Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18

BackgroundOur previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa, but there are several unusual phenotypic features. This study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.ResultsThe complete M18 genome is composed of a single chromosome of 6,327,754 base pairs containing 5684 open reading frames. Seven genomic islands, including two novel prophages and five specific non-phage islands were identified besides the conserved P. aeruginosa core genome. Each prophage contains a putative chitinase coding gene, and the prophage II contains a capB gene encoding a putative cold stress protein. The non-phage genomic islands contain genes responsible for pyoluteorin biosynthesis, environmental substance degradation and type I and III restriction-modification systems. Compared with other P. aeruginosa strains, the fewest number (3) of insertion sequences and the most number (3) of clustered regularly interspaced short palindromic repeats in M18 genome may contribute to the relative genome stability. Although the M18 genome is most closely related to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible to several antimicrobial agents and easier to be erased in a mouse acute lung infection model than the strain LESB58. The whole M18 transcriptomic analysis indicated that 10.6% of the expressed genes are temperature-dependent, with 22 genes up-regulated at 28°C in three non-phage genomic islands and one prophage but none at 37°C.ConclusionsThe P. aeruginosa strain M18 has evolved its specific genomic structures and temperature dependent expression patterns to meet the requirement of its fitness and competitiveness under selective pressures imposed on the strain in rhizosphere niche.

[1]  C. R. Howell Suppression of Pythium ultimum-induced damping-off of cotton seedlings by Pseudomonas fluorescens and its antibiotic, pyoluteorin. , 1980 .

[2]  R. Cook,et al.  Characterization of an antibiotic produced by a strain of Pseudomonas fluorescens inhibitory to Gaeumannomyces graminis var. tritici and Pythium spp , 1986, Antimicrobial Agents and Chemotherapy.

[3]  L. Thomashow,et al.  Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici , 1988, Journal of bacteriology.

[4]  J. Briat Iron assimilation and storage in prokaryotes. , 1992, Journal of general microbiology.

[5]  U Heinemann,et al.  Crystal structure of CspA, the major cold shock protein of Escherichia coli. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[6]  H. Nikaido,et al.  Role of mexA-mexB-oprM in antibiotic efflux in Pseudomonas aeruginosa , 1995, Antimicrobial agents and chemotherapy.

[7]  A. Neely,et al.  Pyoverdin is essential for virulence of Pseudomonas aeruginosa , 1996, Infection and immunity.

[8]  M. Denton,et al.  Spread of β-lactam-resistant Pseudomonas aeruginosa in a cystic fibrosis clinic , 1996 .

[9]  S. Buysens,et al.  Involvement of Pyochelin and Pyoverdin in Suppression of Pythium-Induced Damping-Off of Tomato by Pseudomonas aeruginosa 7NSK2 , 1996, Applied and environmental microbiology.

[10]  C. Winstanley,et al.  Spread of beta-lactam-resistant Pseudomonas aeruginosa in a cystic fibrosis clinic. , 1996, Lancet.

[11]  K. Poole,et al.  Overexpression of the mexC–mexD–oprJ efflux operon in nfxB‐type multidrug‐resistant strains of Pseudomonas aeruginosa , 1996, Molecular microbiology.

[12]  Ross Ihaka,et al.  Gentleman R: R: A language for data analysis and graphics , 1996 .

[13]  N. Gotoh,et al.  Characterization of MexE–MexF–OprN, a positively regulated multidrug efflux system of Pseudomonas aeruginosa , 1997, Molecular microbiology.

[14]  S. Eddy,et al.  tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. , 1997, Nucleic acids research.

[15]  D. F. Sahm,et al.  AmpC beta-lactamases. , 1998 .

[16]  B. Wretlind,et al.  Mechanisms of quinolone resistance in clinical strains of Pseudomonas aeruginosa. , 1998, Microbial drug resistance.

[17]  P. Bakker,et al.  Biocontrol by Phenazine-1-carboxamide-Producing Pseudomonas chlororaphis PCL1391 of Tomato Root Rot Caused by Fusarium oxysporum f. sp. radicis-lycopersici , 1998 .

[18]  S. Salzberg,et al.  Improved microbial gene identification with GLIMMER. , 1999, Nucleic acids research.

[19]  S. Gould,et al.  Characterization of the Pyoluteorin Biosynthetic Gene Cluster of Pseudomonas fluorescens Pf-5 , 1999, Journal of bacteriology.

[20]  S. Lory,et al.  Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen , 2000, Nature.

[21]  D. Werck-Reichhart,et al.  Cytochromes P450: a success story , 2000, Genome Biology.

[22]  S. Lory,et al.  A genomic island in Pseudomonas aeruginosa carries the determinants of flagellin glycosylation , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[23]  I. Kobayashi Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. , 2001, Nucleic acids research.

[24]  Benjamin A. Shoemaker,et al.  CDD: a database of conserved domain alignments with links to domain three-dimensional structure , 2002, Nucleic Acids Res..

[25]  Maynard V. Olson,et al.  Genetic Variation at the O-Antigen Biosynthetic Locus in Pseudomonas aeruginosa , 2002, Journal of bacteriology.

[26]  S. Salzberg,et al.  Fast algorithms for large-scale genome alignment and comparison. , 2002, Nucleic acids research.

[27]  M. Kleerebezem,et al.  Complete genome sequence of Lactobacillus plantarum WCFS1 , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[28]  Qing Yang,et al.  Conservation of genome content and virulence determinants among clinical and environmental isolates of Pseudomonas aeruginosa , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[29]  A. Krogh,et al.  Prediction of lipoprotein signal peptides in Gram‐negative bacteria , 2003, Protein science : a publication of the Protein Society.

[30]  N. Koedam,et al.  Effect of genotype and root colonization in biological control of fusarium wilts in pigeonpea and chickpea by Pseudomonas aeruginosa PNA1. , 2003, Canadian journal of microbiology.

[31]  J. Musarrat,et al.  Characterization of a New Pseudomonas aeruginosa Strain NJ-15 as a Potential Biocontrol Agent , 2003, Current Microbiology.

[32]  A. Danchin,et al.  Bmc Genomics , 2004 .

[33]  Trinad Chakraborty,et al.  GenomeViz: visualizing microbial genomes , 2004, BMC Bioinformatics.

[34]  Daniel G. Lee,et al.  The broad host range pathogen Pseudomonas aeruginosa strain PA14 carries two pathogenicity islands harboring plant and animal virulence genes. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Hong-bo Hu,et al.  Identification and characterization of pltZ, a gene involved in the repression of pyoluteorin biosynthesis in Pseudomonas sp. M18. , 2004, FEMS microbiology letters.

[36]  Xuehong Zhang,et al.  Phenazine-1-carboxylic acid is negatively regulated and pyoluteorin positively regulated by gacA in Pseudomonas sp. M18. , 2004, FEMS microbiology letters.

[37]  Hong-bo Hu,et al.  Isolation and Characterization of a New Fluorescent Pseudomonas Strain that Produces Both Phenazine 1-Carboxylic Acid and Pyoluteorin , 2005 .

[38]  N. Ayyadurai,et al.  Characterization of antifungal metabolite produced by a new strain Pseudomonas aeruginosa PUPa3 that exhibits broad‐spectrum antifungal activity and biofertilizing traits , 2005, Journal of applied microbiology.

[39]  Martin Ester,et al.  Sequence analysis PSORTb v . 2 . 0 : Expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis , 2004 .

[40]  M. Van Sluys,et al.  Xylella and Xanthomonas Mobil'omics. , 2005, Omics : a journal of integrative biology.

[41]  Hong-bo Hu,et al.  Differential Regulation of rsmA Gene on Biosynthesis of Pyoluteorin and Phenazine-1-carboxylic Acid in Pseudomonas sp. M18 , 2005 .

[42]  Xuehong Zhang,et al.  Identification and characterization of a putative ABC transporter PltHIJKN required for pyoluteorin production in Pseudomonas sp. M18. , 2006, Gene.

[43]  Neil Woodford,et al.  The β-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter , 2006 .

[44]  Li Li,et al.  Genomic analysis reveals that Pseudomonas aeruginosa virulence is combinatorial , 2006, Genome Biology.

[45]  S. Diggle,et al.  The galactophilic lectin, LecA, contributes to biofilm development in Pseudomonas aeruginosa. , 2006, Environmental microbiology.

[46]  W. Blankenfeldt,et al.  Phenazine compounds in fluorescent Pseudomonas spp. biosynthesis and regulation. , 2006, Annual review of phytopathology.

[47]  Dong Pei,et al.  Autoinduction of RpoS Biosynthesis in the Biocontrol Strain Pseudomonas sp. M18 , 2007, Current Microbiology.

[48]  N. Woodford,et al.  The beta-lactamase threat in Enterobacteriaceae, Pseudomonas and Acinetobacter. , 2006, Trends in microbiology.

[49]  M. Nei,et al.  MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. , 2007, Molecular biology and evolution.

[50]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[51]  Ibtissem Grissa,et al.  CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats , 2007, Nucleic Acids Res..

[52]  Stephen Lory,et al.  MobilomeFINDER: web-based tools for in silico and experimental discovery of bacterial genomic islands , 2007, Nucleic Acids Res..

[53]  Rajinder K. Gupta,et al.  Bacterial Chitinases: Properties and Potential , 2007, Critical reviews in biotechnology.

[54]  Xuehong Zhang,et al.  An rhl-like quorum-sensing system negatively regulates pyoluteorin production in Pseudomonas sp. M18. , 2007, Microbiology.

[55]  Hong-bo Hu,et al.  QscR Acts as an Intermediate in gacA-Dependent Regulation of PCA Biosynthesis in Pseudomonas sp. M-18 , 2008, Current Microbiology.

[56]  J. Mekalanos,et al.  Threonine phosphorylation post-translationally regulates protein secretion in Pseudomonas aeruginosa , 2007, Nature Cell Biology.

[57]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[58]  L. Marraffini,et al.  CRISPR Interference Limits Horizontal Gene Transfer in Staphylococci by Targeting DNA , 2008, Science.

[59]  D. Hogan,et al.  Pseudomonas aeruginosa-Candida albicans Interactions: Localization and Fungal Toxicity of a Phenazine Derivative , 2008, Applied and Environmental Microbiology.

[60]  A. Franks,et al.  Pseudomonas–Plant Interactions , 2008 .

[61]  J. Rello,et al.  Hybrid Pathogenicity Island PAGI-5 Contributes to the Highly Virulent Phenotype of a Pseudomonas aeruginosa Isolate in Mammals , 2008, Journal of bacteriology.

[62]  B. Birren,et al.  Dynamics of Pseudomonas aeruginosa genome evolution , 2008, Proceedings of the National Academy of Sciences.

[63]  Jun Yu,et al.  VFDB 2008 release: an enhanced web-based resource for comparative pathogenomics , 2007, Nucleic Acids Res..

[64]  Xuehong Zhang,et al.  Las-like quorum-sensing system negatively regulates both pyoluteorin and phenazine-1-carboxylic acid production in Pseudomonas sp. M18 , 2008, Science in China Series C: Life Sciences.

[65]  George A. O'Toole,et al.  In Vivo Growth of Pseudomonas aeruginosa Strains PAO1 and PA14 and the Hypervirulent Strain LESB58 in a Rat Model of Chronic Lung Infection , 2007, Journal of bacteriology.

[66]  Georgios S. Vernikos,et al.  Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens , 2009, Genome Biology.

[67]  Raymond Lo,et al.  Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes , 2008, Nucleic Acids Res..

[68]  Haixia Jiang,et al.  The Distinct Quorum Sensing Hierarchy of las and rhl in Pseudomonas sp. M18 , 2009, Current Microbiology.

[69]  Guo-Ping Zhao,et al.  Complete Genome Sequence of Lactobacillus plantarum JDM1 , 2009, Journal of bacteriology.

[70]  Xuehong Zhang,et al.  Temperature-Dependent Expression of phzM and Its Regulatory Genes lasI and ptsP in Rhizosphere Isolate Pseudomonas sp. Strain M18 , 2009, Applied and Environmental Microbiology.

[71]  George A. Jacoby,et al.  AmpC β-Lactamases , 2009, Clinical Microbiology Reviews.

[72]  Julian Parkhill,et al.  Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. , 2008, Genome research.

[73]  Yuquan Xu,et al.  Medium optimization for phenazine-1-carboxylic acid production by a gacA qscR double mutant of Pseudomonas sp. M18 using response surface methodology. , 2010, Bioresource technology.

[74]  Xuehong Zhang,et al.  Enhancement of phenazine-1-carboxylic acid production using batch and fed-batch culture of gacA inactivated Pseudomonas sp. M18G. , 2010, Bioresource technology.

[75]  P. H. Roy,et al.  Complete Genome Sequence of the Multiresistant Taxonomic Outlier Pseudomonas aeruginosa PA7 , 2010, PloS one.

[76]  Haixia Jiang,et al.  Optimization of phenazine-1-carboxylic acid production by a gacA/qscR-inactivated Pseudomonas sp. M18GQ harboring pME6032Phz using response surface methodology , 2010, Applied Microbiology and Biotechnology.

[77]  A. Gales,et al.  Multidrug-resistant Pseudomonas aeruginosa and Acinetobacter baumannii: resistance mechanisms and implications for therapy , 2010, Expert review of anti-infective therapy.

[78]  Zixin Deng,et al.  mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes , 2010, Nucleic Acids Res..

[79]  T. Pohl,et al.  Genome Diversity of Pseudomonas aeruginosa PAO1 Laboratory Strains , 2009, Journal of bacteriology.

[80]  Zixin Deng,et al.  Pathogenicity Islands PAPI-1 and PAPI-2 Contribute Individually and Synergistically to the Virulence of Pseudomonas aeruginosa Strain PA14 , 2010, Infection and Immunity.

[81]  Z. Lu,et al.  Regulatory Feedback Loop of Two phz Gene Clusters through 5′-Untranslated Regions in Pseudomonas sp. M18 , 2011, PloS one.