Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5

<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas fluorescens </it>Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathog...

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Main Authors: Paulsen Ian T, Loper Joyce E, Mavrodi Dmitri V, Thomashow Linda S
Format: Article
Language:English
Published: BMC 2009-01-01
Series:BMC Microbiology
Online Access:http://www.biomedcentral.com/1471-2180/9/8
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author Paulsen Ian T
Loper Joyce E
Mavrodi Dmitri V
Thomashow Linda S
author_facet Paulsen Ian T
Loper Joyce E
Mavrodi Dmitri V
Thomashow Linda S
author_sort Paulsen Ian T
collection DOAJ
description <p>Abstract</p> <p>Background</p> <p><it>Pseudomonas fluorescens </it>Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, and its sequence has revealed attributes associated with the strain's ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches.</p> <p>Results</p> <p>Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb integrative conjugative element (ICE) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from ICEs found in other <it>Pseudomonas </it>spp., and PFGI-2, which resembles a portion of pathogenicity islands in the genomes of the plant pathogens <it>Pseudomonas syringae </it>and <it>P. viridiflava</it>. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes.</p> <p>Conclusion</p> <p>Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive recombination and have evolved in part via exchange of genetic material with other <it>Pseudomonas </it>spp. having commensal or pathogenic relationships with plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other <it>Pseudomonas </it>spp., they also carry a number of putative niche-specific genes that could affect the survival of <it>P. fluorescens </it>Pf-5 in natural habitats. Most notable are a ~35-kb segment of "cargo" genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4.</p>
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spelling doaj.art-bd0f90516e3a495aaf72b03eb69e88522022-12-22T03:25:29ZengBMCBMC Microbiology1471-21802009-01-0191810.1186/1471-2180-9-8Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5Paulsen Ian TLoper Joyce EMavrodi Dmitri VThomashow Linda S<p>Abstract</p> <p>Background</p> <p><it>Pseudomonas fluorescens </it>Pf-5 is a plant-associated bacterium that inhabits the rhizosphere of a wide variety of plant species and and produces secondary metabolites suppressive of fungal and oomycete plant pathogens. The Pf-5 genome is rich in features consistent with its commensal lifestyle, and its sequence has revealed attributes associated with the strain's ability to compete and survive in the dynamic and microbiologically complex rhizosphere habitat. In this study, we analyzed mobile genetic elements of the Pf-5 genome in an effort to identify determinants that might contribute to Pf-5's ability to adapt to changing environmental conditions and/or colonize new ecological niches.</p> <p>Results</p> <p>Sequence analyses revealed that the genome of Pf-5 is devoid of transposons and IS elements and that mobile genetic elements (MGEs) are represented by prophages and genomic islands that collectively span over 260 kb. The prophages include an F-pyocin-like prophage 01, a chimeric prophage 03, a lambdoid prophage 06, and decaying prophages 02, 04 and 05 with reduced size and/or complexity. The genomic islands are represented by a 115-kb integrative conjugative element (ICE) PFGI-1, which shares plasmid replication, recombination, and conjugative transfer genes with those from ICEs found in other <it>Pseudomonas </it>spp., and PFGI-2, which resembles a portion of pathogenicity islands in the genomes of the plant pathogens <it>Pseudomonas syringae </it>and <it>P. viridiflava</it>. Almost all of the MGEs in the Pf-5 genome are associated with phage-like integrase genes and are integrated into tRNA genes.</p> <p>Conclusion</p> <p>Comparative analyses reveal that MGEs found in Pf-5 are subject to extensive recombination and have evolved in part via exchange of genetic material with other <it>Pseudomonas </it>spp. having commensal or pathogenic relationships with plants and animals. Although prophages and genomic islands from Pf-5 exhibit similarity to MGEs found in other <it>Pseudomonas </it>spp., they also carry a number of putative niche-specific genes that could affect the survival of <it>P. fluorescens </it>Pf-5 in natural habitats. Most notable are a ~35-kb segment of "cargo" genes in genomic island PFGI-1 and bacteriocin genes associated with prophages 1 and 4.</p>http://www.biomedcentral.com/1471-2180/9/8
spellingShingle Paulsen Ian T
Loper Joyce E
Mavrodi Dmitri V
Thomashow Linda S
Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
BMC Microbiology
title Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
title_full Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
title_fullStr Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
title_full_unstemmed Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
title_short Mobile genetic elements in the genome of the beneficial rhizobacterium <it>Pseudomonas fluorescens </it>Pf-5
title_sort mobile genetic elements in the genome of the beneficial rhizobacterium it pseudomonas fluorescens it pf 5
url http://www.biomedcentral.com/1471-2180/9/8
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AT mavrodidmitriv mobilegeneticelementsinthegenomeofthebeneficialrhizobacteriumitpseudomonasfluorescensitpf5
AT thomashowlindas mobilegeneticelementsinthegenomeofthebeneficialrhizobacteriumitpseudomonasfluorescensitpf5