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1. A manually curated compendium of expression profiles for the microbial cell factory Corynebacterium glutamicum

Author

Angela Kranz, Tino Polen, Christian Kotulla, Annette Arndt, Graziella Bosco, Michael Bussmann, Ava Chattopadhyay, Annette Cramer, Cedric-Farhad Davoudi, Ursula Degner, Ramon Diesveld, Raphael Freiherr von Boeselager, Kim Gärtner, Cornelia Gätgens, Tobias Georgi, Christian Geraths, Sabine Haas, Antonia Heyer, Max Hünnefeld, Takeru Ishige, Armin Kabus, Nicolai Kallscheuer, Larissa Kever, Simon Klaffl, Britta Kleine, Martina Kočan, Abigail Koch-Koerfges, Kim J. Kraxner, Andreas Krug, Aileen Krüger, Andreas Küberl, Mohamed Labib, Christian Lange, Christina Mack, Tomoya Maeda, Regina Mahr, Stephan Majda, Andrea Michel, Xenia Morosov, Olga Müller, Arun M. Nanda, Jens Nickel, Jennifer Pahlke, Eugen Pfeifer, Laura Platzen, Paul Ramp, Doris Rittmann, Steffen Schaffer, Sandra Scheele, Stephanie Spelberg, Julia Schulte, Jens-Eric Schweitzer, Georg Sindelar, Ulrike Sorger-Herrmann, Markus Spelberg, Corinna Stansen, Apilaasha Tharmasothirajan, Jan van Ooyen, Philana van Summeren-Wesenhagen, Michael Vogt, Sabrina Witthoff, Lingfeng Zhu, Bernhard J. Eikmanns, Marco Oldiges, Georg Schaumann, Meike Baumgart, Melanie Brocker, Lothar Eggeling, Roland Freudl, Julia Frunzke, Jan Marienhagen, Volker F. Wendisch, and Michael Bott

Subjects
Science
Abstract

Abstract Corynebacterium glutamicum is the major host for the industrial production of amino acids and has become one of the best studied model organisms in microbial biotechnology. Rational strain construction has led to an improvement of producer strains and to a variety of novel producer strains with a broad substrate and product spectrum. A key factor for the success of these approaches is detailed knowledge of transcriptional regulation in C. glutamicum. Here, we present a large compendium of 927 manually curated microarray-based transcriptional profiles for wild-type and engineered strains detecting genome-wide expression changes of the 3,047 annotated genes in response to various environmental conditions or in response to genetic modifications. The replicates within the 927 experiments were combined to 304 microarray sets ordered into six categories that were used for differential gene expression analysis. Hierarchical clustering confirmed that no outliers were present in the sets. The compendium provides a valuable resource for future fundamental and applied research with C. glutamicum and contributes to a systemic understanding of this microbial cell factory. Measurement(s) Gene Expression Analysis Technology Type(s) Two Color Microarray Factor Type(s) WT condition A vs. WT condition B • Plasmid-based gene overexpression in parental strain vs. parental strain with empty vector control • Deletion mutant vs. parental strain Sample Characteristic - Organism Corynebacterium glutamicum Sample Characteristic - Environment laboratory environment Sample Characteristic - Location Germany

Published
2022
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2. The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin–Benson–Bassham cycle

Author

Stephanie Spelberg and Oliver Ebenhöh

Subjects
0106 biological sciences, 0301 basic medicine, Computer science, media_common.quotation_subject, carbon fixation, Context (language use), Review Article, Bioinformatics, 01 natural sciences, Biochemistry, Carbon Cycle, Gibbs phenomenon, 03 medical and health sciences, symbols.namesake, Contradiction, Photosynthesis, Review Articles, media_common, Gibbs effect, Reaction scheme, Carbon Dioxide, Epistemology, Calvin cycle, 030104 developmental biology, symbols, mathematical model, 010606 plant biology & botany
Abstract

The photosynthetic carbon reduction cycle, or Calvin–Benson–Bassham (CBB) cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still the subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle's structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive 14CO2 was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the ‘photosynthetic Gibbs effect’. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by CBB, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the CBB cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that it requires sound theoretical approaches to resolve conflicting interpretations and to provide consistent quantitative explanations.

Published
2018
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3. The importance of the photosynthetic Gibbs effect in the elucidation of the Calvin-Benson-Bassham Cycle

Author

Stephanie Spelberg and Oliver Ebenhoeh

Subjects
Gibbs phenomenon, Structure (mathematical logic), symbols.namesake, Philosophy, media_common.quotation_subject, symbols, Reaction scheme, Subject (philosophy), Contradiction, Context (language use), Epistemology, media_common
Abstract

The photosynthetic carbon reduction cycle, or Calvin-Benson-Bassham Cycle, is now contained in every standard biochemistry textbook. Although the cycle was already proposed in 1954, it is still subject of intense research, and even the structure of the cycle, i.e. the exact series of reactions, is still under debate. The controversy about the cycle’s structure was fuelled by the findings of Gibbs and Kandler in 1956 and 1957, when they observed that radioactive14CO2was dynamically incorporated in hexoses in a very atypical and asymmetrical way, a phenomenon later termed the ‘photosynthetic Gibbs effect’. Now, it is widely accepted that the photosynthetic Gibbs effect is not in contradiction to the reaction scheme proposed by Calvin, Benson and Bassham, but the arguments given have been largely qualitative and hand-waving. To fully appreciate the controversy and to understand the difficulties in interpreting the Gibbs effect, it is illustrative to illuminate the history of the discovery of the Calvin-Benson-Bassham Cycle. We here give an account of central scientific advances and discoveries, which were essential prerequisites for the elucidation of the cycle. Placing the historic discoveries in the context of the modern textbook pathway scheme illustrates the complexity of the cycle and demonstrates why especially dynamic labelling experiments are far from easy to interpret. We conclude by arguing that only mathematical models based on a sound theory are capable of resolving conflicting interpretations and providing a consistent quantitative explanation.

Published
2017
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4. A systems-wide understanding of photosynthetic acclimation in algae and higher plants

Author

Roberto Bassi, Ioannis Dikaios, Brieuc Urbain, Michel Goldschmidt-Clermont, Oliver Ebenhöh, Anna Matuszyńska, Stephanie Spelberg, Julie Maguire, Kailash Adhikari, Adeline Le Monnier, Dipali Singh, Stefano Magni, Giulio Rocco Stella, Lucilla Taddei, Federica Cariti, Claudia Zabke, Fiona Wanjiku Moejes, Antonella Succurro, Kathrin Müller, Giovanni Finazzi, Mark G. Poolman, Valeria Villanova, Serena Flori, Guillaume Cogne, Angela Falciatore, Cluster of Excellence on Plant Sciences (CEPLAS), Institute of Quantitative and Theoretical Biology, Heinrich Heine Universität Düsseldorf = Heinrich Heine University [Düsseldorf], Bantry Marine Research Station, Department of Biological and Medical Sciences, Oxford Brookes University, Department of Biotechnology, University of Tehran-University College of Science, Department of Botany and Plant Biology, University of Geneva, Laboratoire de génie des procédés - environnement - agroalimentaire (GEPEA), Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Université de Nantes (UN)-Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN), Centre National de la Recherche Scientifique (CNRS), Ecole Nationale Vétérinaire Agroalimentaire et de l'Alimentation Nantes Atlantique (ONIRIS), PRES Université Nantes Angers Le Mans (UNAM), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie - Paris 6 (UPMC), Sorbonne Université (SU), UMR 1417 PCV Laboratoire de Physiologie Cellulaire Végétale., Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA), Université Grenoble Alpes [2016-2019] (UGA [2016-2019]), Fermentalg SA, IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT), University of Aberdeen, Marie Curie Initial Training Network project, AccliPhot [PITN-GA-2012-316427], Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-IMT Atlantique Bretagne-Pays de la Loire (IMT Atlantique), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-Centre National de la Recherche Scientifique (CNRS)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN)-Institut Universitaire de Technologie - Nantes (IUT Nantes), Université de Nantes (UN)-Institut Universitaire de Technologie Saint-Nazaire (IUT Saint-Nazaire), Université de Nantes (UN)-Institut Universitaire de Technologie - La Roche-sur-Yon (IUT La Roche-sur-Yon), Université de Nantes (UN)-Ecole Nationale Vétérinaire, Agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Université Bretagne Loire (UBL), Heinrich-Heine-Universität Düsseldorf [Düsseldorf], Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Institut National de la Santé et de la Recherche Médicale (INSERM)-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 Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université Pierre et Marie Curie (Paris 6), Sorbonne Universités, Université Grenoble Alpes (UGA), Ecole Nationale Supérieure des Mines de Nantes (Mines Nantes), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-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)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Université de Nantes (UN)-École nationale vétérinaire, agroalimentaire et de l'alimentation Nantes-Atlantique (ONIRIS)-Centre National de la Recherche Scientifique (CNRS)-Université Bretagne Loire (UBL)-IMT Atlantique (IMT Atlantique), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), IMT Atlantique (IMT Atlantique), Moejes F.W., Matuszynska A., Adhikari K., Bassi R., Cariti F., Cogne G., Dikaios I., Falciatore A., Finazzi G., Flori S., Goldschmidt-Clermont M., Magni S., Maguire J., Le Monnier A., Muller K., Poolman M., Singh D., Spelberg S., Stella G.R., Succurro A., Taddei L., Urbain B., Villanova V., Zabke C., and Ebenhoh O.

Subjects
0301 basic medicine, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Physiology, Acclimatization, Context (language use), PhD training, interdisciplinary training, Plant Science, Biochemistry, biophysics & molecular biology [F05] [Life sciences], Biology, acclimation, Photosynthesis, Models, Biological, modelling, 03 medical and health sciences, Algae, Chlorophyta, application industrielle, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, mathematical modelling, Biochimie, biophysique & biologie moléculaire [F05] [Sciences du vivant], biodiversity, modélisation, micro-algue, Phototroph, photosynthetic system, Ecology, Non-photochemical quenching, Systems Biology, acclimatation photosynthétique, photosynthetic optimisation, Plankton, Plants, analyse rétrospective, biology.organism_classification, industrial application, European Training Network, 030104 developmental biology, Acclimation, microalgal cultivation, non-photochemical quenching, Photosynthetic acclimation, adaptation à la lumière, appareil photosynthétique, Biochemical engineering
Abstract

The ability of phototrophs to colonise different environments relies on robust protection against oxidative stress, a critical requirement for the successful evolutionary transition from water to land. Photosynthetic organisms have developed numerous strategies to adapt their photosynthetic apparatus to changing light conditions in order to optimise their photosynthetic yield, which is crucial for life on Earth to exist. Photosynthetic acclimation is an excellent example of the complexity of biological systems, where highly diverse processes, ranging from electron excitation over protein protonation to enzymatic processes coupling ion gradients with biosynthetic activity, interact on drastically different timescales from picoseconds to hours. Efficient functioning of the photosynthetic apparatus and its protection is paramount for efficient downstream processes, including metabolism and growth. Modern experimental techniques can be successfully integrated with theoretical and mathematical models to promote our understanding of underlying mechanisms and principles. This review aims to provide a retrospective analysis of multidisciplinary photosynthetic acclimation research carried out by members of the Marie Curie Initial Training Project, AccliPhot, placing the results in a wider context. The review also highlights the applicability of photosynthetic organisms for industry, particularly with regards to the cultivation of microalgae. It intends to demonstrate how theoretical concepts can successfully complement experimental studies broadening our knowledge of common principles in acclimation processes in photosynthetic organisms, as well as in the field of applied microalgal biotechnology.

Published
2017
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