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.author Redondo-Nieto, Miguel
dc.contributor.author Barret, Matthieu
dc.contributor.author Morrissey, John P.
dc.contributor.author Germaine, Kieran
dc.contributor.author Martínez-Granero, Francisco
dc.contributor.author Barahona, Emma
dc.contributor.author Navazo, Ana
dc.contributor.author Sánchez-Contreras, María
dc.contributor.author Moynihan, Jennifer A.
dc.contributor.author Muriel, Candela
dc.contributor.author Dowling, David
dc.contributor.author O'Gara, Fergal
dc.contributor.author Martín, Marta
dc.contributor.author Rivilla, Rafael
dc.date.accessioned 2013-08-08T11:50:21Z
dc.date.available 2013-08-08T11:50:21Z
dc.date.issued 2013-01-25
dc.identifier.citation Redondo-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:10.1186/1471-2164-14-54 en
dc.identifier.volume 14 en
dc.identifier.issued 54 en
dc.identifier.issn 1471-2164
dc.identifier.uri http://hdl.handle.net/10468/1217
dc.identifier.doi 10.1186/1471-2164-14-54
dc.description.abstract Background: 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.sponsorship Science 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.format.mimetype application/pdf en
dc.language.iso en en
dc.publisher BMC Genomics en
dc.relation.uri http://www.biomedcentral.com/1471-2164/14/54
dc.rights © 2013 Redondo-Nieto et al.; licensee BioMed Central Ltd. en
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en
dc.subject Pseudomonas fluorescens F113 en
dc.subject Rhizobacterium en
dc.title Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction en
dc.type Article (peer-reviewed) en
dc.internal.authorurl http://publish.ucc.ie/researchprofiles/D010/jmorrissey en
dc.internal.authorcontactother John Morrissey, Microbiology Department, Food Science Building, University College Cork, Cork, Ireland en
dc.internal.availability Full text available en
dc.description.version Published Version en
dc.contributor.funder Environmental Protection Agency en
dc.contributor.funder Marine Institute en
dc.contributor.funder Science Foundation Ireland en
dc.contributor.funder Department of Agriculture, Fisheries and Food, Ireland
dc.contributor.funder European Commission
dc.contributor.funder Health Research Board
dc.contributor.funder Irish Research Council for Science Engineering and Technology
dc.contributor.funder Department of Education, Ireland
dc.description.status Peer reviewed en
dc.identifier.journaltitle BMC Genomics en
dc.internal.IRISemailaddress j.morrissey@ucc.ie en


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© 2013 Redondo-Nieto et al.; licensee BioMed Central Ltd. Except where otherwise noted, this item's license is described as © 2013 Redondo-Nieto et al.; licensee BioMed Central Ltd.
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