Author: "Norbert Rolland" - Searchworks@Jio Institute Digital Library Search Results

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102 results on '"Norbert Rolland"'

1. Obituary: Dominique Job (1947-2022)

Author: Elisabeth Jamet, Marie-Thérèse Esquerré-Tugayé, Karine Gallardo-Guerrero, Norbert Rolland, Michel Zivy, Mélisande Blein-Nicolas, Delphine Vincent, Brigitte Gontero, and Loïc Rajjou
Subjects: Dominique Job, obituary and bibliography, plant physiologist, French Academy of Agriculture, proteomics, Plant culture, SB1-1110
Published: 2023
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2. Paving the way towards future‐proofing our crops

Author: Alexandra Baekelandt, Vandasue L. R. Saltenis, Philippe Nacry, Aleksandra Malyska, Marc Cornelissen, Amrit Kaur Nanda, Abhishek Nair, Peter Rogowsky, Laurens Pauwels, Bertrand Muller, Jonas Collén, Jonas Blomme, Mathias Pribil, Lars B. Scharff, Jessica Davies, Ralf Wilhelm, Norbert Rolland, Jeremy Harbinson, Wout Boerjan, Erik H. Murchie, Alexandra J. Burgess, Jean‐Pierre Cohan, Philippe Debaeke, Sébastien Thomine, Dirk Inzé, René Klein Lankhorst, and Martin A. J. Parry
Subjects: crop productivity, crop yield, future‐proofed crops, future world scenarios, plant research, Agriculture, Agriculture (General), S1-972
Abstract: Abstract To meet the increasing global demand for food, feed, fibre and other plant‐derived products, a steep increase in crop productivity is a scientifically and technically challenging imperative. The CropBooster‐P project, a response to the H2020 call ‘Future proofing our plants’, is developing a roadmap for plant research to improve crops critical for the future of European agriculture by increasing crop yield, nutritional quality, value for non‐food applications and sustainability. However, if we want to efficiently improve crop production in Europe and prioritize methods for crop trait improvement in the coming years, we need to take into account future socio‐economic, technological and global developments, including numerous policy and socio‐economic challenges and constraints. Based on a wide range of possible global trends and key uncertainties, we developed four extreme future learning scenarios that depict complementary future developments. Here, we elaborate on how the scenarios could inform and direct future plant research, and we aim to highlight the crop improvement approaches that could be the most promising or appropriate within each of these four future world scenarios. Moreover, we discuss some key plant technology options that would need to be developed further to meet the needs of multiple future learning scenarios, such as improving methods for breeding and genetic engineering. In addition, other diverse platforms of food production may offer unrealized potential, such as underutilized terrestrial and aquatic species as alternative sources of nutrition and biomass production. We demonstrate that although several methods or traits could facilitate a more efficient crop production system in some of the scenarios, others may offer great potential in all four of the future learning scenarios. Altogether, this indicates that depending on which future we are heading toward, distinct plant research fields should be given priority if we are to meet our food, feed and non‐food biomass production needs in the coming decades.
Published: 2023
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3. CropBooster‐P: Towards a roadmap for plant research to future‐proof crops in Europe

Author: Alexandra Baekelandt, Vandasue L. R. Saltenis, Mathias Pribil, Philippe Nacry, Jeremy Harbinson, Norbert Rolland, Ralf Wilhelm, Jessica Davies, Dirk Inzé, Martin A. J. Parry, and René Klein Lankhorst
Subjects: climate change, crop improvement, crop yield, food supply, H2020, nutritional quality, Agriculture, Agriculture (General), S1-972
Abstract: Abstract The world needs more than double its current agricultural productivity by 2050 to produce enough food and feed, as well as to provide feedstock for the bioeconomy. These future increases will not only need to be sustainable but without comprommising the nutritional quality, and ideally also need to decrease greenhouse gas emissions and increase carbon sequestration to help mitigate the consequences of global climate change. These challenges could be tackled by developing and integrating new future‐proof crops into our food system. The H2020 CropBooster‐P project sets out plant‐centered breeding approaches guided by a broad socio‐economic and societal support. First, the potential approaches for breeding crops with sustainably increased yields adapted to the future climate of Europe are identified. These crop‐breeding options are subsequently prioritized and their adoption considered by experts across the agri‐food system and the wider public, taking into account environmental, economic and other technical criteria. In this way, a specific research agenda to future‐proof our crops was developed, supported by an eventual implementation plan.
Published: 2023
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4. Designing the Crops for the Future; The CropBooster Program

Author: Jeremy Harbinson, Martin A. J. Parry, Jess Davies, Norbert Rolland, Francesco Loreto, Ralf Wilhelm, Karin Metzlaff, and René Klein Lankhorst
Subjects: food supply, climate change, crop yield, sustainability, resource use efficiency, photosynthesis, Biology (General), QH301-705.5
Abstract: The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge.
Published: 2021
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5. Crystal Structure of the Chloroplastic Oxoene Reductase ceQORH from Arabidopsis thaliana

Author: Sarah Mas y mas, Gilles Curien, Cécile Giustini, Norbert Rolland, Jean-Luc Ferrer, and David Cobessi
Subjects: chloroplast envelope quinone oxidoreductase homolog, oxylipins, γ-ketols, α, β-unsaturated carbonyls, X-ray crystallography, Plant culture, SB1-1110
Abstract: Enzymatic and non-enzymatic peroxidation of polyunsaturated fatty acids give rise to accumulation of aldehydes, ketones, and α,β-unsaturated carbonyls of various lengths, known as oxylipins. Oxylipins with α,β-unsaturated carbonyls are reactive electrophile species and are toxic. Cells have evolved several mechanisms to scavenge reactive electrophile oxylipins and decrease their reactivity such as by coupling with glutathione, or by reduction using NAD(P)H-dependent reductases and dehydrogenases of various substrate specificities. Plant cell chloroplasts produce reactive electrophile oxylipins named γ-ketols downstream of enzymatic lipid peroxidation. The chloroplast envelope quinone oxidoreductase homolog (ceQORH) from Arabidopsis thaliana was previously shown to reduce the reactive double bond of γ-ketols. In marked difference with its cytosolic homolog alkenal reductase (AtAER) that displays a high activity toward the ketodiene 13-oxo-9(Z),11(E)-octadecadienoic acid (13-KODE) and the ketotriene 13-oxo-9(Z), 11(E), 15(Z)-octadecatrienoic acid (13-KOTE), ceQORH binds, but does not reduce, 13-KODE and 13-KOTE. Crystal structures of apo-ceQORH and ceQORH bound to 13-KOTE or to NADP+ and 13-KOTE have been solved showing a large ligand binding site, also observed in the structure of the cytosolic alkenal/one reductase. Positioning of the α,β-unsaturated carbonyl of 13-KOTE in ceQORH-NADP+-13-KOTE, far away from the NADP+ nicotinamide ring, provides a rational for the absence of activity with the ketodienes and ketotrienes. ceQORH is a monomeric enzyme in solution whereas other enzymes from the quinone oxidoreductase family are stable dimers and a structural explanation of this difference is proposed. A possible in vivo role of ketodienes and ketotrienes binding to ceQORH is also discussed.
Published: 2017
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6. Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana.

Author: Hubert Mayerhofer, Emeline Sautron, Norbert Rolland, Patrice Catty, Daphné Seigneurin-Berny, Eva Pebay-Peyroula, and Stéphanie Ravaud
Subjects: Medicine, Science
Abstract: Copper is a crucial ion in cells, but needs to be closely controlled due to its toxic potential and ability to catalyse the formation of radicals. In chloroplasts, an important step for the proper functioning of the photosynthetic electron transfer chain is the delivery of copper to plastocyanin in the thylakoid lumen. The main route for copper transport to the thylakoid lumen is driven by two PIB-type ATPases, Heavy Metal ATPase 6 (HMA6) and HMA8, located in the inner membrane of the chloroplast envelope and in the thylakoid membrane, respectively. Here, the crystal structures of the nucleotide binding domain of HMA6 and HMA8 from Arabidopsis thaliana are reported at 1.5Å and 1.75Å resolution, respectively, providing the first structural information on plants Cu+-ATPases. The structures reveal a compact domain, with two short helices on both sides of a twisted beta-sheet. A double mutant, aiding in the crystallization, provides a new crystal contact, but also avoids an internal clash highlighting the benefits of construct modifications. Finally, the histidine in the HP motif of the isolated domains, unable to bind ATP, shows a side chain conformation distinct from nucleotide bound structures.
Published: 2016
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7. Oligomeric status and nucleotide binding properties of the plastid ATP/ADP transporter 1: toward a molecular understanding of the transport mechanism.

Author: Aurélien Deniaud, Pankaj Panwar, Annie Frelet-Barrand, Florent Bernaudat, Céline Juillan-Binard, Christine Ebel, Norbert Rolland, and Eva Pebay-Peyroula
Subjects: Medicine, Science
Abstract: BACKGROUND: Chloroplast ATP/ADP transporters are essential to energy homeostasis in plant cells. However, their molecular mechanism remains poorly understood, primarily due to the difficulty of producing and purifying functional recombinant forms of these transporters. METHODOLOGY/PRINCIPAL FINDINGS: In this work, we describe an expression and purification protocol providing good yields and efficient solubilization of NTT1 protein from Arabidopsis thaliana. By biochemical and biophysical analyses, we identified the best detergent for solubilization and purification of functional proteins, LAPAO. Purified NTT1 was found to accumulate as two independent pools of well folded, stable monomers and dimers. ATP and ADP binding properties were determined, and Pi, a co-substrate of ADP, was confirmed to be essential for nucleotide steady-state transport. Nucleotide binding studies and analysis of NTT1 mutants lead us to suggest the existence of two distinct and probably inter-dependent binding sites. Finally, fusion and deletion experiments demonstrated that the C-terminus of NTT1 is not essential for multimerization, but probably plays a regulatory role, controlling the nucleotide exchange rate. CONCLUSIONS/SIGNIFICANCE: Taken together, these data provide a comprehensive molecular characterization of a chloroplast ATP/ADP transporter.
Published: 2012
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8. Heterologous expression of membrane proteins: choosing the appropriate host.

Author: Florent Bernaudat, Annie Frelet-Barrand, Nathalie Pochon, Sébastien Dementin, Patrick Hivin, Sylvain Boutigny, Jean-Baptiste Rioux, Daniel Salvi, Daphné Seigneurin-Berny, Pierre Richaud, Jacques Joyard, David Pignol, Monique Sabaty, Thierry Desnos, Eva Pebay-Peyroula, Elisabeth Darrouzet, Thierry Vernet, and Norbert Rolland
Subjects: Medicine, Science
Abstract: BackgroundMembrane proteins are the targets of 50% of drugs, although they only represent 1% of total cellular proteins. The first major bottleneck on the route to their functional and structural characterisation is their overexpression; and simply choosing the right system can involve many months of trial and error. This work is intended as a guide to where to start when faced with heterologous expression of a membrane protein.Methodology/principal findingsThe expression of 20 membrane proteins, both peripheral and integral, in three prokaryotic (E. coli, L. lactis, R. sphaeroides) and three eukaryotic (A. thaliana, N. benthamiana, Sf9 insect cells) hosts was tested. The proteins tested were of various origins (bacteria, plants and mammals), functions (transporters, receptors, enzymes) and topologies (between 0 and 13 transmembrane segments). The Gateway system was used to clone all 20 genes into appropriate vectors for the hosts to be tested. Culture conditions were optimised for each host, and specific strategies were tested, such as the use of Mistic fusions in E. coli. 17 of the 20 proteins were produced at adequate yields for functional and, in some cases, structural studies. We have formulated general recommendations to assist with choosing an appropriate system based on our observations of protein behaviour in the different hosts.Conclusions/significanceMost of the methods presented here can be quite easily implemented in other laboratories. The results highlight certain factors that should be considered when selecting an expression host. The decision aide provided should help both newcomers and old-hands to select the best system for their favourite membrane protein.
Published: 2011
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9. Lactococcus lactis, an alternative system for functional expression of peripheral and intrinsic Arabidopsis membrane proteins.

Author: Annie Frelet-Barrand, Sylvain Boutigny, Lucas Moyet, Aurélien Deniaud, Daphné Seigneurin-Berny, Daniel Salvi, Florent Bernaudat, Pierre Richaud, Eva Pebay-Peyroula, Jacques Joyard, and Norbert Rolland
Subjects: Medicine, Science
Abstract: BackgroundDespite their functional and biotechnological importance, the study of membrane proteins remains difficult due to their hydrophobicity and their low natural abundance in cells. Furthermore, into established heterologous systems, these proteins are frequently only produced at very low levels, toxic and mis- or unfolded. Lactococcus lactis, a gram-positive lactic bacterium, has been traditionally used in food fermentations. This expression system is also widely used in biotechnology for large-scale production of heterologous proteins. Various expression vectors, based either on constitutive or inducible promoters, are available for this system. While previously used to produce bacterial and eukaryotic membrane proteins, the ability of this system to produce plant membrane proteins was until now not tested.Methodology/principal findingsThe aim of this work was to test the expression, in Lactococcus lactis, of either peripheral or intrinsic Arabidopsis membrane proteins that could not be produced, or in too low amount, using more classical heterologous expression systems. In an effort to easily transfer genes from Gateway-based Arabidopsis cDNA libraries to the L. lactis expression vector pNZ8148, we first established a cloning strategy compatible with Gateway entry vectors. Interestingly, the six tested Arabidopsis membrane proteins could be produced, in Lactococcus lactis, at levels compatible with further biochemical analyses. We then successfully developed solubilization and purification processes for three of these proteins. Finally, we questioned the functionality of a peripheral and an intrinsic membrane protein, and demonstrated that both proteins were active when produced in this system.Conclusions/significanceAltogether, these data suggest that Lactococcus lactis might be an attractive system for the efficient and functional production of difficult plant membrane proteins.
Published: 2010
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10. Proteomics Evidence of a Systemic Response to Desiccation in the Resurrection Plant Haberlea rhodopensis

Author: Petko Mladenov, Diana Zasheva, Sébastien Planchon, Céline C. Leclercq, Denis Falconet, Lucas Moyet, Sabine Brugière, Daniela Moyankova, Magdalena Tchorbadjieva, Myriam Ferro, Norbert Rolland, Jenny Renaut, Dimitar Djilianov, Xin Deng, Institute of Botany [Beijing] (IB-CAS), Chinese Academy of Sciences [Beijing] (CAS), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), Agrobioinstitute, Agricultural Academy Bulgaria, Bulgarian Academy of Sciences (BAS), Luxembourg Institute of Science and Technology (LIST), LIPID, Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA), Medical University of Sofia [Bulgarie], The Fonds National de la Recherche, Luxembourg (Project SMARTWALL C15/SR/10240550), CAS PRESIDENT’S INTERNATIONAL FELLOWSHIP INITIATIVE GRANT (2021PB0101), National Key R&D program of China (2021YFE0102600), Bulgarian Science Fund (KP06-H-41-IP-Kitai), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), ANR-17-EURE-0003,CBH-EUR-GS,CBH-EUR-GS(2017), Martin-Laffon, Jacqueline, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, and CBH-EUR-GS - - CBH-EUR-GS2017 - ANR-17-EURE-0003 - EURE - VALID
Subjects: dehydrin, Organic Chemistry, drought stress, systems biology, General Medicine, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, Catalysis, Computer Science Applications, subcellular fractionation, [SDV.BV.BOT] Life Sciences [q-bio]/Vegetal Biology/Botanics, Inorganic Chemistry, resurrection plant, proteomics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], [SDV.BBM.GTP] Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Physical and Theoretical Chemistry, Molecular Biology, Spectroscopy
Abstract: International audience; Global warming and drought stress are expected to have a negative impact on agricultural productivity. Desiccation-tolerant species, which are able to tolerate the almost complete desiccation of their vegetative tissues, are appropriate models to study extreme drought tolerance and identify novel approaches to improve the resistance of crops to drought stress. In the present study, to better understand what makes resurrection plants extremely tolerant to drought, we performed transmission electron microscopy and integrative large-scale proteomics, including organellar and phosphorylation proteomics, and combined these investigations with previously published transcriptomic and metabolomics data from the resurrection plant Haberlea rhodopensis. The results revealed new evidence about organelle and cell preservation, posttranscriptional and posttranslational regulation, photosynthesis, primary metabolism, autophagy, and cell death in response to desiccation in H. rhodopensis. Different protective intrinsically disordered proteins, such as late embryogenesis abundant (LEA) proteins, thaumatin-like proteins (TLPs), and heat shock proteins (HSPs), were detected. We also found a constitutively abundant dehydrin in H. rhodopensis whose phosphorylation levels increased under stress in the chloroplast fraction. This integrative multi-omics analysis revealed a systemic response to desiccation in H. rhodopensis and certain targets for further genomic and evolutionary studies on DT mechanisms and genetic engineering towards the improvement of drought tolerance in crops.
Published: 2022
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11. Designing the Crops for the Future; The CropBooster Program

Author: Jess Davies, Francesco Loreto, Norbert Rolland, Martin A. J. Parry, René Klein Lankhorst, Ralf Wilhelm, Jeremy Harbinson, Karin Metzlaff, Wageningen University and Research [Wageningen] (WUR), Lancaster Environment Centre, Lancaster University, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Grenoble Alpes (UGA), National Research Council of Italy | Consiglio Nazionale delle Ricerche (CNR), University of Naples Federico II = Università degli studi di Napoli Federico II, Julius Kühn-Institut (JKI), European Plant Science Organisation, European Project: 817690,H2020, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Consiglio Nazionale delle Ricerche (CNR), Università degli studi di Napoli Federico II, Harbinson, Jeremy, Parry, Martin A. J., Davies, Je, Rolland, Norbert, Loreto, Francesco, Wilhelm, Ralf, Metzlaff, Karin, and Klein Lankhorst, René
Subjects: 0106 biological sciences, 0301 basic medicine, Breeding, 01 natural sciences, 7. Clean energy, 11. Sustainability, Climate change, resource use efficiency, Photosynthesis, Biology (General), biodiversity, 2. Zero hunger, education.field_of_study, Food security, BioSolar Cells, Biodiversity, Bioeconomy, sustainability, Natural resource, CO, International Action, Biofysica, climate change, Sustainability, CO2, General Agricultural and Biological Sciences, Opinion, QH301-705.5, Population, Biophysics, Food supply, Biology, General Biochemistry, Genetics and Molecular Biology, 12. Responsible consumption, 03 medical and health sciences, Crop yield, education, Environmental planning, bioeconomy, Sustainable development, photosynthesis, General Immunology and Microbiology, business.industry, [SDV.SA.AEP]Life Sciences [q-bio]/Agricultural sciences/Agriculture, economy and politics, 15. Life on land, crop yield, food supply, 030104 developmental biology, Climate change mitigation, 13. Climate action, Agriculture, breeding, Resource use efficiency, business, 010606 plant biology & botany
Abstract: Simple Summary Our climate is changing and the world population is growing to an estimated 10 billion people by 2050. This may cause serious problems in global food supply, protection of the environment and safeguarding Earth’s biodiversity. To face these challenges, agriculture will have to adapt and a key element in this will be the development of “future-proof” crops. These crops will not only have to be high-yielding, but also should be able to withstand future climate conditions and will have to make very efficient use of scarce resources such as water, phosphorus and minerals. Future crops should not only sustainably give access to sufficient, nutritious, and diverse food to a worldwide growing population, but also support the circular bio-based economy and contribute to a lower atmospheric CO2 concentration to counteract global warming. Future-proofing our crops is an urgent issue and a challenging goal that only can be realized by large-scale, international research cooperation. We call for international action and propose a pan-European research and innovation initiative, the CropBooster Program, to mobilize the European plant research community and all interested actors in agri-food research and innovation to face the challenge. Abstract The realization of the full objectives of international policies targeting global food security and climate change mitigation, including the United Nation’s Sustainable Development Goals, the Paris Climate Agreement COP21 and the European Green Deal, requires that we (i) sustainably increase the yield, nutritional quality and biodiversity of major crop species, (ii) select climate-ready crops that are adapted to future weather dynamic and (iii) increase the resource use efficiency of crops for sustainably preserving natural resources. Ultimately, the grand challenge to be met by agriculture is to sustainably provide access to sufficient, nutritious and diverse food to a worldwide growing population, and to support the circular bio-based economy. Future-proofing our crops is an urgent issue and a challenging goal, involving a diversity of crop species in differing agricultural regimes and under multiple environmental drivers, providing versatile crop-breeding solutions within wider socio-economic-ecological systems. This goal can only be realized by a large-scale, international research cooperation. We call for international action and propose a pan-European research initiative, the CropBooster Program, to mobilize the European plant research community and interconnect it with the interdisciplinary expertise necessary to face the challenge.
Published: 2021
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12. Calmodulin is involved in the dual subcellular location of two chloroplast proteins

Author: Laura Perrot, Imen Bouchnak, Stéphane Miras, Daphné Seigneurin-Berny, Daniel Salvi, Marcel Kuntz, Lucas Moyet, Norbert Rolland, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), French National Research Agency (ANR)ANR-10-LABX-49-01French National Research Agency (ANR)ANR-06-GPLA-0003French National Research Agency (ANR)ANR-2010-BLAN-1610-01French National Research Agency (ANR)ANR-10-LABX-49-01INRA Plant Biology and Breeding Division ANR-10-LABX-49-01French Atomic Energy Commission French National Research Agency (ANR)ANR-15-IDEX-02French National Research Agency (ANR) Centre National de la Recherche Scientifique (CNRS) INRA, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-06-GPLA-0003,GPLA06024G,Glyco-chloroplast : Identification of signals controlling the protein trafficking between the secretory pathway and the chloroplast(2006), ANR-10-BLAN-1610,Chloro-Pro,Régulation de la dynamique du protéome chloroplastique(2010), ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, and ANR-15-IDEX-02,DATA@UGA,Grenoble Alpes Data Institute(2016)
Subjects: 0301 basic medicine, Chloroplasts, Calmodulin, Arabidopsis, Plant Biology, Biochemistry, Chloroplast membrane, plant molecular biology, Chloroplast Proteins, 03 medical and health sciences, Bimolecular fluorescence complementation, Cytosol, chloroplast, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Calcium Signaling, Plastids, Plastid, Molecular Biology, Binding Sites, 030102 biochemistry & molecular biology, biology, Arabidopsis Proteins, Chemistry, Membrane Proteins, Cell Biology, Compartmentalization (psychology), Subcellular location, Cell Compartmentation, Cell biology, subcellular fractionation, Chloroplast, 030104 developmental biology, Chloroplast envelope, subcellular organelle, plant biochemistry, biology.protein, calmodulin (CaM), Protein Binding
Abstract: International audience; Cell compartmentalization is an essential process by which eukaryotic cells separate and control biological processes. While calmodulins are well known to regulate catalytic properties of their targets, we show here their involvement in the subcellular location of two plant proteins. Both proteins exhibit a dual location, namely in the cytosol in addition to their association to plastids (where they are known to fulfil their role). One of these proteins, ceQORH, a long-chain fatty acid reductase, was analysed in more details and its calmodulin binding site identified by specific mutations. Such a mutated form is predominantly targeted to plastids at the expense of its cytosolic location. The second protein, TIC32, was also shown to be dependent on its calmodulin binding site for retention in the cytosol. Complementary approaches (bimolecular fluorescence complementation and reverse genetics) demonstrated that the calmodulin isoform CAM5 is specifically involved in the retention of ceQORH in the cytosol. This study identifies a new role for calmodulin and sheds new light on the intriguing CaM-binding properties of hundreds of plastid proteins, despite no CaM or CaM-like proteins were identified in plastids.
Published: 2019
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13. Unravelling hidden components of the chloroplast envelope proteome: opportunities and limits of better MS sensitivity

Author: Daniel Salvi, Norbert Rolland, Lucas Moyet, Imen Bouchnak, Marianne Tardif, Sabine Brugière, Marcel Kuntz, Sophie Le Gall, Dynamique du protéome et biogenèse du chloroplaste (ChloroGenesis), Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), French National Research Agency (ANR) ANR-15-IDEX-02 ANR-10-LABX-49-01 ANR-10-INBS-08, Institut National de la Recherche Agronomique (INRA), ANR-15-IDEX-0002,UGA,IDEX UGA(2015), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Etude de la dynamique des protéomes (EDyP), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), ANR-15-IDEX-02,DATA@UGA,Grenoble Alpes Data Institute(2016), ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, ANR-10-INBS-08-01/10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)
Subjects: Cell Extracts, Chloroplasts, Proteome, Arabidopsis thaliana, Arabidopsis, Plant Biology, Cellular organelles, Biochemistry, Chloroplast membrane, Subcellular Separation, Chloroplast, Cell fractionation, Analytical Chemistry, 03 medical and health sciences, Chloroplast Proteins, Organelle, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastid, Databases, Protein, Molecular Biology, 030304 developmental biology, 0303 health sciences, Subcellular analysis, Mass spectrometry, Chemistry, Arabidopsis Proteins, Subcellular localization, Research, 030302 biochemistry & molecular biology, Membrane Proteins, food and beverages, Proteins, Intracellular Membranes, Chloroplast envelope, Biogenesis, Subcellular Fractions
Abstract: By quantitatively comparing the proteomes of total leaf (crude cell extract) from Arabidopsis and purified chloroplast envelope fractions, this study makes available a novel parameter (calculated Enrichment Factor) for each putative envelope protein. This parameter provides important information to enable the more confident identification of genuine envelope components, distinguishing them from contaminants from other cellular/chloroplast compartments., Graphical Abstract Highlights Identification of previously undetected chloroplast envelope proteins. Up to date manual annotation of genuine (or shared) envelope components. New hypotheses for localizations, functions, interactions among cell compartments. A new resource of significant value to the broader plant science community., The chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling the exchange of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides etc.) of the plant cell. However, unraveling the contents of the chloroplast envelope proteome remains a difficult challenge; many proteins constituting this functional double membrane system remain to be identified. Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.4% of the whole cell proteome). In other words, most envelope proteins are so rare at the cell, chloroplast, or even envelope level, that they remained undetectable using targeted MS studies. Cross-contamination of chloroplast subcompartments by each other and by other cell compartments during cell fractionation, impedes accurate localization of many envelope proteins. The aim of the present study was to take advantage of technologically improved MS sensitivity to better define the proteome of the chloroplast envelope (differentiate genuine envelope proteins from contaminants). This MS-based analysis relied on an enrichment factor that was calculated for each protein identified in purified envelope fractions as compared with the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1269 proteins were detected in purified envelope fractions, of which, 462 could be assigned an envelope localization by combining MS-based spectral count analyses with manual annotation using data from the literature and prediction tools. Many of such proteins being previously unknown envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.
Published: 2019
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14. The Main Functions of Plastids

Author: Norbert, Rolland, Imen, Bouchnak, Lucas, Moyet, Daniel, Salvi, and Marcel, Kuntz
Subjects: Plastids, Energy Metabolism, Biological Evolution
Abstract: Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.
Published: 2018

15. AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins

Author: Daniel, Salvi, Sylvain, Bournais, Lucas, Moyet, Imen, Bouchnak, Marcel, Kuntz, Christophe, Bruley, and Norbert, Rolland
Subjects: Proteomics, Chloroplasts, Databases, Factual, Arabidopsis Proteins, Computational Biology, Plastids, Thylakoids
Abstract: Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO ( http://at-chloro.prabi.fr/at_chloro/ ) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.
Published: 2018

16. AT_CHLORO: The First Step When Looking for Information About Subplastidial Localization of Proteins

Author: Christophe Bruley, Sylvain Bournais, Norbert Rolland, Lucas Moyet, Daniel Salvi, Imen Bouchnak, Marcel Kuntz, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Marechal Eric, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)
Subjects: 0301 basic medicine, Chemistry, Subcellular localization, [SDV]Life Sciences [q-bio], food and beverages, macromolecular substances, Stroma, Plant, Chloroplast membrane, Chloroplast, 03 medical and health sciences, 030104 developmental biology, Envelope, Thylakoid, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Biophysics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastid, Chloroplast Proteins, Plastid envelope, Intermembrane space, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; Plastids contain several key subcompartments. The two limiting envelope membranes (inner and outer membrane of the plastid envelope with an intermembrane space between), an aqueous phase (stroma), and an internal membrane system terms (thylakoids) formed of flat compressed vesicles (grana) and more light structures (lamellae). The thylakoid vesicles delimit another discrete soluble compartment, the thylakoid lumen. AT_CHLORO (http://at-chloro.prabi.fr/at_chloro/) is a unique database supplying information about the subplastidial localization of proteins. It was created from simultaneous proteomic analyses targeted to the main subcompartments of the chloroplast from Arabidopsis thaliana (i.e., envelope, stroma, thylakoid) and to the two subdomains of thylakoid membranes (i.e., grana and stroma lamellae). AT_CHLORO assembles several complementary information (MS-based experimental data, curated functional annotations and subplastidial localization, links to other public databases and references) which give a comprehensive overview of the current knowledge about the subplastidial localization and the function of chloroplast proteins, with a specific attention given to chloroplast envelope proteins.
Published: 2018
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17. Preparation of membrane fractions (envelope, thylakoids, grana and stroma lamellae) from Arabidopsis chloroplasts for quantitative proteomic investigations and other studies

Author: Daniel Salvi, Daphné Seigneurin-Berny, Lucas Moyet, Norbert Rolland, Martino Tomizioli, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), H. P. Mock, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Martin-Laffon, Jacqueline
Subjects: 0301 basic medicine, Plastid membrane, Arabidopsis thaliana, food and beverages, Plant, Biology, Chloroplast membrane, Cell biology, Chloroplast, 03 medical and health sciences, 030104 developmental biology, Membrane, Stroma, Thylakoid, Organelle, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Inner membrane, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS
Abstract: Chloroplasts are semiautonomous organelles found in plants and protists. They are surrounded by a double membrane system, or envelope. These envelope membranes contain machineries to import nuclear-encoded proteins, and transporters for ions or metabolites, but are also essential for a range of plastid-specific metabolisms. The inner membrane surrounds a stroma, which is the site of the carbon chemistry of photosynthesis. Chloroplasts also contain an internal membrane system, or thylakoids, where the light phase of photosynthesis occurs. The thylakoid membranes themselves have a bipartite structure, consisting of grana stacks interconnected by stroma lamellae. These thylakoid membranes however form a continuous network that encloses a single lumenal space. Chloroplast-encoded or targeted proteins are thus addressed to various sub-compartments that turn out to be flexible systems and whose main functions can be modulated by alterations in the relative levels of their components. This article describes procedures developed to recover highly purified chloroplast membrane fractions (i.e., envelope, crude thylakoid membranes, as well as the two main thylakoid subdomains, grana and stroma lamellae), starting from Percoll-purified Arabidopsis chloroplasts. Immunological markers are also listed that can be used to assess the purity of these fractions and reveal specific contaminations by other plastid membrane compartments. The methods described here are compatible with chloroplast proteome dynamic studies relying on targeted quantitative proteomic investigations.
Published: 2018

18. The Main Functions of Plastids

Author: Lucas Moyet, Daniel Salvi, Marcel Kuntz, Imen Bouchnak, Norbert Rolland, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Marechal Eric, and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: Proteomics, 0301 basic medicine, Nuclear gene, fungi, Functional redundancy, food and beverages, Plant, Mitochondrion, Biology, Chloroplast, 03 medical and health sciences, Metabolism, 030104 developmental biology, Evolutionary biology, Organelle, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Function, Plastid, Function (biology)
Abstract: International audience; Plastids are semiautonomous organelles like mitochondria, and derive from a cyanobacterial ancestor that was engulfed by a host cell. During evolution, they have recruited proteins originating from the nuclear genome, and only parts of their ancestral metabolic properties were conserved and optimized to limit functional redundancy with other cell compartments. Furthermore, large disparities in metabolic functions exist among various types of plastids, and the characterization of their various metabolic properties is far from being accomplished. In this review, we provide an overview of the main functions, known to be achieved by plastids or shared by plastids and other compartments of the cell. In short, plastids appear at the heart of all main plant functions.
Published: 2018
Full Text: View/download PDF

19. Preparation of Membrane Fractions (Envelope, Thylakoids, Grana, and Stroma Lamellae) from Arabidopsis Chloroplasts for Quantitative Proteomic Investigations and Other Studies

Author: Lucas, Moyet, Daniel, Salvi, Martino, Tomizioli, Daphné, Seigneurin-Berny, and Norbert, Rolland
Subjects: Proteomics, Chloroplasts, Arabidopsis Proteins, Arabidopsis, Intracellular Membranes, Cell Fractionation
Abstract: Chloroplasts are semiautonomous organelles found in plants and protists. They are surrounded by a double membrane system, or envelope. These envelope membranes contain machineries to import nuclear-encoded proteins, and transporters for ions or metabolites, but are also essential for a range of plastid-specific metabolisms. The inner membrane surrounds a stroma, which is the site of the carbon chemistry of photosynthesis. Chloroplasts also contain an internal membrane system, or thylakoids, where the light phase of photosynthesis occurs. The thylakoid membranes themselves have a bipartite structure, consisting of grana stacks interconnected by stroma lamellae. These thylakoid membranes however form a continuous network that encloses a single lumenal space. Chloroplast-encoded or targeted proteins are thus addressed to various sub-compartments that turn out to be flexible systems and whose main functions can be modulated by alterations in the relative levels of their components. This article describes procedures developed to recover highly purified chloroplast membrane fractions (i.e., envelope, crude thylakoid membranes, as well as the two main thylakoid subdomains, grana and stroma lamellae), starting from Percoll-purified Arabidopsis chloroplasts. Immunological markers are also listed that can be used to assess the purity of these fractions and reveal specific contaminations by other plastid membrane compartments. The methods described here are compatible with chloroplast proteome dynamic studies relying on targeted quantitative proteomic investigations.
Published: 2017

20. ChloroKB:a web-application for the integration of knowledge related to chloroplast metabolic network

Author: Daphné Seigneurin-Berny, Sylvain Bournais, Christophe Bruley, Claude Alban, Gilles Curien, Marianne Tardif, Marcel Kuntz, Stéphane Ravanel, Pauline Gloaguen, Michel Matringe, Myriam Ferro, Yves Vandenbrouck, Norbert Rolland, Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire Biologie, Informatique et Mathématiques, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), ANR (GRAL Labex, Grenoble Alliance for Integrated Structural Cell Biology) [ANR-10-LABEX-04], ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Etude de la dynamique des protéomes (EDyP), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and ANR–10–LABEX–04 ,GRAL,Labex
Subjects: 0301 basic medicine, Chloroplasts, Traceability, Arabidopsis thaliana, Physiology, Knowledge Bases, [SDV]Life Sciences [q-bio], Arabidopsis, Metabolic network, Context (language use), Plant Science, Computational biology, Bioinformatics, Chloroplast, Metabolic engineering, Knowledge base, 03 medical and health sciences, Software, Genetics, Web application, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, Internet, biology, business.industry, Plant, Breakthrough Technologies, biology.organism_classification, Biocuration, Biological network visualization, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Metabolism, Metabolic pathways, business, Metabolic Networks and Pathways, Subcellular Fractions
Abstract: International audience; Higher plants, as autotrophic organisms, are effective sources of molecules. They hold great promise for metabolic engineering, but the behavior of plant metabolism at the network level is still incompletely described. Although structural models (stoichiometry matrices) and pathway databases are extremely useful, they cannot describe the complexity of the metabolic context, and new tools are required to visually represent integrated biocurated knowledge for use by both humans and computers. Here, we describe ChloroKB, a Web application (http://chlorokb.fr/) for visual exploration and analysis of the Arabidopsis (Arabidopsis thaliana) metabolic network in the chloroplast and related cellular pathways. The network was manually reconstructed through extensive biocuration to provide transparent traceability of experimental data. Proteins and metabolites were placed in their biological context (spatial distribution within cells, connectivity in the network, participation in supramolecular complexes, and regulatory interactions) using CellDesigner software. The network contains 1,147 reviewed proteins (559 localized exclusively in plastids, 68 in at least one additional compartment, and 520 outside the plastid), 122 proteins awaiting biochemical/genetic characterization, and 228 proteins for which genes have not yet been identified. The visual presentation is intuitive and browsing is fluid, providing instant access to the graphical representation of integrated processes and to a wealth of refined qualitative and quantitative data. ChloroKB will be a significant support for structural and quantitative kinetic modeling, for biological reasoning, when comparing novel data with established knowledge, for computer analyses, and for educational purposes. ChloroKB will be enhanced by continuous updates following contributions from plant researchers.
Published: 2017
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21. Glycerolipids in photosynthesis: Composition, synthesis and trafficking

Author: Denis Falconet, Maryse A. Block, Laurence Boudière, Giovanni Finazzi, Dimitris Petroutsos, Sylvaine Roy, Olivier Bastien, Fabrice Rébeillé, Eric Maréchal, Norbert Rolland, Morgane Michaud, Juliette Jouhet, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Région Rhône-Alpes and Labex GRAL (Grenoble Alliance for Integrated Structural Cell Biology), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: Cyanobacteria, Galactolipid, [SDV]Life Sciences [q-bio], Biophysics, plant, Review, Monogalactosyldiacylglycerol, Photosynthesis, Thylakoids, Biochemistry, lipids, chemistry.chemical_compound, Membrane Lipids, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Digalactosyldiacylglycerol, Phosphatidylglycerol, biology, Protein Stability, food and beverages, Biological Transport, Cell Biology, biology.organism_classification, chloroplast membranes, Biosynthetic Pathways, Chloroplast, Metabolic pathway, Membrane, Eukaryotic Cells, chemistry, Prokaryotic Cells, Thylakoid, Sulfoquinovosyldiacylglycerol, Glycolipids, Sulfolipid
Abstract: International audience; : Glycerolipids constituting the matrix of photosynthetic membranes, from cyanobacteria to chloroplasts of eukaryotic cells, comprise monogalactosyldiacylglycerol, digalactosyldiacylglycerol, sulfoquinovosyldiacylglycerol and phosphatidylglycerol. This review covers our current knowledge on the structural and functional features of these lipids in various cellular models, from prokaryotes to eukaryotes. Their relative proportions in thylakoid membranes result from highly regulated and compartmentalized metabolic pathways, with a cooperation, in the case of eukaryotes, of non-plastidic compartments. This review also focuses on the role of each of these thylakoid glycerolipids in stabilizing protein complexes of the photosynthetic machinery, which might be one of the reasons for their fascinating conservation in the course of evolution. This article is part of a Special Issue entitled: Dynamic and ultrastructure of bioenergetic membranes and their components.
Published: 2014
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22. Structural Insights into the Nucleotide-Binding Domains of the P1B-type ATPases HMA6 and HMA8 from Arabidopsis thaliana

Author: Eva Pebay-Peyroula, Norbert Rolland, Hubert Mayerhofer, Patrice Catty, Daphné Seigneurin-Berny, Emeline Sautron, Stéphanie Ravaud, Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Physiologie cellulaire et végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Ravaud, Stephanie, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), European Community's Seventh Framework Programme FP7 [HEALTH-F4-2007-201924], Grenoble Alliance for Integrated Structural Cell Biology GRAL [ANR-10-LABX-49-01], Institut Universitaire de France, French Centre National de la Recherche Scientifique, University Grenoble Alpes, EDICT Consortium, European Project: 201924,EC:FP7:HEALTH,FP7-HEALTH-2007-A,EDICT(2008), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, Adenosine Triphosphatase, Protein Structure Comparison, Models, Molecular, Chloroplasts, Arabidopsis, lcsh:Medicine, Plant Science, Crystallography, X-Ray, Chloroplast membrane, Biochemistry, Protein structure, Macromolecular Structure Analysis, Chemical Precipitation, Amino Acids, lcsh:Science, Plastocyanin, Adenosine Triphosphatases, Multidisciplinary, Crystallography, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Organic Compounds, Nucleotides, Physics, Chemical Reactions, food and beverages, Condensed Matter Physics, Enzymes, Chemistry, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], Cyclic nucleotide-binding domain, Thylakoid, Physical Sciences, Crystal Structure, Cellular Structures and Organelles, Cellular Types, Basic Amino Acids, Crystallization, Research Article, Protein Binding, Protein Structure, Materials by Structure, Plant Cell Biology, Protein domain, Materials Science, Biology, Crystals, 03 medical and health sciences, Protein Domains, Plant Cells, Inner membrane, Solid State Physics, Histidine, Amino Acid Sequence, Molecular Biology, Binding Sites, Arabidopsis Proteins, Organic Chemistry, lcsh:R, Phosphatases, Chemical Compounds, Biology and Life Sciences, Proteins, Cell Biology, Electron transport chain, 030104 developmental biology, Biophysics, Enzymology, lcsh:Q, Sequence Alignment, Copper
Abstract: International audience; Copper is a crucial ion in cells, but needs to be closely controlled due to its toxic potential and ability to catalyse the formation of radicals. In chloroplasts, an important step for the proper functioning of the photosynthetic electron transfer chain is the delivery of copper to plastocyanin in the thylakoid lumen. The main route for copper transport to the thylakoid lumen is driven by two PIB-type ATPases, Heavy Metal ATPase 6 (HMA6) and HMA8, located in the inner membrane of the chloroplast envelope and in the thylakoid membrane, respectively. Here, the crystal structures of the nucleotide binding domain of HMA6 and HMA8 from Arabidopsis thaliana are reported at 1.5Å and 1.75Å resolution, respectively, providing the first structural information on plants Cu+-ATPases. The structures reveal a compact domain, with two short helices on both sides of a twisted beta-sheet. A double mutant, aiding in the crystallization, provides a new crystal contact, but also avoids an internal clash highlighting the benefits of construct modifications. Finally, the histidine in the HP motif of the isolated domains, unable to bind ATP, shows a side chain conformation distinct from nucleotide bound structures.
Published: 2016
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23. Identification of Two Conserved Residues Involved in Copper Release from Chloroplast PIB-1-ATPases

Author: Cécile Giustini, Emeline Sautron, Thuy Van Dang, Daniel Salvi, Patrice Catty, Lucas Moyet, Serge Crouzy, Norbert Rolland, Daphné Seigneurin-Berny, Physiologie cellulaire et végétale (LPCV), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat a l'Energie Atomique et aux Energies Alternatives, Centre National de la Recherche Scientifique, French National Institute for Agricultural Research, University of Grenoble Alpes, GRAL Labex [ANR-10-LABX-49-01], CEA, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0301 basic medicine, Saccharomyces cerevisiae, Amino Acid Motifs, Arabidopsis, chemistry.chemical_element, Plant Biology, Biochemistry, Chloroplast membrane, Thylakoids, 03 medical and health sciences, chloroplast, ATPase, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Histidine, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Plastocyanin, Adenosine Triphosphatases, 030102 biochemistry & molecular biology, biology, Arabidopsis Proteins, food and beverages, Cell Biology, biology.organism_classification, Copper release site, Copper, Recombinant Proteins, Chloroplast, Lactococcus lactis, 030104 developmental biology, chemistry, PIB-1-ATPases, Thylakoid, plant biochemistry, copper transport, copper release site, Thylakoid Membrane Proteins, Cysteine
Abstract: International audience; Copper is an essential transition metal for living organisms. In the plant model Arabidopsis thaliana, half of the copper content is localized in the chloroplast and, as a cofactor of plastocyanin, copper is essential for photosynthesis. Within the chloroplast, copper delivery to plastocyanin involves two transporters of the PIB-1-ATPases subfamily, HMA6 at the chloroplast envelope and HMA8, in the thylakoid membranes. Both proteins are high affinity copper transporters but share distinct enzymatic properties. In the present work, the comparison of 140 sequences of PIB-1-ATPases revealed a conserved region unusually rich in histidine and cysteine residues in the TMA-L1 region of eukaryotic chloroplast copper ATPases. To evaluate the role of these residues, we mutated them in HMA6 and HMA8. Mutants of interest were selected from phenotypic tests in yeast and produced in Lactococcus lactis for further biochemical characterizations using phosphorylation assays from ATP and Pi. Combining functional and structural data, we highlight the importance of the cysteine and the first histidine of the Cx3Hx2H motif in the process of copper release from HMA6 and HMA8, and propose a copper pathway through the membrane domain of these transporters. Finally our work suggests a more general role of the histidine residue in the transport of copper by PIB-1-ATPases.
Published: 2016
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24. Membrane Protein Production in Lactococcus lactis for Functional Studies

Author: Daphne, Seigneurin-Berny, Martin S, King, Emiline, Sautron, Lucas, Moyet, Patrice, Catty, François, André, Norbert, Rolland, Edmund R S, Kunji, and Annie, Frelet-Barrand
Subjects: Lactococcus lactis, Bacterial Proteins, Genetic Vectors, Gene Expression, Membrane Proteins, Protein Engineering, Recombinant Proteins
Abstract: Due to their unique properties, expression and study of membrane proteins in heterologous systems remains difficult. Among the bacterial systems available, the Gram-positive lactic bacterium, Lactococcus lactis, traditionally used in food fermentations, is nowadays widely used for large-scale production and functional characterization of bacterial and eukaryotic membrane proteins. The aim of this chapter is to describe the different possibilities for the functional characterization of peripheral or intrinsic membrane proteins expressed in Lactococcus lactis.
Published: 2016

25. MASCP Gator: An Aggregation Portal for the Visualization of Arabidopsis Proteomics Data

Author: Ian Castleden, Stefanie Wienkoop, Matthias Hirsch-Hoffmann, Hirofumi Nakagami, Klaas J. van Wijk, Sandra K. Tanz, Christophe Bruley, Norbert Rolland, Joshua L. Heazlewood, Sacha Baginsky, Steven P. Briggs, Wilhelm Gruissem, A. Harvey Millar, R R Schmidt, Katja Baerenfaller, Alexandra M. E. Jones, Hiren J. Joshi, Waltraud X. Schulze, Volker Egelhofer, Tetsuro Toyoda, Wolfram Weckwerth, Qi Sun, Joint BioEnergy Institute, Department of Biology, Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Max Planck Institute of Molecular Plant Physiology (MPI-MP), Max-Planck-Gesellschaft, Department of plant Biology, Cornell University, Molecular Systems Biology, universite de Vienne, Laboratoire d'Etude de la Dynamique des Proteomes, Institut National de la Santé et de la Recherche Médicale (INSERM), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, The Sainsbury Laboratory, Sainsbury Laboratory, Division of Biology, University of California [San Diego] (UC San Diego), University of California-University of California, Centre of Excellence for Computational Systems Biology, The University of Western Australia (UWA), Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks, Cornell University [New York], Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), The Sainsbury Laboratory [Norwich] (TSL), University of California (UC)-University of California (UC), U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research [DE-AC02-05CH11231], AGRON-OMICS [LSHG-CT-2006-037704], Australian Research Council, Australian Research Council Centre of Excellence in Plant Energy Biology, Ministry of Education, Culture, Sports, Science and Technology [21770059], Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Bioinformatics, Physiology, Research areas, Arabidopsis, plant, Plant Science, Proteomics, 01 natural sciences, World Wide Web, User-Computer Interface, 03 medical and health sciences, proteomics, Resource (project management), online resources, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Phosphorylation, Databases, Protein, database, 030304 developmental biology, Internet, 0303 health sciences, biology, Arabidopsis Proteins, business.industry, data mining, Hyperlink, biology.organism_classification, Visualization, Identification (information), information networks, aggregator, The Internet, business, Protein Kinases, 010606 plant biology & botany
Abstract: Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (H.J.J., J.L.H.); Department of Biology, Eidgenossisch Technische Hochschule Zurich, CH-8092 Zurich, Switzerland (M. H.-H., K. B., W. G.); Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, 06120 Halle (Saale), Germany (S. B.); Max-Planck Institute for Molecular Plant Physiology, 14476 Potsdam-Golm, Germany (R. S., W. X. S.); Department of Plant Biology, Cornell University, Ithaca, New York 14853 (Q. S., K.J.v.W.); Molecular Systems Biology, University of Vienna, 1090 Vienna, Austria (V. E., S. W., W. W.); Institut National de la Sante et de la Recherche Medicale, Laboratoire d'Etude de la Dynamique des Proteomes, U880, F-38000 Grenoble, France (C. B.); Commissariat a l'Energie Atomique et aux Energies Alternatives, Direction des Sciences du Vivant, Institut de Recherches en Technologies et Sciences pour le Vivant, F-38000 Grenoble, France (C.B., N.R.); Universite Joseph Fourier, F-38000 Grenoble, France (C. B., N.R.); CNRS, Laboratoire de Physiologie Cellulaire Vegetale, UMR5168, F-38000 Grenoble, France (N.R.); INRA, UMR1200, F-38000 Grenoble, France (N.R.); RIKEN Plant Science Center and RIKEN Bioinformatics and Systems Engineering Division, Tsurumi-ku, Yokohama 230-0045, Japan (T.T., H.N.); The Sainsbury Laboratory, John Innes Centre, Norwich Research Park, Norwich NR4 7UH, United Kingdom (A.M.J.); Division of Biology, University of California San Diego, La Jolla, California 92093 (S.P.B.); and Centre of Excellence for Computational Systems Biology (I.C.) and Australian Research Council Centre of Excellence in Plant Energy Biology and Centre for Comparative Analysis of Biomolecular Networks (I.C., S.K.T., A.H.M.), University of Western Australia, Crawley 6009, Western Australia, Australia
Published: 2010
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26. Plant organelle proteomics: Collaborating for optimal cell function

Author: Pascale Jolivet, John H. Doonan, Jacques Bourguignon, Thierry Chardot, Konstantinos G. Alexiou, Niranjan Chakraborty, Geneviève Ephritikhine, Norbert Rolland, Myriam Ferro, Michel Jaquinod, Ganesh Kumar Agrawal, and Randeep Rakwal
Subjects: 0106 biological sciences, 0303 health sciences, biology, Chemistry, food and beverages, Condensed Matter Physics, Proteomics, biology.organism_classification, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, Analytical Chemistry, Cell biology, 03 medical and health sciences, Arabidopsis, Organelle, Proteome, Organelle biogenesis, Plastid, Spectroscopy, Function (biology), Organism, 030304 developmental biology, 010606 plant biology & botany
Abstract: Organelle proteomics describes the study of proteins present in organelle at a particular instance during the whole period of their life cycle in a cell. Organelles are specialized membrane bound structures within a cell that function by interacting with cytosolic and luminal soluble proteins making the protein composition of each organelle dynamic. Depending on organism, the total number of organelles within a cell varies, indicating their evolution with respect to protein number and function. For example, one of the striking differences between plant and animal cells is the plastids in plants. Organelles have their own proteins, and few organelles like mitochondria and chloroplast have their own genome to synthesize proteins for specific function and also require nuclear-encoded proteins. Enormous work has been performed on animal organelle proteomics. However, plant organelle proteomics has seen limited work mainly due to: (i) inter-plant and inter-tissue complexity, (ii) difficulties in isolation of subcellular compartments, and (iii) their enrichment and purity. Despite these concerns, the field of organelle proteomics is growing in plants, such as Arabidopsis, rice and maize. The available data are beginning to help better understand organelles and their distinct and/or overlapping functions in different plant tissues, organs or cell types, and more importantly, how protein components of organelles behave during development and with surrounding environments. Studies on organelles have provided a few good reviews, but none of them are comprehensive. Here, we present a comprehensive review on plant organelle proteomics starting from the significance of organelle in cells, to organelle isolation, to protein identification and to biology and beyond. To put together such a systematic, in-depth review and to translate acquired knowledge in a proper and adequate form, we join minds to provide discussion and viewpoints on the collaborative nature of organelles in cell, their proper function and evolution.
Published: 2010
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27. Chloroplast Proteomics and the Compartmentation of Plastidial Isoprenoid Biosynthetic Pathways

Author: Daphné Seigneurin-Berny, Norbert Rolland, Jérôme Garin, Christophe Masselon, Myriam Ferro, Jacques Joyard, Daniel Salvi, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: Chlorophyll, Proteomics, 0106 biological sciences, Chloroplasts, proteome, Arabidopsis, plant, Plant Science, Biology, 01 natural sciences, isoprenoid biosynthesis, 03 medical and health sciences, chloroplast, Stroma, subcellular localization, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Plastids, Plastid, Databases, Protein, Molecular Biology, Plant Proteins, 030304 developmental biology, 0303 health sciences, Sequence Homology, Amino Acid, food and beverages, metabolic pathway, Chloroplast, Biochemistry, Plant protein, Thylakoid, Proteome, Chloroplast Proteins, metabolism, 010606 plant biology & botany
Abstract: International audience; Recent advances in the proteomic field have allowed high-throughput experiments to be conducted on chloroplast samples. Many proteomic investigations have focused on either whole chloroplast or sub-plastidial fractions. To date, the Plant Protein Database (PPDB, Sun et al., 2009) presents the most exhaustive chloroplast proteome available online. However, the accurate localization of many proteins that were identified in different sub-plastidial compartments remains hypothetical. Ferro et al. (2009) went a step further into the knowledge of Arabidopsis thaliana chloroplast proteins with regards to their accurate localization within the chloroplast by using a semi-quantitative proteomic approach known as spectral counting. Their proteomic strategy was based on the accurate mass and time tags (AMT) database approach and they built up AT_CHLORO, a comprehensive chloroplast proteome database with sub-plastidial localization and curated information on envelope proteins. Comparing these two extensive databases, we focus here on about 100 enzymes involved in the synthesis of chloroplast-specific isoprenoids. Well known pathways (i.e. compartmentation of the methyl erythritol phosphate biosynthetic pathway, of tetrapyrroles and chlorophyll biosynthesis and breakdown within chloroplasts) validate the spectral counting-based strategy. The same strategy was then used to identify the precise localization of the biosynthesis of carotenoids and prenylquinones within chloroplasts (i.e. in envelope membranes, stroma, and/or thylakoids) that remains unclear until now.
Published: 2009
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28. A Proteomic Survey of Chlamydomonas reinhardtii Mitochondria Sheds New Light on the Metabolic Plasticity of the Organelle and on the Nature of the -Proteobacterial Mitochondrial Ancestor

Author: Brigitte Gontero, Oliver Deusch, Jérôme Garin, Marianne Tardif, Norbert Rolland, Sabine Brugière, Tal Dagan, Jacques Joyard, William Martin, Annie Adrait, Robert van Lis, Lauriane Kuhn, Ariane Atteia, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire d'étude de la dynamique des protéomes (LEDyP), Université Joseph Fourier - Grenoble 1 (UJF)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM), Institute of Botany, Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Bioénergétique et Ingénierie des Protéines (BIP ), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, carbon metabolism, Algae, proteome, Chlamydomonas reinhardtii, nucleotide metabolism, Mitochondrion, phylogeny, 01 natural sciences, Genome, Oxidative Phosphorylation, 03 medical and health sciences, evolution, Organelle, Genetics, Animals, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Alphaproteobacteria, 030304 developmental biology, 0303 health sciences, biology, Chlamydomonas, metabolic pathway, sequence homology, bioinformatics, Vitamin biosynthesis, biology.organism_classification, Biological Evolution, Cell biology, mitochondria, enzyme, vitamin biosynthesis, targeting prediction, Proteome, Eukaryote, protein import, protein, metabolism, 010606 plant biology & botany
Abstract: Mitochondria play a key role in the life and death of eukaryotic cells, yet the full spectrum of mitochondrial functions is far from being fully understood, especially in photosynthetic organisms. To advance our understanding of mitochondrial functions in a photosynthetic cell, an extensive proteomic survey of Percoll-purified mitochondria from the metabolically versatile, hydrogen-producing green alga Chlamydomonas reinhardtii was performed. Different fractions of purified mitochondria from Chlamydomonas cells grown under aerobic conditions were analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry after protein separation on sodium dodecyl sulfate polyacrylamide gel electrophoresis or on blue-native polyacrylamide gel electrophoresis. Of the 496 nonredundant proteins identified, 149 are known or predicted to reside in other cellular compartments and were thus excluded from the molecular and evolutionary analyses of the Chlamydomonas proteome. The mitochondrial proteome of the photosynthetic alga reveals important lineage-specific differences with other mitochondrial proteomes, reflecting the high metabolic diversity of the organelle. Some mitochondrial metabolic pathways in Chlamydomonas appear to combine typical mitochondrial enzymes and bacterial-type ones, whereas others are unknown among mitochondriate eukaryotes. The comparison of the Chlamydomonas proteins to their identifiable homologs predicted from 354 sequenced genomes indicated that Arabidopsis is the most closely related nonalgal eukaryote. Furthermore, this phylogenomic analysis shows that free-living alpha-proteobacteria from the metabolically versatile orders Rhizobiales and Rhodobacterales better reflect the gene content of the ancestor of the chlorophyte mitochondria than parasitic alpha-proteobacteria with reduced and specialized genomes.
Published: 2009
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29. The chloroplast membrane associated ceQORH putative quinone oxidoreductase reduces long-chain, stress-related oxidized lipids

Author: Gilles Curien, Jean-Luc Montillet, Jean-Luc Ferrer, David Cobessi, Alexander N. Grechkin, Michel Matringe, Cécile Giustini, Norbert Rolland, Sarah Mas-y-Mas, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Biologie végétale et microbiologie environnementale - UMR7265 (BVME), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Laboratoire d'Ecophysiologie Moléculaire des Plantes (LEMP), Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Kazan Institute of Biochemistry and Biophysics, ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Protéines de Protection des Végétaux (PPV), Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), French National Research Agency GRAL Labex ANR-10-LABX-49-01, Russian Academy of Sciences, Labex GRAL (Alliance Grenobloise pour la Biologie Structurale et Cellulaire integrees), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Aix Marseille Université (AMU)-Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Subjects: 0301 basic medicine, Chloroplasts, Membrane lipids, Lipoxygenase, reactive electrophile species, Arabidopsis, gamma-ketols, Cyclopentanes, Plant Science, Horticulture, Biology, Quinone oxidoreductase, oxylipin, Biochemistry, Chloroplast membrane, Membrane Lipids, 03 medical and health sciences, Quinone Reductases, chloroplast, Inner membrane, alkenone reductase, Oxylipins, Jasmonate, Molecular Biology, ComputingMilieux_MISCELLANEOUS, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Arabidopsis Proteins, Quinones, Membrane Proteins, General Medicine, jasmonate, Chloroplast, Metabolic pathway, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Fatty Acids, Unsaturated, Oxidation-Reduction
Abstract: International audience; Under oxidative stress conditions the lipid constituents of cells can undergo oxidation whose frequent consequence is the production of highly reactive alpha,beta-unsaturated carbonyls. These molecules are toxic because they can add to biomolecules (such as proteins and nucleic acids) and several enzyme activities cooperate to eliminate these reactive electrophile species. CeQORH (chloroplast envelope Quinone Oxidoreductase Homolog, At4g13010) is associated with the inner membrane of the chloroplast envelope and imported into the organelle by an alternative import pathway. In the present study, we show that the recombinant ceQORH exhibits the activity of a NADPH-dependent alpha,beta-unsaturated oxoene reductase reducing the double bond of medium-chain (C >= 9) to long-chain (18 carbon atoms) reactive electrophile species deriving from poly-unsaturated fatty acid peroxides. The best substrates of ceQORH are 13-lipoxygenase-derived gamma-ketols. gamma-Ketols are spontaneously produced in the chloroplast from the unstable allene oxide formed in the biochemical pathway leading to 12-oxo-phytodienoic acid, a precursor of the defense hormone jasmonate. In chloroplasts, ceQORH could detoxify 13-lipoxygenase-derived gamma-ketols at their production sites in the membranes. This finding opens new routes toward the understanding of gamma-ketols role and detoxification.
Published: 2016
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30. Membrane Protein Production in Lactococcus lactis for Functional Studies

Author: Lucas Moyet, Edmund R.S. Kunji, Martin S. King, Annie Frelet-Barrand, Emiline Sautron, Patrice Catty, François André, Daphné Seigneurin-Berny, Norbert Rolland, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Mitochondrial Biology Unit, Medical Research Council, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Franche-Comté Électronique Mécanique, Thermique et Optique - Sciences et Technologies (UMR 6174) (FEMTO-ST), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Centre National de la Recherche Scientifique (CNRS), Medical Research Council [MC_U105663139], Mus-Veteau Isabelle, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Paris-Sud - Paris 11 (UP11)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Université de Franche-Comté (UFC)-Centre National de la Recherche Scientifique (CNRS)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Université de Technologie de Belfort-Montbeliard (UTBM), Laboratoire de physiologie cellulaire végétale ( LPCV ), Institut National de la Recherche Agronomique ( INRA ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Laboratoire de Chimie et Biologie des Métaux ( LCBM - UMR 5249 ), Université Joseph Fourier - Grenoble 1 ( UJF ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Grenoble Alpes ( UGA ), Institut de Biologie Intégrative de la Cellule ( I2BC ), Université Paris-Saclay-Centre National de la Recherche Scientifique ( CNRS ) -Commissariat à l'énergie atomique et aux énergies alternatives ( CEA ) -Université Paris-Sud - Paris 11 ( UP11 ), Mus-Veteau, I., Wellcome Trust-Medical Research Council Cambridge Stem Cell Institute, University of Cambridge [UK] (CAM), Université de Technologie de Belfort-Montbeliard (UTBM)-Ecole Nationale Supérieure de Mécanique et des Microtechniques (ENSMM)-Centre National de la Recherche Scientifique (CNRS)-Université de Franche-Comté (UFC), Université Bourgogne Franche-Comté [COMUE] (UBFC)-Université Bourgogne Franche-Comté [COMUE] (UBFC), and ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010)
Subjects: 0301 basic medicine, Heterologous, Expression, law.invention, 03 medical and health sciences, Transport assays, law, Gene expression, Membrane proteins, Protocol, Functional studies, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], [ SDV.BBM ] Life Sciences [q-bio]/Biochemistry, Molecular Biology, ComputingMilieux_MISCELLANEOUS, 030102 biochemistry & molecular biology, biology, [ SDV ] Life Sciences [q-bio], Lactococcus lactis, food and beverages, Protein engineering, biology.organism_classification, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], 030104 developmental biology, Biochemistry, Membrane protein, Recombinant DNA, Protein overexpression, Bacteria
Abstract: International audience; Due to their unique properties, expression and study of membrane proteins in heterologous systems remains difficult. Among the bacterial systems available, the Gram-positive lactic bacterium, Lactococcus lactis, traditionally used in food fermentations, is nowadays widely used for large-scale production and functional characterization of bacterial and eukaryotic membrane proteins. The aim of this chapter is to describe the different possibilities for the functional characterization of peripheral or intrinsic membrane proteins expressed in Lactococcus lactis.
Published: 2016
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31. No plastidial calmodulin-like proteins detected by two targeted mass-spectrometry approaches and GFP fusion proteins

Author: Daniel Salvi, Mathieu Baudet, Martine Neveu, Elisa Dell’Aglio, Myriam Ferro, Alexandra Kraut, David Macherel, Norbert Rolland, Gilles Curien, Martin-Laffon, Jacqueline, BLANC - Régulation de la dynamique du protéome chloroplastique - - Chloro-Pro2010 - ANR-10-BLAN-1610 - BLANC - VALID, Mediterranean Center for Environment and Biodiversity - - CeMEB2010 - ANR-10-LABX-0004 - LABX - VALID, Infrastructure Française de Protéomique - - ProFI2010 - ANR-10-INBS-0008 - INBS - VALID, Physiologie cellulaire et végétale (LPCV), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Etude de la dynamique des protéomes (EDyP ), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, ANR [ANR-2010-BLAN-1610-01 Chloro-Pro], Labex GRAL (Alliance Grenobloise pour la Biologie Structurale et Cellulaire Integrées : [ANR-10-LABEX-04], [ANR10-INSB-08 ProFI, Proteomics French Infrastructure], CEA DSV (IRTELIS International Program)., ANR-10-BLAN-1610,Chloro-Pro,Régulation de la dynamique du protéome chloroplastique(2010), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-INBS-0008,ProFI,Infrastructure Française de Protéomique(2010), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Etude de la dynamique des protéomes (EDyP), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), ANR–10–LABEX–04 ,GRAL,Labex, ANR10-INSB-08,ProFI,Proteomics French Infrastructure, Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)
Subjects: 0301 basic medicine, Proteomics, Calmodulin, Arabidopsis thaliana, Plastid, Plant Science, Vacuole, Mitochondrion, plastide, Biochemistry, Chloroplast, CaM-like protein, Purification protocol, 03 medical and health sciences, Cytosol, GFP fusion, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, calmoduline, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, protéomique, Molecular Biology, biology, chloroplaste, Mass spectrometry, Subcellular localization, Protein, Plant, Peroxisome, Cell biology, 030104 developmental biology, Targeted mass spectrometry, biology.protein, Calcium regulation, CaM-like proteins
Abstract: Supplementary data: http://dx.doi.org/10.1016/j.neps.2016.08.001; International audience; Background: CaM-like proteins (CMLs) are localized in the cytosol and others in organelles such as the mitochondria, the peroxisomes and the vacuole. To date, although several plastidial proteins were identified as CaM/CML interactors, no CMLs were assigned to the chloroplast. Absence of clues about the genetic identity of plastidial CMLs prevents investigating their regulatory role. Results: To improve our understanding of plastidial Ca2+ regulation, we attempted to identify plastidial CMLs with two large scale, CaM-specific proteomic approaches, and GFP-fusions. Conclusions: Despite the use of several different approaches no plastidial CML could be identified. GFP fusion of CML 35 CML36 and CML41 indicate a cytosolic localization.
Published: 2016
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32. Ions channels/transporters and chloroplast regulation

Author: Valeria Villanova, Dimitris Petroutsos, Daphné Seigneurin-Berny, Serena Flori, Giovanni Finazzi, Emeline Sautron, Martino Tomizioli, Norbert Rolland, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Fermentalg, Project 'Mixoalgues' (INRABAP Department grant)- Project 'Elici-TAG-Screening' (Region Rhone Alpes)- Marie Curie Initial Training Network Accliphot (FP7-PEOPLE-2012-ITN, 316427), ANR-10-LABX-0004,CeMEB,Mediterranean Center for Environment and Biodiversity(2010), ANR-10-GENM-0002,Chloro-types,Adaptation du chloroplaste aux stress abiotiques : utilisation de la protéomique pour révéler les phénotypes moléculaires(2010), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), ANR–10–LABEX–04 ,GRAL,Labex, ANR-2010- GENOM-BTV-002-01,Chloro-Types, Finazzi G., Petroutsos D., Tomizioli M., Flori S., Sautron E., Villanova V., Rolland N., and Seigneurin-Berny D.
Subjects: 0106 biological sciences, Chloroplasts, Arabidopsis thaliana, Physiology, Anion Transport Proteins, Arabidopsis, 01 natural sciences, Chloroplast membrane, Thylakoids, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Photosynthesis, Molecular Biology, Cation Transport Proteins, 030304 developmental biology, 0303 health sciences, Ion Transport, biology, ATP synthase, Chemiosmosis, Arabidopsis Proteins, Membrane Transport Proteins, Cell Biology, Plant, biology.organism_classification, Cell biology, Chloroplast, Cell metabolism, Biochemistry, Chloroplast envelope, Thylakoid, Proton motive force, biology.protein, Calcium, Homeostasis, 010606 plant biology & botany, Ions trafficking
Abstract: International audience; Ions play fundamental roles in all living cells and their gradients are often essential to fuel transports, to regulate enzyme activities and to transduce energy within and between cells. Their homeostasis is therefore an essential component of the cell metabolism. Ions must be imported from the extracellular matrix to their final subcellular compartments. Among them, the chloroplast is a particularly interesting example because there, ions not only modulate enzyme activities, but also mediate ATP synthesis and actively participate in the building of the photosynthetic structures by promoting membrane-membrane interaction. In this review, we first provide a comprehensive view of the different machineries involved in ion trafficking and homeostasis in the chloroplast, and then discuss peculiar functions exerted by ions in the frame of photochemical conversion of absorbed light energy.
Published: 2015
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33. Analytical ultracentrifugation and preliminary X-ray studies of the chloroplast envelope quinone oxidoreductase homologue from Arabidopsis thaliana

Author: Cécile Giustini, Norbert Rolland, Jean Luc Ferrer, David Cobessi, Gilles Curien, Sarah Mas y mas, Institut de biologie structurale (IBS - UMR 5075), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes (UGA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Beamline FIP-BM30A ESRF, ANR-10-INBS-0005-02,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10- LABX-49-01,Labex GRAL,Labex GRAL, Institut de biologie structurale (IBS - UMR 5075 ), Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), FRISBI project (ANR-10-INSB-05-0, GRAL project (ANR-10- LABX-49-01), ANR-10-INBS-0005,FRISBI,Infrastructure Française pour la Biologie Structurale Intégrée(2010), ANR-10-LABX-0049,GRAL,Grenoble Alliance for Integrated Structural Cell Biology(2010), Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Arabidopis thaliana, Chloroplasts, Quinone oxidoreductase homologue, Substrate specificity, Molecular Sequence Data, Biophysics, Arabidopsis, Quinone oxidoreductase, Biochemistry, Chloroplast membrane, Research Communications, Structural Biology, Oxidoreductase, Transit Peptide, Genetics, NAD(P)H Dehydrogenase (Quinone), [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Amino Acid Sequence, Peptide sequence, Purification, Transit peptide, chemistry.chemical_classification, biology, Arabidopsis Proteins, Protein, Membrane, food and beverages, Plant, Crystallisation, Condensed Matter Physics, biology.organism_classification, Chloroplast, chemistry, Chloroplast envelope, Enzyme, Analytical ultracentrifugation, Crystallization, Ultracentrifugation, CeQORH, Cloning
Abstract: Quinone oxidoreductases reduce a broad range of quinones and are widely distributed among living organisms. The chloroplast envelope quinone oxidoreductase homologue (ceQORH) fromArabidopsis thalianabinds NADPH, lacks a classical N-terminal and cleavable chloroplast transit peptide, and is transported through the chloroplast envelope membrane by an unknown alternative pathway without cleavage of its internal chloroplast targeting sequence. To unravel the fold of this targeting sequence and its substrate specificity, ceQORH fromA. thalianawas overexpressed inEscherichia coli, purified and crystallized. Crystals of apo ceQORH were obtained and a complete data set was collected at 2.34 Å resolution. The crystals belonged to space groupC2221, with two molecules in the asymmetric unit.
Published: 2015
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34. [Untitled]

Author: Ariane Vlerick, Norbert Rolland, Jacques Joyard, Fabrice Homblé, and Jean Marie Ruysschaert
Subjects: 0106 biological sciences, 0303 health sciences, Physiology, Chemistry, food and beverages, Cell Biology, 01 natural sciences, Chloride, Chloroplast membrane, Chloroplast, 03 medical and health sciences, Membrane, Biochemistry, Stroma, Ionic strength, Chloride channel, medicine, Biophysics, Ion channel, 030304 developmental biology, 010606 plant biology & botany, medicine.drug
Abstract: Several anions such as Cl−, NO− 2, SO2− 4, and PO3− 4 are known to modulate the photosynthetic activity. Moreover, the chloroplast metabolism requires the exchange of both inorganic and organic (e.g., triose phosphate, dicarboxylic acid, ATP) anions between the cytoplasmand the stroma. A chloride channel form the chloroplast envelope was reconstituted in planar lipid bilayers. We show that the channel is active in conditions prevailing in the plant. The open probability increases with the ionic strength of the experimental solutions and is maximal at 0 mV. This suggests that the channel could play a role in the osmotic regulation of the chloroplast. Amino group reagents affect the channel activity in a way that demonstrated that lysine residues are important for channel gating but not for ATP binding. Together, our results provide new information on the functioning of this channel in the chloroplast envelope membranes. They indicate that the open probability of the channel is low (P o ≤ 0.2) in vivo and that this channel can account for the chloride flux through the chloroplast envelope.
Published: 2003
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35. Functional Expression of Plant Membrane Proteins in Lactococcus lactis

Author: Annie Frelet-Barrand, Daniel Salvi, Lucas Moyet, Emeline Sautron, Sylvain Boutigny, Daphné Seigneurin-Berny, Norbert Rolland, Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Stress Oxydants et Détoxication (LSOD), Département Biochimie, Biophysique et Biologie Structurale (B3S), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), García-Fruitós, Elena, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), E, Garcia-Fruitos, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: biology, Chemistry, Lactococcus, [SDV]Life Sciences [q-bio], Lactococcus lactis, Heterologous, food and beverages, biology.organism_classification, protein overexpression, Membrane, Biochemistry, Membrane protein, Solubilization, Functional expression, Protocol, membrane protein, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Lactococcus lacti, Heterologous protein, bacteria, Bacteria, ComputingMilieux_MISCELLANEOUS
Abstract: International audience; The study of most membrane proteins remains challenging due to their hydrophobicity and their low natural abundance in cells. Lactococcus lactis, a Gram-positive lactic bacterium, has been traditionally used in food fermentations and is nowadays widely used in biotechnology for large-scale production of heterologous proteins. This system has been successfully used for the production of prokaryotic and eukaryotic membrane proteins. The purpose of this chapter is to provide detailed protocols for (1) the expression of plant peripheral or intrinsic membrane proteins and then for (2) their solubilization, from Lactococcus membranes, for further purification steps and biochemical characterization.
Published: 2015
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36. In vivo spectroscopy and NMR metabolite fingerprinting approaches to connect the dynamics of photosynthetic and metabolic phenotypes in resurrection plant Haberlea rhodopensis during desiccation and recovery

Author: Petko Mladenov, Vasiliy Goltsev, Norbert Rolland, Anne-Marie Boisson, Daniela Moyankova, Svetlana Simova, Dimitar Djilianov, Sabine Brugière, Magdalena Tchorbadjieva, Vasilena Krasteva, Giovanni Finazzi, Myriam Ferro, Diana Zasheva, Kalina Alipieva, Richard Bligny, Martin-Laffon, Jacqueline, Agricultural Academy, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Bulgarian Academy of Sciences, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Софийски университет = Sofia University, Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences (BAS), Operational programme 'Human resources Development', European Social Fund of the European Union [BG051PO001], COST-STSM-FA0603-5623, Rolland, Norbert, Djilianovl, Dimitar, Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), University of Sofia, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)
Subjects: déshydratation, Drought stress, Photosystem II, phenotype, ved/biology.organism_classification_rank.species, Resurrection plant, Plant Science, resurrection plant, drought stress, photosynthesis, metabolism, haberlea rhodopensis, lcsh:Plant culture, Photosynthesis, Photosystem I, Botany, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, lcsh:SB1-1110, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, photosynthèse, métabolisme, Photosystem, Haberlea, Original Research, sécheresse, réaction au stress, Vegetal Biology, biology, ved/biology, fungi, food and beverages, Valine, Plant, biology.organism_classification, rehydratation, Metabolic pathway, phénotype, Haberlea rhodopensis, Metabolism, propriété spectroscopique, lipids degradation, Biophysics, Desiccation, Aminoacids, Biologie végétale
Abstract: The resurrection plant Haberlea rhodopensis was used to study dynamics of drought response of photosynthetic machinery parallel with changes in primary metabolism. A relation between leaf water content and photosynthetic performance was established, enabling us to perform a non-destructive evaluation of the plant water status during stress. Spectroscopic analysis of photosynthesis indicated that, at variance with linear electron flow involving photosystem (PS) I and II, cyclic electron flow around PSI remains active till almost full dry state at the expense of the linear electron flow, due to the changed protein organization of photosynthetic apparatus. We suggest that, this activity could have a photoprotective role and prevent a complete drop in adenosine triphosphate (ATP), in the absence of linear electron flow, to fuel specific energy-dependent processes necessary for the survival of the plant, during the late states of desiccation. The NMR fingerprint show significant metabolic changes in several pathways. Due to the declining of linear electron flow accompanied by biosynthetic reactions during desiccation, a reduction of the ATP pool during drought was observed, which was fully and quickly recovered after plants rehydration. We found a decline of valine accompanied by lipid degradation during stress, likely to provide alternative carbon sources for sucrose accumulation at late stages of desiccation. This accumulation, as well as the increased levels of glycerophosphodiesters during drought stress could provide osmoprotection to the cells.
Published: 2015
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37. Integral membrane proteins of the chloroplast envelope: Identification and subcellular localization of new transporters

Author: Jacques Joyard, Daphné Seigneurin-Berny, Jérôme Garin, Myriam Ferro, Norbert Rolland, Hélène Riviere-Rolland, Thierry Vermat, Didier Grunwald, Daniel Salvi, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)
Subjects: 0106 biological sciences, Chloroplasts, Proteome, In silico, Molecular Sequence Data, [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Computational biology, Biology, Polymerase Chain Reaction, 01 natural sciences, Chloroplast membrane, 03 medical and health sciences, Spinacia oleracea, BIOLOGIE CELLULAIRE, Inner membrane, Plastids, Plastid envelope, Integral membrane protein, DNA Primers, Plant Proteins, 030304 developmental biology, 0303 health sciences, Multidisciplinary, BIOCHIMIE, Membrane Proteins, Intracellular Membranes, Biological Sciences, BASE DE DONNEES, Molecular biology, Transmembrane protein, Membrane protein, Solvents, Carrier Proteins, METHODE PAGE, Subcellular Fractions, 010606 plant biology & botany
Abstract: A two-membrane system, or envelope, surrounds plastids. Because of the integration of chloroplast metabolism within the plant cell, the envelope is the site of many specific transport activities. However, only a few proteins involved in the processes of transport across the chloroplast envelope have been identified already at the molecular level. To discover new envelope transporters, we developed a subcellular proteomic approach, which is aimed to identify the most hydrophobic envelope proteins. This strategy combined the use of highly purified and characterized membrane fractions, extraction of the hydrophobic proteins with organic solvents, SDS/PAGE separation, and tandem mass spectrometry analysis. To process the large amount of MS/MS data, a blast -based program was developed for searching in protein, expressed sequence tag, and genomic plant databases. Among the 54 identified proteins, 27 were new envelope proteins, with most of them bearing multiple α-helical transmembrane regions and being very likely envelope transporters. The present proteomic study also allowed us to identify common features among the known and newly identified putative envelope inner membrane transporters. These features were used to mine the complete Arabidopsis genome and allowed us to establish a virtual plastid envelope integral protein database. Altogether, both proteomic and in silico approaches identified more than 50 candidates for the as yet previously uncharacterized plastid envelope transporters. The predictable function of some of these proteins opens up areas of investigation that may lead to a better understanding of the chloroplast metabolism. The present subcellular proteomic approach is amenable to the analysis of the hydrophobic core of other intracellular membrane systems.
Published: 2002
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38. Functional expression of plant membrane proteins in Lactococcus lactis

Author: Sylvain, Boutigny, Emeline, Sautron, Annie, Frelet-Barrand, Lucas, Moyet, Daniel, Salvi, Norbert, Rolland, and Daphné, Seigneurin-Berny
Subjects: Lactococcus lactis, Gene Expression, Membrane Proteins, Biotechnology, Plant Proteins
Abstract: The study of most membrane proteins remains challenging due to their hydrophobicity and their low natural abundance in cells. Lactococcus lactis, a Gram-positive lactic bacterium, has been traditionally used in food fermentations and is nowadays widely used in biotechnology for large-scale production of heterologous proteins. This system has been successfully used for the production of prokaryotic and eukaryotic membrane proteins. The purpose of this chapter is to provide detailed protocols for (1) the expression of plant peripheral or intrinsic membrane proteins and then for (2) their solubilization, from Lactococcus membranes, for further purification steps and biochemical characterization.
Published: 2014

39. Deciphering Thylakoid Sub-compartments using a Mass Spectrometry-based Approach

Author: Daniel Salvi, Lucas Moyet, Lisa M. Breckels, Daphné Seigneurin-Berny, Cosmin Lazar, Thomas Burger, Sabine Brugière, Giovanni Finazzi, Norbert Rolland, Myriam Ferro, Anne-Marie Hesse, Kathryn S. Lilley, Martino Tomizioli, Laurent Gatto, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), French National Research Agency (Grenoble Alliance for Integrated Structural Cell Biology) [ANR-2010-GENOM-BTV-002-01 Chloro-Types, ANR-10-LABEX-04 GRAL Labex, ANR-10-INBS-08 ProFI], EU FP7 program (Prime-XS project) [262067], Marie Curie Initial Training Network Accliphot [316427], Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: Proteomics, 0106 biological sciences, Arabidopsis, Biology, Photosynthesis, Thylakoids, 01 natural sciences, Biochemistry, Mass Spectrometry, Analytical Chemistry, 03 medical and health sciences, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Organelle, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, Plant Proteins, 030304 developmental biology, 0303 health sciences, food and beverages, Biological membrane, Articles, Chloroplast, Membrane, Thylakoid, Quantasome, 010606 plant biology & botany
Abstract: International audience; Photosynthesis has shaped atmospheric and ocean chemistries and probably changed the climate as well, as oxygen is released from water as part of the photosynthetic process. In photosynthetic eukaryotes, this process occurs in the chloroplast, an organelle containing the most abundant biological membrane, the thylakoids. The thylakoids of plants and some green algae are structurally inhomogeneous, consisting of two main domains: the grana, which are piles of membranes gathered by stacking forces, and the stroma-lamellae, which are unstacked thylakoids connecting the grana. The major photosynthetic complexes are unevenly distributed within these compartments because of steric and electrostatic constraints. Although proteomic analysis of thylakoids has been instrumental to define its protein components, no extensive proteomic study of subthylakoid localization of proteins in the BBY (grana) and the stroma-lamellae fractions has been achieved so far. To fill this gap, we performed a complete survey of the protein composition of these thylakoid subcompartments using thylakoid membrane fractionations. We employed semiquantitative proteomics coupled with a data analysis pipeline and manual annotation to differentiate genuine BBY and stroma-lamellae proteins from possible contaminants. About 300 thylakoid (or potentially thylakoid) proteins were shown to be enriched in either the BBY or the stroma-lamellae fractions. Overall, present findings corroborate previous observations obtained for photosynthetic proteins that used nonproteomic approaches. The originality of the present proteomic relies in the identification of photosynthetic proteins whose differential distribution in the thylakoid subcompartments might explain already observed phenomenon such as LHCII docking. Besides, from the present localization results we can suggest new molecular actors for photosynthesis-linked activities. For instance, most PsbP-like subunits being differently localized in stroma-lamellae, these proteins could be linked to the PSI-NDH complex in the context of cyclic electron flow around PSI. In addition, we could identify about a hundred new likely minor thylakoid (or chloroplast) proteins, some of them being potential regulators of the chloroplast physiology.
Published: 2014
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40. Organic solvent extraction as a versatile procedure to identify hydrophobic chloroplast membrane proteins

Author: Daphné Seigneurin-Berny, Myriam Ferro, Daniel Salvi, Jacques Joyard, Agnès Chapel, Norbert Rolland, and Jérôme Garin
Subjects: Gel electrophoresis, Chloroplasts, Chromatography, Chemistry, Detergents, Clinical Biochemistry, Peripheral membrane protein, Membrane Proteins, Biochemistry, Mass Spectrometry, Transmembrane protein, Analytical Chemistry, Membrane, Solubility, Membrane protein, Thylakoid, Proteome, Solvents, Electrophoresis, Polyacrylamide Gel, Salts, Organic Chemicals, Integral membrane protein
Abstract: As a complementary approach to genome projects, proteomic analyses have been set up to identify new gene products. One of the major challenges in proteomics concerns membrane proteins, especially the minor ones. A procedure based on the differential extraction of membrane proteins in chloroform/methanol mixtures, was tested on the two different chloroplast membrane systems: envolope and thylakoid membranes. Combining the use of classical sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and mass spectrometry analyses, this procedure enabled identification of hydrophobic proteins. The propensity of hydrophobic proteins to partition in chloroform/methanol mixtures was directly correlated with the number of amino acid residues/number of putative transmembrane regions (Res/TM ratio). Regardless of the particular case of some lipid-interacting proteins, chloroform/methanol extractions allowed enrichment of hydrophobic proteins and exclusion of hydrophilic proteins from both membrane systems, thus demonstrating the versatility of the procedure.
Published: 2000
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41. Plant ribosome recycling factor homologue is a chloroplastic protein and is bactericidal in Escherichia coli carrying temperature-sensitive ribosome recycling factor

Author: Christine Miège, Jacques Joyard, Laszlo Janosi, Catherine Cheniclet, Akira Kaji, Norbert Rolland, Emeline Teyssier, Maryse A. Block, Masahiro Shuda, and Jean-Pierre Carde
Subjects: Ribosomal Proteins, Chloroplasts, Light, Molecular Sequence Data, Ribosome Recycling Factor, medicine.disease_cause, Ribosome, Spinacia oleracea, Ribosomal protein, Complementary DNA, Escherichia coli, medicine, Amino Acid Sequence, RNA, Messenger, Cloning, Molecular, Gene, Peptide sequence, Plant Proteins, Multidisciplinary, Base Sequence, Sequence Homology, Amino Acid, biology, Temperature, Proteins, Biological Sciences, Recombinant Proteins, Anti-Bacterial Agents, Chloroplast, Biochemistry, biology.protein, Ribosomes
Abstract: We have isolated a protein, mature RRFHCP, from chloroplasts of spinach ( Spinacia oleracea L.) that shows 46% sequence identity and 66% sequence homology with ribosome recycling factor (RRF) of Escherichia coli . RRF recycles ribosomes through disassembly of the posttermination complex. From the cDNA analysis and from the amino-terminal sequencing of the isolated protein, the mature RRFHCP was deduced to have a M r of 21,838 with 193 aa. It lacks the 78-aa chloroplast targeting sequence encoded by the RRFHCP cDNA sequence. The RRFHCP synthesized in vitro was imported into isolated chloroplasts with simultaneous conversion to the mature RRFHCP. Transcription of the gene coding for RRFHCP was not dependent on light, yet it was limited mostly to photosynthetic tissues in which only one transcript size was detected. Mature RRFHCP exerted a bactericidal effect on E. coli carrying temperature-sensitive RRF at the permissive temperature whereas wild-type E. coli was not affected.
Published: 1999
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42. HMA1 and PAA1, two chloroplast envelope PIB-ATPases, play distinct roles in chloroplast copper homeostasis

Author: Annie Frelet-Barrand, Giovanni Finazzi, Norbert Rolland, Corinne Rivasseau, Daphné Seigneurin-Berny, Marinus Pilon, Emeline Sautron, Sylvain Boutigny, Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Biology department and program in molecular plant biology, University of Colorado [Boulder], Grant from the US National Science Foundation (IOS-0847442), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0106 biological sciences, Arabidopsis thaliana, Physiology, ATPase, Mutant, Arabidopsis, chemistry.chemical_element, Gene Expression, plant, Plant Science, 01 natural sciences, Chloroplast membrane, Gene Expression Regulation, Enzymologic, PIB ATPase, 03 medical and health sciences, chloroplast, Gene Expression Regulation, Plant, medicine, Chloroplast Proton-Translocating ATPases, Homeostasis, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cell damage, 030304 developmental biology, Adenosine Triphosphatases, 0303 health sciences, biology, Arabidopsis Proteins, envelope transporter, food and beverages, Transporter, biology.organism_classification, medicine.disease, Plants, Genetically Modified, Copper, Chloroplast, Plant Leaves, Phenotype, Biochemistry, chemistry, Seedlings, copper, Mutation, biology.protein, metal homeostasis, 010606 plant biology & botany
Abstract: International audience; Copper is an essential micronutrient but it is also potentially toxic as copper ions can catalyse the production of free radicals, which result in various types of cell damage. Therefore, copper homeostasis in plant and animal cells must be tightly controlled. In the chloroplast, copper import is mediated by a chloroplast-envelope PIB-type ATPase, HMA6/PAA1. Copper may also be imported by HMA1, another chloroplast-envelope PIB-ATPase. To get more insights into the specific functional roles of HMA1 and PAA1 in copper homeostasis, this study analysed the phenotypes of plants affected in the expression of both HMA1 and PAA1 ATPases, as well as of plants overexpressing HMA1 in a paa1 mutant background. The results presented here provide new evidence associating HMA1 with copper homeostasis in the chloroplast. These data suggest that HMA1 and PAA1 behave as distinct pathways for copper import and targeting to the chloroplast. Finally, this work also provides evidence for an alternative route for copper import into the chloroplast mediated by an as-yet unidentified transporter that is neither HMA1 nor PAA1
Published: 2014
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43. Lactococcus lactis: Recent Developments in Functional Expression of Membrane Proteins

Author: Marcel Delaforge, Daphné Seigneurin-Berny, François Andre, Norbert Rolland, Annie Frelet-Barrand, and Sana Bakari
Subjects: Membrane protein, Functional expression, Gene expression, Lactococcus lactis, medicine, Prokaryotic expression, A protein, Computational biology, Biology, medicine.disease_cause, biology.organism_classification, Escherichia coli, Microbiology
Abstract: Membrane proteins (MPs) play key roles in most important cellular processes ranging from cell-to-cell communication to signaling processes. Despite recent improvements, the expression of functionally folded MPs in sufficient amounts for functional and structural characterization remains a challenge. Indeed, it is still difficult to predict whether a protein can be overproduced in a functional state in some expression system(s), although studies of high-throughput screens have been issued in recent years. Prokaryotic expression systems present several advantages over eukaryotic ones. Among them, Lactococcus lactis (L. lactis) has emerged in the past years as a good alternative expression system to Escherichia coli. The purpose of this chapter is to describe L. lactis and its tightly inducible system, nisin-controlled gene expression (NICE), for the expression of MPs from both prokaryotic and eukaryotic origins. Moreover, we will describe the functional characterization of some MPs produced in L. lactis.
Published: 2014
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44. Complementary biochemical approaches applied to the identification of plastidial calmodulin-binding proteins

Author: Sabine Brugière, Daniel Salvi, Michel Matringe, Faustine Delpierre, Gilles Curien, Daphné Seigneurin-Berny, Cécile Giustini, Elisa Dell’Aglio, Lucas Moyet, Norbert Rolland, Mathieu Baudet, Myriam Ferro, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Labex GRAL (Alliance Grenobloise pour la Biologie Structurale et Cellulaire Intégrées), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: 0106 biological sciences, calmodulin, CaM-binding protein, Chloroplasts, animal structures, Calmodulin, Arabidopsis thaliana, proteome, Arabidopsis, plant, 01 natural sciences, 03 medical and health sciences, affinity chromatography, chloroplast, Spinacia oleracea, Organelle, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Plant Proteins, 030304 developmental biology, mass spectrometry, 0303 health sciences, calcium, biology, Arabidopsis Proteins, Gene Expression Profiling, biology.organism_classification, Calmodulin-binding proteins, 3. Good health, Plant Leaves, Chloroplast, Phosphotransferases (Alcohol Group Acceptor), Biochemistry, Proteome, biology.protein, Calmodulin-Binding Proteins, NAD+ kinase, Signal transduction, metabolism, Protein Binding, Signal Transduction, 010606 plant biology & botany, Biotechnology
Abstract: International audience; Ca(2+)/Calmodulin (CaM)-dependent signaling pathways play a major role in the modulation of cell responses in eukaryotes. In the chloroplast, few proteins such as the NAD(+) kinase 2 have been previously shown to interact with CaM, but a general picture of the role of Ca(2+)/CaM signaling in this organelle is still lacking. Using CaM-affinity chromatography and mass spectrometry, we identified 210 candidate CaM-binding proteins from different Arabidopsis and spinach chloroplast sub-fractions. A subset of these proteins was validated by an optimized in vitro CaM-binding assay. In addition, we designed two fluorescence anisotropy assays to quantitatively characterize the binding parameters and applied those assays to NAD(+) kinase 2 and selected candidate proteins. On the basis of our results, there might be many more plastidial CaM-binding proteins than previously estimated. In addition, we showed that an array of complementary biochemical techniques is necessary in order to characterize the mode of interaction of candidate proteins with CaM.
Published: 2013
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45. PredAlgo: a new subcellular localization prediction tool dedicated to green algae

Author: Laurent Cournac, Olivier Vallon, Sabine Brugière, Michael Specht, Norbert Rolland, Ariane Atteia, Myriam Ferro, Michael Hippler, Guillaume Cogne, Gilles Peltier, Christophe Bruley, Marianne Tardif, Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institute for Plant Biochemistry and Biotechnology, Westfälische Wilhelms-Universität Münster (WWU), Biologie cellulaire et moléculaire des plantes et des bactéries (BCMPB), Université de la Méditerranée - Aix-Marseille 2-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Physiologie membranaire et moléculaire du chloroplaste (PMMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), 'Bundesministerium für Bildung und Forschung' Grant 0315265C (GOFORSYS partner Golmer Forschungseinheit für Systembiologie)., Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université de la Méditerranée - Aix-Marseille 2, Bioénergie et Microalgues (EBM), Institut de Biosciences et Biotechnologies d'Aix-Marseille (ex-IBEB) (BIAM), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), Environnement, Bioénergie, Microalgues et Plantes (EBMP), and Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)-Direction de Recherche Fondamentale (CEA) (DRF (CEA))
Subjects: 0106 biological sciences, Chloroplasts, Algae, organellar import, Prasinophyceae, Chlamydomonas reinhardtii, transit peptide, Computational biology, Proteomics, 01 natural sciences, 03 medical and health sciences, proteomics, chloroplast, Transit Peptide, Botany, subcellular localization, Genetics, mitochondrion, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, mass spectrometry, 0303 health sciences, biology, Trebouxiophyceae, Algal Proteins, Computational Biology, biology.organism_classification, Mitochondria, secretory pathway, Chloroplast, Proteome, Neural Networks, Computer, Chloroplast Proteins, protein, Software, 010606 plant biology & botany
Abstract: International audience; The unicellular green alga Chlamydomonas reinhardtii is a prime model for deciphering processes occurring in the intracellular compartments of the photosynthetic cell. Organelle-specific proteomic studies have started to delineate its various subproteomes, but sequence-based prediction software is necessary to assign proteins subcellular localizations at whole genome scale. Unfortunately, existing tools are oriented toward land plants and tend to mispredict the localization of nuclear-encoded algal proteins, predicting many chloroplast proteins as mitochondrion targeted. We thus developed a new tool called PredAlgo that predicts intracellular localization of those proteins to one of three intracellular compartments in green algae: the mitochondrion, the chloroplast, and the secretory pathway. At its core, a neural network, trained using carefully curated sets of C. reinhardtii proteins, divides the N-terminal sequence into overlapping 19-residue windows and scores the probability that they belong to a cleavable targeting sequence for one of the aforementioned organelles. A targeting prediction is then deduced for the protein, and a likely cleavage site is predicted based on the shape of the scoring function along the N-terminal sequence. When assessed on an independent benchmarking set of C. reinhardtii sequences, PredAlgo showed a highly improved discrimination capacity between chloroplast- and mitochondrion-localized proteins. Its predictions matched well the results of chloroplast proteomics studies. When tested on other green algae, it gave good results with Chlorophyceae and Trebouxiophyceae but tended to underpredict mitochondrial proteins in Prasinophyceae. Approximately 18% of the nuclear-encoded C. reinhardtii proteome was predicted to be targeted to the chloroplast and 15% to the mitochondrion.
Published: 2012
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46. Prediction of subplastidial localization of chloroplast proteins from spectral count data - Comparison of machine learning algorithms

Author: Thomas Burger, Samuel Wieczorek, Christophe Masselon, Daniel Salvi, Norbert Rolland, Myriam Ferro, Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de Biologie à Grande Échelle (BGE - UMR S1038), Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes (UGA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG)
Subjects: food and beverages, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract: To study chloroplast metabolism and functions, subplastidial localization is a prerequisite to achieve protein functional characterization. As the accurate localization of many chloroplast proteins often remains hypothetical, we set up a proteomics strategy in order to assign the accurate subplastidial localization. A comprehensive study of Arabidopsis thaliana chloroplast proteome has been carried out in our group [1], involving high performance mass spectrometry analyses of highly fractionated chloroplasts. In particular, spectral count data were acquired for the three major chloroplast sub-fractions (stroma, thylakoids and envelope) obtained by sucrose gradient purification. As the distribution of spectral counts over compartments is a fair predicator of relative abundance of proteins [2], it was justified to propose a prime statistical model [1] relating spectral counts to subplastidial localization. This predictive model was based on a logistic regression, and demonstrated an accuracy rate of 84% for chloroplast proteins. In the present work, we conducted a comparative study of various machine learning techniques to generate a predictive model of subplastidial localization of chloroplast proteins based on spectral count data.
Published: 2012

47. The biosynthetic capacities of the plastids and integration between cytoplasmic and chloroplast processes

Author: Giovanni Finazzi, Marcel Kuntz, Gilles Curien, Daphné Seigneurin-Berny, Norbert Rolland, Eric Maréchal, Michel Matringe, Stéphane Ravanel, Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)
Subjects: 0106 biological sciences, MESH: Oxidation-Reduction, Cytoplasm, Chloroplasts, envelope transporters, plant, MESH: Carbon Dioxide, 01 natural sciences, Chloroplast Proteins, MESH: Cell Compartmentation, Cell Compartmentation, MESH: Chloroplast Proteins, Plastids, Photosynthesis, plastid, MESH: Evolution, Molecular, MESH: Photosynthesis, 0303 health sciences, MESH: Symbiosis, Endosymbiosis, MESH: Proteomics, food and beverages, MESH: Plastids, MESH: Cyanobacteria, Cell biology, Chloroplast, Protein Transport, Oxidation-Reduction, MESH: Protein Transport, Nuclear gene, chloroplast/cytosol exchange, review, Biology, Cyanobacteria, Evolution, Molecular, 03 medical and health sciences, proteomics, Plant Cells, Genetics, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastid, Symbiosis, 030304 developmental biology, MESH: Chloroplasts, MESH: Cytoplasm, fungi, Carbon Dioxide, MESH: Plant Cells, Cytosol, MESH: Organelle Size, Organelle Size, cell compartment, metabolism, 010606 plant biology & botany
Abstract: Document Type : Book Chapter; International audience; Plastids are semiautonomous organelles derived from cyanobacterial ancestors. Following endosymbiosis, plastids have evolved to optimize their functions, thereby limiting metabolic redundancy with other cell compartments. Contemporary plastids have also recruited proteins produced by the nuclear genome of the host cell. In addition, many genes acquired from the cyanobacterial ancestor evolved to code for proteins that are targeted to cell compartments other than the plastid. Consequently, metabolic pathways are now a patchwork of enzymes of diverse origins, located in various cell compartments. Because of this, a wide range of metabolites and ions traffic between the plastids and other cell compartments. In this review, we provide a comprehensive analysis of the well-known, and of the as yet uncharacterized, chloroplast/cytosol exchange processes, which can be deduced from what is currently known about compartmentation of plant-cell metabolism.
Published: 2012
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48. Subcellular and sub-organellar proteomics as a complementary tool to study the evolution of the plastid proteome

Author: Norbert Rolland, Marcel Kuntz, Laboratoire de physiologie cellulaire végétale (LPCV), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Bullerwell, C., Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Recherche Agronomique (INRA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), and Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])
Subjects: 0106 biological sciences, proteome, plant, Computational biology, Biology, Proteomics, 01 natural sciences, 03 medical and health sciences, chloroplast, Transit Peptide, Organelle, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Plastid, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, fungi, food and beverages, Molecular biology, Protein subcellular localization prediction, Amino acid, Chloroplast, chemistry, Proteome, protein, 010606 plant biology & botany
Abstract: Plastids fulfill a number of essential functions, including photosynthesis, assimilation of nitrogen and sulfur, synthesis of amino acids, fatty acids, and many secondary metabolites. Pure computation-based predictions are limited in predicting plastid proteomes, and proteomic and especially subcellular proteomics studies are essential to provide an in-depth evaluation of the plastid proteome. The aim of this chapter was to highlight some of the current data, generated by plastids proteomics, in terms of functions, compartmentation, and evolution of this organelle.
Published: 2012
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49. Biochemical Characterization of AtHMA6/PAA1, a Chloroplast Envelope Cu(I)-ATPase

Author: Patrice Catty, Roger Miras, Sylvain Boutigny, Daphné Seigneurin-Berny, Norbert Rolland, Jacques Joyard, Laboratoire de Chimie et Biologie des Métaux (LCBM - UMR 5249), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Direction de Recherche Fondamentale (CEA) (DRF (CEA)), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Laboratoire de physiologie cellulaire végétale (LPCV), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut de Biosciences et de Biotechnologies de Grenoble (ex-IRTSV) (BIG), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), CEA, CEA-PM project, CNRS, INRA, University of Grenoble, Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes (UGA)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Joseph Fourier - Grenoble 1 (UJF)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA)-Université Grenoble Alpes (UGA), Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019])-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche Interdisciplinaire de Grenoble (IRIG), Université Joseph Fourier - Grenoble 1 (UJF)-Institut National de la Recherche Agronomique (INRA)-Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), and Martin-Laffon, Jacqueline
Subjects: 0106 biological sciences, Chloroplasts, Arabidopsis thaliana, ATPase, Arabidopsis, ATPases, Plant Biology, plant, 01 natural sciences, Biochemistry, Chloroplast membrane, 03 medical and health sciences, parasitic diseases, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Chloroplast Proton-Translocating ATPases, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Molecular Biology, chloroplast envelope, P-TYPE ATPASE, METAL TRANSPORT, SACCHAROMYCES-CEREVISIAE, ARCHAEOGLOBUS-FULGIDUS, FUNCTIONAL EXPRESSION, COPPER HOMEOSTASIS, ENTEROCOCCUS-HIRAE, COFACTOR DELIVERY, P-1B-TYPE ATPASE, ARABIDOPSIS, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, Ion Transport, biology, urogenital system, Arabidopsis Proteins, Lactococcus lactis, food and beverages, Cell Biology, Cations, Monovalent, biology.organism_classification, Yeast, carbohydrates (lipids), Chloroplast, enzyme, Enzyme, chemistry, copper, metal transporter, biology.protein, Phosphorylation, lipids (amino acids, peptides, and proteins), 010606 plant biology & botany
Abstract: International audience; Copper is an essential plant micronutrient playing key roles in cellular processes, among them photosynthesis. In Arabidopsis thaliana, copper delivery to chloroplasts, mainly studied by genetic approaches, is thought to involve two P(IB)-type ATPases: AtHMA1 and AtHMA6/PAA1. The lack of biochemical characterization of AtHMA1 and PAA1, and more generally of plant P(IB)-type ATPases, is due to the difficulty of getting high amounts of these membrane proteins in an active form, either from their native environment or after expression in heterologous systems. In this study, we report the first biochemical characterization of PAA1, a plant copper-transporting ATPase. PAA1 produced in Lactococcus lactis is active, forming an aspartyl phosphate intermediate in the presence of ATP and the adequate metal ion. PAA1 can also be phosphorylated using inorganic phosphate in the absence of transition metal. Both phosphorylation types allowed us to demonstrate that PAA1 is activated by monovalent copper ions (and to a lower extent by silver ions) with an apparent affinity in the micromolar range. In agreement with these biochemical data, we also demonstrate that when expressed in yeast, PAA1 induces increased sensitivities to copper and silver. These data provide the first enzymatic characterization of a P(IB-1)-type plant ATPase and clearly identify PAA1 as a high affinity Cu(I) transporter of the chloroplast envelope.
Published: 2011
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50. Preparation of envelope membrane fractions from Arabidopsis chloroplasts for proteomic analysis and other studies

Author: Daniel, Salvi, Lucas, Moyet, Daphné, Seigneurin-Berny, Myriam, Ferro, Jacques, Joyard, and Norbert, Rolland
Subjects: Plant Leaves, Proteomics, Chloroplasts, Blotting, Western, Arabidopsis, Povidone, Electrophoresis, Polyacrylamide Gel, Intracellular Membranes, Chemical Fractionation, Cell Fractionation, Silicon Dioxide, Biomarkers, Mass Spectrometry
Abstract: Plastids are semiautonomous organelles restricted to plants and protists. These plastids are surrounded by a double membrane system, or envelope. These envelope membranes contain machineries to import nuclear-encoded proteins, and transporters for ions or metabolites, but are also essential for a range of plastid-specific metabolisms. Targeted semiquantitative proteomic investigations have revealed specific cross-contaminations by other cell or plastid compartments that may occur during chloroplast envelope purification. This article describes procedures developed to recover highly purified envelope fractions starting from Percoll-purified Arabidopsis chloroplasts, gives an overview of possible cross-contaminations, provides some tricks to limit these cross-contaminations, and lists immunological markers and methods that can be used to assess the purity of the envelope fractions.
Published: 2011

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