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41 results on '"Gregor Mendel Institute of Molecular Plant Biology (GMI)"'

1. Chaperone-like protein DAY plays critical roles in photomorphogenesis

Author

Sung Hee Lee, Hee-Kyung Ahn, Tak Lee, Insuk Lee, Hyun Sook Pai, Ilyeong Choi, Dong Hye Seo, Ji Woo Kim, Ho Seok Lee, Huikyong Cho, Jae Hee Kim, Julian Bünting, Young Eun Jeon, Youssef Belkhadir, D. Lee, Tae Wuk Kim, Jung Min Lee, Man Ho Oh, Ahn, Hee-Kyung [0000-0002-8884-0156], Lee, Tak [0000-0001-7008-7605], Lee, Du-Hwa [0000-0003-4106-7730], Lee, Insuk [0000-0003-3146-6180], Belkhadir, Youssef [0000-0001-7149-7139], Pai, Hyun-Sook [0000-0003-1345-5840], Apollo - University of Cambridge Repository, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Yonsei University Seoul, Korea, University of East Anglia [Norwich] (UEA), Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), College of Life Sciences and Biotechnology, Korea University, Chungnam National University (CNU), Hanyang University, Vienna Biocenter - VBC [Austria], and Yonsei University

Subjects
0106 biological sciences, 0301 basic medicine, Chlorophyll, Chloroplasts, Light, [SDV]Life Sciences [q-bio], Arabidopsis, General Physics and Astronomy, 631/449/2653/1359, 01 natural sciences, chemistry.chemical_compound, 38/1, Gene Expression Regulation, Plant, Morphogenesis, Brassinosteroid, RNA-Seq, 14/19, 13/89, Multidisciplinary, biology, Chemistry, article, Plant morphogenesis, Plant physiology, food and beverages, Plants, Genetically Modified, Recombinant Proteins, Cell biology, Chloroplast, Transmembrane domain, Gene Knockdown Techniques, Photomorphogenesis, 38/39, Microtubule-Associated Proteins, Signal Transduction, Science, 38/90, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, Brassinosteroids, Etiolation, Light responses, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Endomembrane system, 14/35, 631/449/2686, Arabidopsis Proteins, fungi, Membrane Proteins, General Chemistry, HSP40 Heat-Shock Proteins, 030104 developmental biology, Seedlings, Chaperone (protein), Mutation, 14/63, biology.protein, Protein Kinases, Biogenesis, 010606 plant biology & botany
Abstract

Photomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARK AND YELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments., Chloroplast development and brassinosteroid (BR) signaling both regulate plant photomorphogenesis. Here the authors show that DAY, a DnaJ-like domain-containing membrane protein, regulates both processes by binding and stabilizing both BRI1, the BR receptor, and POR, a key enzyme in chlorophyll biosynthesis.

Published
2021
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2. Role of Polycomb in the control of transposable elements

Author

Sandra Duharcourt, Angélique Déléris, Frédéric Berger, 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), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Institut Jacques Monod (IJM (UMR_7592)), Université de Paris (UP)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité), This work was supported by Centre National de la Recherche Scientifique, the LABEX Who Am I? (ANR-11-LABX-0071, ANR-11-IDEX-0005-02), the Agence Nationale de la Recherche (ANR-18-CE12-0005-04, ANR-19-CE12-0015-01 to S.D., ANR-19-CE12-0033-01 to A.D.), and theAustrian Science Fund (FWF grants P30802, P32054, and TAI304 to F.B.), ANR-11-LABX-0071,WHO AM I,Determinants de l'Identité : de la molécule à l'individu(2011), ANR-11-IDEX-0005,USPC,Université Sorbonne Paris Cité(2011), ANR-18-CE12-0005,LaMarque,Transitions évolutives dans la reconnaissance du 'soi' génomique: petits ARN, facteurs spécifiques de séquence et méthylation de l'ADN(2018), ANR-19-CE12-0015,POLYCHROME,Complexe Polycomb chez la paramécie: interaction avec la machinerie des petits ARN et spécificité de substrats(2019), and ANR-19-CE12-0033,COMPTES,COopération, COmpensation, COmpétition: interactions complexes entre Méthylation de l'ADN et Polycomb dans le contrôle des Eléments Transposables d'ArabidopsiS(2019)

Subjects
Transposable element, Heterochromatin, Mutant, Polycomb-Group Proteins, macromolecular substances, Histones, 03 medical and health sciences, chemistry.chemical_compound, 0302 clinical medicine, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Genetics, Animals, Humans, Gene, 030304 developmental biology, 0303 health sciences, biology, Polycomb Repressive Complex 2, DNA Methylation, Histone, chemistry, Evolutionary biology, DNA methylation, DNA Transposable Elements, biology.protein, PRC2, 030217 neurology & neurosurgery, DNA
Abstract

It is generally considered that Polycomb Repressive Complex (PRC)2 deposits the histone mark H3K27me3 on silent protein-coding genes, while transposable elements are repressed by DNA and/or H3K9 methylation. Yet, there is increasing evidence that PRC2 also targets and even silences transposable elements in representatives of several distantly related eukaryotic lineages. In plants and animals, H3K27me3 is present on transposable elements in mutants and specific cell types devoid of DNA methylation. In this Opinion, we summarize the experimental evidence for this phenomenon across the eukaryotic kingdom, and discuss its functional and evolutionary significance. We hypothesize that an ancestral role of Polycomb group (PcG) proteins was to silence transposable elements.

Published
2021

3. Loss of two families of SPX domain-containing proteins required for vacuolar polyphosphate accumulation coincides with the transition to phosphate storage in green plants

Author

Liam Dolan, Benoît Menand, Houqing Zeng, Hongyu Zhao, Long Wang, Lei Xu, Xianqing Jia, Keke Yi, Yuxin Zhang, Yiyong Zhu, Key Laboratory of Plant Nutrition and Fertilizers, Ministry of Agriculture and Rural Affairs, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Chinese Academy of Agricultural Sciences (CAAS), Nanjing Agricultural University (NAU), Luminy Génétique et Biophysique des Plantes (LGBP), 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), College of Life and Environmental Sciences, Hangzhou Normal University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic-based Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China, European Project: 787613,DENOVO-P, Nanjing Agricultural University, 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)-Aix Marseille Université (AMU)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, SPX-VTC, [SDV]Life Sciences [q-bio], SPX-SLC, plant evolution, chemistry.chemical_element, Chlamydomonas reinhardtii, Plant Science, Vacuole, Viridiplantae, 01 natural sciences, 03 medical and health sciences, Polyphosphates, Homeostasis, Molecular Biology, Phylogeny, Plant Proteins, biology, Permease, Phosphorus, Chlamydomonas, polyphosphate, biology.organism_classification, Solute carrier family, vacuolar phosphate, 030104 developmental biology, Biochemistry, chemistry, Chaperone (protein), Vacuoles, biology.protein, 010606 plant biology & botany, Molecular Chaperones
Abstract

International audience; Phosphorus is an essential nutrient for plants. It is stored as inorganic phosphate (Pi) in the vacuoles of land plants but as inorganic polyphosphate (polyP) in chlorophyte algae. Although it is recognized that the SPXMajor Facilitator Superfamily (MFS) and VPE proteins are responsible for Pi influx and efflux, respectively, across the tonoplast in land plants, the mechanisms that underlie polyP homeostasis and the transition of phosphorus storage forms during the evolution of green plants remain unclear. In this study, we showed that CrPTC1, encoding a protein with both SPX and SLC (permease solute carrier 13) domains for Pi transport, and CrVTC4, encoding a protein with both SPX and vacuolar transporter chaperone (VTC) domains for polyP synthesis, are required for vacuolar polyP accumulation in the chlorophyte Chlamydomonas reinhardtii. Phylogenetic analysis showed that the SPX-SLC, SPX-VTC, and SPX-MFS proteins were present in the common ancestor of green plants (Viridiplantae). The SPX-SLC and SPX-VTC proteins are conserved among species that store phosphorus as vacuolar polyP and absent from genomes of plants that store phosphorus as vacuolar Pi. By contrast, SPX-MFS genes are present in the genomes of streptophytes that store phosphorus as Pi in the vacuoles. These results suggest that loss of SPX-SLC and SPX-VTC genes and functional conservation of SPX-MFS proteins during the evolution of streptophytes accompanied the change from ancestral polyP storage to Pi storage.

Published
2020

4. DEK influences the trade-off between growth and 1 arrest via H2A.Z-nucleosomes in Arabidopsis

Author

Brestovitsky, Anna, Ezer, Daphne, Waidmann, Sascha, Maslen, Sarah, Balcerowicz, Martin, Cortijo, Sandra, Charoensawan, Varodom, Rhodes, Daniela, Jonak, Claudia, Wigge, Philip, Sainsbury Laboratory Cambridge University (SLCU), University of Cambridge [UK] (CAM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Natural Resources and Life Sciences (BOKU), Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-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), Nanyang Technological University [Singapour], Sainsbury Laboratory Cambridge, University of Natural Resources and Applied Life Sciences (BOKU), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)

Subjects
stomatognathic diseases, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

The decision of whether to grow and proliferate or to restrict growth and develop resilience to stress is a key biological trade-off. In plants, constitutive growth results in increased sensitivity to environmental stress1,2. The underlying mechanisms controlling this decision are however not well understood. We used temperature as a cue to discover regulators of this process in plants, as it both enhances growth and development rates within a specific range and is also a stress at extremes. We found that the conserved chromatin-associated protein DEK plays a central role in balancing the response between growth and arrest in Arabidopsis, and it does this via H2A.Z-nucleosomes. DEK target genes show two distinct categories of chromatin architecture based on the distribution of H2A.Z in +1 nucleosome and gene body, and these predict induction or repression by DEK. We show that these chromatin signatures of DEK target genes are conserved in human cells, suggesting that DEK may act through an evolutionarily conserved mechanism to control the balance between growth and arrest in plants and animals.

Published
2020

5. Arabidopsis proteins with a transposon-related domain act in gene silencing

Author

Yoko, Ikeda, Thierry, Pélissier, Pierre, Bourguet, Claude, Becker, Marie-Noëlle, Pouch-Pélissier, Romain, Pogorelcnik, Magdalena, Weingartner, Detlef, Weigel, Jean-Marc, Deragon, Olivier, Mathieu, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Université de Perpignan Via Domitia (UPVD), Laboratoire d'Informatique, de Modélisation et d'optimisation des Systèmes (LIMOS), SIGMA Clermont (SIGMA Clermont)-Université d'Auvergne - Clermont-Ferrand I (UdA)-Ecole Nationale Supérieure des Mines de St Etienne-Centre National de la Recherche Scientifique (CNRS)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Université d'Auvergne - Clermont-Ferrand I (UdA)-SIGMA Clermont (SIGMA Clermont)-Ecole Nationale Supérieure des Mines de St Etienne (ENSM ST-ETIENNE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Retroelements, Arabidopsis Proteins, [SDV]Life Sciences [q-bio], Science, Centromere, Arabidopsis, Nuclear Proteins, food and beverages, DNA Methylation, Article, Evolution, Molecular, Protein Domains, Heterochromatin, DNA Transposable Elements, Gene Silencing, RNA, Small Interfering, ComputingMilieux_MISCELLANEOUS
Abstract

Transposable elements (TEs) are prevalent in most eukaryotes, and host genomes have devised silencing strategies to rein in TE activity. One of these, transcriptional silencing, is generally associated with DNA methylation and short interfering RNAs. Here we show that the Arabidopsis genes MAIL1 and MAIN define an alternative silencing pathway independent of DNA methylation and short interfering RNAs. Mutants for MAIL1 or MAIN exhibit release of silencing and appear to show impaired condensation of pericentromeric heterochromatin. Phylogenetic analysis suggests not only that MAIL1 and MAIN encode a retrotransposon-related plant mobile domain, but also that host plant mobile domains were captured by DNA transposons during plant evolution. Our results reveal a role for Arabidopsis proteins with a transposon-related domain in gene silencing., Host genomes have evolved multiple silencing mechanisms to repress transposable element activity. Here Ikeda et al. show that the Arabidopsis MAIL1 and MAIN genes encode a retrotransposon-related plant mobile domain and define an alternative silencing pathway largely independent of DNA methylation and siRNAs.

Published
2017

6. Molecular characterization of Chlamydomonas reinhardtii telomeres and telomerase mutants

Author

Eberhard, Stephan, Valuchova, Sona, Ravat, Julie, Fulneček, Jaroslav, Jolivet, Pascale, Bujaldon, Sandrine, Lemaire, Stéphane, Wollman, Francis-André, Teixeira, Maria Teresa, Riha, Karel, Xu, Zhou, Physiologie membranaire et moléculaire du chloroplaste (PMMC), Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes (LBMCE), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-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), Sorbonne Université (SU)-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), Institut de Biologie Paris Seine (IBPS), and Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Base Sequence, [SDV]Life Sciences [q-bio], Genetic Variation, Telomere Homeostasis, [SDV.BBM.BM]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Molecular biology, macromolecular substances, Telomere, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Amino Acid Sequence, Telomerase, Research Articles, Chlamydomonas reinhardtii, Polymorphism, Restriction Fragment Length, Telomere Shortening, Research Article, Repetitive Sequences, Nucleic Acid
Abstract

This study characterizes the sequence, end structure, and length distribution of Chlamydomonas reinhardtii telomeres and shows that telomerase mutants are defective in telomere maintenance., Telomeres are repeated sequences found at the end of the linear chromosomes of most eukaryotes and are required for chromosome integrity. Expression of the reverse-transcriptase telomerase allows for extension of telomeric repeats to counteract natural telomere shortening. Although Chlamydomonas reinhardtii, a photosynthetic unicellular green alga, is widely used as a model organism in photosynthesis and flagella research, and for biotechnological applications, the biology of its telomeres has not been investigated in depth. Here, we show that the C. reinhardtii (TTTTAGGG)n telomeric repeats are mostly nondegenerate and that the telomeres form a protective structure, with a subset ending with a 3′ overhang and another subset presenting a blunt end. Although telomere size and length distributions are stable under various standard growth conditions, they vary substantially between 12 genetically close reference strains. Finally, we identify CrTERT, the gene encoding the catalytic subunit of telomerase and show that telomeres shorten progressively in mutants of this gene. Telomerase mutants eventually enter replicative senescence, demonstrating that telomerase is required for long-term maintenance of telomeres in C. reinhardtii.

Published
2019

7. Ancient hybridization and strong adaptation to viruses across African vervet monkey populations

Author

Svardal, Hannes, Jasinska, Anna, Apetrei, Cristian, Coppola, Giovanni, Huang, Yu, Schmitt, Christopher, Jacquelin, Béatrice, Ramensky, Vasily, Müller-Trutwin, Michaela, Antonio, Martin, Weinstock, George, Grobler, J. Paul, Dewar, Ken, Wilson, Richard, Turner, Trudy, Warren, Wesley, Freimer, Nelson, Nordborg, Magnus, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of California [Los Angeles] (UCLA), University of California (UC), Polish Academy of Sciences (PAN), University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE), Shanghai Institute of Materia Medica, Chinese Academy of Sciences [Changchun Branch] (CAS), Boston University [Boston] (BU), HIV, Inflammation et persistance - HIV, Inflammation and Persistence, Institut Pasteur [Paris] (IP), Moscow Institute of Physics and Technology [Moscow] (MIPT), Medical Research Council Unit The Gambia (MRC), The Jackson Laboratory [Bar Harbor] (JAX), University of the Free State [South Africa] (UFS), McGill University = Université McGill [Montréal, Canada], University of Wisconsin - Milwaukee, The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), H.S. has been supported by a travel grant from the Austrian Ministry of Science and Research. C.A. is supported by RO1 AI119346 from the National Institute of Allergy and Infectious Diseases (NIAID). We acknowledge the support of the National Institute of Neurological Disorders and Stroke (NINDS) Informatics Center for Neurogenetics and Neurogenomics (P30 NS062691). We would like to thank F. Gao for assistance with microarray data analysis., Samples were collected through the UCLA Systems Biology Sample Repository funded by US National Institutes of Health grants R01RR016300 and R01OD010980 to N.F. For permits allowing us to collect samples, we thank the Gambia Department of Parks & Wildlife Management, the Botswana Ministry of Environment & Wildlife and Tourism, the Ghana Wildlife Division, Forestry Commission, the Zambia Wildlife Authority, the Ethiopian Wildlife Conservation Authority, the Ministry of Forestry & the Environment, Department of Environmental Affairs, South Africa, the Department of Economic Development and Environmental Affairs, Eastern Cape, the Department of Tourism, Environmental and Economic Affairs, Free State, Ezemvelo KZN Wildlife, KwaZulu-Natal, and the Department of Economic Development, Environment and Tourism, Limpopo. We also thank G. Redmond and the St. Kitts Biomedical Research Foundation for facilitating sample collection in St. Kitts and Nevis. We thank J. Brenchley, K. Reimann (R24OD010976), and J. Baulu and the Barbados Primate Research Center and Wildlife Reserve for providing samples of Tanzanian origin and Barbadian vervets. For help with sample collection and processing, we thank J. Danzy-Cramer, Y. Jung, O. Morton and J. Freimer. We thank J. Kamm for discussion, Ü. Seren, J. Wasserscheid and N. Juretic for IT support, and R. Halai for help with figure design, University of California, HIV, Inflammation et persistance, Institut Pasteur [Paris], and University of the Free State [South Africa]

Subjects
CD4-Positive T-Lymphocytes, animal diseases, [SDV]Life Sciences [q-bio], Simian Acquired Immunodeficiency Syndrome, medicine.disease_cause, Medical and Health Sciences, 0302 clinical medicine, Reticulate, Chlorocebus aethiops, Gene Regulatory Networks, Vervet monkey, Phylogeny, Genetics, 0303 health sciences, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Simian immunodeficiency virus, Biological Sciences, Phenotype, Host-Pathogen Interactions, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, Biotechnology, Physiological, Biology, 03 medical and health sciences, Acquired immunodeficiency syndrome (AIDS), Genetic, Species Specificity, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], parasitic diseases, medicine, Animals, Adaptation, Gene, Hybridization, 030304 developmental biology, Gene Expression Profiling, Human Genome, Genetic Variation, biology.organism_classification, medicine.disease, Macaca mulatta, Gene Ontology, Good Health and Well Being, Africa, African Green Monkey, 030217 neurology & neurosurgery, Developmental Biology
Abstract

Vervet monkeys (genusChlorocebus, also known as African green monkeys), are highly abundant in savannahs and riverine forests throughout sub-Saharan Africa. They are amongst the most widely distributed nonhuman primates, show considerable phenotypic diversity, and have long been an important biomedical model for a variety of human diseases and in vaccine research. They are particularly interesting for HIV/AIDS research as they are the most abundant natural hosts of simian immunodeficiency virus (SIV), a close relative of HIV. Here we present the first genome-wide survey of polymorphism in vervets, using sequencing data from 163 individuals sampled from across Africa and the Caribbean islands where vervets were introduced during the colonial era. We find high diversity, within and between taxa, and clear evidence that taxonomic divergence was reticulate rather than following a simple branching pattern. A scan for diversifying selection across vervet taxa yields gene enrichments much stronger than in similar studies on humans. In particular, we report strong and highly polygenic selection signals affecting viral processes --- in line with recent evidence that proposes a driving role for viruses in protein evolution in mammals. Furthermore, selection scores are highly elevated in genes whose human orthologs interact with HIV, and in genes that show a response to experimental SIV infection in vervet monkeys but not in rhesus macaques, suggesting that part of the signal reflects taxon-specific adaptation to SIV. Intriguingly, rather than affecting genes with antiviral and inflammatory-related functions, selection in vervets appears to have primarily targeted genes involved in the transcriptional regulation of viruses, and in particular those that are harmful only under immunodeficiency, suggesting adaptation to living with SIV rather than defense against infection.

Published
2019

8. Crowdsourced assessment of common genetic contribution to predicting anti-TNF treatment response in rheumatoid arthritis

Author

Sieberts, Solveig K., Zhu, Fan, García-García, Javier, Stahl, Eli, Pratap, Abhishek, Pandey, Gaurav, Pappas, Dimitrios, Aguilar, Daniel, Anton, Bernat, Bonet, Jaume, Eksi, Ridvan, Fornés, Oriol, Guney, Emre, Li, Hongdong, Marín, Manuel Alejandro, Panwar, Bharat, Planas-Iglesias, Joan, Poglayen, Daniel, Cui, Jing, Falcao, Andre O., Suver, Christine, Hoff, Bruce, Balagurusamy, Venkat S. K., Dillenberger, Donna, Neto, Elias Chaibub, Norman, Thea, Aittokallio, Tero, Ammad-ud-din, Muhammad, Azencott, Chloe-Agathe, Bellón, Víctor, Boeva, Valentina, Bunte, Kerstin, Chheda, Himanshu, Cheng, Lu, Corander, Jukka, Dumontier, Michel, Goldenberg, Anna, Gopalacharyulu, Peddinti, Hajiloo, Mohsen, Hidru, Daniel, Jaiswal, Alok, Kaski, Samuel, Khalfaoui, Beyrem, Khan, Suleiman Ali, Kramer, Eric R., Marttinen, Pekka, Mezlini, Aziz M., Molparia, Bhuvan, Pirinen, Matti, Saarela, Janna, Samwald, Matthias, Stoven, Véronique, Tang, Hao, Tang, Jing, Torkamani, Ali, Vert, Jean-Phillipe, Wang, Bo, Wang, Tao, Wennerberg, Krister, Wineinger, Nathan E., Xiao, Guanghua, Xie, Yang, Yeung, Rae, Zhan, Xiaowei, Zhao, Cheng, Calaza, Manuel, Elmarakeby, Haitham, Heath, Lenwood S., Long, Quan, Moore, Jonathan D., Opiyo, Stephen Obol, Savage, Richard S., Zhu, Jun, Greenberg, Jeff, Kremer, Joel, Michaud, Kaleb, Barton, Anne, Coenen, Marieke, Mariette, Xavier, Miceli, Corinne, Shadick, Nancy, Weinblatt, Michael, de Vries, Niek, Tak, Paul P., Gerlag, Danielle, Huizinga, Tom W. J., Kurreeman, Fina, Allaart, Cornelia F., Louis Bridges Jr., S., Criswell, Lindsey, Moreland, Larry, Klareskog, Lars, Saevarsdottir, Saedis, Padyukov, Leonid, Gregersen, Peter K., Friend, Stephen, Plenge, Robert, Stolovitzky, Gustavo, Oliva, Baldo, Guan, Yuanfang, Mangravite, Lara M., Bridges, S. Louis, Intelligent Systems, Institute for Molecular Medicine Finland, Department of Mathematics and Statistics, Helsinki Institute for Information Technology, Jukka Corander / Principal Investigator, Department of Computer Science, Janna Saarela / Principal Investigator, Krister Wennerberg / Principal Investigator, Biostatistics Helsinki, Statistical and population genetics, AII - Amsterdam institute for Infection and Immunity, Clinical Immunology and Rheumatology, Zhejiang University, Universidad del Pais Vasco / Euskal Herriko Unibertsitatea [Espagne] (UPV/EHU), Commonwealth Scientific and Industrial Research Organisation [Canberra] (CSIRO), DYNBIO LEGOS, Laboratoire d'études en Géophysique et océanographie spatiales (LEGOS), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Météo-France -Centre National de la Recherche Scientifique (CNRS), Institut d'Ecologia Aquàtica, Universitat de Girona (UdG), Department of Medical Genetics, Faculty of Medicine-Child and Family Research Institute-Centre for Molecular Medicine and Therapeutics-University of British Columbia (UBC), China Agricultural University (CAU), Computational Intelligence Research Group (CA3), Centre of Technology and Systems (CTS), Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Faculdade de Ciências e Tecnologia = School of Science & Technology (FCT NOVA), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA)-Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Cancer et génome: Bioinformatique, biostatistiques et épidémiologie d'un système complexe, Mines Paris - PSL (École nationale supérieure des mines de Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut Curie [Paris]-Institut National de la Santé et de la Recherche Médicale (INSERM), Centre de Bioinformatique (CBIO), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL), Hefei University of Technology (HFUT), Stanford Center for BioMedical Informatics Research (BMIR), Stanford University, Service de génétique [Rouen], CHU Rouen, Normandie Université (NU)-Normandie Université (NU)-Université de Rouen Normandie (UNIROUEN), Normandie Université (NU), Technical Research Centre of Finland, VTT Technical Research Centre of Finland (VTT), U.S. Food and Drug Administration (FDA), Jet Propulsion Laboratory (JPL), NASA-California Institute of Technology (CALTECH), Profium Oy [Helsinki], Chinese Academy of Agricultural Sciences (CAAS), Business School [Hohai University], Hohai University, Institute of Industrial Economics [Hohai University], State Key Laboratory of Medical Genetics of China, Hunan Medical College, State Key Laboratory of Advanced Special Steel, Shanghai University, Quantitative Biomedical Research Center (QBRC), University of Texas Southwestern Medical Center [Dallas], Harold C. Simmons Comprehensive Cancer Center [Dallas, TX, États-Unis], Laboratoire de recherche en Hydrodynamique, Énergétique et Environnement Atmosphérique (LHEEA), École Centrale de Nantes (ECN)-Centre National de la Recherche Scientifique (CNRS), China National Research Center of Intelligent Equipment for Agriculture [Beijing] (NRCIEA), Centro Nacional de Análisi Genómico (CNAG), Centro Nacional de Análisis Genómico, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Mechanical and Aerospace Engineering [Univ California Davis] (MAE - UC Davis), University of California [Davis] (UC Davis), University of California (UC)-University of California (UC), Tongji University, Laboratory for Measles and Rubella, Laboratoire National de Santé [Luxembourg] (LNS), Department of Human Genetics, Radboud University Medical Center [Nijmegen], INSERM U1012, AP-HP Hôpital Bicêtre (Le Kremlin-Bicêtre), School of biosciences and biotechnology, University of Camerino, Università degli Studi di Camerino = University of Camerino (UNICAM), Division of Rheumatology, Immunology and Allergy and Partners Asthma Center, Brigham and Women's Hospital [Boston], Department of Health Education and Promotion, Maastricht University [Maastricht], University of Amsterdam [Amsterdam] (UvA), Department of rheumatology, Leiden University Medical Center (LUMC), Universiteit Leiden-Universiteit Leiden, Rheumatology Unit, Department of Medicine, University of California [San Francisco] (UC San Francisco), University of California (UC), Rheumatology Unit, Karolinska Institutet [Stockholm], Merck & Co. Inc, Structural Bioinformatics Group (GRIB), Barcelona Research Park of Biomedicine (PRBB), Universitat Pompeu Fabra [Barcelona] (UPF), Capital Normal University [Beijing], Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut national des sciences de l'Univers (INSU - CNRS)-Observatoire Midi-Pyrénées (OMP), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Météo France-Centre National d'Études Spatiales [Toulouse] (CNES)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), MINES ParisTech - École nationale supérieure des mines de Paris, California Institute of Technology (CALTECH)-NASA, Department of Mechanical and Aerospace Engineering [Davis], University of California-University of California, Università degli Studi di Camerino (UNICAM), University of California [San Francisco] (UCSF), University of California, Sage Bionetworks, University of Michigan, Ann Arbor, Pompeu Fabra University, Icahn School of Medicine at Mount Sinai, Corrona LLC, Northeastern University, Harvard University, University of Lisbon, IBM, INSERM U900, University of Helsinki, University of Toronto, Scripps Research Institute, Medical University of Vienna, University of Texas at Dallas, New York University, Albany Medical College, Arthritis Research Center Foundation, Radboud University Nijmegen, INSERM U1184, University of Amsterdam, Glaxo Smith Kline, Leiden University, University of Alabama at Birmingham, University of California San Francisco, University of Pittsburgh, Karolinska Institutet, North Shore-Long Island Jewish Health System, Merck, Aalto-yliopisto, and Aalto University

Subjects
Male, 0301 basic medicine, General Physics and Astronomy, Arthritis, Genome-wide association study, Bioinformatics, DISEASE, Arthritis, Rheumatoid, Cohort Studies, Missing heritability problem, MISSING HERITABILITY, Medicine, Certolizumab pegol, RISK, Multidisciplinary, Antibodies, Monoclonal, Middle Aged, Prognosis, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], 3. Good health, STACKED GENERALIZATION, Treatment Outcome, Antirheumatic Agents, Crowdsourcing, Biomarker (medicine), Female, Erratum, medicine.drug, Adult, Science, Context (language use), Antibodies, Monoclonal, Humanized, Polymorphism, Single Nucleotide, Article, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, INFLIXIMAB, Journal Article, Humans, SNP, Genetic Predisposition to Disease, GENOME-WIDE ASSOCIATION, METAANALYSIS, Aged, ta113, Tumor Necrosis Factor-alpha, business.industry, NETWORK INFERENCE, COMPLEX TRAITS, Artritis reumatoide -- Tractament, CLINICAL-RESPONSE, General Chemistry, 113 Computer and information sciences, medicine.disease, Infliximab, 030104 developmental biology, 3121 General medicine, internal medicine and other clinical medicine, Certolizumab Pegol, business, RC
Abstract

Rheumatoid arthritis (RA) affects millions world-wide. While anti-TNF treatment is widely used to reduce disease progression, treatment fails in ∼one-third of patients. No biomarker currently exists that identifies non-responders before treatment. A rigorous community-based assessment of the utility of SNP data for predicting anti-TNF treatment efficacy in RA patients was performed in the context of a DREAM Challenge (http://www.synapse.org/RA_Challenge). An open challenge framework enabled the comparative evaluation of predictions developed by 73 research groups using the most comprehensive available data and covering a wide range of state-of-the-art modelling methodologies. Despite a significant genetic heritability estimate of treatment non-response trait (h2=0.18, P value=0.02), no significant genetic contribution to prediction accuracy is observed. Results formally confirm the expectations of the rheumatology community that SNP information does not significantly improve predictive performance relative to standard clinical traits, thereby justifying a refocusing of future efforts on collection of other data., Rheumatoid arthritis patients respond differently to anti-TNF treatment. Using community-based challenge, the authors show that currently available data does not reveal meaningful genetic predictors of response to anti-TNF therapy, thus confirming clinical observations.

Published
2016

9. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

Author

Seunghee Lee, Jetty S.S. Ammiraju, Railson Schreinert dos Santos, Ann Danowitz, Shu-Min Kao, Li Zhang, Chengjun Zhang, Cheng chieh Wu, Dongying Gao, Carlos E.M. Londono, Scott A. Jackson, Yi Liao, Mingsheng Chen, Chuanzhu Fan, Andrea Zuccolo, Muhua Wang, Christos Noutsos, Rod A. Wing, Manyuan Long, Robert J Henry, Marie-Christine Carpentier, Kshirod K. Jena, Aiko Iwata, Yue-Ie C. Hsing, Jose Luis Goicoechea, Bin Han, Richard Cooke, Joshua C. Stein, Luis F. Rivera, Thomas Wicker, Dario Copetti, Fu Jin Wei, Claude Becker, Paul L. Sanchez, Qi Feng, Andrea R. Gschwend, Ramil Mauleon, Carlos A. Machado, Derrick J. Zwickl, Daniel da Rosa Farias, Jayson Talag, Dave Flowers, Eric Lasserre, Nickolai Alexandrov, Yeisoo Yu, Moaine El Baidouri, Luciano Carlos da Maia, Jeremy Schmutz, Dave Kudrna, Olivier Panaud, Kenneth L. McNally, Xiang Song, Kevin G. Nyberg, Nori Kurata, Qiang Zhao, Kapeel Chougule, Jhih wun Zeng, Antonio Costa de Oliveira, Jianwei Zhang, Doreen Ware, Jun Wang, Detlef Weigel, Sharon Wei, Julie Jacquemin, Michael J. Sanderson, Ecology and Evolutionary Biology [Tucson] (EEB), University of Arizona, Dipartimento Sci Agr & Ambientali, Università degli Studi di Udine - University of Udine [Italie], Wuhan University [China], University of Georgia [USA], Chinese Academy of Agricultural Mechanization Sciences (CCCME), Laboratoire Génome et développement des plantes (LGDP), Université de Perpignan Via Domitia (UPVD)-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Tsukuba University of Technology, Graduate School of Comprehensive Human Sciences, Université de Tsukuba = University of Tsukuba, Sismologie (IPGS) (IPGS-Sismologie), Institut de physique du globe de Strasbourg (IPGS), Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut national des sciences de l'Univers (INSU - CNRS)-Centre National de la Recherche Scientifique (CNRS), United States Department of Energy, Institute of Plant Biology, University of Zurich, Plant Genomics and Breeding Center, Department of Biology, and Cold Spring Harbor Laboratory

Subjects
0301 basic medicine, Crops, Agricultural, Evolution, Genetic Speciation, [SDV]Life Sciences [q-bio], Plant genetics, Introgression, Genomics, Crops, Oryza, Genome, Medical and Health Sciences, Evolution, Molecular, Domestication, 03 medical and health sciences, Molecular evolution, Phylogenetics, Genetics, ComputingMilieux_MISCELLANEOUS, Phylogeny, Conserved Sequence, 2. Zero hunger, Agricultural, biology, food and beverages, Molecular, Genetic Variation, Plant, 15. Life on land, Biological Sciences, biology.organism_classification, 030104 developmental biology, Evolutionary biology, Genome, Plant, Developmental Biology
Abstract

The genus Oryza is a model system for the study of molecular evolution over time scales ranging from a few thousand to 15 million years. Using 13 reference genomes spanning the Oryza species tree, we show that despite few large-scale chromosomal rearrangements rapid species diversification is mirrored by lineage-specific emergence and turnover of many novel elements, including transposons, and potential new coding and noncoding genes. Our study resolves controversial areas of the Oryza phylogeny, showing a complex history of introgression among different chromosomes in the young 'AA' subclade containing the two domesticated species. This study highlights the prevalence of functionally coupled disease resistance genes and identifies many new haplotypes of potential use for future crop protection. Finally, this study marks a milestone in modern rice research with the release of a complete long-read assembly of IR 8 'Miracle Rice', which relieved famine and drove the Green Revolution in Asia 50 years ago.

Published
2018

10. Transposons: a blessing curse

Author

Dubin, Manu, Scheid, Ortrun, Becker, Claude, Laboratoire de Génétique et Evolution des Populations Végétales, Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS), Gregor Mendel Institute of Molecular Plant Biology (GMI), and Austrian Academy of Sciences (OeAW)

Subjects
[SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, food and beverages, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics
Abstract

International audience; The genomes of most plant species are dominated by transposable elements (TEs). Once considered as ‘junk DNA’, TEs are now known to have a major role in driving genome evolution. Over the last decade, it has become apparent that some stress conditions and other environmental stimuli can drive bursts of activity of certain TE families and consequently new TE insertions. These can give rise to altered gene expression patterns and phenotypes, with new TE insertions sometimes causing flanking genes to become transcriptionally responsive to the same stress conditions that activated the TE in the first place. Such connections between TE-mediated increases in diversity and an accelerated rate of genome evolution provide powerful mechanisms for plants to adapt more rapidly to new environmental conditions. This review will focus on environmentally induced transposition, the mechanisms by which it alters gene expression, and the consequences for plant genome evolution and breeding.

Published
2018

11. The rate and potential relevance of new mutations in a colonizing plant lineage

Author

Verena J. Schuenemann, Jia-Hui Chen, Rob W. Ness, Wolfgang Busch, Dominik G. Grimm, Hernán A. Burbano, Claude Becker, Radka Slovak, Benjamin Brachi, Claudia Setzer, Johannes Krause, Joy Bergelson, Ella Reiter, Detlef Weigel, Moises Exposito-Alonso, Joerg Hagmann, Max-Planck-Institut, Eberhard Karls Universität Tübingen = Eberhard Karls University of Tuebingen, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Chinese Academy of Sciences (CAS), Department of Ecology and Evolution [Chicago], University of Chicago, Department of Biology, and Northern Arizona University [Flagstaff]

Subjects
0301 basic medicine, 0106 biological sciences, Cancer Research, Mutation rate, [SDV]Life Sciences [q-bio], Arabidopsis, Population genetics, Plant Weeds, Plant Science, medicine.disease_cause, Plant Genetics, méthode de croisement, 01 natural sciences, Genome, Gene flow, Negative selection, Mutation Rate, Plant Genomics, amérique du nord, Genetics (clinical), Phylogeny, Data Management, Mutation, 0303 health sciences, Natural selection, Chemical Reactions, Eukaryota, Phylogenetic Analysis, Genomics, Plants, Phylogenetics, Chemistry, Phenotype, Experimental Organism Systems, Physical Sciences, Genome, Plant, Research Article, Biotechnology, Gene Flow, Computer and Information Sciences, Substitution Mutation, Lineage (genetic), lcsh:QH426-470, Plant Development, Brassica, Biology, Research and Analysis Methods, Methylation, 010603 evolutionary biology, Evolution, Molecular, 03 medical and health sciences, Model Organisms, Plant and Algal Models, medicine, Genetics, Evolutionary Systematics, Selection, Genetic, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Crosses, Genetic, Selection (genetic algorithm), Taxonomy, 030304 developmental biology, Evolutionary Biology, Population Biology, arabidopsis thaliana, Organisms, Biology and Life Sciences, Computational Biology, Selfing, Sequence Analysis, DNA, Genome Analysis, Genomic Libraries, Genome Annotation, lcsh:Genetics, 030104 developmental biology, Evolutionary biology, Plant Biotechnology, Directed Molecular Evolution, Introduced Species, Population Genetics
Abstract

By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by “natural evolution experiments” that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions—the subset of mutations that survived natural selection and drift–, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance., PLoS Genetics, 14 (2), ISSN:1553-7390, ISSN:1553-7404

Published
2018

12. Insights into Land Plant Evolution Garnered from the Marchantia polymorpha Genome

Author

Akifumi Sugiyama, Efraín De Luna, Hideya Fukuzawa, Yuki Hirakawa, Yoshihiro Yoshitake, Jeremy Schmutz, Minoru Kubo, Sabine Zachgo, Sumio Sugano, Satoshi Naramoto, Isabel Monte, Juan Caballero-Pérez, Takashi Okamoto, Feng Chen, Keita Kinose, Rui Sun, Bruno Catarino, Shin-ichiro Inoue, Tomokazu Kawashima, Yasukazu Nakamura, Masaaki Umeda, Masayuki Tsuzuki, Junko Kyozuka, John L. Bowman, Mitsuru Kakita, Chia-Wei Lu, Eduardo Flores-Sandoval, Takayuki Kohchi, Christian R. Boehm, Kimitsune Ishizaki, D. Magnus Eklund, Shih-Shun Lin, Makoto Shirakawa, Jim Haseloff, Moritz Rövekamp, Hirofumi Nakagami, Anna Lipzen, Yuichiro Watanabe, Kazuhiko Nishitani, Noriyuki Suetsugu, Keisuke Inoue, Marc W. Schmid, Yosuke Kawai, Hirokazu Tomogane, Robert A. Martienssen, Shengqiang Shu, Ryuichi Nishihama, Ulf Lagercrantz, Miya Mizutani, Liam Dolan, Tom Dierschke, Frédéric Berger, Felix Althoff, Kevin M. Davies, Ueli Grossniklaus, Bence Galik, Asao Fujiyama, Sureshkumar Balasubrmanian, Ryusuke Yokoyama, Takashi Ueda, Izumi Yotsui, Toshinori Kinoshita, Misato Ohtani, Eri Koide, Kazufumi Yazaki, Shinichiro Sawa, Jane Grimwood, Diane Bauer, Mario A. Arteaga-Vazquez, Sakiko Ishida, Takahiro Hamada, Roberto Solano, Alexander J. Hetherington, Daniel Grimanelli, Stevie N. Florent, Erika Lindquist, Ryosuke Sano, Kenji Komatsu, Catherine Adam, Asuka Higo, Sarah Kopischke, Hope Hundley, Rebecca A. Mosher, Jerry Jenkins, Naoki Minamino, Hideki Nagasaki, Mizuki Takenaka, Kerrie Barry, Takashi Araki, Nobuyoshi Mochizuki, Anke Reinders, Mihails Delmans, Yuji Kohara, Yoko Ikeda, Daisuke Takezawa, Mansi Chovatia, Ana E. Dorantes-Acosta, Taku Demura, Masaki Okumura, Qidong Jia, Takehiko Kanazawa, Yutaka Suzuki, Megan Kennedy, Jeremy Phillips, Bernardo Pollak, Liam N. Briginshaw, Shohei Yamaoka, Shota Chiyoda, Alexander Spunde, John M. Ward, Masaharu Mizutani, Katsuyuki T. Yamato, Shiori S Aki, Boehm, Christian [0000-0002-6633-7998], Haseloff, Jim [0000-0003-4793-8058], Pollak, Bernardo [0000-0003-2329-7401], Apollo - University of Cambridge Repository, Monash University [Clayton], Department of Energy / Joint Genome Institute (DOE), Los Alamos National Laboratory (LANL), Kobe University, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Nara Institute of Science and Technology, Monash University [Melbourne], The University of Tennessee [Knoxville], Osnabrück University of Applied Sciences (OS UAS), Hochschule Osnabrück, Diversité, adaptation, développement des plantes (UMR DIADE), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Earth Science and Astrononomy [Tokyo], The University of Tokyo (UTokyo), National Institute for Basic Biology [Okazaki] (NIBB), Graduate University for Advanced Studies [Hayama] (SOKENDAI), Cold Spring Harbor Laboratory (CSHL), Centro Nacional de Biotecnología [Madrid] (CNB-CSIC), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), RIKEN Center for Sustainable Resource Science [Yokohama] (RIKEN CSRS), RIKEN - Institute of Physical and Chemical Research [Japon] (RIKEN), Max Planck Institute for Plant Breeding Research (MPIPZ), Tokyo Metropolitan University [Tokyo] (TMU), Kumamoto University, Biocomputing Unit [Madrid], Research Institute for Sustainable Humanosphere (RISH), Kyoto University [Kyoto], University of Ulm (UUlm), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), and Kyoto University

Subjects
inorganic chemicals, 0301 basic medicine, Flora, Transcription, Genetic, [SDV]Life Sciences [q-bio], Marchantia polymorpha, Adaptation, Biological, macromolecular substances, Genome, General Biochemistry, Genetics and Molecular Biology, Evolutionsbiologi, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Marchantia, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, sex chromosome, Biological sciences, Plant evolution, Medical And Health Sciences, Evolutionary Biology, biology, Ecology, fungi, food and beverages, Molecular Sequence Annotation, Biological evolution, Biological Sciences, 15. Life on land, biology.organism_classification, charophycean algae, Biological Evolution, 030104 developmental biology, Embryophyta, Terrestrial ecosystem, land plant evolution, auxin, Genome, Plant, Developmental Biology, Signal Transduction
Abstract

The evolution of land flora transformed the terrestrial environment. Land plants evolved from an ancestral charophycean alga from which they inherited developmental, biochemical, and cell biological attributes. Additional biochemical and physiological adaptations to land, and a life cycle with an alternation between multicellular haploid and diploid generations that facilitated efficient dispersal of desiccation tolerant spores, evolved in the ancestral land plant. We analyzed the genome of the liverwort Marchantia polymorpha, a member of a basal land plant lineage. Relative to charophycean algae, land plant genomes are characterized by genes encoding novel biochemical pathways, new phytohormone signaling pathways (notably auxin), expanded repertoires of signaling pathways, and increased diversity in some transcription factor families. Compared with other sequenced land plants, M. polymorpha exhibits low genetic redundancy in most regulatory pathways, with this portion of its genome resembling that predicted for the ancestral land plant., 陸上植物の祖先の特徴をもつ苔類ゼニゴケの全ゲノム構造を解明. 京都大学プレスリリース. 2017-10-06.

Published
2017

13. Patterns of Polymorphism at the Self-Incompatibility Locus in 1,083 Arabidopsis thaliana Genomes

Author

Isabelle Fobis-Loisy, Xavier Vekemans, Vincent Castric, Quan Long, Magnus Nordborg, Pauline M. Goubet, Anne-Catherine Holl, Elisa Prat, Dazhe Meng, Takashi Tsuchimatsu, Alexander Platzer, William Marande, Hélène Bergès, Sophie Gallina, Gregor Mendel Institute, Austrian Academy of Sciences, Vienna Biocenter, Department of Biology, Chiba University, Inage-ku, Chiba, Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo), Université de Lille-Centre National de la Recherche Scientifique (CNRS), Lab Reprod & Dev Plantes, École normale supérieure - Lyon (ENS Lyon), Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Gregor Mendel Institute (GMI) - Vienna Biocenter (VBC), Austrian Academy of Sciences (OeAW), University of Calgary, Gregor Mendel Institute of Molecular Plant Biology (GMI), JSPS KAKENHI [15K18583], ANR-11-BSV7-013-03, ANR-11-JSV7-008-01, European Research Council [648321], ANR-13-BSV7-0013,BugsInACell,Accommodation intracellulaire des bactéries symbiotiques fixatrices d'azote(2013), ANR-13-JSV7-0003,DOMEVOL,Mecanismes et evolution de la dominance(2013), Évolution, Écologie et Paléontologie (Evo-Eco-Paleo) - UMR 8198 (Evo-Eco-Paléo (EEP)), and École normale supérieure de Lyon (ENS de Lyon)

Subjects
0106 biological sciences, evolution of selfing, Arabidopsis, Locus (genetics), Self-Fertilization, Biology, Genes, Plant, 01 natural sciences, Genome, self-incompatibility, Haplogroup, Evolution, Molecular, 03 medical and health sciences, 1001 genomes project, evolutionary transition, Amino Acid Sequence, Alleles, Phylogeny, Discoveries, ComputingMilieux_MISCELLANEOUS, Plant Proteins, 030304 developmental biology, Genetics, 0303 health sciences, Polymorphism, Genetic, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Arabidopsis Proteins, Haplotype, Breakpoint, Selfing, 15. Life on land, Fixation (population genetics), Haplotypes, Mutation, Recombination, 010606 plant biology & botany
Abstract

Although the transition to selfing in the model plantArabidopsis thalianainvolved the loss of the self-incompatibility (SI) system, it clearly did not occur due to the fixation of a single inactivating mutation at the locus determining the specificities of SI (the S-locus). At least three groups of divergent haplotypes (haplogroups), corresponding to ancient functional S-alleles, have been maintained at this locus, and extensive functional studies have shown that all three carry distinct inactivating mutations. However, the historical process of loss of SI is not well understood, in particular its relation with the last glaciation. Here, we took advantage of recently published genomic re-sequencing data in 1,083Arabidopsis thalianaaccessions that we combined with BAC sequencing to obtain polymorphism information for the whole S-locus region at a species-wide scale. The accessions differed by several major rearrangements including large deletions and inter-haplogroup recombinations, forming a set of haplogroups that are widely distributed throughout the native range and largely overlap geographically. ‘Relict’A.thalianaaccessions that directly derive from glacial refugia are polymorphic at the S-locus, suggesting that the three haplogroups were already present when glacial refugia from the last Ice Age became isolated. Inter-haplogroup recombinant haplotypes were highly frequent, and detailed analysis of recombination breakpoints suggested multiple independent origins. These findings suggest that the complete loss of SI inA.thalianainvolved independent self-compatible mutants that arose prior to the last Ice Age, and experienced further rearrangements during post-glacial colonization.

Published
2017

14. Zinc availability modulates plant growth and 1 immune responses via AZI1

Author

Bouain, Nadia, Satbhai, Santosh B., Saenchai, Chorpet, Desbrosses, Guilhem, Berthomieu, Pierre, Busch, Wolfgang, Rouached, Hatem, Biochimie et Physiologie Moléculaire des Plantes (BPMP), Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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), Salk Institute for Biological Studies, Plant Molecular and Cellular Biology Laboratory, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Space Research Institute of Austrian Academy of Sciences (IWF), Vienna Biocenter, Biochimie et Physiologie Moléculaire des Plantes ( BPMP ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Equipe Hormones, Nutriments et Développement (HoNuDe) ( HONUDE ), Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Université de Montpellier ( UM ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Austrian Academy of Sciences, Equipe Electrophysiologie de la nutrition minérale et des symbioses racinaires ( ELSA ), Equipe Adaptation des plantes aux métaux ( METAUX ), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Hormones, Nutriments et Développement (HoNuDe) (HONUDE), Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Equipe Electrophysiologie de la nutrition minérale et des symbioses racinaires (ELSA), and Equipe Adaptation des plantes aux métaux (METAUX)

Subjects
[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, acide azelaique, croissance racinaire, nonanedioic acid, arabidopsis thaliana, zinc, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, carence en zinc, régulation de la croissance
Abstract

preprint déposé dans bioRxiv; Zinc is an essential micronutrient for all living organisms and is involved in a plethora of processes including growth and development, and immunity. However, it is unknown if there is a common genetic and molecular basis underlying multiple facets of zinc function. Here we used natural variation in Arabidopsis thaliana to study the role of zinc in regulating growth. We identify allelic variation of the systemic immunity gene AZI1 as a key for determining root growth responses to low zinc conditions. We further demonstrate that this gene is important for modulating root growth depending on the zinc and defence status. Finally, we show that the interaction of the immunity signal azelaic acid and zinc level to regulate root growth is conserved in rice. This work demonstrates that there is a common genetic and molecular basis for multiple zinc dependent processes and that nutrient cues can determine the balance of plant growth and immune responses in plants.

Published
2017

15. Ecological plant epigenetics: Evidence from model and non-model species, and the way forward

Author

Sonja J. Prohaska, Koen J. F. Verhoeven, Claude Becker, Marie Mirouze, Christina L. Richards, Peter F. Stadler, Etienne Bucher, Christian Lampei, Walter Durka, Lars Opgenoorth, Emiliano Trucchi, Jan Engelhardt, Ovidiu Paun, Conchita Alonso, Bence Gáspár, Stefan A. Rensing, Ilkka Kronholm, Vít Latzel, Maria Colomé-Tatché, Kristian K. Ullrich, Andreas Gogol-Döring, Thomas P. van Gurp, Katrin Heer, Oliver Bossdorf, Ivo Grosse, University of South Florida [Tampa] (USF), Estación Biológica de Doñana (EBD), Consejo Superior de Investigaciones Científicas [Madrid] (CSIC), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Plant Evolutionary Ecology, University of Tübingen, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, European Research Institute for the Biology of Ageing [Groningen] (ERIBA), University Medical Center Groningen [Groningen] (UMCG), Helmholtz Zentrum München = German Research Center for Environmental Health, TUM School of Life Sciences Weihenstephan, Technische Universität Munchen - Université Technique de Munich [Munich, Allemagne] (TUM), Helmholtz Zentrum für Umweltforschung = Helmholtz Centre for Environmental Research (UFZ), German Centre for Integrative Biodiversity Research (iDiv), Institut für Informatik [Leipzig], Universität Leipzig, Institut für Informatik / Institute of Computer Science [Halle], Martin-Luther-University Halle-Wittenberg, Netherlands Institute of Ecology - NIOO-KNAW (NETHERLANDS), Philipps Universität Marburg = Philipps University of Marburg, University of Jyväskylä (JYU), Institute of Plant Breeding, Seed Science and Population Genetics, Universität Hohenheim, Institute of Botany of the Czech Academy of Sciences (IB / CAS), Czech Academy of Sciences [Prague] (CAS), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Department of Botany and Biodiversity Research, University of Vienna [Vienna], Santa Fe Institute, Centre for Biological Signaling Studies [Freiburg] (BIOSS), University of Freiburg [Freiburg], Max Planck Institute for Mathematics in the Sciences (MPI-MiS), Max-Planck-Gesellschaft, Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences [Oslo], Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO)-Faculty of Mathematics and Natural Sciences [Oslo], University of Oslo (UiO)-University of Oslo (UiO), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), Université Paris-Sud - Paris 11 (UP11)-Centre National de la Recherche Scientifique (CNRS), Helmholtz Zentrum für Umweltforschung (UFZ), Inst Comp Sci, Martin-Luther-Universität Halle Wittenberg (MLU), Institute of Experimental Ecology Germany, Conservation Biology and Ecology, Universität Ulm - Ulm University [Ulm, Allemagne], Department of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research (MPIPZ), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Carl-Maria-von-Weber-Gesamtausgabe, Universität Paderborn (UPB), Department of Zoology [Oxford], University of Oxford [Oxford], 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), Centre National de la Recherche Scientifique (CNRS)-Université Paris-Sud - Paris 11 (UP11), and Terrestrial Ecology (TE)

Subjects
0106 biological sciences, 0301 basic medicine, EPIGENOMIC DIVERSITY, [SDV]Life Sciences [q-bio], Species distribution, INDIVIDUAL VARIATION, Phenotypic plasticity, 01 natural sciences, Genome, phenotypic plasticity, Epigenesis, Genetic, DNA METHYLATION VARIATION, ComputingMilieux_MISCELLANEOUS, 0303 health sciences, Ecology, bioinformatiikka, genomiikka, Genomics, Plants, Bioinformatics, ecological epigenetics, genomics, response to environment, Ecology, Evolution, Behavior and Systematics, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Habitat, epigenetiikka, international, PHYSCOMITRELLA-PATENS, PERENNIAL HERB, kasviekologia, Ecological epigenetics, SEQUENCING DATA, Evolution, Ecology (disciplines), Biology, 010603 evolutionary biology, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Polyploid, Behavior and Systematics, kasvit, Epigenetics, Ecosystem, 030304 developmental biology, HERB HELLEBORUS-FOETIDUS, Ecological Epigenetics, Phenotypic Plasticity, Response To Environment, Ambientale, Response to environment, DNA Methylation, 15. Life on land, Ecological realism, Plant ecology, 030104 developmental biology, ARABIDOPSIS-THALIANA, Bioinformatics, ecological epigenetics, genomics, phenotypic plasticity, response to environment, Adaptation, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, NATURAL-POPULATIONS
Abstract

Growing evidence shows that epigenetic mechanisms contribute to complex traits, with implications across many fields of biology. In plant ecology, recent studies have attempted to merge ecological experiments with epigenetic analyses to elucidate the contribution of epigenetics to plant phenotypes, stress responses, adaptation to habitat, and range distributions. While there has been some progress in revealing the role of epigenetics in ecological processes, studies with non-model species have so far been limited to describing broad patterns based on anonymous markers of DNA methylation. In contrast, studies with model species have benefited from powerful genomic resources, which contribute to a more mechanistic understanding but have limited ecological realism. Understanding the significance of epigenetics for plant ecology requires increased transfer of knowledge and methods from model species research to genomes of evolutionarily divergent species, and examination of responses to complex natural environments at a more mechanistic level. This requires transforming genomics tools specifically for studying non-model species, which is challenging given the large and often polyploid genomes of plants. Collaboration among molecular geneticists, ecologists and bioinformaticians promises to enhance our understanding of the mutual links between genome function and ecological processes.

Published
2017

16. Live-cell analysis of DNA methylation during sexual reproduction in Arabidopsis reveals context and sex-specific dynamics controlled by noncanonical RdDM

Author

Benjamin Selles, Matthias Van Durme, Robert A. Martienssen, Andrea J. Schorn, Frédéric Berger, Daphné Autran, Moritz K. Nowack, Caroline Michaud, Thiet Minh Vu, Daniel Grimanelli, Mathieu Ingouff, Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Cold Spring Harbor Laboratory (CSHL), Universiteit Gent = Ghent University (UGENT), Vlaams Instituut voor Biotechnologie [Ghent, Belgique] (VIB), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), and Universiteit Gent = Ghent University [Belgium] (UGENT)

Subjects
0301 basic medicine, CHROMATIN, EPIGENETIC INHERITANCE, Arabidopsis, ENDOSPERM, Biology, sensors, DEMETHYLATION, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Cell Line, HETEROCHROMATIN, reproduction, 03 medical and health sciences, Mice, Epigenetics of physical exercise, Sex Factors, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Histone methylation, Genetics, Animals, Epigenetics, PLANT, RNA-Directed DNA Methylation, Embryonic Stem Cells, Epigenomics, SMALL RNA, EARLY EMBRYOGENESIS, DNA methylation, THALIANA, Arabidopsis Proteins, Reproduction, Biology and Life Sciences, reprogramming, Methylation, DNA-Directed RNA Polymerases, Methyltransferases, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, DNA Methylation, Plants, Genetically Modified, GENOME, 030104 developmental biology, Gene Expression Regulation, Single-Cell Analysis, Reprogramming, Resource/Methodology, Developmental Biology
Abstract

Cytosine methylation is a key epigenetic mark in many organisms, important for both transcriptional control and genome integrity. While relatively stable during somatic growth, DNA methylation is reprogrammed genome-wide during mammalian reproduction. Reprogramming is essential for zygotic totipotency and to prevent transgenerational inheritance of epimutations. However, the extent of DNA methylation reprogramming in plants remains unclear. Here, we developed sensors reporting with single-cell resolution CG and non-CG methylation in Arabidopsis. Live imaging during reproduction revealed distinct and sex-specific dynamics for both contexts. We found that CHH methylation in the egg cell depends on DOMAINS REARRANGED METHYLASE 2 (DRM2) and RNA polymerase V (Pol V), two main actors of RNA-directed DNA methylation, but does not depend on Pol IV. Our sensors provide insight into global DNA methylation dynamics at the single-cell level with high temporal resolution and offer a powerful tool to track CG and non-CG methylation both during development and in response to environmental cues in all organisms with methylated DNA, as we illustrate in mouse embryonic stem cells.

Published
2017

17. Mapping the subcellular mechanical properties of live cells in tissues with fluorescence emission-Brillouin imaging

Author

Stephanie Werner, Lijuan Zhang, Thomas Greb, Yvon Jaillais, Kareem Elsayad, Jixiang Kong, Edmundo R. Sánchez Guajardo, Marçal Gallemí, Youssef Belkhadir, Vienna Biocenter Core Facilities, Partenaires INRAE, Austrian Academy of Sciences (OeAW), University Medical Center Göttingen (UMG), Gregor Mendel Institute of Molecular Plant Biology (GMI), Institute of Science and Technology [Austria] (IST Austria), Vienna Biocenter, Reproduction et développement des plantes (RDP), Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de la Recherche Agronomique (INRA)-École normale supérieure - Lyon (ENS Lyon), Centre for Organismal Studies, Universität Heidelberg [Heidelberg], Austrian Federal Ministry of Science, Research Economy, City of Vienna through the VBCF, Austrian Academy of Science through the Gregor Mendel Institute, Austrian Science Fund (FWF) P25594-168 B21, German Research Foundation (DFG) GR 2104/4-1, Institute of Science and Technology [Klosterneuburg, Austria] (IST Austria), École normale supérieure de Lyon (ENS de Lyon)-Institut National de la Recherche Agronomique (INRA)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), and Universität Heidelberg [Heidelberg] = Heidelberg University

Subjects
0301 basic medicine, [SDV]Life Sciences [q-bio], Hydrostatic pressure, Arabidopsis, 01 natural sciences, Biochemistry, 010309 optics, Extracellular matrix, 03 medical and health sciences, 0103 physical sciences, Extracellular, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Molecular Biology, biology, Chemistry, Cell Biology, biology.organism_classification, Cell biology, Extracellular Matrix, Multicellular organism, 030104 developmental biology, Microscopy, Fluorescence, Cytoplasm, Mutation, Signal transduction, Developmental biology
Abstract

International audience; Extracellular matrices (ECMs) are central to the advent of multicellular life, and their mechanical properties are modulated by and impinge on intracellular signaling pathways that regulate vital cellular functions. High spatial-resolution mapping of mechanical properties in live cells is, however, extremely challenging. Thus, our understanding of how signaling pathways process physiological signals to generate appropriate mechanical responses is limited. We introduce fluorescence emission-Brillouin scattering imaging (FBi), a method for the parallel and all-optical measurements of mechanical properties and fluorescence at the submicrometer scale in living organisms. Using FBi, we showed that changes in cellular hydrostatic pressure and cytoplasm viscoelasticity modulate the mechanical signatures of plant ECMs. We further established that the measured "stiffness" of plant ECMs is symmetrically patterned in hypocotyl cells undergoing directional growth. Finally, application of this method to Arabidopsis thaliana with photoreceptor mutants revealed that red and far-red light signals are essential modulators of ECM viscoelasticity. By mapping the viscoelastic signatures of a complex ECM, we provide proof of principle for the organism-wide applicability of FBi for measuring the mechanical outputs of intracellular signaling pathways. As such, our work has implications for investigations of mechanosignaling pathways and developmental biology.

Published
2016

18. Epigenome confrontation triggers immediate reprogramming of DNA methylation and transposon silencing in Arabidopsis thaliana F1 epihybrids

Author

Claude Becker, Detlef Weigel, Mélanie Rigal, Yoko Ikeda, Jane Devos, Romain Pogorelcnik, Olivier Mathieu, Thierry Pélissier, Génétique, Reproduction et Développement (GReD), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de la Santé et de la Recherche Médicale (INSERM), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), Department of Molecular Biology, Max Planck Institute for Developmental Biology, Max-Planck-Gesellschaft-Max-Planck-Gesellschaft, and Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Genetics, Multidisciplinary, [SDV]Life Sciences [q-bio], food and beverages, Epigenome, Biology, 03 medical and health sciences, 030104 developmental biology, Epigenetics of physical exercise, PNAS Plus, DNA methylation, Epigenetics, Reprogramming, Transposons as a genetic tool, RNA-Directed DNA Methylation, ComputingMilieux_MISCELLANEOUS, Epigenomics
Abstract

Genes and transposons can exist in variable DNA methylation states, with potentially differential transcription. How these epialleles emerge is poorly understood. Here, we show that crossing an Arabidopsis thaliana plant with a hypomethylated genome and a normally methylated WT individual results, already in the F1 generation, in widespread changes in DNA methylation and transcription patterns. Novel nonparental and heritable epialleles arise at many genic loci, including a locus that itself controls DNA methylation patterns, but with most of the changes affecting pericentromeric transposons. Although a subset of transposons show immediate resilencing, a large number display decreased DNA methylation, which is associated with de novo or enhanced transcriptional activation and can translate into transposon mobilization in the progeny. Our findings reveal that the combination of distinct epigenomes can be viewed as an epigenomic shock, which is characterized by a round of epigenetic variation creating novel patterns of gene and TE regulation.

Published
2016

19. TDM1 Regulation Determines the Number of Meiotic Divisions

Author

Arp Schnittger, Hirofumi Harashima, Yuko Nomura, Laurence Cromer, Karel Riha, Sylvie Jolivet, Raphael Mercier, Wayne Crismani, Marta Cifuentes, Charlotte Renne, Keiko Sugimoto, Hirofumi Nakagami, Petra Bulankova, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, RIKEN Plant Science Center, Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Hamburg, Masaryk University [Brno] (MUNI), Czech Science Foundation [14-22346S], Japan Society for the Promotion of Science (JSPS) [26291064, 26650106, 15H01247], Fondation Simone et Cino del Duca, INRA BAP department, Labex Saclay Plant Sciences-SPS [ANR-10-LABX-0040-SPS], European Project: 281659,EC:FP7:ERC,ERC-2011-StG_20101109,MEIOSIGHT(2012), and Mercier, Raphaël

Subjects
0301 basic medicine, Cancer Research, [SDV]Life Sciences [q-bio], Arabidopsis, Genetic recombination, Biochemistry, Tubulin, [SDV.IDA]Life Sciences [q-bio]/Food engineering, Cell Cycle and Cell Division, Post-Translational Modification, Phosphorylation, Genetics (clinical), Genes, Dominant, Genetics, biology, Chromosome Biology, Meiosis, Phosphothreonine, Cell Processes, Ploidy, Research Article, Protein Binding, lcsh:QH426-470, Haploidisation, Models, Biological, Anaphase-Promoting Complex-Cyclosome, Chromosomes, Plant, 03 medical and health sciences, Cyclin-dependent kinase, Cyclins, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, Interkinesis, Telophase, Genetic Testing, Molecular Biology, Ecology, Evolution, Behavior and Systematics, Metaphase, Arabidopsis Proteins, Meiosis II, Biology and Life Sciences, Proteins, Epistasis, Genetic, Cell Biology, Tetraploidy, lcsh:Genetics, Protein Subunits, 030104 developmental biology, Mutation, biology.protein, Anaphase, Peptides
Abstract

Cell cycle control must be modified at meiosis to allow two divisions to follow a single round of DNA replication, resulting in ploidy reduction. The mechanisms that ensure meiosis termination at the end of the second and not at the end of first division are poorly understood. We show here that Arabidopsis thaliana TDM1, which has been previously shown to be essential for meiotic termination, interacts directly with the Anaphase-Promoting Complex. Further, mutations in TDM1 in a conserved putative Cyclin-Dependant Kinase (CDK) phosphorylation site (T16-P17) dominantly provoked premature meiosis termination after the first division, and the production of diploid spores and gametes. The CDKA;1-CYCA1.2/TAM complex, which is required to prevent premature meiotic exit, phosphorylated TDM1 at T16 in vitro. Finally, while CYCA1;2/TAM was previously shown to be expressed only at meiosis I, TDM1 is present throughout meiosis. These data, together with epistasis analysis, lead us to propose that TDM1 is an APC/C component whose function is to ensure meiosis termination at the end of meiosis II, and whose activity is inhibited at meiosis I by CDKA;1-TAM-mediated phosphorylation to prevent premature meiotic exit. This provides a molecular mechanism for the differential decision of performing an additional round of division, or not, at the end of meiosis I and II, respectively., Author Summary Meiosis is a fundamental process for sexually reproducing organisms that creates genetic diversity within populations. A key feature of meiosis is the reduction of the number of chromosomes, from two sets to one set, prior to fertilization. This reduction in chromosome number is due to two cell divisions following a single round of DNA replication. In this study, we analysed the mechanism which controls the number of cell divisions, ensuring that meiotic termination occurs after the second meiotic division, and not at the end of the first division. We used the model plant Arabidopsis thaliana to show that the gene TDM1 has a central role in regulating meiotic cell divisions. The integrity of the gene affects whether one, two or three meiotic divisions will occur. We further explain the relationship between TDM1 and its regulator the cyclin TAM, and how they work together to produce reproductive cells with a reduced number of chromosomes. This tightly controlled mechanism ensures the transmission of the correct number of chromosomes from one generation to the next.

Published
2016

20. The genome of the vervet ( Chlorocebus aethiops sabaeus )

Author

Nicoletta Archidiacono, Jennifer F. Hughes, George M. Weinstock, Yoon Jung, Christopher A. Schmitt, Angela Noll, Nelson B. Freimer, Matthew J. Jorgensen, Jennifer J. Tuscher, Nam Tran, Jason M. Brenchley, David H. O’Connor, Matthew W. Hahn, Eugene Redmond, Alex Nisbett, Roland Zahn, Hannes Svardal, Gary P. Schroth, Raquel García-Pérez, Magnus Nordborg, Nikoleta Juretic, Michael J. Montague, Gregg W.C. Thomas, Michel M. Dione, Julie A. Karl, Anna J. Jasinska, Wesley C. Warren, Jay R. Kaplan, Richard K. Wilson, Patrick Minx, Bronwen Aken, Mariano Rocchi, Colby Chiang, Françoise Thibaud-Nissen, Jessica Wasserscheid, Vasily Ramensky, Oi Wa Choi, Gennady Churakov, Roscoe Stanyon, Yu S. Huang, David Webb, Brian J. Raney, Jörn E. Schmitz, Milinn Kremitzki, Beatrice Jacquelin, Michaela Müller-Trutwin, Juergen Schmitz, Rishi Nag, Tomas Marques-Bonet, LaDeana W. Hillier, Martin Antonio, Tina Graves, Trudy R. Turner, Kim Kyung, Ken Dewar, Chad Tomlinson, Roger W. Wiseman, Oronzo Capozzi, The McDonnell Genome Institute (MGI), Washington University in Saint Louis (WUSTL), Semel Institute for Neuroscience and Human Behavior [Los Angeles, Ca], University of California [Los Angeles] (UCLA), University of California-University of California, Institute of Bioorganic Chemistry [Poznań], Polska Akademia Nauk = Polish Academy of Sciences (PAN), Institució Catalana de Recerca i Estudis Avançats (ICREA), Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Gregor Mendel Institute of Molecular Plant Biology (GMI), Austrian Academy of Sciences (OeAW), University of Bari Aldo Moro (UNIBA), Whitehead Institute, Massachusetts Institute of Technology (MIT), McGill University = Université McGill [Montréal, Canada], University of Wisconsin - Milwaukee, University of the Free State [South Africa], University of Wisconsin-Madison, Beth Israel Deaconess Medical Center [Boston] (BIDMC), Harvard Medical School [Boston] (HMS), Crucell Holland B.V, St. Kitts Biomedical Research Foundation, Régulation des Infections Rétrovirales, Institut Pasteur [Paris], National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Medical Research Council Unit The Gambia (MRC), Illumina Incorporated [San Diego, CA, USA], Wake Forest School of Medicine [Winston-Salem], Wake Forest Baptist Medical Center, Indiana University [Bloomington], Indiana University System, University of California [Santa Cruz] (UCSC), University of California, European Molecular Biology Laboratory [Hinxton], Institute of Experimental Pathology (ZMBE), Westfälische Wilhelms-Universität Münster (WWU), Institute for Evolution and Biodiversity (IEB), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), National Center for Biotechnology Information (NCBI), The Jackson Laboratory [Bar Harbor] (JAX), Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory., We thank the following organizations for providing sampling permits and permissions: Ethiopian Wildlife Conservation Authority, Zambia Wildlife Authority, Wildlife Division, Forestry Commission, Republic of Ghana, and Gambia Department of Parks and Wildlife Management. We thank Dr. James L. Blanchard and Dr. Ivona Pandrea for vervet samples used to characterize MHC. We thank Josh McMichael and Josh Peck for figure assistance. We thank Joanne Nelson and Barbara Gillam for data submission. We thank the members of the library production group led by Catrina Fronick and sequencing led by Matt Cordes. We also thank the Medical Research Council Unit (MRC), The Gambia for their assistance, as well as all the veterinarians who worked with us to safely obtain samples., National Institutes of Health (US), National Human Genome Research Institute (US), Agence Nationale de Recherches sur le SIDA et les Hépatites Virales (France), Agence Nationale de la Recherche (France), Ministero dell'Istruzione, dell'Università e della Ricerca, Genome Canada, EMBO, Wellcome Trust, University of California (UC)-University of California (UC), Università degli studi di Bari Aldo Moro = University of Bari Aldo Moro (UNIBA), University of the Free State [South Africa] (UFS), Institut Pasteur [Paris] (IP), University of California [Santa Cruz] (UC Santa Cruz), University of California (UC), Westfälische Wilhelms-Universität Münster = University of Münster (WWU), and Università degli Studi di Firenze = University of Florence (UniFI)

Subjects
animal diseases, [SDV]Life Sciences [q-bio], Chlorocebus aethiops, Cercopithecus aethiops, Medical and Health Sciences, Major Histocompatibility Complex, MESH: Animals, MESH: Genetic Variation, MESH: Phylogeny, Genetics (clinical), Phylogeny, MESH: Evolution, Molecular, Gene Rearrangement, education.field_of_study, Cercopithecini, Genome, biology, MESH: Genomics, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], MESH: Karyotype, Genomics, Biological Sciences, 3. Good health, Rhesus macaque, Phylogeography, MESH: Phylogeography, [SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology, [SDE]Environmental Sciences, Complete Genome assembly, primates, cercopithecini, Infection, Biotechnology, MESH: Computational Biology, Resource, Evolution, Bioinformatics, MESH: Gene Rearrangement, Population, Karyotype, Simis, Old World monkey, MESH: Molecular Sequence Annotation, [SDV.BID]Life Sciences [q-bio]/Biodiversity, Chromosome Painting, Evolution, Molecular, MESH: Major Histocompatibility Complex, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], parasitic diseases, Genetics, Animals, MESH: Genome, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, education, [SDV.GEN]Life Sciences [q-bio]/Genetics, Genètica animal, MESH: Chromosome Painting, Human Genome, Molecular, Computational Biology, Genetic Variation, Molecular Sequence Annotation, Gene rearrangement, biology.organism_classification, MESH: Cercopithecus aethiops, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Evolutionary biology, African Green Monkey
Abstract

Warren, Wesley C. et al., We describe a genome reference of the African green monkey or vervet (Chlorocebus aethiops). This member of the Old World monkey (OWM) superfamily is uniquely valuable for genetic investigations of simian immunodeficiency virus (SIV), for which it is the most abundant natural host species, and of a wide range of health-related phenotypes assessed in Caribbean vervets (C. a. sabaeus), whose numbers have expanded dramatically since Europeans introduced small numbers of their ancestors from West Africa during the colonial era. We use the reference to characterize the genomic relationship between vervets and other primates, the intra-generic phylogeny of vervet subspecies, and genome-wide structural variations of a pedigreed C. a. sabaeus population. Through comparative analyses with human and rhesus macaque, we characterize at high resolution the unique chromosomal fission events that differentiate the vervets and their close relatives from most other catarrhine primates, in whom karyotype is highly conserved. We also provide a summary of transposable elements and contrast these with the rhesus macaque and human. Analysis of sequenced genomes representing each of the main vervet subspecies supports previously hypothesized relationships between these populations, which range across most of sub-Saharan Africa, while uncovering high levels of genetic diversity within each. Sequence-based analyses of major histocompatibility complex (MHC) polymorphisms reveal extremely low diversity in Caribbean C. a. sabaeus vervets, compared to vervets from putatively ancestral West African regions. In the C. a. sabaeus research population, we discover the first structural variations that are, in some cases, predicted to have a deleterious effect; future studies will determine the phenotypic impact of these variations., Funding to R.K.W. was provided by NIH-NHGRI grant 5U54HG00307907. Support for the Vervet Research Colony was provided by NIH grant RR019963/OD010965 to J.R.K. Funding to N.B.F. was provided by NIH grants R01RR016300 and R01OD010980. The French National Agency for Research on AIDS and Viral Hepatitis (ANRS) provided funding to M.C.M.-T. Funding to M.R. and R.S. was provided by the Ministero della Universita’ e della Ricerca. Funding to K.D. was provided by Genome Canada and Genome Quebec. B.A. and R.N. acknowledge support from the Wellcome Trust (grant number WT095908) and the European Molecular Biology Laboratory.

Published
2015

21. Comparisons of two receptor-MAPK pathways in a single cell-type reveal mechanisms of signalling specificity.

Author

Ma Y, Flückiger I, Nicolet J, Pang J, Dickinson JB, De Bellis D, Emonet A, Fujita S, and Geldner N

Subjects
Mitogen-Activated Protein Kinases metabolism, Mitogen-Activated Protein Kinases genetics, Gene Expression Regulation, Plant, Signal Transduction, Transcription Factors metabolism, Transcription Factors genetics, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins metabolism, Arabidopsis Proteins genetics, MAP Kinase Signaling System, Plant Roots genetics, Plant Roots metabolism
Abstract

Cells harbour numerous receptor pathways to respond to diverse stimuli, yet often share common downstream signalling components. Mitogen-activated protein kinase (MPK) cascades are an example of such common hubs in eukaryotes. How such common hubs faithfully transduce distinct signals within the same cell-type is insufficiently understood, yet of fundamental importance for signal integration and processing in plants. We engineered a unique genetic background allowing direct comparisons of a developmental and an immunity pathway in one cell-type, the Arabidopsis root endodermis. We demonstrate that the two pathways maintain distinct functional and transcriptional outputs despite common MPK activity patterns. Nevertheless, activation of different MPK kinases and MPK classes led to distinct functional readouts, matching observed pathway-specific readouts. On the basis of our comprehensive analysis of core MPK signalling elements, we propose that combinatorial activation within the MPK cascade determines the differential regulation of an endodermal master transcription factor, MYB36, that drives pathway-specific gene activation., (© 2024. The Author(s).)

Published
2024
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22. Long days induce adaptive secondary dormancy in the seeds of the Mediterranean plant Aethionema arabicum.

Author

Mérai Z, Graeber K, Xu F, Donà M, Lalatović K, Wilhelmsson PKI, Fernandez-Pozo N, Rensing SA, Leubner-Metzger G, Mittelsten Scheid O, and Dolan L

Subjects
Photoperiod, Gene Expression Regulation, Plant, Plant Proteins genetics, Plant Proteins metabolism, Gibberellins metabolism, Seasons, Seedlings growth & development, Seedlings physiology, Adaptation, Physiological, Plant Dormancy, Seeds growth & development, Seeds physiology, Germination, Brassicaceae physiology
Abstract

Secondary dormancy is an adaptive trait that increases reproductive success by aligning seed germination with permissive conditions for seedling establishment. Aethionema arabicum is an annual plant and member of the Brassicaceae that grows in environments characterized by hot and dry summers. Aethionema arabicum seeds may germinate in early spring when seedling establishment is permissible. We demonstrate that long-day light regimes induce secondary dormancy in the seeds of Aethionema arabicum (CYP accession), repressing germination in summer when seedling establishment is riskier. Characterization of mutants screened for defective secondary dormancy demonstrated that RGL2 mediates repression of genes involved in gibberellin (GA) signaling. Exposure to high temperature alleviates secondary dormancy, restoring germination potential. These data are consistent with the hypothesis that long-day-induced secondary dormancy and its alleviation by high temperatures may be part of an adaptive response limiting germination to conditions permissive for seedling establishment in spring and autumn., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2024 Elsevier Inc. All rights reserved.)

Published
2024
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23. Live Imaging of the Shoot Apical Meristem of Intact, Soil-Grown, Flowering Arabidopsis Plants.

Author

Bradamante G

Abstract

All aerial organs in plants originate from the shoot apical meristem, a specialized tissue at the tip of a plant, enclosing a few stem cells. Understanding developmental dynamics within this tissue in relation to internal and external stimuli is of crucial importance. Imaging the meristem at the cellular level beyond very early stages requires the apex to be detached from the plant body, a procedure that does not allow studies in living, intact plants over longer periods. This protocol describes a new confocal microscopy method with the potential to image the shoot apical meristem of an intact, soil-grown, flowering Arabidopsis plant over several days. The setup opens new avenues to study apical stem cells, their interconnection with the whole plant, and their responses to environmental stimuli. Key features • Novel dissection and imaging method of the shoot apical meristem of Arabidopsis . • Procedure performed with intact, soil-grown, flowering plants. • Possibility of long-term live imaging of the shoot apical meristem. • Protocol can be adapted to different plant species., Competing Interests: Competing interestsThe author declares not to have any conflict of interest., (©Copyright : © 2024· The Authors; This is an open access article under the CC BY-NC license.)

Published
2024
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24. Micropillar arrays, wide window acquisition and AI-based data analysis improve comprehensiveness in multiple proteomic applications.

Author

Matzinger M, Schmücker A, Yelagandula R, Stejskal K, Krššáková G, Berger F, Mechtler K, and Mayer RL

Subjects
Proteome metabolism, Chromatin, Artificial Intelligence, Proteomics methods, Peptides
Abstract

Comprehensive proteomic analysis is essential to elucidate molecular pathways and protein functions. Despite tremendous progress in proteomics, current studies still suffer from limited proteomic coverage and dynamic range. Here, we utilize micropillar array columns (µPACs) together with wide-window acquisition and the AI-based CHIMERYS search engine to achieve excellent proteomic comprehensiveness for bulk proteomics, affinity purification mass spectrometry and single cell proteomics. Our data show that µPACs identify ≤50% more peptides and ≤24% more proteins, while offering improved throughput, which is critical for large (clinical) proteomics studies. Combining wide precursor isolation widths of m/z 4-12 with the CHIMERYS search engine identified +51-74% and +59-150% more proteins and peptides, respectively, for single cell, co-immunoprecipitation, and multi-species samples over a conventional workflow at well-controlled false discovery rates. The workflow further offers excellent precision, with CVs <7% for low input bulk samples, and accuracy, with deviations <10% from expected fold changes for regular abundance two-proteome mixes. Compared to a conventional workflow, our entire optimized platform discovered 92% more potential interactors in a protein-protein interaction study on the chromatin remodeler Smarca5/Snf2h. These include previously described Smarca5 binding partners and undescribed ones including Arid1a, another chromatin remodeler with key roles in neurodevelopmental and malignant disorders., (© 2024. The Author(s).)

Published
2024
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25. RHO of plant signaling was established early in streptophyte evolution.

Author

Mulvey H and Dolan L

Subjects
Phylogeny, Plants, Chlorophyta, Embryophyta genetics, Streptophyta physiology
Abstract

The algal ancestors of land plants underwent a transition from a unicellular to a multicellular body plan. 1 This transition likely took place early in streptophyte evolution, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. 2 How this transition was brought about is unknown; however, it was likely facilitated by the evolution of novel mechanisms to spatially regulate morphogenesis. In land plants, RHO of plant (ROP) signaling plays a conserved role in regulating polarized cell growth and cell division orientation to orchestrate morphogenesis. 3 ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes. , 4 how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes., 5 , 6 , 7 , 8 ROP constitutes a plant-specific subfamily of the RHO GTPases, which are more widely conserved throughout eukaryotes. 9 , 10 Although the RHO family originated in early eukaryotes, 11 , 12 how and when the ROP subfamily originated had remained elusive. Here, we demonstrate that ROP signaling was established early in the streptophyte lineage, sometime after the divergence of the Chlorokybophyceae/Mesostigmatophyceae lineage, but before the divergence of the Klebsormidiophyceae lineage. This period corresponds to when the unicellular-to-multicellular transition likely took place in the streptophytes. In addition to being critical for the complex morphogenesis of extant land plants, we speculate that ROP signaling contributed to morphological evolution in early streptophytes., Competing Interests: Declaration of interests L.D. is a founder of MoA Technology. He is also a member of the company’s board and its scientific advisory board., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2023
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26. Immunopeptidomics in the Era of Single-Cell Proteomics.

Author

Mayer RL and Mechtler K

Abstract

Immunopeptidomics, as the analysis of antigen peptides being presented to the immune system via major histocompatibility complexes (MHC), is being seen as an imperative tool for identifying epitopes for vaccine development to treat cancer and viral and bacterial infections as well as parasites. The field has made tremendous strides over the last 25 years but currently still faces challenges in sensitivity and throughput for widespread applications in personalized medicine and large vaccine development studies. Cutting-edge technological advancements in sample preparation, liquid chromatography as well as mass spectrometry, and data analysis, however, are currently transforming the field. This perspective showcases how the advent of single-cell proteomics has accelerated this transformation of immunopeptidomics in recent years and will pave the way for even more sensitive and higher-throughput immunopeptidomics analyses.

Published
2023
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27. RHO GTPase of plants regulates polarized cell growth and cell division orientation during morphogenesis.

Author

Mulvey H and Dolan L

Subjects
Cell Division, Plants metabolism, Plant Proteins genetics, Plant Proteins metabolism, Morphogenesis, rho GTP-Binding Proteins genetics, Marchantia genetics
Abstract

Cell polarity-broadly defined as the asymmetric distribution of cellular activities and subcellular components within a cell-determines the geometry of cell growth and division during development. RHO GTPase proteins regulate the establishment of cell polarity and are conserved among eukaryotes. RHO of plant (ROP) proteins are a subgroup of RHO GTPases that are required for cellular morphogenesis in plants. However, how ROP proteins modulate the geometry of cell growth and division during the morphogenesis of plant tissues and organs is not well understood. To investigate how ROP proteins function during tissue development and organogenesis, we characterized the function of the single-copy ROP gene of the liverwort Marchantia polymorpha (MpROP). M. polymorpha develops morphologically complex three-dimensional tissues and organs exemplified by air chambers and gemmae, respectively. Mprop loss-of-function mutants form defective air chambers and gemmae, indicating ROP function is required for tissue development and organogenesis. During air chamber and gemma development in wild type, the MpROP protein is enriched to sites of polarized growth at the cell surface and accumulates at the expanding cell plate of dividing cells. Consistent with these observations, polarized cell growth is lost and cell divisions are misoriented in Mprop mutants. We propose that ROP regulates both polarized cell growth and cell division orientation in a coordinated manner to orchestrate tissue development and organogenesis in land plants., Competing Interests: Declaration of interests L.D. is a founder of MoA Technology. He is also a member of the company's board and its scientific advisory board., (Copyright © 2023 The Authors. Published by Elsevier Inc. All rights reserved.)

Published
2023
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28. Label-free single cell proteomics utilizing ultrafast LC and MS instrumentation: A valuable complementary technique to multiplexing.

Author

Matzinger M, Mayer RL, and Mechtler K

Subjects
Mass Spectrometry methods, Proteome analysis, Proteomics methods, Algorithms
Abstract

The ability to map a proteomic fingerprint to transcriptomic data would master the understanding of how gene expression translates into actual phenotype. In contrast to nucleic acid sequencing, in vitro protein amplification is impossible and no single cell proteomic workflow has been established as gold standard yet. Advances in microfluidic sample preparation, multi-dimensional sample separation, sophisticated data acquisition strategies, and intelligent data analysis algorithms have resulted in major improvements to successfully analyze such tiny sample amounts with steadily boosted performance. However, among the broad variation of published approaches, it is commonly accepted that highest possible sensitivity, robustness, and throughput are still the most urgent needs for the field. While many labs have focused on multiplexing to achieve these goals, label-free SCP is a highly promising strategy as well whenever high dynamic range and unbiased accurate quantification are needed. We here focus on recent advances in label-free single-cell mass spectrometry workflows and try to guide our readers to choose the best method or combinations of methods for their specific applications. We further highlight which techniques are most propitious in the future and which applications but also limitations we foresee for the field., (© 2023 The Authors. Proteomics published by Wiley-VCH GmbH.)

Published
2023
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30. Phytochromes mediate germination inhibition under red, far-red, and white light in Aethionema arabicum.

Author

Mérai Z, Xu F, Musilek A, Ackerl F, Khalil S, Soto-Jiménez LM, Lalatović K, Klose C, Tarkowská D, Turečková V, Strnad M, and Mittelsten Scheid O

Subjects
Germination genetics, Seeds genetics, Hormones metabolism, Phytochrome genetics, Phytochrome metabolism, Arabidopsis metabolism, Brassicaceae genetics, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
Abstract

The view on the role of light during seed germination stems mainly from studies with Arabidopsis (Arabidopsis thaliana), where light is required to initiate this process. In contrast, white light is a strong inhibitor of germination in other plants, exemplified by accessions of Aethionema arabicum, another member of Brassicaceae. Their seeds respond to light with gene expression changes of key regulators converse to that of Arabidopsis, resulting in opposite hormone regulation and prevention of germination. However, the photoreceptors involved in this process in A. arabicum remain unknown. Here, we screened a mutant collection of A. arabicum and identified koy-1, a mutant that lost light inhibition of germination due to a deletion in the promoter of HEME OXYGENASE 1, the gene for a key enzyme in the biosynthesis of the phytochrome chromophore. koy-1 seeds were unresponsive to red- and far-red light and hyposensitive under white light. Comparison of hormone and gene expression between wild type and koy-1 revealed that very low light fluence stimulates germination, while high irradiance of red and far-red light is inhibitory, indicating a dual role of phytochromes in light-regulated seed germination. The mutation also affects the ratio between the 2 fruit morphs of A. arabicum, suggesting that light reception via phytochromes can fine-tune several parameters of propagation in adaptation to conditions in the habitat., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2023. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Published
2023
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31. Robust and Easy-to-Use One-Pot Workflow for Label-Free Single-Cell Proteomics.

Author

Matzinger M, Müller E, Dürnberger G, Pichler P, and Mechtler K

Subjects
Workflow, Reproducibility of Results, Cell Line, Proteomics, Proteome analysis
Abstract

The analysis of ultralow input samples or even individual cells is essential to answering a multitude of biomedical questions, but current proteomic workflows are limited in their sensitivity and reproducibility. Here, we report a comprehensive workflow that includes improved strategies for all steps, from cell lysis to data analysis. Thanks to convenient-to-handle 1 μL sample volume and standardized 384-well plates, the workflow is easy for even novice users to implement. At the same time, it can be performed semi-automatized using CellenONE, which allows for the highest reproducibility. To achieve high throughput, ultrashort gradient lengths down to 5 min were tested using advanced μ-pillar columns. Data-dependent acquisition (DDA), wide-window acquisition (WWA), data-independent acquisition (DIA), and commonly used advanced data analysis algorithms were benchmarked. Using DDA, 1790 proteins covering a dynamic range of four orders of magnitude were identified in a single cell. Using DIA, proteome coverage increased to more than 2200 proteins identified from single-cell level input in a 20 min active gradient. The workflow enabled differentiation of two cell lines, demonstrating its suitability to cellular heterogeneity determination.

Published
2023
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32. Mendelian and non-Mendelian genetics in model plants.

Author

Mittelsten Scheid O

Subjects
Inheritance Patterns genetics, Plants genetics
Abstract

The "Mendelian Rules" of inheritance are cornerstones of genetics, described in Mendel's seminal publication from 1866. The experimental results and their interpretation have been discussed in numerous ways. This perspective emphasizes the contribution of Mendel's preparations prior to his crossing experiments to the discovery of Mendelian genetics. This thoughtful experimental design, and some fortune, avoided pitfalls that could have resulted in non-Mendelian inheritance., (� American Society of Plant Biologists 2022. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Published
2022
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33. Innate, translation-dependent silencing of an invasive transposon in Arabidopsis.

Author

Oberlin S, Rajeswaran R, Trasser M, Barragán-Borrero V, Schon MA, Plotnikova A, Loncsek L, Nodine MD, Marí-Ordóñez A, and Voinnet O

Subjects
DNA Transposable Elements genetics, Gene Expression Regulation, Plant, RNA, Small Interfering genetics, Arabidopsis genetics, Arabidopsis metabolism, Arabidopsis Proteins genetics, Arabidopsis Proteins metabolism
Abstract

Co-evolution between hosts' and parasites' genomes shapes diverse pathways of acquired immunity based on silencing small (s)RNAs. In plants, sRNAs cause heterochromatinization, sequence degeneration, and, ultimately, loss of autonomy of most transposable elements (TEs). Recognition of newly invasive plant TEs, by contrast, involves an innate antiviral-like silencing response. To investigate this response's activation, we studied the single-copy element EVADÉ (EVD), one of few representatives of the large Ty1/Copia family able to proliferate in Arabidopsis when epigenetically reactivated. In Ty1/Copia elements, a short subgenomic mRNA (shGAG) provides the necessary excess of structural GAG protein over the catalytic components encoded by the full-length genomic flGAG-POL. We show here that the predominant cytosolic distribution of shGAG strongly favors its translation over mostly nuclear flGAG-POL. During this process, an unusually intense ribosomal stalling event coincides with mRNA breakage yielding unconventional 5'OH RNA fragments that evade RNA quality control. The starting point of sRNA production by RNA-DEPENDENT-RNA-POLYMERASE-6 (RDR6), exclusively on shGAG, occurs precisely at this breakage point. This hitherto-unrecognized "translation-dependent silencing" (TdS) is independent of codon usage or GC content and is not observed on TE remnants populating the Arabidopsis genome, consistent with their poor association, if any, with polysomes. We propose that TdS forms a primal defense against EVD de novo invasions that underlies its associated sRNA pattern., (© 2021 The Authors. Published under the terms of the CC BY 4.0 license.)

Published
2022
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34. QUAREP-LiMi: A community-driven initiative to establish guidelines for quality assessment and reproducibility for instruments and images in light microscopy.

Author

Nelson G, Boehm U, Bagley S, Bajcsy P, Bischof J, Brown CM, Dauphin A, Dobbie IM, Eriksson JE, Faklaris O, Fernandez-Rodriguez J, Ferrand A, Gelman L, Gheisari A, Hartmann H, Kukat C, Laude A, Mitkovski M, Munck S, North AJ, Rasse TM, Resch-Genger U, Schuetz LC, Seitz A, Strambio-De-Castillia C, Swedlow JR, Alexopoulos I, Aumayr K, Avilov S, Bakker GJ, Bammann RR, Bassi A, Beckert H, Beer S, Belyaev Y, Bierwagen J, Birngruber KA, Bosch M, Breitlow J, Cameron LA, Chalfoun J, Chambers JJ, Chen CL, Conde-Sousa E, Corbett AD, Cordelieres FP, Nery ED, Dietzel R, Eismann F, Fazeli E, Felscher A, Fried H, Gaudreault N, Goh WI, Guilbert T, Hadleigh R, Hemmerich P, Holst GA, Itano MS, Jaffe CB, Jambor HK, Jarvis SC, Keppler A, Kirchenbuechler D, Kirchner M, Kobayashi N, Krens G, Kunis S, Lacoste J, Marcello M, Martins GG, Metcalf DJ, Mitchell CA, Moore J, Mueller T, Nelson MS, Ogg S, Onami S, Palmer AL, Paul-Gilloteaux P, Pimentel JA, Plantard L, Podder S, Rexhepaj E, Royon A, Saari MA, Schapman D, Schoonderwoert V, Schroth-Diez B, Schwartz S, Shaw M, Spitaler M, Stoeckl MT, Sudar D, Teillon J, Terjung S, Thuenauer R, Wilms CD, Wright GD, and Nitschke R

Subjects
Reference Standards, Reproducibility of Results, Microscopy
Abstract

A modern day light microscope has evolved from a tool devoted to making primarily empirical observations to what is now a sophisticated , quantitative device that is an integral part of both physical and life science research. Nowadays, microscopes are found in nearly every experimental laboratory. However, despite their prevalent use in capturing and quantifying scientific phenomena, neither a thorough understanding of the principles underlying quantitative imaging techniques nor appropriate knowledge of how to calibrate, operate and maintain microscopes can be taken for granted. This is clearly demonstrated by the well-documented and widespread difficulties that are routinely encountered in evaluating acquired data and reproducing scientific experiments. Indeed, studies have shown that more than 70% of researchers have tried and failed to repeat another scientist's experiments, while more than half have even failed to reproduce their own experiments. One factor behind the reproducibility crisis of experiments published in scientific journals is the frequent underreporting of imaging methods caused by a lack of awareness and/or a lack of knowledge of the applied technique. Whereas quality control procedures for some methods used in biomedical research, such as genomics (e.g. DNA sequencing, RNA-seq) or cytometry, have been introduced (e.g. ENCODE), this issue has not been tackled for optical microscopy instrumentation and images. Although many calibration standards and protocols have been published, there is a lack of awareness and agreement on common standards and guidelines for quality assessment and reproducibility. In April 2020, the QUality Assessment and REProducibility for instruments and images in Light Microscopy (QUAREP-LiMi) initiative was formed. This initiative comprises imaging scientists from academia and industry who share a common interest in achieving a better understanding of the performance and limitations of microscopes and improved quality control (QC) in light microscopy. The ultimate goal of the QUAREP-LiMi initiative is to establish a set of common QC standards, guidelines, metadata models and tools, including detailed protocols, with the ultimate aim of improving reproducible advances in scientific research. This White Paper (1) summarizes the major obstacles identified in the field that motivated the launch of the QUAREP-LiMi initiative; (2) identifies the urgent need to address these obstacles in a grassroots manner, through a community of stakeholders including, researchers, imaging scientists, bioimage analysts, bioimage informatics developers, corporate partners, funding agencies, standards organizations, scientific publishers and observers of such; (3) outlines the current actions of the QUAREP-LiMi initiative and (4) proposes future steps that can be taken to improve the dissemination and acceptance of the proposed guidelines to manage QC. To summarize, the principal goal of the QUAREP-LiMi initiative is to improve the overall quality and reproducibility of light microscope image data by introducing broadly accepted standard practices and accurately captured image data metrics., (© 2021 The Authors. Journal of Microscopy published by JohnWiley & Sons Ltd on behalf of Royal Microscopical Society.)

Published
2021
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35. The EpiDiverse Plant Epigenome-Wide Association Studies (EWAS) Pipeline.

Author

Can SN, Nunn A, Galanti D, Langenberger D, Becker C, Volmer K, Heer K, Opgenoorth L, Fernandez-Pozo N, and Rensing SA

Abstract

Bisulfite sequencing is a widely used technique for determining DNA methylation and its relationship with epigenetics, genetics, and environmental parameters. Various techniques were implemented for epigenome-wide association studies (EWAS) to reveal meaningful associations; however, there are only very few plant studies available to date. Here, we developed the EpiDiverse EWAS pipeline and tested it using two plant datasets, from P. abies (Norway spruce) and Q. lobata (valley oak). Hence, we present an EWAS implementation tested for non-model plant species and describe its use.

Published
2021
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36. Polyploidy-associated paramutation in Arabidopsis is determined by small RNAs, temperature, and allele structure.

Author

Bente H, Foerster AM, Lettner N, and Mittelsten Scheid O

Subjects
Gene Order, Gene Silencing, RNA Interference, Alleles, Arabidopsis genetics, Mutation, Polyploidy, RNA, Plant, RNA, Small Untranslated, Temperature
Abstract

Paramutation is a form of non-Mendelian inheritance in which the expression of a paramutable allele changes when it encounters a paramutagenic allele. This change in expression of the paramutable alleles is stably inherited even after segregation of both alleles. While the discovery of paramutation and studies of its underlying mechanism were made with alleles that change plant pigmentation, paramutation-like phenomena are known to modulate the expression of other traits and in other eukaryotes, and many cases have probably gone undetected. It is likely that epigenetic mechanisms are responsible for the phenomenon, as paramutation forms epialleles, genes with identical sequences but different expression states. This could account for the intergenerational inheritance of the paramutated allele, providing profound evidence that triggered epigenetic changes can be maintained over generations. Here, we use a case of paramutation that affects a transgenic selection reporter gene in tetraploid Arabidopsis thaliana. Our data suggest that different types of small RNA are derived from paramutable and paramutagenic epialleles. In addition, deletion of a repeat within the epiallele changes its paramutability. Further, the temperature during the growth of the epiallelic hybrids determines the degree and timing of the allelic interaction. The data further make it plausible why paramutation in this system becomes evident only in the segregating F2 population of tetraploid plants containing both epialleles. In summary, the results support a model for polyploidy-associated paramutation, with similarities as well as distinctions from other cases of paramutation., Competing Interests: The authors have declared that no competing interests exist.

Published
2021
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37. Ustilago maydis effector Jsi1 interacts with Topless corepressor, hijacking plant jasmonate/ethylene signaling.

Author

Darino M, Chia KS, Marques J, Aleksza D, Soto-Jiménez LM, Saado I, Uhse S, Borg M, Betz R, Bindics J, Zienkiewicz K, Feussner I, Petit-Houdenot Y, and Djamei A

Subjects
Ascomycota, Basidiomycota, Co-Repressor Proteins, Cyclopentanes, Ethylenes, Fungal Proteins, Oxylipins, Zea mays, Plant Diseases, Ustilago
Abstract

Ustilago maydis is the causal agent of maize smut disease. During the colonization process, the fungus secretes effector proteins that suppress immune responses and redirect the host metabolism in favor of the pathogen. As effectors play a critical role during plant colonization, their identification and functional characterization are essential to understanding biotrophy and disease. Using biochemical, molecular, and transcriptomic techniques, we performed a functional characterization of the U. maydis effector Jasmonate/Ethylene signaling inducer 1 (Jsi1). Jsi1 interacts with several members of the plant corepressor family Topless/Topless related (TPL/TPR). Jsi1 expression in Zea mays and Arabidopsis thaliana leads to transcriptional induction of the ethylene response factor (ERF) branch of the jasmonate/ethylene (JA/ET) signaling pathway. In A. thaliana, activation of the ERF branch leads to biotrophic susceptibility. Jsi1 likely activates the ERF branch via an EAR (ET-responsive element binding-factor-associated amphiphilic repression) motif, which resembles EAR motifs from plant ERF transcription factors, that interacts with TPL/TPR proteins. EAR-motif-containing effector candidates were identified from different fungal species, including Magnaporthe oryzae, Sporisorium scitamineum, and Sporisorium reilianum. Interaction between plant TPL proteins and these effector candidates from biotrophic and hemibiotrophic fungi indicates the convergent evolution of effectors modulating the TPL/TPR corepressor hub., (© 2020 The Authors New Phytologist © 2020 New Phytologist Foundation.)

Published
2021
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38. ARADEEPOPSIS, an Automated Workflow for Top-View Plant Phenomics using Semantic Segmentation of Leaf States.

Author

Hüther P, Schandry N, Jandrasits K, Bezrukov I, and Becker C

Subjects
Arabidopsis cytology, Computational Biology, Genome-Wide Association Study, Genotype, Image Processing, Computer-Assisted, Phenotype, Plant Leaves cytology, Plant Leaves genetics, Semantics, Arabidopsis genetics, Phenomics, Software, Workflow
Abstract

Linking plant phenotype to genotype is a common goal to both plant breeders and geneticists. However, collecting phenotypic data for large numbers of plants remain a bottleneck. Plant phenotyping is mostly image based and therefore requires rapid and robust extraction of phenotypic measurements from image data. However, because segmentation tools usually rely on color information, they are sensitive to background or plant color deviations. We have developed a versatile, fully open-source pipeline to extract phenotypic measurements from plant images in an unsupervised manner. ARADEEPOPSIS (https://github.com/Gregor-Mendel-Institute/aradeepopsis) uses semantic segmentation of top-view images to classify leaf tissue into three categories: healthy, anthocyanin rich, and senescent. This makes it particularly powerful at quantitative phenotyping of different developmental stages, mutants with aberrant leaf color and/or phenotype, and plants growing in stressful conditions. On a panel of 210 natural Arabidopsis ( Arabidopsis thaliana ) accessions, we were able to not only accurately segment images of phenotypically diverse genotypes but also to identify known loci related to anthocyanin production and early necrosis in genome-wide association analyses. Our pipeline accurately processed images of diverse origin, quality, and background composition, and of a distantly related Brassicaceae. ARADEEPOPSIS is deployable on most operating systems and high-performance computing environments and can be used independently of bioinformatics expertise and resources., (© 2020 American Society of Plant Biologists. All rights reserved.)

Published
2020
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39. Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.

Author

Griss J, Stanek F, Hudecz O, Dürnberger G, Perez-Riverol Y, Vizcaíno JA, and Mechtler K

Subjects
Algorithms, Databases, Protein, Humans, Cluster Analysis, Mass Spectrometry methods, Proteome analysis, Proteomics methods
Abstract

Label-free quantification has become a common-practice in many mass spectrometry-based proteomics experiments. In recent years, we and others have shown that spectral clustering can considerably improve the analysis of (primarily large-scale) proteomics data sets. Here we show that spectral clustering can be used to infer additional peptide-spectrum matches and improve the quality of label-free quantitative proteomics data in data sets also containing only tens of MS runs. We analyzed four well-known public benchmark data sets that represent different experimental settings using spectral counting and peak intensity based label-free quantification. In both approaches, the additionally inferred peptide-spectrum matches through our spectra-cluster algorithm improved the detectability of low abundant proteins while increasing the accuracy of the derived quantitative data, without increasing the data sets' noise. Additionally, we developed a Proteome Discoverer node for our spectra-cluster algorithm which allows anyone to rebuild our proposed pipeline using the free version of Proteome Discoverer.

Published
2019
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40. apQuant: Accurate Label-Free Quantification by Quality Filtering.

Author

Doblmann J, Dusberger F, Imre R, Hudecz O, Stanek F, Mechtler K, and Dürnberger G

Subjects
Algorithms, Benchmarking, Peptides analysis, Computational Biology methods, Proteomics methods
Abstract

Label-free quantification of shotgun proteomics data is a frequently used strategy, offering high dynamic range, sensitivity, and the ability to compare a high number of samples without additional labeling effort. Here, we present a bioinformatics approach that significantly improves label-free quantification results. We employ Percolator to assess the quality of quantified peptides. This allows to extract accurate and reliable quantitative results based on false discovery rate. Benchmarking our approach on previously published public data shows that it considerably outperforms currently available algorithms. apQuant is available free of charge as a node for Proteome Discoverer.

Published
2019
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41. RANK rewires energy homeostasis in lung cancer cells and drives primary lung cancer.

Author

Rao S, Sigl V, Wimmer RA, Novatchkova M, Jais A, Wagner G, Handschuh S, Uribesalgo I, Hagelkruys A, Kozieradzki I, Tortola L, Nitsch R, Cronin SJ, Orthofer M, Branstetter D, Canon J, Rossi J, D'Arcangelo M, Botling J, Micke P, Fleur L, Edlund K, Bergqvist M, Ekman S, Lendl T, Popper H, Takayanagi H, Kenner L, Hirsch FR, Dougall W, and Penninger JM

Subjects
Alveolar Epithelial Cells metabolism, Animals, Cell Respiration, Cells, Cultured, Energy Metabolism, Female, Gonadal Steroid Hormones physiology, Homeostasis, Humans, Lung metabolism, Lung Neoplasms drug therapy, Male, Mice, Mitochondria metabolism, Neoplastic Stem Cells metabolism, Proto-Oncogene Proteins p21(ras) genetics, Receptor Activator of Nuclear Factor-kappa B antagonists & inhibitors, Receptor Activator of Nuclear Factor-kappa B genetics, Receptor Activator of Nuclear Factor-kappa B metabolism, Respiratory Mucosa metabolism, Lung Neoplasms metabolism, Receptor Activator of Nuclear Factor-kappa B physiology
Abstract

Lung cancer is the leading cause of cancer deaths. Besides smoking, epidemiological studies have linked female sex hormones to lung cancer in women; however, the underlying mechanisms remain unclear. Here we report that the receptor activator of nuclear factor-kB (RANK), the key regulator of osteoclastogenesis, is frequently expressed in primary lung tumors, an active RANK pathway correlates with decreased survival, and pharmacologic RANK inhibition reduces tumor growth in patient-derived lung cancer xenografts. Clonal genetic inactivation of KRas in mouse lung epithelial cells markedly impairs the progression of G12D -driven lung cancer, resulting in a significant survival advantage. Mechanistically, RANK rewires energy homeostasis in human and murine lung cancer cells and promotes expansion of lung cancer stem-like cells, which is blocked by inhibiting mitochondrial respiration. Our data also indicate survival differences in KRas -driven lung cancer between male and female mice, and we show that female sex hormones can promote lung cancer progression via the RANK pathway. These data uncover a direct role for RANK in lung cancer and may explain why female sex hormones accelerate lung cancer development. Inhibition of RANK using the approved drug denosumab may be a therapeutic drug candidate for primary lung cancer. G12D -driven lung cancer, resulting in a significant survival advantage. Mechanistically, RANK rewires energy homeostasis in human and murine lung cancer cells and promotes expansion of lung cancer stem-like cells, which is blocked by inhibiting mitochondrial respiration. Our data also indicate survival differences in KRas G12D -driven lung cancer between male and female mice, and we show that female sex hormones can promote lung cancer progression via the RANK pathway. These data uncover a direct role for RANK in lung cancer and may explain why female sex hormones accelerate lung cancer development. Inhibition of RANK using the approved drug denosumab may be a therapeutic drug candidate for primary lung cancer., (© 2017 Rao et al.; Published by Cold Spring Harbor Laboratory Press.)

Published
2017
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