Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Ian T. Paulsen; Caroline M. Press; Jacques Ravel; Donald Y. Kobayashi; Garry S. A. Myers; Dmitri V. Mavrodi; Robert T. DeBoy; Rekha Seshadri; Qinghu Ren; Ramana Madupu; Robert J. Dodson; A. Scott Durkin; Lauren M. Brinkac; Sean C. Daugherty; Stephen A. Sullivan; Mary J. Rosovitz; Michelle L. Gwinn; Liwei Zhou; Davd J. Schneider; Samuel W. Cartinhour; William C. Nelson; Janice Weidman; Kisha Watkins; Kevin Tran; Hoda Khouri; Elizabeth A. Pierson; Leland S. Pierson; Linda S. Thomashow; Joyce E. Loper

doi:10.1038/nbt1110

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Ian T. Paulsen^*, Caroline M. Press, Jacques Ravel, Donald Y. Kobayashi, Garry S. A. Myers, Dmitri V. Mavrodi, Robert T. DeBoy, Rekha Seshadri, Qinghu Ren, Ramana Madupu, Robert J. Dodson, A. Scott Durkin, Lauren M. Brinkac, Sean C. Daugherty, Stephen A. Sullivan, Mary J. Rosovitz, Michelle L. Gwinn, Liwei Zhou, Davd J. Schneider, Samuel W. CartinhourWilliam C. Nelson, Janice Weidman, Kisha Watkins, Kevin Tran, Hoda Khouri, Elizabeth A. Pierson, Leland S. Pierson, Linda S. Thomashow, Joyce E. Loper

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

540 Citations (Scopus)

Abstract

Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.

Original language	English
Pages (from-to)	873-878
Number of pages	6
Journal	Nature Biotechnology
Volume	23
Issue number	7
DOIs	https://doi.org/10.1038/nbt1110
Publication status	Published - 2005
Externally published	Yes

Bibliographical note

A corrigendum for this article exists and can be found in Nature Biotechnology, vol. 24, no. 4, p. 466. DOI: 10.1038/nbt0406-466b

Access to Document

10.1038/nbt1110

Cite this

Paulsen, I. T., Press, C. M., Ravel, J., Kobayashi, D. Y., Myers, G. S. A., Mavrodi, D. V., DeBoy, R. T., Seshadri, R., Ren, Q., Madupu, R., Dodson, R. J., Durkin, A. S., Brinkac, L. M., Daugherty, S. C., Sullivan, S. A., Rosovitz, M. J., Gwinn, M. L., Zhou, L., Schneider, D. J., ... Loper, J. E. (2005). Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5. Nature Biotechnology, 23(7), 873-878. https://doi.org/10.1038/nbt1110

@article{d6b4b9f54a4b4670a90a5cadc702c5b6,

title = "Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5",

abstract = "Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.",

author = "Paulsen, {Ian T.} and Press, {Caroline M.} and Jacques Ravel and Kobayashi, {Donald Y.} and Myers, {Garry S. A.} and Mavrodi, {Dmitri V.} and DeBoy, {Robert T.} and Rekha Seshadri and Qinghu Ren and Ramana Madupu and Dodson, {Robert J.} and Durkin, {A. Scott} and Brinkac, {Lauren M.} and Daugherty, {Sean C.} and Sullivan, {Stephen A.} and Rosovitz, {Mary J.} and Gwinn, {Michelle L.} and Liwei Zhou and Schneider, {Davd J.} and Cartinhour, {Samuel W.} and Nelson, {William C.} and Janice Weidman and Kisha Watkins and Kevin Tran and Hoda Khouri and Pierson, {Elizabeth A.} and Pierson, {Leland S.} and Thomashow, {Linda S.} and Loper, {Joyce E.}",

note = "A corrigendum for this article exists and can be found in Nature Biotechnology, vol. 24, no. 4, p. 466. DOI: 10.1038/nbt0406-466b",

year = "2005",

doi = "10.1038/nbt1110",

language = "English",

volume = "23",

pages = "873--878",

journal = "Nature Biotechnology",

issn = "1087-0156",

publisher = "Springer, Springer Nature",

number = "7",

}

Paulsen, IT, Press, CM, Ravel, J, Kobayashi, DY, Myers, GSA, Mavrodi, DV, DeBoy, RT, Seshadri, R, Ren, Q, Madupu, R, Dodson, RJ, Durkin, AS, Brinkac, LM, Daugherty, SC, Sullivan, SA, Rosovitz, MJ, Gwinn, ML, Zhou, L, Schneider, DJ, Cartinhour, SW, Nelson, WC, Weidman, J, Watkins, K, Tran, K, Khouri, H, Pierson, EA, Pierson, LS, Thomashow, LS & Loper, JE 2005, 'Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5', Nature Biotechnology, vol. 23, no. 7, pp. 873-878. https://doi.org/10.1038/nbt1110

TY - JOUR

T1 - Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

AU - Paulsen, Ian T.

AU - Press, Caroline M.

AU - Ravel, Jacques

AU - Kobayashi, Donald Y.

AU - Myers, Garry S. A.

AU - Mavrodi, Dmitri V.

AU - DeBoy, Robert T.

AU - Seshadri, Rekha

AU - Ren, Qinghu

AU - Madupu, Ramana

AU - Dodson, Robert J.

AU - Durkin, A. Scott

AU - Brinkac, Lauren M.

AU - Daugherty, Sean C.

AU - Sullivan, Stephen A.

AU - Rosovitz, Mary J.

AU - Gwinn, Michelle L.

AU - Zhou, Liwei

AU - Schneider, Davd J.

AU - Cartinhour, Samuel W.

AU - Nelson, William C.

AU - Weidman, Janice

AU - Watkins, Kisha

AU - Tran, Kevin

AU - Khouri, Hoda

AU - Pierson, Elizabeth A.

AU - Pierson, Leland S.

AU - Thomashow, Linda S.

AU - Loper, Joyce E.

N1 - A corrigendum for this article exists and can be found in Nature Biotechnology, vol. 24, no. 4, p. 466. DOI: 10.1038/nbt0406-466b

PY - 2005

Y1 - 2005

N2 - Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.

AB - Pseudomonas fluorescens Pf-5 is a plant commensal bacterium that inhabits the rhizosphere and produces secondary metabolites that suppress soilborne plant pathogens. The complete sequence of the 7.1-Mb Pf-5 genome was determined. We analyzed repeat sequences to identify genomic islands that, together with other approaches, suggested P. fluorescens Pf-5's recent lateral acquisitions include six secondary metabolite gene clusters, seven phage regions and a mobile genomic island. We identified various features that contribute to its commensal lifestyle on plants, including broad catabolic and transport capabilities for utilizing plant-derived compounds, the apparent ability to use a diversity of iron siderophores, detoxification systems to protect from oxidative stress, and the lack of a type III secretion system and toxins found in related pathogens. In addition to six known secondary metabolites produced by P. fluorescens Pf-5, three novel secondary metabolite biosynthesis gene clusters were also identified that may contribute to the biocontrol properties of P. fluorescens Pf-5.

UR - http://www.scopus.com/inward/record.url?scp=23344440104&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/record.url?scp=33645735327&partnerID=8YFLogxK

UR - http://doi.org/10.1038/nbt0406-466b

U2 - 10.1038/nbt1110

DO - 10.1038/nbt1110

M3 - Article

C2 - 15980861

AN - SCOPUS:23344440104

SN - 1087-0156

VL - 23

SP - 873

EP - 878

JO - Nature Biotechnology

JF - Nature Biotechnology

IS - 7

ER -

Complete genome sequence of the plant commensal Pseudomonas fluorescens Pf-5

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this