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

Autor: Rafael Rivilla, Matthieu Barret, Miguel Redondo-Nieto, John P. Morrissey, David N. Dowling, Fergal O'Gara, Kieran J. Germaine, Marta Martín, Emma Barahona, Francisco Martínez-Granero, Candela Muriel, Jennifer A. Moynihan, María Sánchez-Contreras, Ana Navazo
Přispěvatelé: Departamento de Biologia, Facultad de Ciencias, Universidad Autonoma de Madrid (UAM), University College Cork (UCC), Institute of Technology Carlow, European Project: 256596,EC:FP7:PEOPLE,FP7-PEOPLE-2009-RG,MEXT REGULATION(2010), Research at UAM was funded by grants MICROAMBIENTE-CM (to R.R.), BIO2009-08254 (to M.M.), and Marie Curie MIGENOF113 (to M.S.-C. and R.R.). This research was supported in parts by grants awarded to FOG by the Science Foundation of Ireland (07IN.1/B948, 08/RFP/GEN1295, 08/RFP/ GEN1319, SFI09/RFP/BMT2350), the Department of Agriculture, Fisheries and Food (RSF grants 06–321 and 06–377, FIRM grants 06RDC459 06RDC506 and 08RDC629), the European Commission (MTKD-CT-2006-042062, Marie Curie TOK:TRAMWAYS, EU256596, MicroB3-287589-OCEAN2012, MACUMBA-CP-TP 311975, PharmaSea-CP-TP 312184), IRCSET (05/EDIV/FP107/INTERPAM, EMBARK), the Marine Institute Beaufort award (C&CRA 2007/082), the Environmental Protection Agency (EPA 2006-PhD-S-21, EPA 2008-PhD-S-2) and the HRB (RP/2006/271, RP/2007/290, HRA/2009/146). The Lab of KG & DD was in part funded by an SFI Tida award and the Department of Education TSR III Agribiotics project. The authors would like to acknowledge the Centro de Computación Científica at Universidad Autónoma de Madrid and the Boole Centre for Research in Informatics at University College Cork for providing access to computational facilities., UAM. Departamento de Biología, Universidad Autónoma de Madrid (UAM)
Jazyk: angličtina
Rok vydání: 2013
Předmět:
Prophages
Genetic code
[SDV]Life Sciences [q-bio]
Denitrification pathway
Bacterial strain
Gene sequence
Genome
flagellar gene
Phylogeny
Plant growth
2. Zero hunger
Genetics
0303 health sciences
Rhizosphere
biology
Chemotaxis
Competitive colonization ability
Genomics
Plants
Biología y Biomedicina / Biología
Adaptation
Physiological
enviroCORE - IT Carlow
abietic acid
core genome
Pseudomonas brassicacearum
Host-Pathogen Interactions
Host pathogen interaction
polar flagellum
Research Article
Biotechnology
lcsh:QH426-470
lcsh:Biotechnology
Plant Development
Rhizobacterium
fluorescens group
Pseudomonas fluorescens
Bacterial genome
Azospirillum brasilense
Microbiology
03 medical and health sciences
Evolutionary history
Bacterial Proteins
VI secretion system
Pseudomonas
lcsh:TP248.13-248.65
Animals
Gene
Prophage
030304 developmental biology
Whole genome sequencing
030306 microbiology
Pseudomonas fluorescens F113
biology.organism_classification
Nonhuman
III secretion
lcsh:Genetics
Streptomyces rochei
Genome
Bacterial
Maximum likelihood
Sinorhizobium meliloti
Zdroj: BMC Genomics
BMC Genomics, BioMed Central, 2013, 14 (1), pp.1-17. ⟨10.1186/1471-2164-14-54⟩
BMC Genomics, Vol 14, Iss 1, p 54 (2013)
Biblos-e Archivo. Repositorio Institucional de la UAM
instname
BMC Genomics, 2013, 14 (1), pp.1-17. ⟨10.1186/1471-2164-14-54⟩
BMC Genomics 1 (14), 1-17. (2013)
ISSN: 1471-2164
Popis: 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.The electronic version of this article is the complete one and can be found online at http://www.biomedcentral.com/1471-2164/14/54
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
This research was supported in parts by grants awarded to FOG by the Science Foundation of Ireland (07IN.1/B948, 08/RFP/GEN1295, 08/RFP/GEN1319, SFI09/RFP/BMT2350); the Department of Agriculture, Fisheries and Food (RSF grants 06–321 and 06–377; FIRM grants 06RDC459 06RDC506 and 08RDC629); the European Commission (MTKD-CT-2006-042062, Marie Curie TOK:TRAMWAYS, EU256596, MicroB3-287589-OCEAN2012, MACUMBA-CP-TP 311975; PharmaSea-CP-TP 312184); IRCSET (05/EDIV/FP107/INTERPAM, EMBARK), the Marine Institute Beaufort award (C&CRA 2007/082), the Environmental Protection Agency (EPA 2006-PhD-S-21, EPA 2008-PhD-S-2) and the HRB (RP/2006/271, RP/2007/290, HRA/2009/146). The Lab of KG & DD was in part funded by an SFI Tida award and the Department of Education TSR III Agribiotics project.
Databáze: OpenAIRE
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