Use of in vivo expression technology to identify genes important in growth and survival of Pseudomonas fluorescens Pf0-1 in soil: Discovery of expressed sequences with novel genetic organization

Journal of Bacteriology

Volumn 186, Issue 21, 2004, Pages 7411-7419

  Silby, Mark W ^a   Levy, Stuart B ^a  

^a TUFTS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL GROWTH; BACTERIAL SURVIVAL; CONTROLLED STUDY; CULTURE MEDIUM; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; GENE SEQUENCE; GENE TECHNOLOGY; GENETIC ORGANIZATION; GRAM NEGATIVE BACTERIUM; IN VIVO EXPRESSION TECHNOLOGY; LABORATORY; NONHUMAN; NUCLEOTIDE SEQUENCE; NUTRIENT UPTAKE; PRIORITY JOURNAL; PSEUDOMONAS FLUORESCENS; SOIL;

BACTERIAL PROTEINS; BACTERIOLOGICAL TECHNIQUES; CULTURE MEDIA; DIAMINOPIMELIC ACID; GENE EXPRESSION REGULATION, BACTERIAL; GENES, BACTERIAL; MUTATION; PROMOTER REGIONS (GENETICS); PSEUDOMONAS FLUORESCENS; RECOMBINANT FUSION PROTEINS; SOIL MICROBIOLOGY; TRANSCRIPTION, GENETIC;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; PROKARYOTA; PSEUDOMONAS; PSEUDOMONAS FLUORESCENS;

EID: 6044274610     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.186.21.7411-7419.2004     Document Type: Article

References (46)

1. Altschul, S. F., W. Gish, W. Miller, E. W. Myers, and D. J. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215:403-410.
2. Black, P. N., C. C. DiRusso, A. K. Metzger, and T. L. Heimert. 1992. Cloning, sequencing, and expression of the fadD gene of Escherichia coli encoding acyl coenzyme A synthetase. J. Biol. Chem. 267:25513-25520.
3. Boch, J., V. Joardar, L. Gao, T. L. Robertson, M. Lim, and B. N. Kunkel. 2002. Identification of Pseudomonas syringae pv. tomato genes induced during infection of Arabidopsis thaliana. Mol. Microbiol. 44:73-88.
4. Camilli, A., and J. J. Mekalanos. 1995. Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol. Microbiol. 18:671-683.
5. Casaz, P., A. Happel, J. Keithan, D. L. Read, S. R. Strain, and S, B. Levy. 2001. The Pseudomonas fluorescens transcription activator AdnA is required for adhesion and motility. Microbiology 147:355-361.
6. Compeau, G., B. J. Al-Achi, E. Platsouka, and S. B. Levy. 1988. Survival of rifampin-resistant mutants of Pseudomonas fluorescens and Pseudomonas putida in soil systems. Appl. Environ. Microbiol. 54:2432-2438.
7. Danielsen, S., M. Kilstrup, K. Barilla, B. Jochimsen, and J. Neuhard. 1992. Characterization of the Escherichia coli codBA operon encoding cytosine permease and cytosine deaminase. Mol. Microbiol. 6:1335-1344.
8. DeFlaun, M. F., B. M. Marshall, E.-P. Kulle, and S. B. Levy. 1994. Tn5 insertion mutants of Pseudomonas fluorescens defective in adhesion to soil and seeds. Appl. Environ. Microbiol. 60:2637-2642.
9. DeFlaun, M. F., A. S. Tanzer, A. L. McAteer, B. Marshall, and S. B. Levy. 1990. Development of an adhesion assay and characterization of an adhesion-deficient mutant of Pseudomonas fluorescens. Appl. Environ. Microbiol. 56:112-119.
10. Finkel, S. E., and R. Kolter. 2001. DNA as a nutrient: novel role for bacterial competence gene homologs. J. Bacteriol. 183:6288-6293.
11. Gal, M., G. M. Preston, R. C. Massey, A. J. Spiers, and P. B. Rainey. 2003. Genes encoding a cellulosic polymer contribute toward the ecological success of Pseudomonas fluorescens SBW25 on plant surfaces. Mol. Ecol. 12:3109-3121.
12. Gennis, R. B., and V. Stewart. 1996. Respiration, p. 217-261. In F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 1. ASM Press, Washington, D. C.
13. Haydon, D. J., and J. R. Guest. 1991. A new family of bacterial regulatory proteins. FEMS Microbiol. Lett. 79:291-296.
14. Johansson, J., and P. Cossart. 2003. RNA-mediated control of virulence gene expression in bacterial pathogens. Trends Microbiol. 11:280-285.
15. Kirner, S., S. Krauss, G. Sury, S. T. Lam, J. M. Ligon, and K. H. van Pee. 1996. The non-haem chloroperoxidase from Pseudomonas fluorescens and its relationship to pyrrolnitrin biosynthesis. Microbiology 142:2129-2135.
16. Lai, Y.-C., H.-L. Peng, and H.-Y. Chang. 2001. Identification of genes induced in vivo during Klebsiella pneumoniae CG43 infection. Infect. Immun. 69:7140-7145.
17. Lee, S.-W., and D. A. Cooksey. 2000. Genes expressed in Pseudomonasputida during colonization of a plant-pathogenic fungus. Appl. Environ. Microbiol. 66:2764-2772.
18. Mahan, M. J., D. M. Heithoff, R. L. Sinsheimer, and D. A. Low. 2000. Assessment of bacterial pathogenesis by analysis of gene expression in the host. Annu. Rev. Genet. 34:139-164.
19. Mahan, M. J., J. M. Slauch, and J. J. Mekalanos. 1993. Selection of bacterial virulence genes that are specifically induced in host tissues. Science 259:686-688.
20. Mahan, M. J., J. W. Tobias, J. M. Slauch, P. C. Hanna, R. J. Collier, and J. J. Mekalanos. 1995. Antibiotic-based selection for bacterial genes that are specifically induced during infection of a host. Proc. Natl. Acad. Sci. USA 92:669-673.
21. Marshall, B., E. A. Robleto, R. Wetzler, P. Kulle, P. Casaz, and S. B. Levy. 2001. The adnA transcriptional factor affects persistence and spread of Pseudomonas fluorescens under natural field conditions. Appl. Environ. Microbiol. 67:852-857.
22. Masse, E., N. Majdalani, and S. Gottesman. 2003. Regulatory roles for small RNAs in bacteria. Curr. Opin. Microbiol. 6:120-124.
23. Matthews, M., and C. R. Roy. 2000. Identification and subcellular localization of the Legionella pneumophila IcmX protein: a factor essential for establishment of a replicative organelle in eukaryotic host cells. Infect. Immun. 68:3971-3982.
24. Monds, R. D., M. W. Silby, and H. K. Mahanty. 2001. Expression of the Pho regulon negatively regulates biofilm formation by Pseudomonas aureofaciens PA147-2. Mol. Microbiol. 42:415-426.
25. Muse, W. B., C. J. Rosario, and R. A. Bender. 2003. Nitrogen regulation of the codBA (cytosine deaminase) operon from Escherichia coll by the nitrogen assimilation control protein, NAC. J. Bacteriol. 185:2920-2926.
26. Nielsen, H., J. Engelbrecht, S. Brunak, and G. von Heijne. 1997. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 10:1-6.
27. Osbourn, A. E., C. E. Barber, and M. J. Daniels. 1987. Identification of plant-induced genes of the bacterial pathogen Xanthomonas campestris pathovar campestris using a promoter-probe plasmid. EMBO J. 6:23-28.
28. O'Toole, G. A., K. A. Gibbs, P. W. Hager, P. V. Phibbs, Jr., and R. Kolter. 2000. The global carbon metabolism regulator Crc is a component of a signal transduction pathway required for biofilm development by Pseudomonas aeruginosa. J. Bacteriol. 182:425-431.
29. O'Toole, G. A., and R. Kolter. 1998. Initiation of biofilm formation in Pseudomonas fluorescens WCS365 proceeds via multiple, convergent signalling pathways: a genetic analysis. Mol. Microbiol. 28:449-461.
30. Parales, R. E., and C. S. Harwood. 1993. Construction and use of a new broad-host-range lacZ transcriptional fusion vector, pHRP309, for gram-bacteria. Gene 133:23-30.
31. Parke, D., D. A. D'Argenio, and L. N. Ornston. 2000. Bacteria are not what they eat: that is why they are so diverse. J. Bacteriol. 182:257-263.
32. Rainey, P. B. 1999. Adaptation of Pseudomonas fluorescens to the plant rhizosphere. Environ. Microbiol. 1:243-257.
33. Rainey, P. B., D. M. Heithoff, and M. J. Mahan. 1997. Single-step conjugative cloning of bacterial gene fusions involved in microbe-host interactions. Mol. Gen. Genet. 256:84-87.
34. Rainey, P. B., and G. M. Preston. 2000. In vivo expression technology strategies: valuable tools for biotechnology. Curr. Opin. Biotechnol. 11:440-444.
35. Rajagopalan, K. V. 1996. Biosynthesis of the molybdenum cofactor, p. 674-679. in F. C. Neidhardt, R. Curtiss III, J. L. Ingraham, E. C. C. Lin, K. B. Low, B. Magasanik, W. S. Reznikoff, M. Riley, M. Schaechter, and H. E. Umbarger (ed.), Escherichia coli and Salmonella, 2nd ed., vol. 1. ASM Press, Washington, D.C.
36. Rediers, H., V. Bonnecarrère, P. B. Rainey, K. Hamonts, J. Vanderleyden, and R. De Mot. 2003. Development and application of a dapB-based in vivo expression technology system to study colonization of rice by the endophytic nitrogen-fixing bacterium Pseudomonas stutzen A15. Appl. Environ. Microbiol. 69:6864-6874.
37. Rigali, S., A. Derouaux, F. Giannotta, and J. Dusart. 2002. Subdivision of the helix-turn-helix GntR family of bacterial regulators in the FadR, HutC, MocR, and YtrA subfamilies. J. Biol. Chem. 277:12507-12515.
38. Robleto, E. A., I. Lopez-Hernandez, M. W. Silby, and S. B. Levy. 2003. Genetic analysis of the AdnA regulon in Pseudomonas fluorescens: nonessential role of flagella in adhesion to sand and biofilm formation. J. Bacteriol. 185:453-460.
39. Sambrook, J., and D. W. Russell. 2001. Molecular cloning: a laboratory manual, 3rd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
40. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
41. Silby, M. W., P. B. Rainey, and S. B. Levy. 2004. IVET experiments in Pseudomonas fluorescens reveal cryptic promoters at loci associated with recognizable overlapping genes. Microbiology 150:518-520.
42. Simon, R., U. Priefer, and A. Punier. 1983. A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram-negative bacteria. Bio/Technology 1:784-791.
43. Stover, C. K., X. Q. Pham, A. L. Erwin, S. D. Mizoguchi, P. Warrener, M. J. Hickey, F. S. Brinkman, W. O. Hufhagle, D. J. Kowalik, M. Lagrou, R. L. Garber, L. Goltry, E. Tolentino, S. Westbrock-Wadman, Y. Yuan, L. L. Brody, S. N. Coulter, K. R. Folger, A. Kas, K. Larbig, R. Lim, K. Smith, D. Spencer, G. K. Wong, Z. Wu, I. T. Paulsen, J. Reizer, M. H. Saier, R. E. Hancock, S. Lory, and M. V. Olson. 2000. Complete genome sequence of Pseudomonas aeruginosa PA01, an opportunistic pathogen. Nature 406:959-964.
44. Wagner, E. G., and R. W. Simons. 1994. Antisense RNA control in bacteria, phages, and plasmids. Annu. Rev. Microbiol. 48:713-742.
45. Wang, J., A. Mushegian, S. Lory, and S. Jin. 1996. Large-scale isolation of candidate virulence genes of Pseudomonas aeruginosa by in vivo selection. Proc. Natl. Acad. Sci. USA 93:10434-10439.
46. You, S. Y., S. Cosloy, and H. Schulz. 1989. Evidence for the essential function of 2,4-dienoyl-coenzyme A reductase in the beta-oxidation of unsaturated fatty acids in vivo. Isolation and characterization of an Escherichia coli mutant with a defective 2,4-dienoyl-coenzyme A reductase. J. Biol. Chem. 264:16489-16495.