Comparative analysis of temperature-dependent transcriptome of Pseudomonas aeruginosa strains from rhizosphere and human habitats

Applied Microbiology and Biotechnology

Volumn 96, Issue 4, 2012, Pages 1007-1019

  Wu, Da Qiang ^a   Li, Yaqian ^a   Xu, Yuquan ^a  

^a Shanghai Jiao Tong University   (China)

Author keywords

Microarray; Pseudomonas aeruginosa; Temperature dependent; Transcriptome

Indexed keywords

COMPARATIVE ANALYSIS; COMPLETE GENOMES; GENOME STRUCTURES; HUMAN HABITATS; P.AERUGINOSA; PSEUDOMONAS AERUGINOSA; TEMPERATURE CHANGES; TEMPERATURE DEPENDENT; TRANSCRIPTOME PROFILES; TRANSCRIPTOMES;

BACTERIA; GENES; GROWTH TEMPERATURE; MICROARRAYS; SOILS;

STRAIN;

TRANSCRIPTOME;

ADAPTATION; BACTERIOLOGY; BACTERIUM; COMPARATIVE STUDY; GENE EXPRESSION; GENOME; HABITAT TYPE; HOMINID; RHIZOSPHERE; TEMPERATURE EFFECT;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CONTROLLED STUDY; MICROARRAY ANALYSIS; NONHUMAN; OPERON; PSEUDOMONAS AERUGINOSA; RHIZOSPHERE; TEMPERATURE;

BACTERIAL PROTEINS; ECOSYSTEM; GENE EXPRESSION REGULATION, BACTERIAL; HUMANS; PSEUDOMONAS AERUGINOSA; PSEUDOMONAS INFECTIONS; RHIZOSPHERE; SOIL MICROBIOLOGY; TRANSCRIPTOME;

PSEUDOMONAS AERUGINOSA;

EID: 84870984614     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4466-5     Document Type: Article

References (50)

1. Anjaiah V, Cornelis P, Koedam N (2003) Effect of genotype and root colonization in biological control of fusarium wilts in pigeonpea and chickpea by Pseudomonas aeruginosa PNA1. Can J Microbiol 49:85-91
2. Attila C, Ueda A, Wood TK (2008) PA2663 (PpyR) increases biofilm formation in Pseudomonas aeruginosa PAO1 through the psl operon and stimulates virulence and quorum-sensing phenotypes. Appl Microbiol Biotechnol 78:293-307
3. Balasubramanian D, Mathee K (2009) Comparative transcriptome analyses of Pseudomonas aeruginosa. Hum Genomics 3:349-361
4. Bernard CS, Bordi C, Termine E, Filloux A, de Bentzmann S (2009) Organization and PprB-dependent control of the Pseudomonas aeruginosa tad Locus, involved in Flp pilus biology. J Bacteriol 191:1961-1973
5. Brencic A, Lory S (2009) Determination of the regulon and identification of novel mRNA targets of Pseudomonas aeruginosa RsmA. Mol Microbiol 72:612-632
6. Burrowes E, Baysse C, Adams C, O'Gara F (2006) Influence of the regulatory protein RsmA on cellular functions in Pseudomonas aeruginosa PAO1, as revealed by transcriptome analysis. Microbiology 152:405-418
7. Buysens S, Heungens K, Poppe J, Hofte M (1996) Involvement of pyochelin and pyoverdin in suppression of Pythium-induced damping-off of tomato by Pseudomonas aeruginosa 7NSK2. Appl Environ Microbiol 62:865-871
8. Cao YR, Wang Q, Jin RX, Jiang Y, Lai HX, He WX, Xu LH, Jiang CL (2010) Planosporangium mesophilum sp. nov., isolated from rhizosphere soil of Bletilla striata. Int J Syst Evol Microbiol 61:1330-1333
9. Cianciotto NP (2005) Type II secretion: a protein secretion system for all seasons. Trends Microbiol 13:581-588
10. Desai JD, Banat IM (1997) Microbial production of surfactants and their commercial potential. Microbiol Mol Biol R 61:47-64
11. Dodey GP, Bolivar R, Fainstein V, Jadeja L (1983) Infections caused by Pseudomonas aeruginosa. Rev Infect Dis 5:279-313
12. Dubern JF, Diggle SP (2008) Quorum sensing by 2-Alkyl-4-quinolones in Pseudomonas aeruginosa and other bacterial species. Mol Biosyst 4:882-888
13. Duzan HM, Mabood F, Souleimanov A, Smith DL (2006) Nod Bj-V (C18:1, MeFuc) production by Bradyrhizobium japonicum (USDA110, 532C) at suboptimal growth temperatures. J Plant Physiol 163:107-111
14. Förster-Fromme K, Jendrossek D (2008) Biochemical characterization of isovaleryl-CoA dehydrogenase (LiuA) of Pseudomonas aeruginosa and the importance of liu genes fora functional catabolic pathway of methyl-branched compounds. FEMS Microbiol Lett 286:78-84
15. Ghai R, Hain T, Chakraborty T (2004) GenomeViz: visualizing microbial genomes. BMC Bioinformatics 5:198
16. Hardalo C, Edberg SC (1997) Pseudomonas aeruginosa: assessment of risk from drinking water. Crit Rev Microbiol 23:47-75
17. Hauser AR (2009) The type III secretion system of Pseudomonas aeruginosa: infection by injection. Nat Rev Microbiol 7:654-665
18. Hoboth C, Hoffmann R, Eichner A, Henke C, Schmoldt S, Imhof A, Heesemann J, Hogardt M (2009) Dynamics of adaptive microevolution of hypermutable Pseudomonas aeruginosa during chronic pulmonary infection in patients with cystic fibrosis. J Infect Dis 200:118-130
19. Hoffman LR, Richardson AR, Houston LS, Kulasekara HD, Martens-Habbena W, Klausen M, Burns JL, Stahl DA, Hassett DJ, Fang FC, Miller SI (2010) Nutrient availability as a mechanism for selection of antibiotic tolerant Pseudomonas aeruginosa within the CF airway. PLoS Pathog 6:e1000712
20. Holloway BW (1955) Genetic recombination in Pseudomonas aeruginosa. J Gen Microbiol 13:572-581
21. Huang X, Zhu D, Ge Y, Hu H, Zhang X, Xu Y (2004) Identification and characterization of pltZ, a gene involved in the repression of pyoluteorin biosynthesis in Pseudomonas sp. M18. FEMS Microbiol Lett 232:197-202
22. Huang X, Yan A, Zhang X, Xu Y (2006) Identification and characterization of a putative ABC transporter PltHIJKN required for pyoluteorin production in Pseudomonas sp. M18. Gene 376:68-78
23. Ihaka R, Gentleman R (1996) R: a language for data analysis and graphics. J Comput Graph Stat 5:299-314
24. Knight CG, Zhang XX, Gunn A, Brenner T, Jackson RW, Giddens SR, Prabhakar S, Zitzmann N, Rainey PB (2010) Testing temperatureinduced proteomic changes in the plant-Associated bacterium Pseudomonas fluorescens SBW25. Environ Microbiol Rep 2:396-402
25. Kobayashi I (2001) Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Nucleic Acids Res 29:3742-3756
26. Kumar RS, Ayyadurai N, Pandiaraja P, Reddy AV, Venkateswarlu Y, Prakash O, Sakthivel N (2005) Characterization of antifungal metabolite produced by a new strain Pseudomonas aeruginosa PUPa3 that exhibits broad-spectrum antifungal activity and biofertilizing traits. J Appl Microbiol 98:145-154
27. Livak KJ, Schmittgen TD (2001) Analysis of relative gene expression data using real-Time quantitative PCR and the 2-ΔΔCT method. Methods 25:402-408
28. Marchler-Bauer A, Panchenko AR, Shoemaker BA, Thiessen PA, Geer LY, Bryant SH (2002) CDD: a database of conserved domain alignments with links to domain three-dimensional structure. Nucleic Acids Res 30:281-283
29. Mathee K, Narasimhan G, Valdes C, Qiu X, Matewish JM, Koehrsen M, Rokas A, Yandava CN, Engels R, Zeng E, Olavarietta R, Doud M, Smith RS, Montgomery P, White JR, Godfrey PA, Kodira C, Birren B, Galagan JE, Lory S (2008) Dynamics of Pseudomonas aeruginosa genome evolution. Proc Natl Acad Sci U S A 105:3100-3105
30. Mira NP, Madeira A, Moreira AS, Coutinho CP, Sá-Correia I (2011) Genomic expression analysis reveals strategies of Burkholderia cenocepacia to adapt to cystic fibrosis patients' airways and antimicrobial therapy. PLoS One 6:e28831
31. Nouaille S, Even S, Charlier C, Le Loir Y, Cocaign-Bousquet M, Loubière P (2009) Transcriptomic response of Lactococcus lactis in mixed culture with Staphylococcus aureus. Appl Environ Microbiol 75:4473-4482
32. Palleroni NJ (2010) The Pseudomonas story. Environl Microbiol 12:1377-1383
33. Poole K, McKay GA (2003) Iron acquisition and its control in Pseudomonas aeruginosa: many roads lead to Rome. Front Biosci 8: d661-686
34. Pribat A, Blaby IK, Lara-Núnez A, Gregory JF 3rd, de Crécy-Lagard V, Hanson AD (2010) FolX and FolM are essential for tetrahydromonapterin synthesis in Escherichia coli and Pseudomonas aeruginosa. J Bacteriol 192:475-482
35. Rodríguez-Rojas A, Mena A, Martin S, Borrell N, Oliver A, Blázquez J (2009) Inactivation of the hmgA gene of Pseudomonas aeruginosa leads to pyomelanin hyperproduction, stress resistance and increased persistence in chronic lung infection. Microbiology 155:1050-1057
36. Salunkhe P, Töpfer T, Buer J, Tümmler B (2005) Genome-wide transcriptional profiling of the steady-state response of Pseudomonas aeruginosa to hydrogen peroxide. J Bacteriol 187:2565-2572
37. Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z (2010) mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes. Nucleic Acids Res 38(Suppl):W194-200
38. Silby MW, Cerdeno-Tárraga AM, Vernikos GS, Giddens SR, Jackson RW, Preston GM, Zhang XX, Moon CD, Gehrig SM, Godfrey SA, Knight CG, Malone JG, Robinson Z, Spiers AJ, Harris S, Challis GL, Yaxley AM, Harris D, Seeger K, Murphy L, Rutter S, Squares R, Quail MA, Saunders E, Mavromatis K, Brettin TS, Bentley SD, Hothersall J, Stephens E, Thomas CM, Parkhill J, Levy SB, Rainey PB, Thomson NR (2009) Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens. Genome Biol 10:R51
39. Small DA, Chang W, Toghrol F, Bentley WE (2007) Comparative global transcription analysis of sodium hypochlorite, peracetic acid, and hydrogen peroxide on Pseudomonas aeruginosa. Appl Microbiol Biotechnol 76:1093-1105
40. Smillie CS, Smith MB, Friedman J, Cordero OX, David LA, Alm EJ (2011) Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244
41. Smith EE, Buckley DG, Wu Z, Saenphimmachak C, Hoffman LR, D'Argenio DA, Miller SI, Ramsey BW, Speert DP, Moskowitz SM, Burns JL, Kaul R, Olson MV (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc Natl Acad Sci U S A 103:8487-8492
42. Söderberg MA, Rossier O, Cianciotto NP (2004) The type II protein secretion system of Legionella pneumophila promotes growth at low temperatures. J Bacteriol 186:3712-3720
43. Stover CK, Pham XQ, Erwin AL, Mizoguchi SD, Warrener P, Hickey MJ, Brinkman FS, Hufnagle WO, Kowalik DJ, Lagrou M, Garber RL, Goltry L, Tolentino E, Westbrock-Wadman S, Yuan Y, Brody LL, Coulter SN, Folger KR, Kas A, Larbig K, Lim R, Smith K, Spencer D, Wong GK, Wu Z, Paulsen IT, Reizer J, Saier MH, Hancock RE, Lory S, Olson MV (2000) Complete genome sequence of Pseudomonas aeruginosa PAO1, an opportunistic pathogen. Nature 406:959-964
44. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637
45. Termine E, Michel GP (2009) Transcriptome and secretome analyses of the adaptive response of Pseudomonas aeruginosa to suboptimal growth temperature. Int Microbiol 12:7-12
46. Werck-Reichhart D, Feyereisen R (2000) Cytochromes P450: a success story. Genome Biol 1: REVIEWS3003
47. Wilderman PJ, Vasil AI, Johnson Z, Wilson MJ, Cunliffe HE, Lamont IL, Vasil ML (2001) Characterization of an endoprotease (PrpL) encoded by a PvdS-regulated gene in Pseudomonas aeruginosa. Infect Immun 69:5385-5394
48. Winsor GL, Van Rossum T, Lo R, Khaira B, Whiteside MD, Hancock RE, Brinkman FS (2009) Pseudomonas Genome Database: facilitating user-friendly, comprehensive comparisons of microbial genomes. Nucleic Acids Res 37:D483-488
49. Winstanley C, Langille MG, Fothergill JL, Kukavica-Ibrulj I, Paradis-Bleau C, Sanschagrin F, Thomson NR, Winsor GL, Quail MA, Lennard N, Bignell A, Clarke L, Seeger K, Saunders D, Harris D, Parkhill J, Hancock RE, Brinkman FS, Levesque RC (2009) Newly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa. Genome Res 19:12-23
50. Wu DQ, Ye J, Ou HY, Wei X, Huang X, He YW, Xu Y (2011) Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18. BMC Genomics 12:438