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

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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.funderEnvironmental Protection Agencyen
dc.contributor.funderMarine Instituteen
dc.contributor.funderScience Foundation Irelanden
dc.contributor.funderDepartment of Agriculture, Fisheries and Food, Ireland
dc.contributor.funderEuropean Commission
dc.contributor.funderHealth Research Board
dc.contributor.funderIrish Research Council for Science Engineering and Technology
dc.contributor.funderDepartment of Education, Ireland
dc.date.accessioned2013-08-08T11:50:21Z
dc.date.available2013-08-08T11:50:21Z
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.sponsorshipScience Foundation of Ireland (07IN.1/B948, 08/RFP/GEN1295, 08/RFP/ GEN1319, SFI09/RFP/BMT2350, Tida award); Department of Agriculture, Fisheries and Food (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 ); IRCSET (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); HRB (RP/2006/271, RP/2007/290, HRA/2009/146); Department of Education (TSR III Agribiotics project)en
dc.description.statusPeer revieweden
dc.description.versionPublished Versionen
dc.format.mimetypeapplication/pdfen
dc.identifier.citationRedondo-Nieto et al.: Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction. BMC Genomics 2013 14:54. doi:10.1186/1471-2164-14-54en
dc.identifier.doi10.1186/1471-2164-14-54
dc.identifier.issn1471-2164
dc.identifier.issued54en
dc.identifier.journaltitleBMC Genomicsen
dc.identifier.urihttps://hdl.handle.net/10468/1217
dc.identifier.volume14en
dc.language.isoenen
dc.publisherBMC Genomicsen
dc.relation.urihttp://www.biomedcentral.com/1471-2164/14/54
dc.rights© 2013 Redondo-Nieto et al.; licensee BioMed Central Ltd.en
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en
dc.subjectPseudomonas fluorescens F113en
dc.subjectRhizobacteriumen
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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