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Genome-wide identification of bacterial plant colonization genes

Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizi...

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Autores principales: Cole, Benjamin J., Feltcher, Meghan E., Waters, Robert J., Wetmore, Kelly M., Mucyn, Tatiana S., Ryan, Elizabeth M., Wang, Gaoyan, Ul-Hasan, Sabah, McDonald, Meredith, Yoshikuni, Yasuo, Malmstrom, Rex R., Deutschbauer, Adam M., Dangl, Jeffery L., Visel, Axel
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627942/
https://www.ncbi.nlm.nih.gov/pubmed/28938018
http://dx.doi.org/10.1371/journal.pbio.2002860
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author Cole, Benjamin J.
Feltcher, Meghan E.
Waters, Robert J.
Wetmore, Kelly M.
Mucyn, Tatiana S.
Ryan, Elizabeth M.
Wang, Gaoyan
Ul-Hasan, Sabah
McDonald, Meredith
Yoshikuni, Yasuo
Malmstrom, Rex R.
Deutschbauer, Adam M.
Dangl, Jeffery L.
Visel, Axel
author_facet Cole, Benjamin J.
Feltcher, Meghan E.
Waters, Robert J.
Wetmore, Kelly M.
Mucyn, Tatiana S.
Ryan, Elizabeth M.
Wang, Gaoyan
Ul-Hasan, Sabah
McDonald, Meredith
Yoshikuni, Yasuo
Malmstrom, Rex R.
Deutschbauer, Adam M.
Dangl, Jeffery L.
Visel, Axel
author_sort Cole, Benjamin J.
collection PubMed
description Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes.
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spelling pubmed-56279422017-10-20 Genome-wide identification of bacterial plant colonization genes Cole, Benjamin J. Feltcher, Meghan E. Waters, Robert J. Wetmore, Kelly M. Mucyn, Tatiana S. Ryan, Elizabeth M. Wang, Gaoyan Ul-Hasan, Sabah McDonald, Meredith Yoshikuni, Yasuo Malmstrom, Rex R. Deutschbauer, Adam M. Dangl, Jeffery L. Visel, Axel PLoS Biol Methods and Resources Diverse soil-resident bacteria can contribute to plant growth and health, but the molecular mechanisms enabling them to effectively colonize their plant hosts remain poorly understood. We used randomly barcoded transposon mutagenesis sequencing (RB-TnSeq) in Pseudomonas simiae, a model root-colonizing bacterium, to establish a genome-wide map of bacterial genes required for colonization of the Arabidopsis thaliana root system. We identified 115 genes (2% of all P. simiae genes) with functions that are required for maximal competitive colonization of the root system. Among the genes we identified were some with obvious colonization-related roles in motility and carbon metabolism, as well as 44 other genes that had no or vague functional predictions. Independent validation assays of individual genes confirmed colonization functions for 20 of 22 (91%) cases tested. To further characterize genes identified by our screen, we compared the functional contributions of P. simiae genes to growth in 90 distinct in vitro conditions by RB-TnSeq, highlighting specific metabolic functions associated with root colonization genes. Our analysis of bacterial genes by sequence-driven saturation mutagenesis revealed a genome-wide map of the genetic determinants of plant root colonization and offers a starting point for targeted improvement of the colonization capabilities of plant-beneficial microbes. Public Library of Science 2017-09-22 /pmc/articles/PMC5627942/ /pubmed/28938018 http://dx.doi.org/10.1371/journal.pbio.2002860 Text en https://creativecommons.org/publicdomain/zero/1.0/ This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 (https://creativecommons.org/publicdomain/zero/1.0/) public domain dedication.
spellingShingle Methods and Resources
Cole, Benjamin J.
Feltcher, Meghan E.
Waters, Robert J.
Wetmore, Kelly M.
Mucyn, Tatiana S.
Ryan, Elizabeth M.
Wang, Gaoyan
Ul-Hasan, Sabah
McDonald, Meredith
Yoshikuni, Yasuo
Malmstrom, Rex R.
Deutschbauer, Adam M.
Dangl, Jeffery L.
Visel, Axel
Genome-wide identification of bacterial plant colonization genes
title Genome-wide identification of bacterial plant colonization genes
title_full Genome-wide identification of bacterial plant colonization genes
title_fullStr Genome-wide identification of bacterial plant colonization genes
title_full_unstemmed Genome-wide identification of bacterial plant colonization genes
title_short Genome-wide identification of bacterial plant colonization genes
title_sort genome-wide identification of bacterial plant colonization genes
topic Methods and Resources
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5627942/
https://www.ncbi.nlm.nih.gov/pubmed/28938018
http://dx.doi.org/10.1371/journal.pbio.2002860
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