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Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions
Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations....
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Published in: | Proceedings of the National Academy of Sciences - PNAS 2005-11, Vol.102 (48), p.17454-17459 |
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creator | Mark, G.L Dow, J.M Kiely, P.D Higgins, H Haynes, J Baysse, C Abbas, A Foley, T Franks, A Morrissey, J |
description | Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis. |
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Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.</description><identifier>ISSN: 0027-8424</identifier><identifier>EISSN: 1091-6490</identifier><identifier>DOI: 10.1073/pnas.0506407102</identifier><identifier>PMID: 16301542</identifier><language>eng</language><publisher>United States: National Academy of Sciences</publisher><subject>Amino acids ; Bacteria ; Beta vulgaris ; Beta vulgaris - microbiology ; Biological Sciences ; Biosynthesis ; Energy metabolism ; Flowers & plants ; Gene expression ; Gene Expression Profiling ; Gene Expression Regulation, Bacterial ; gene induction ; Genes ; Genes, Bacterial - genetics ; Genomes ; Genomics - methods ; messenger RNA ; microarray technology ; Microbiology ; Mutation - genetics ; Oligonucleotide Array Sequence Analysis ; Plant interaction ; Plant roots ; Plant Roots - chemistry ; Plant Roots - microbiology ; Plants ; Pseudomonas aeruginosa ; Pseudomonas aeruginosa - genetics ; Pseudomonas aeruginosa - metabolism ; Reverse Transcriptase Polymerase Chain Reaction ; Rhizosphere ; Root exudates ; soil bacteria ; Species Specificity ; sugar beet ; Symbiosis ; transcription (genetics)</subject><ispartof>Proceedings of the National Academy of Sciences - PNAS, 2005-11, Vol.102 (48), p.17454-17459</ispartof><rights>Copyright 2005 National Academy of Sciences of the United States of America</rights><rights>Copyright National Academy of Sciences Nov 29, 2005</rights><rights>Copyright © 2005, The National Academy of Sciences 2005</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c553t-9cd6780583add8fe9f297cffdbed8aac0e2c4f31ae4e444d05077988b679bf773</citedby><cites>FETCH-LOGICAL-c553t-9cd6780583add8fe9f297cffdbed8aac0e2c4f31ae4e444d05077988b679bf773</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Uhttp://www.pnas.org/content/102/48.cover.gif</thumbnail><linktopdf>$$Uhttps://www.jstor.org/stable/pdf/4152499$$EPDF$$P50$$Gjstor$$H</linktopdf><linktohtml>$$Uhttps://www.jstor.org/stable/4152499$$EHTML$$P50$$Gjstor$$H</linktohtml><link.rule.ids>230,314,727,780,784,885,27924,27925,53791,53793,58238,58471</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/16301542$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mark, G.L</creatorcontrib><creatorcontrib>Dow, J.M</creatorcontrib><creatorcontrib>Kiely, P.D</creatorcontrib><creatorcontrib>Higgins, H</creatorcontrib><creatorcontrib>Haynes, J</creatorcontrib><creatorcontrib>Baysse, C</creatorcontrib><creatorcontrib>Abbas, A</creatorcontrib><creatorcontrib>Foley, T</creatorcontrib><creatorcontrib>Franks, A</creatorcontrib><creatorcontrib>Morrissey, J</creatorcontrib><title>Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions</title><title>Proceedings of the National Academy of Sciences - PNAS</title><addtitle>Proc Natl Acad Sci U S A</addtitle><description>Molecules exuded by plant roots are thought to act as signals to influence the ability of microbial strains to colonize the roots and to survive in the rhizosphere. Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.</description><subject>Amino acids</subject><subject>Bacteria</subject><subject>Beta vulgaris</subject><subject>Beta vulgaris - microbiology</subject><subject>Biological Sciences</subject><subject>Biosynthesis</subject><subject>Energy metabolism</subject><subject>Flowers & plants</subject><subject>Gene expression</subject><subject>Gene Expression Profiling</subject><subject>Gene Expression Regulation, Bacterial</subject><subject>gene induction</subject><subject>Genes</subject><subject>Genes, Bacterial - genetics</subject><subject>Genomes</subject><subject>Genomics - methods</subject><subject>messenger RNA</subject><subject>microarray technology</subject><subject>Microbiology</subject><subject>Mutation - genetics</subject><subject>Oligonucleotide Array Sequence Analysis</subject><subject>Plant interaction</subject><subject>Plant roots</subject><subject>Plant Roots - chemistry</subject><subject>Plant Roots - microbiology</subject><subject>Plants</subject><subject>Pseudomonas aeruginosa</subject><subject>Pseudomonas aeruginosa - genetics</subject><subject>Pseudomonas aeruginosa - metabolism</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>Rhizosphere</subject><subject>Root exudates</subject><subject>soil bacteria</subject><subject>Species Specificity</subject><subject>sugar beet</subject><subject>Symbiosis</subject><subject>transcription (genetics)</subject><issn>0027-8424</issn><issn>1091-6490</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2005</creationdate><recordtype>article</recordtype><recordid>eNqFkUFv1DAQhSMEokvhzAVBxAGJQ1rbsWP7UglVLSBV4kB7tpxkvHiVjYPtLOXfM9GuusClJ49mPr-ZN1MUryk5o0TW59No0xkRpOFEUsKeFCtKNK0arsnTYkUIk5XijJ8UL1LaEEK0UOR5cUKbmlDB2ar4dRvtmLropxy2UE4xOD_4cV0GV7a2yxC9HcoIaQpjglTmUMYQcgn3c28zJnwPY_bOY7iGcUmMuzDsoMeg3PouhhaqabBjxgTKoaZHqZfFM2eHBK8O72lxd311e_mluvn2-evlp5uqE6LOle76RioiVG37XjnQjmnZOde30CtrOwKs466mFjhwzntchZRaqbaRunVS1qfFxV53mtst9B0OG-1gpui3Nv42wXrzb2X0P8w67AzFRk3ToMCHg0AMP2dI2Wx96mBARxDmZBqluOBcPgoy3HijmUDw_X_gJsxxxC0sTI09lULofA_hAlOK4B5GpsQspzfL6c3x9Pjj7d9Oj_zh1gh8PADLz6McM1wZKtGFcfMwZLjPyJaPsIi82SOblEN8YDgVjGuN5Xf7srPB2HX0ydx9X_wRnJ4Jous_4-jZlA</recordid><startdate>20051129</startdate><enddate>20051129</enddate><creator>Mark, G.L</creator><creator>Dow, J.M</creator><creator>Kiely, P.D</creator><creator>Higgins, H</creator><creator>Haynes, J</creator><creator>Baysse, C</creator><creator>Abbas, A</creator><creator>Foley, T</creator><creator>Franks, A</creator><creator>Morrissey, J</creator><general>National Academy of Sciences</general><general>National Acad Sciences</general><scope>FBQ</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7QG</scope><scope>7QL</scope><scope>7QP</scope><scope>7QR</scope><scope>7SN</scope><scope>7SS</scope><scope>7T5</scope><scope>7TK</scope><scope>7TM</scope><scope>7TO</scope><scope>7U9</scope><scope>8FD</scope><scope>C1K</scope><scope>FR3</scope><scope>H94</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7T7</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20051129</creationdate><title>Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions</title><author>Mark, G.L ; 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Differential bacterial responses to signals from different plant species may mediate the selection of specific rhizosphere populations. Very little, however, is known about the effects of plant exudates on patterns of bacterial gene expression. Here, we have tested the concept that plant root exudates modulate expression of bacterial genes involved in establishing microbe-plant interactions. We have examined the influence on the Pseudomonas aeruginosa PA01 transcriptome of exudates from two varieties of sugarbeet that select for genetically distinct pseudomonad populations in the rhizosphere. The response to the two exudates showed only a partial overlap; the majority of those genes with altered expression was regulated in response to only one of the two exudates. Genes with altered expression included those with functions previously implicated in microbe-plant interactions, such as aspects of metabolism, chemotaxis and type III secretion, and a subset with putative or unknown function. Use of a panel of mutants with targeted disruptions allowed us to identify previously uncharacterized genes with roles in the competitive ability of P. aeruginosa in the rhizosphere within this subset. No genes with host-specific effects were identified. Homologues of the genes identified occur in the genomes of both beneficial and pathogenic root-associated bacteria, suggesting that this strategy may help to elucidate molecular interactions that are important for biocontrol, plant growth promotion, and plant pathogenesis.</abstract><cop>United States</cop><pub>National Academy of Sciences</pub><pmid>16301542</pmid><doi>10.1073/pnas.0506407102</doi><tpages>6</tpages><oa>free_for_read</oa></addata></record> |
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subjects | Amino acids Bacteria Beta vulgaris Beta vulgaris - microbiology Biological Sciences Biosynthesis Energy metabolism Flowers & plants Gene expression Gene Expression Profiling Gene Expression Regulation, Bacterial gene induction Genes Genes, Bacterial - genetics Genomes Genomics - methods messenger RNA microarray technology Microbiology Mutation - genetics Oligonucleotide Array Sequence Analysis Plant interaction Plant roots Plant Roots - chemistry Plant Roots - microbiology Plants Pseudomonas aeruginosa Pseudomonas aeruginosa - genetics Pseudomonas aeruginosa - metabolism Reverse Transcriptase Polymerase Chain Reaction Rhizosphere Root exudates soil bacteria Species Specificity sugar beet Symbiosis transcription (genetics) |
title | Transcriptome profiling of bacterial responses to root exudates identifies genes involved in microbe-plant interactions |
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