A method adapting microarray technology for signature-tagged mutagenesis of Desulfovibrio desulfuricans G20 and Shewanella oneidensis MR-1 in anaerobic sediment survival experiments

Applied and Environmental Microbiology

Volumn 71, Issue 11, 2005, Pages 7064-7074

  Groh, Jennifer L ^a   Luo, Qingwei ^a   Ballard, Jimmy D ^b   Krumholz, Lee R ^a  

^a UNIVERSITY OF OKLAHOMA   (United States)

^b UNIVERSITY OF OKLAHOMA COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIOLOGY; BIOLOGICAL ORGANS; DATA ACQUISITION; GENES; MATHEMATICAL MODELS; SEDIMENTS;

MICROARRAY TECHNOLOGY; SIGNATURE-TAGGED MUTAGENESIS (STM); SURVIVAL GENES;

MUTAGENESIS;

BACTERIUM;

ANAEROBIC BACTERIUM; ANAEROBIC CAPACITY; ARTICLE; BACTERIAL SURVIVAL; CHEMOTAXIS; DESULFOVIBRIO DESULFURICANS; GENE EXPRESSION; GENE FUNCTION; GENE IDENTIFICATION; MICROARRAY ANALYSIS; MUTAGENESIS; NONHUMAN; PLASMID; SEDIMENT; SHEWANELLA ONEIDENSIS; SIGNATURE TAGGED MUTAGENESIS; TRANSPOSON;

ANAEROBIOSIS; BACTERIAL PROTEINS; CARDIOPULMONARY RESUSCITATION; DESULFOVIBRIO DESULFURICANS; DNA TRANSPOSABLE ELEMENTS; DNA, BACTERIAL; GENE EXPRESSION PROFILING; GEOLOGIC SEDIMENTS; MUTAGENESIS, INSERTIONAL; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLASMIDS; SHEWANELLA;

BACTERIA (MICROORGANISMS); DESULFOVIBRIO DESULFURICANS; SHEWANELLA ONEIDENSIS; SHEWANELLA ONEIDENSIS MR-1;

EID: 32044474842     PISSN: 00992240     EISSN: None     Source Type: Journal    
DOI: 10.1128/AEM.71.11.7064-7074.2005     Document Type: Article

References (57)

1. Akerley, B. J., E. J. Rubin, A. Camilli, D. J. Lampe, H. M. Robertson, and J. J. Mekalanos. 1998. Systematic identification of essential genes by in vitro mariner mutagenesis. Proc. Natl. Acad. Sci. USA 95:8927-8932.
2. Alexeyev, M. F., and I. N. Shokolenko. 1995. Mini-Tn10 transposon derivatives for insertion mutagenesis and gene delivery into the chromosome of Gram-negative bacteria. Gene 160:59-62.
3. Ausubel, F. M., R. Brent, R. E. Kingston, D. D. Moore, J. G. Seidman, J. A. Smith, and K. Struhl. 1987. Current protocols in molecular biology. Green Publishing Associates, New York, N.Y.
4. Beeman, R. E., and J. M. Suflita. 1990. Environmental factors influencing methanogenesis in a shallow anoxic aquifer: a field and laboratory study. J. Ind. Microbiol. 5:45-58.
5. Beeman, R. E., and J. M. Suflita. 1987. Microbial ecology of a shallow unconfined ground water aquifer polluted by municipal landfill leachate. Microb. Ecol. 14:39-54.
6. Cannac, V., M. S. Caffrey, G. Voordouw, and M. A. Cusanovich. 1991. Expression of the gene encoding cytochrome c3 from the sulfate-reducing bacterium Desulfovibrio vulgaris in the purple photosynthetic bacterium Rhodobacter sphaeroides. Arch. Biochem. Biophys. 286:629-632.
7. Chiang, S. L., and J. J. Mekalanos. 1998. Use of signature-tagged transposon mutagenesis to identify Vibrio cholerae genes critical for colonization. Mol. Microbiol. 27:797-805.
8. Chiang, S. L., J. J. Mekalanos, and D. W. Holden. 1999. In vivo genetic analysis of bacterial virulence. Annu. Rev. Microbiol. 53:129-154.
9. Childers, S. E., S. Ciufo, and D. R. Lovley. 2002. Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 416:767-769.
10. Dennis, J. J., and G. J. Zylstra. 1998. Plasposons: modular self-cloning minitransposon derivatives for rapid genetic analysis of gram-negative bacterial genomes. Appl. Environ. Microbiol. 64:2710-2715.
11. Dyson, P. J. 1999. Isolation and development of transposons. Methods Microbiol. 29:133-167.
12. Fu, R., J. D. Wall, and G. Voordouw. 1994. DcrA, a c-type heme-containing methyl-accepting protein from Desulfovibrio vulgaris Hildenborough, senses the oxygen concentration or redox potential of the environment. J. Bacteriol. 176:344-350.
13. Ganesh, R., K. G. Robinson, G. D. Reed, and G. S. Sayler. 1997. Reduction of hexavalent uranium from organic complexes by sulfate- and iron-reducing bacteria. Appl. Environ. Microbiol. 63:4385-4391.
14. Handfield, M., and R. C. Levesque. 1999. Strategies for isolation of in vivo expressed genes from bacteria. FEMS Microbiol. Rev. 23:69-91.
15. Hansen, T. A. 1994. Metabolism of sulfate-reducing prokaryotes. Antonie Leeuwenhoek 66:165-185.
16. Hayes, F. 2003. Transposon-based strategies for microbial functional genomics and proteomics. Annu. Rev. Genet. 37:3-29.
17. Heidelberg, J. F., I. T. Paulsen, K. E. Nelson, E. J. Gaidos, W. C. Nelson, T. D. Read, J. A. Eisen, R. Seshadri, N. Ward, B. Methe, R. A. Clayton, T. Meyer, A. Tsapin, J. Scott, M. Beanan, L. Brinkac, S. Daugherty, R. T. DeBoy, R. J. Dodson, A. S. Durkin, D. H. Haft, J. F. Kolonay, R. Madupu, J. D. Peterson, L. A. Umayam, O. White, A. M. Wolf, J. Vamathevan, J. Weidman, M. Impraim, K. Lee, K. Berry, C. Lee, J. Mueller, H. Khouri, J. Gill, T. R. Utterback, L. A. McDonald, T. V. Feldblyum, H. O. Smith, J. C. Venter, K. H. Nealson, and C. M. Fraser. 2002. Genome sequence of the dissimilatory metal ion-reducing bacterium Shewanella oneidensis. Nat. Biotechnol. 20:1118-1123.
18. Hendrixson, D. R., and V. J. DiRita. 2004. Identification of Campylobacter jejuni genes involved in commensal colonization of the chick gastrointestinal tract. Mol. Microbiol. 52:471-484.
19. Hensel, M., J. E. Shea, C. Gleeson, M. D. Jones, E. Dalton, and D. W. Holden. 1995. Simultaneous identification of bacterial virulence genes by negative selection. Science 269:400-403.
20. + antiporters in survival of Vibrio cholerae in a saline environment. J. Bacteriol. 185:1236-1244.
21. Heungens, K., C. E. Cowles, and H. Goodrich-Blair. 2002. Identification of Xenorhabdus nematophila genes required for mutualistic colonization of Steinernema carpocapsae nematodes. Mol. Microbiol. 45:1337-1353.
22. Karlyshev, A. V., P. C. F. Oyston, K. Williams, G. C. Clark, R. W. Titball, E. A. Winzeler, and B. W. Wren. 2001. Application of high-density array-based signature-tagged mutagenesis to discover novel Yersinia virulence-associated genes. Infect. Immun. 69:7810-7819.
23. Kennedy, M. J., and J. G. Lawless. 1985. Role of chemotaxis in the ecology of denitrifiers. Appl. Environ. Microbiol. 49:109-114.
24. Kim, C. H., D. R. Helinski, and G. Ditta. 1986. Overlapping transcription of the nifA regulatory gene in Rhizobium meliloti. Gene 50:141-148.
25. Kleckner, N., J. Bender, and S. Gottesman. 1991. Uses of transposons with emphasis on Tn10. Methods Enzymol. 204:139-180.
26. Lehoux, D. E., and R. C. Levesque. 2000. Detection of genes essential in specific niches by signature-tagged mutagenesis. Curr. Opin. Biotechnol. 11:434-439.
27. Lehoux, D. E., F. Sanschagrin, I. Kukavica-Ibrulj, E. Potvin, and R. C. Levesque. 2004. Identification of novel pathogenicity genes by PCR signature-tagged mutagenesis and related technologies, p. 289-304. In N. Woodford and A. P. Johnson (ed.), Genomics, proteomics, and clinical bacteriology, vol. 266. Humana Press, Totowa, N.J.
28. Lehoux, D. E., F. Sanschagrin, and R. C. Levesque. 1999. Defined oligonucleotide tag pools and PCR screening in signature-tagged mutagenesis of essential genes from bacteria. BioTechniques 26:473-480.
29. Lloyd, J. R., J. Chesnes, S. Glasauer, D. J. Bunker, F. R. Livens, and D. R. Lovley. 2002. Reduction of actinides and fission products by Fe(III)-reducing bacteria. Geomicrobiol. J. 19:103-120.
30. Lockhart, D. J., H. Dong, M. C. Byrne, M. T. Follettie, M. V. Gallo, M. S. Chee, M. Mittmann, C. Wang, M. Kobayashi, H. Horton, and E. L. Brown. 1996. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat. Biotechnol. 14:1675-1680.
31. Lovley, D. R., D. E. Holmes, and K. P. Nevin. 2004. Dissimilatory Fe(III) and Mn(IV) reduction. Adv. Microb. Physiol. 49:219-286.
32. Lovley, D. R., and E. J. P. Phillips. 1986. Availability of trivalent iron for microbial reduction in bottom sediments of the freshwater tidal Potomac River. Appl. Environ. Microbiol. 52:751-757.
33. Lovley, D. R., and E. J. P. Phillips. 1986. Organic matter mineralization with reduction of ferric iron in anaerobic sediments. Appl. Environ. Microbiol. 51:683-689.
34. Mecsas, J. 2002. Use of signature-tagged mutagenesis in pathogenesis studies. Curr. Opin. Microbiol. 5:33-37.
35. Mei, J.-M., F. Nourbakhsh, C. W. Ford, and D. W. Holden. 1997. Identification of Staphylococcus aureus virulence genes in a murine model of bacteremia using signature-tagged mutagenesis. Mol. Microbiol. 26:399-407.
36. Merrell, D. S., D. L. Hava, and A. Camilli. 2002. Identification of novel factors involved in colonization and acid tolerance of Vibrio cholerae. Mol. Microbiol. 43:1471-1491.
37. Myers, C. R., and J. M. Myers. 1997. Replication of plasmids with the p15A origin in Shewanella putrefaciens MR-1. Lett. Appl. Microbiol. 24:221-225.
38. Myers, C. R., and K. H. Nealson. 1988. Bacterial manganese reduction and growth with manganese oxide as the sole electron acceptor. Science 240:1319-1321.
39. Nealson, K. H., D. P. Moser, and D. A. Saffarini. 1995. Anaerobic electron acceptor chemotaxis in Shewanella putrefaciens. Appl. Environ. Microbiol. 61:1551-1554.
40. Newman, D. K., and R. Kolter. 2000. A role for excreted quinones in extracellular electron transfer. Nature 405:94-97.
41. 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.
42. Postgate, J. R. 1984. The sulfate reducing bacteria, 2nd ed. Cambridge University Press, Cambridge, United Kingdom.
43. Potvin, E., D. E. Lehoux, I. Kukavica-Ibrulj, K. L. Richard, F. Sanschagrin, G. W. Lau, and R. C. Levesque. 2003. In vivo functional genomics of Pseudomonas aeruginosa for high-throughput screening of new virulence factors and antibacterial targets. Environ. Microbiol. 5:1294-1308.
44. Rapp, B. J., and J. D. Wall. 1987. Genetic transfer in Desulfovibrio desulfuricans. Proc. Natl. Acad. Sci. USA 84:9128-9130.
45. Rubin, E. J., B. J. Akerley, V. N. Novik, D. J. Lampe, R. N. Husson, and J. J. Mekalanos. 1999. In vivo transposition of mariner-based elements in enteric bacteria and mycobacteria. Proc. Natl. Acad. Sci. USA 96:1645-1650.
46. Schena, M., R. A. Heller, T. P. Theriault, K. Konrad, E. Lachenmeier, and R. W. Davis. 1998. Microarrays: biotechnology's discovery platform for functional genomics. Trends Biotechnol. 16:301-306.
47. Shalon, D., S. J. Smith, and P. O. Brown. 1996. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res. 6:639-645.
48. Shoemaker, D. D., D. A. Lashkari, D. Morris, M. Mittmann, and R. W. Davis. 1996. Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy. Nat. Genet. 14:450-456.
49. Smidt, H., J. Van der Oost, and W. M. De Vos. 2001. Development of a gene cloning and inactivation system for halorespiring Desulfitobacterium dehalogenans. Appl. Environ. Microbiol. 67:591-597.
50. Steger, J. L., C. Vincent, J. D. Ballard, and L. R. Krumholz. 2002. Desulfovibrio sp. genes involved in the metabolism of hydrogen and lactate. Appl. Environ. Microbiol. 68:1932-1937.
51. Stewart, R. C., and F. W. Dahlquist. 1987. Molecular components of bacterial chemotaxis. Chem. Rev. 87:997-1025.
52. Voordouw, G., and S. Brenner. 1986. Cloning and sequencing of the gene encoding cytochrome c3 from Desulfovibrio vulgaris (Hildenborough). Eur. J. Biochem. 159:347-351.
53. Wall, J. D., C. L. Hemme, B. Rapp-Giles, J. A. Ringbauer, L. Casalot, and T. Giblin. 2003. Genes and genetic manipulations of Desulfovibrio, p. 85-98. In M. W. Adams, J. G. Ferry, L. L. Barton, M. K. Johnson, and L. G. Ljungdahl (ed.), Biochemistry and physiology of anaerobic bacteria. Springer, New York, N. Y.
54. Wall, J. D., T. Murnan, J. Argyle, R. S. English, and B. J. Rapp-Giles. 1996. Transposon mutagenesis in Desulfovibrio desulfuricans: development of a random mutagenesis tool from Tn7. Appl. Environ. Microbiol. 62:3762-3767.
55. Wall, J. D., B. J. Rapp-Giles, and M. Rousset. 1993. Characterization of a small plasmid from Desulfovibrio desulfuricans and its use for shuttle vector construction. J. Bacteriol. 175:4121-4128.
56. Winzeler, E. A., D. D. Shoemaker, A. Astromoff, H. Liang, K. Anderson, B. Andre, R. Bangham, R. Benito, J. D. Boeke, H. Bussey, A. M. Chu, C. Connelly, K. Davis, F. Dietrich, S. W. Dow, M. El Bakkoury, F. Foury, S. H. Friend, E. Gentalen, G. Giaever, J. H. Hegemann, T. Jones, M. Laub, H. Liao, N. Liebundguth, D. J. Lockhart, A. Lucau-Danila, M. Lussier, N. M'Rabet, P. Menard, M. Mittmann, C. Pai, C. Rebischung, J. L. Revuelta, L. Riles, C. J. Roberts, P. Ross-MacDonald, B. Scherens, M. Snyder, S. Sookhai-Mahadeo, R. K. Storms, S. Veronneau, M. Voet, G. Volckaert, T. R. Ward, R. Wysocki, G. S. Yen, K. Yu, K. Zimmermann, P. Philippsen, M. Johnston, and R. W. Davis. 1999. Functional characterization of the S. cerevisiae genome by gene deletion and parallel analysis. Science 285:901-906.
57. Wolk, C. P., Y. Cai, and J. M. Panoff. 1991. Use of a transposon with luciferase as a reporter to identify environmentally responsive genes in a cyanobacterium. Proc. Natl. Acad. Sci. USA 88:5355-5359.