Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction

dc.contributor.authorRedondo-Nieto, Miguel
dc.contributor.authorBarret, Matthieu
dc.contributor.authorMorrissey, John P.
dc.contributor.authorGermaine, Kieran
dc.contributor.authorMartínez-Granero, Francisco
dc.contributor.authorBarahona, Emma
dc.contributor.authorNavazo, Ana
dc.contributor.authorSánchez-Contreras, María
dc.contributor.authorMoynihan, Jennifer A.
dc.contributor.authorMuriel, Candela
dc.contributor.authorDowling, David
dc.contributor.authorO'Gara, Fergal
dc.contributor.authorMartín, Marta
dc.contributor.authorRivilla, Rafael
dc.contributor.funderHealth Research Boarden
dc.contributor.funderIrish Research Council for Science Engineering and Technologyen
dc.contributor.funderMarine Instituteen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderComunidad de Madrid, Spain
dc.contributor.funderMinisterio de Educación, Cultura y Deporte, Spain
dc.contributor.funderDepartment of Agriculture, Fisheries and Food, Ireland
dc.contributor.funderEuropean Commission
dc.contributor.funderEnvironmental Protection Agency
dc.contributor.funderDepartment of Education and Skills, Ireland
dc.date.accessioned2016-02-25T17:01:28Z
dc.date.available2016-02-25T17:01:28Z
dc.date.issued2013-01-25
dc.description.abstractBackground: Pseudomonas fluorescens F113 is a plant growth-promoting rhizobacterium (PGPR) isolated from the sugar-beet rhizosphere. This bacterium has been extensively studied as a model strain for genetic regulation of secondary metabolite production in P. fluorescens, as a candidate biocontrol agent against phytopathogens, and as a heterologous host for expression of genes with biotechnological application. The F113 genome sequence and annotation has been recently reported. Results: Comparative analysis of 50 genome sequences of strains belonging to the P. fluorescens group has revealed the existence of five distinct subgroups. F113 belongs to subgroup I, which is mostly composed of strains classified as P. brassicacearum. The core genome of these five strains is highly conserved and represents approximately 76% of the protein-coding genes in any given genome. Despite this strong conservation, F113 also contains a large number of unique protein-coding genes that encode traits potentially involved in the rhizocompetence of this strain. These features include protein coding genes required for denitrification, diterpenoids catabolism, motility and chemotaxis, protein secretion and production of antimicrobial compounds and insect toxins. Conclusions: The genome of P. fluorescens F113 is composed of numerous protein-coding genes, not usually found together in previously sequenced genomes, which are potentially decisive during the colonisation of the rhizosphere and/or interaction with other soil organisms. This includes genes encoding proteins involved in the production of a second flagellar apparatus, the use of abietic acid as a growth substrate, the complete denitrification pathway, the possible production of a macrolide antibiotic and the assembly of multiple protein secretion systems.en
dc.description.sponsorshipComunidad de Madrid (MICROAMBIENTE-CM grant to Rafael Rivilla); Ministerio de Educación, Cultura y Deporte, Spain (BIO2009-08254 grant to Marta Martín); Science Foundation Ireland (SFI Grants 07IN.1/B948, 08/RFP/GEN1295, 08/RFP/GEN1319, SFI09/RFP/BMT2350 to Fergal O'Gara); Department of Agriculture, Fisheries and Food, Ireland (RSF grants 06–321 and 06–377; FIRM grants 06RDC459 06RDC506 and 08RDC629); European Commission (MTKD-CT-2006-042062; Marie Curie TOK:TRAMWAYS; EU256596; MicroB3-287589-OCEAN2012; MACUMBA-CP-TP 311975; PharmaSea-CP-TP 312184; Marie Curie MIGENOF113 to María Sánchez-Contreras and Rafael Rivilla); Irish Research Council for Science Engineering and Technology (05/EDIV/FP107/INTERPAM, EMBARK);Marine Institute (Beaufort Award C&CRA 2007/082); Environmental Protection Agency (EPA 2006-PhD-S-21, EPA 2008-PhD-S-2); Health Research Board (RP/2006/271, RP/2007/290, HRA/2009/146); Science Foundation Ireland (Tida Award); Department of Education and Skills, Ireland (TSR III Agribiotics Project)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.articleid54
dc.identifier.citationREDONDO-NIETO, M., BARRET, M., MORRISSEY, J., GERMAINE, K., MARTÍNEZ-GRANERO, F., BARAHONA, E., NAVAZO, A., SÁNCHEZ-CONTRERAS, M., MOYNIHAN, J. A., MURIEL, C., DOWLING, D., O’GARA, F., MARTÍN, M. & RIVILLA, R. 2013. Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics, 14:54, 1-17.en
dc.identifier.doi10.1186/1471-2164-14-54
dc.identifier.endpage17en
dc.identifier.issn1471-2164
dc.identifier.journaltitleBMC Genomicsen
dc.identifier.startpage1en
dc.identifier.urihttps://hdl.handle.net/10468/2399
dc.identifier.volume14en
dc.language.isoenen
dc.publisherBioMed Central Ltd.en
dc.rights© Redondo-Nieto et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.en
dc.rights.urihttp://​creativecommons.​org/​licenses/​by/​2.​0en
dc.subjectVI secretion systemen
dc.subjectCompetitive colonization abilityen
dc.subjectIII secretionen
dc.subjectStreptomyces rocheien
dc.subjectMaximum likelihooden
dc.subjectPlant growthen
dc.subjectEvolutionary historyen
dc.subjectAzospirillum brasilenseen
dc.subjectSinorhizobium melilotien
dc.titleGenome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interactionen
dc.typeArticle (peer-reviewed)en
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