Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

被引：300

作者：

Silby, Mark W. ^{[2
,3
]}

Cerdeno-Tarraga, Ana M. ^{[1
]}

Vernikos, Georgios S. ^{[1
]}

Giddens, Stephen R. ^{[4
]}

Jackson, Robert W. ^{[4
,5
]}

Preston, Gail M. ^{[4
]}

Zhang, Xue-Xian ^{[6
]}

Moon, Christina D. ^{[4
]}

Gehrig, Stefanie M. ^{[4
]}

Godfrey, Scott A. C. ^{[4
]}

Knight, Christopher G. ^{[4
]}

Malone, Jacob G. ^{[4
]}

Robinson, Zena ^{[4
]}

Spiers, Andrew J. ^{[4
]}

Harris, Simon ^{[1
]}

Challis, Gregory L. ^{[7
]}

Yaxley, Alice M. ^{[8
]}

Harris, David ^{[1
]}

Seeger, Kathy ^{[1
]}

Murphy, Lee ^{[1
]}

Rutter, Simon ^{[1
]}

Squares, Rob ^{[1
]}

Quail, Michael A. ^{[1
]}

Saunders, Elizabeth ^{[9
]}

Mavromatis, Konstantinos ^{[10
]}

Brettin, Thomas S. ^{[9
]}

Bentley, Stephen D. ^{[1
]}

Hothersall, Joanne ^{[11
]}

Stephens, Elton ^{[11
]}

Thomas, Christopher M. ^{[11
]}

Parkhill, Julian ^{[1
]}

Levy, Stuart B. ^{[2
,3
]}

Rainey, Paul B. ^{[6
,12
]}

Thomson, Nicholas R. ^{[1
]}

机构：

[1] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

[2] Tufts Univ, Sch Med, Ctr Adaptat Genet & Drug Resistance, Boston, MA 02111 USA

[3] Tufts Univ, Sch Med, Dept Mol Biol & Microbiol, Boston, MA 02111 USA

[4] Univ Oxford, Dept Plant Sci, Oxford OX1 3RB, England

[5] Univ Reading, Sch Biol Sci, Reading RG6 6AJ, Berks, England

[6] Massey Univ, N Shore Mail Ctr, New Zealand Inst Adv Study, Auckland, New Zealand

[7] Univ Warwick, Dept Chem, Coventry CV4 7AL, W Midlands, England

[8] Univ Warwick, Dept Biol Sci, Coventry CV4 7AL, W Midlands, England

[9] Los Alamos Natl Lab, Biosci Div, DOE Joint Genome Inst, Los Alamos, NM 87545 USA

[10] Joint Genome Inst, Dept Energys, Genome Biol Program, Walnut Creek, CA 94598 USA

[11] Univ Birmingham, Dept Biosci, Birmingham B15 2TT, W Midlands, England

[12] Massey Univ Auckland, Allan Wilson Ctr Mol Ecol & Evolut, N Shore Mail Ctr, Auckland, New Zealand

来源：

GENOME BIOLOGY | 2009年 / 10卷 / 05期

基金：

英国生物技术与生命科学研究理事会;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; VIVO EXPRESSION TECHNOLOGY; EXPERIMENTAL POPULATIONS; ADAPTIVE DIVERGENCE; BACTERIAL GENOMES; ESCHERICHIA-COLI; SBW25; ACQUISITION; GROWTH; SOIL;

D O I：

10.1186/gb-2009-10-5-r51

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

引用

页数：16

共 75 条

[11] SURVIVAL OF RIFAMPIN-RESISTANT MUTANTS OF PSEUDOMONAS-FLUORESCENS AND PSEUDOMONAS-PUTIDA IN SOIL SYSTEMS [J].

COMPEAU, G ;

ALACHI, BJ ;

PLATSOUKA, E ;

LEVY, SB .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 1988, 54 (10) :2432-2438

[12] Development of a multilocus sequence typing scheme for the opportunistic pathogen Pseudomonas aeruginosa [J].

Curran, B ;

Jonas, D ;

Grundmann, H ;

Pitt, T ;

Dowson, CG .

JOURNAL OF CLINICAL MICROBIOLOGY, 2004, 42 (12) :5644-5649

[13] Bacterial Genomes as new gene homes:: The genealogy of ORFans in E-coli [J].

Daubin, V ;

Ochman, H .

GENOME RESEARCH, 2004, 14 (06) :1036-1042

[14] Genome-based discovery, structure prediction and functional analysis of cyclic lipopeptide antibiotics in Pseudomonas species [J].

de Bruijn, Irene ;

de Kock, Maarten J. D. ;

Yang, Meng ;

de Waard, Pieter ;

van Beek, Teris A. ;

Raaijmakers, Jos M. .

MOLECULAR MICROBIOLOGY, 2007, 63 (02) :417-428

[15] Small mobile sequences in bacteria display diverse structure/function motifs [J].

Delihas, Nicholas .

MOLECULAR MICROBIOLOGY, 2008, 67 (03) :475-481

[16] RECOMBINATION IN ESCHERICHIA-COLI AND THE DEFINITION OF BIOLOGICAL SPECIES [J].

DYKHUIZEN, DE ;

GREEN, L .

JOURNAL OF BACTERIOLOGY, 1991, 173 (22) :7257-7268

[17] MUSCLE: multiple sequence alignment with high accuracy and high throughput [J].

Edgar, RC .

NUCLEIC ACIDS RESEARCH, 2004, 32 (05) :1792-1797

[18] Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas fluorescens NCIMB 10586 [J].

El-Sayed, AK ;

Hothersall, J ;

Cooper, SM ;

Stephens, E ;

Simpson, TJ ;

Thomas, CM .

CHEMISTRY & BIOLOGY, 2003, 10 (05) :419-430

[19] Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces [J].

Gal, M ;

Preston, GM ;

Massey, RC ;

Spiers, AJ ;

Rainey, PB .

MOLECULAR ECOLOGY, 2003, 12 (11) :3109-3121

[20] Mutational activation of niche-specific genes provides insight into regulatory networks and bacterial function in a complex environment [J].

Giddens, Stephen R. ;

Jackson, Robert W. ;

Moon, Christina D. ;

Jacobs, Michael A. ;

Zhang, Xue-Xian ;

Gehrig, Stefanie M. ;

Rainey, Paul B. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (46) :18247-18252

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