1. Comparative analysis of Ralstonia solanacearum methylomes
- Author
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Erill, Ivan, Puigvert, Marina, Legrand, Ludovic, Guarischi-Sousa, Rodrigo, Vandecasteele, Céline, Setubal, João C., Genin, Stephane, Guidot, Alice, Valls, Marc, Department of Biological Sciences, The Open University [Milton Keynes] (OU), CSIC- IRTA- UAB -UB, Center for Research in Agricultural Genomics, Department of Genetics, The University of Texas M.D. Anderson Cancer Center [Houston], Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo (USP), GeT PlaGe, Genotoul, Institut National de la Recherche Agronomique (INRA), Spanish Ministry of Economy and Competitiveness projects : AGL2013-46898-R, AGL2016-78002-R, U.S. National Science Foundation : MCB-1158056, CERCA Program of the Catalan Government (Generalitat de Catalunya), University of Maryland, Baltimore County Office of Research, 'Severo Ochoa Program for Centers of Excellence in R&D' of the Spanish Ministry of Economy and Competitiveness, SEV-2015-0533, COST Action SUSTAIN from the European Union : FA1208, doctoral fellowship : 2012/15197-1, Sao Paulo Research Foundation (FAPESP), CNPq : 304881/2015-5, Universitat de Barcelona, France Genomique National infrastructure, as part of 'Investissement d'avenir' program, Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Maryland [Baltimore County] (UMBC), University of Maryland System, Consejo Superior de Investigaciones Científicas [Spain] (CSIC), Universitat Autònoma de Barcelona (UAB), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Spanish Ministry of Economy and Competitiveness projects AGL2013-46898-RAGL2016-78002-RNational Science Foundation (NSF)MCB-1158056CERCA Program of the Catalan Government (Generalitat de Catalunya) University of Maryland Baltimore County Office of Research 'Severo Ochoa Program for Centers of Excellence in RAMP, D' of the Spanish Ministry of Economy and Competitiveness SEV-2015-0533COST Action SUSTAIN from the European Union FA1208doctoral fellowship 2012/15197-1Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP) National Council for Scientific and Technological Development (CNPq)304881/2015-5Universitat de Barcelona French National Research Agency (ANR), Ministerio de Economía y Competitividad (España), National Science Foundation (US), Generalitat de Catalunya, European Commission, Sao Paulo Research Foundation, Universidad de Barcelona, Agence Nationale de la Recherche (France), The Open University [Milton Keynes] ( OU ), University of Texas M.D. Anderson Cancer Center, Interactions plantes-microorganismes et santé végétale, Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ) -Institut National de la Recherche Agronomique ( INRA ), Universidade de São Paulo ( USP ), and Institut National de la Recherche Agronomique ( INRA )
- Subjects
Epigenomics ,[ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology ,comparative analysis ,transposon ,[SDV]Life Sciences [q-bio] ,Plant Science ,comparative genomics ,adaptation ,Ralstonia ,methylome ,nucleotide modification ,epigenomics ,transcriptional ,regulation ,genome ,Transcriptional regulation ,[ SDV.MP ] Life Sciences [q-bio]/Microbiology and Parasitology ,plante pathogène ,Phytopatogenic bacteria ,[SDV.BV]Life Sciences [q-bio]/Vegetal Biology ,transcriptional regulation ,Bacteris fitopatògens ,pathologie végétale ,Transposon ,Vegetal Biology ,Genome ,Comparative genomics ,Microbiology and Parasitology ,food and beverages ,analyse comparative ,biochemical phenomena, metabolism, and nutrition ,Microbiologie et Parasitologie ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Ralstonia solanacearum ,Methylome ,Biologie végétale ,Nucleotide modification - Abstract
Ralstonia solanacearum is an important soil-borne plant pathogen with broad geographical distribution and the ability to cause wilt disease in many agriculturally important crops. Genome sequencing of multiple R. solanacearum strains has identified both unique and shared genetic traits influencing their evolution and ability to colonize plant hosts. Previous research has shown that DNA methylation can drive speciation and modulate virulence in bacteria, but the impact of epigenetic modifications on the diversification and pathogenesis of R. solanacearum is unknown. Sequencing of R. solanacearum strains GMI1000 and UY031 using Single Molecule Real-Time technology allowed us to perform a comparative analysis of R. solanacearum methylomes. Our analysis identified a novel methylation motif associated with a DNA methylase that is conserved in all complete Ralstonia spp. genomes and across the Burkholderiaceae, as well as a methylation motif associated to a phage-borne methylase unique to R. solanacearum UY031. Comparative analysis of the conserved methylation motif revealed that it is most prevalent in gene promoter regions, where it displays a high degree of conservation detectable through phylogenetic footprinting. Analysis of hyper- and hypo-methylated loci identified several genes involved in global and virulence regulatory functions whose expression may be modulated by DNA methylation. Analysis of genome-wide modification patterns identified a significant correlation between DNA modification and transposase genes in R. solanacearum UY031, driven by the presence of a high copy number of ISrso3 insertion sequences in this genome and pointing to a novel mechanism for regulation of transposition. These results set a firm foundation for experimental investigations into the role of DNA methylation in R. solanacearum evolution and its adaptation to different plants., This work was funded by the Spanish Ministry of Economy and Competitiveness projects AGL2013-46898-R and AGL2016-78002-R to MV and by a U.S. National Science Foundation (MCB-1158056) award to IE. We also acknowledge financial support from the CERCA Program of the Catalan Government (Generalitat de Catalunya), the University of Maryland, Baltimore County Office of Research, the “Severo Ochoa Program for Centers of Excellence in R&D” 2016–2019 (SEV-2015-0533) of the Spanish Ministry of Economy and Competitiveness and the COST Action SUSTAIN (FA1208) from the European Union. RG is the recipient of a doctoral fellowship [grant 2012/15197-1, São Paulo Research Foundation (FAPESP)]. JS has a researcher fellowship from CNPq (304881/2015-5). MP holds an APIF doctoral fellowship from Universitat de Barcelona. This work was also performed in collaboration with the GeT core facility, Toulouse, France (http://get.genotoul.fr), and was supported by France Génomique National infrastructure, funded as part of “Investissement d'avenir” program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09).
- Published
- 2017
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