Mutational analysis of the ompA promoter from Flavobacterium johnsoniae

Journal of Bacteriology

Volumn 189, Issue 14, 2007, Pages 5108-5118

  Chen, Shicheng ^a   Bagdasarian, Michael ^a   Kaufman, Michael G ^b   Bates, Adam K ^a   Walker, Edward D ^a  

^a Michigan State University ^*  (United States)

^b MICHIGAN STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SUBSTITUTION; ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTEROIDES FRAGILIS; CONTROLLED STUDY; ESCHERICHIA COLI; FLAVOBACTERIUM JOHNSONIAE; GENE MUTATION; GENE SEQUENCE; MUTATIONAL ANALYSIS; NONHUMAN; NUCLEOTIDE SEQUENCE; OMPA GENE; PRIORITY JOURNAL; PROMOTER REGION; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION;

AMINO ACID SEQUENCE; BACTERIAL OUTER MEMBRANE PROTEINS; BASE SEQUENCE; DNA MUTATIONAL ANALYSIS; FLAVOBACTERIUM; GENOME, BACTERIAL; MOLECULAR SEQUENCE DATA; POINT MUTATION; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; TRANSCRIPTION INITIATION SITE;

BACTEROIDES FRAGILIS; BACTEROIDETES; ESCHERICHIA COLI; FLAVOBACTERIUM; FLAVOBACTERIUM JOHNSONIAE; PROTEOBACTERIA;

EID: 34447513132     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.00401-07     Document Type: Article

References (60)

1. Agarwal, N., and A. K. Tyagi. 2006. Mycobacterial transcriptional signals: requirements for recognition by RNA polymerase and optimal transcriptional activity. Nucleic Acids Res. 34:4245-4257.
2. Alvarez, B., P. Secades, M. J. McBride, and J. A. Guijarro. 2004. Development of genetic techniques for the psychrotrophic fish pathogen Flavobacterium psychrophilum. Appl. Environ. Microbiol. 70:581-587.
3. Bannantine, J. P., R. G. Barletta, C. O. Thoen, and R. E. Andrews, Jr. 1997. Identification of Mycobacterium paratuberculosis gene expression signals. Microbiology 143:921-928.
4. Bayley, D. P., E. R. Rocha, and C. J. Smith. 2000. Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol. Lett. 193:149-154.
5. Blain, F., A. L. Tkalec, Z. Shao, C. Poulin, M. Pedneault, K. Gu, B. Eggimann, J. Zimmermann, and H. Su. 2002. Expression system for high levels of GAG lyase gene expression and study of the hepA upstream region in Flavobacterium heparinum. J. Bacteriol. 184:3242-3252.
6. Borriss, M., E. Helmke, R. Hanschke, and T. Schweder. 2003. Isolation and characterization of marine psychrophilic phage-host systems from Arctic sea ice. Extremophiles 7:377-384.
7. Bostanci, N., R. Allaker, U. Johansson, M. Rangarajan, M. A. Curtis, F. J. Hughes, and I. J. McKay. 2007. Interleukin-1α stimulation in monocytes by periodontal bacteria: antagonistic effects of Porphyromonas gingivalis. Oral Microbiol. Immunol. 22:52-60.
8. Braun, D. C., and D. C. Stein. 2004. The lgtABCDE gene cluster, involved in lipooligosaccharide biosynthesis in Neisseria gonorrhoeae, contains multiple promoter sequences. J. Bacteriol. 186:1038-1049.
9. Braun, T. F., M. K. Khubbar, D. A. Saffarini, and M. J. McBride. 2005. Flavobacterium johnsoniae gliding motility genes identified by mariner mutagenesis. J. Bacteriol. 187:6943-6952.
10. Braun, T. F., and M. J. McBride. 2005. Flavobacterium johnsoniae GldJ is a lipoprotein that is required for gliding motility. J. Bacteriol. 187:2628-2637.
11. Cerdeño-Tárraga, A. M., S. Patrick, L. C. Crossman, G. Blakely, V. Abratt, N. Lennard, I. Poxton, B. Duerden, B. Harris, M. A. Quail, A. Barron, L. Clark, C. Corton, J. Doggett, M. T. G. Holden, N. Larke, A. Line, A. Lord, H. Norbertczak, D. Ormond, C. Price, E. Rabbinowitsch, J. Woodward, B. Barrell, and J. Parkhill. 2005. Extensive DNA inversions in the B. fragilis genome control variable gene expression. Science 307:1463-1465.
12. Chen, S., M. Bagdasarian, M. G. Kaufman, and E. D. Walker. 2007. Characterization of strong promoters from an environmental Flavobacterium hibemum strain using a green fluorescent protein-based reporter system. Appl. Environ. Microbiol. 73:1089-1100.
13. Chen, S., M. Bagdasarian, M. G. Kaufman, and E. D. Walker. 2007. Organization of a partial S10 operon and its transcriptional analysis in Flavobacterium hibernum strain W22. FEMS Microbiol. Lett. 267:38-45.
14. Cottrell, M. T., and D. L. Kirchman. 2000. Natural assemblages of marine proteobacteria and members of the Cytophaga-Flavobacter cluster consuming low- and high-molecular-weight dissolved organic matter. Appl. Environ. Microbiol. 66:1692-1697.
15. Decostere, A., F. Haesebrouck, G. Charlier, and R. Ducatelle. 1999. The association of Flavobacterium columnare strains of high and low virulence with gill tissue of black mollies (Poecilia sphenops). Vet. Microbiol. 67:287-298.
16. Dombroski, A. J., B. D. Johnson, M. Lonetto, and C. A. Gross. 1996. The sigma subunit of Escherichia coli RNA polymerase senses promoter spacing. Proc. Natl. Acad. Sci. USA 93:8858-8862.
17. Doree, S. M., and M. H. Mulks. 2001. Identification of an Actinobacillus pleuropneumoniae consensus promoter structure. J. Bacteriol. 183:1983-1989.
18. Dsouza, M., N. Larsen, and R. Overbeek. 1997. Searching for patterns in genomic data. Trends Genet. 13:497-498.
19. Estrem, S. T., T. Gaal, W. Ross, and R. L. Gourse. 1998. Identification of an UP element consensus sequence for bacterial promoters. Proc. Natl. Acad. Sci. USA 95:9761-9766.
20. Gourse, R. L., W. Ross, and T. Gaal. 2000. UPs and downs in bacterial transcription initiation: the role of the alpha subunit of RNA polymerase in promoter recognition. Mol. Microbiol. 37:687-695.
21. Harley, C. B., and R. P. Reynolds. 1987. Analysis of E. coli promoter sequences. Nucleic Acids Res. 15:2343-2361.
22. Helmann, J. D. 1995. Compilation and analysis of Bacillus subtilis σ∧-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res. 23:2351-2360.
23. Hunnicutt, D. W., M. J. Kempf, and M. J. McBride. 2002. Mutations in Flavobacterium johnsoniae gldF and gldG disrupt gliding motility and interfere with membrane localization of GldA. J. Bacteriol. 184:2370-2378.
24. Hunnicutt, D. W., and M. J. McBride. 2000. Cloning and characterization of the Flavobacterium johnsoniae gliding-motility genes gldB and gldC. J. Bacteriol. 182:911-918.
25. Hunnicutt, D. W., and M. J. McBride. 2001. Cloning and characterization of the Flavobacterium johnsoniae gliding motility genes gldD and gldE. J. Bacteriol. 183:4167-4175.
26. Iyer, L. M., E. V. Koonin, and L. Aravind. 2004. Evolution of bacterial RNA polymerase: implications for large-scale bacterial phylogeny, domain accretion, and horizontal gene transfer. Gene 335:73.
27. Jackson, C. A., B. Hoffmann, N. Slakeski, S. Cleal, A. J. Hendtlass, and E. C. Reynolds. 2000. A consensus Porphyromonas gingivalis promoter sequence. FEMS Microbiol. Lett. 186:133-138.
28. Kempf, M. J., and M. J. McBride. 2000. Transposon insertions in the Flavobacterium johnsoniae ftsX gene disrupt gliding motility and cell division. J. Bacteriol. 182:1671-1679.
29. Kill, K., T. T. Binnewies, T. Sicheritz-Ponten, H. Willenbrock, P. F. Hallin, T. M. Wassenaar, and D. W. Ussery. 2005. Genome update: sigma factors in 240 bacterial genomes. Microbiology 151:3147-3150.
30. Kirchman, D. L. 2002. The ecology of Cytophaga-Flavobacteria in aquatic environments. FEMS Microbiol. Ecol. 39:91-100.
31. Kirchman, D. L., L. V. Yu, and M. T. Cottrell. 2003. Diversity and abundance of uncultured Cytophaga-like bacteria in the Delaware Estuary. Appl. Environ. Microbiol. 69:6587-6596.
32. Kuwahara, T., A. Yamashita, H. Hirakawa, H. Nakayama, H. Toh, N. Okada, S. Kuhara, M. Hattori, T. Hayashi, and Y. Ohnishi. 2004. Genomic analysis of Bacteroides fragilis reveals extensive DNA inversions regulating cell surface adaptation. Proc. Natl. Acad. Sci. USA 101:14919-14924.
33. Kuznedelov, K., L. Minakhin, A. Niedziela-Majka, S. L. Dove, D. Rogulja, B. E. Nickels, A. Hochschild, T. Heyduk, and K. Severinov. 2002. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295:855-857.
34. Liu, M., M. Tolstorukov, V. Zhurkin, S. Garges, and S. Adhya. 2004. A mutant spacer sequence between -35 and -10 elements makes the Plac promoter hyperactive and cAMP receptor protein-independent. Proc. Natl. Acad. Sci. USA 101:6911-6916.
35. MacLellan, S. R., A. M. MacLean, and T. M. Finan. 2006. Promoter pre-diction in the rhizobia. Microbiology 152:1751-1763.
36. Malakooti, J., S. P. Wang, and B. Ely. 1995. A consensus promoter sequence for Caulobacter crescentus genes involved in biosynthetic and housekeeping functions. J. Bacteriol. 177:4372-4376.
37. Manch-Citron, J. N., P. J. Shahani, and R. Schneider. 2001. Cloning, characterization, and possible origin of the Prevotella loescheii dnaK homolog. Curr. Microbiol. 42:82-88.
38. McBride, M. J., and T. F. Braun. 2004. GldI is a lipoprotein that is required for Flavobacterium johnsoniae gliding motility and chitin utilization. J. Bacteriol. 186:2295-2302.
39. McBride, M. J., T. F. Braun, and J. L. Brust. 2003. Flavobacterium johnsoniae GldH is a lipoprotein that is required for gliding motility and chitin utilization. J. Bacteriol. 185:6648-6657.
40. McBride, M. J., and M. J. Kempf. 1996. Development of techniques for the genetic manipulation of the gliding bacterium Cytophaga johnsonae. J. Bacteriol. 178:583-590.
41. Nelson, S. S., and M. J. McBride. 2006. Mutations in Flavobacterium johnsoniae secDF result in defects in gliding motility and chitin utilization. J. Bacteriol. 188:348-351.
42. Nematollahi, A., A. Decostere, F. Pasmans, and F. Haesebrouck. 2003. Flavobacterium psychrophilum infections in salmonid fish. J. Fish Dis. 26:563-574.
43. Nishikawa, K., F. Yoshimura, and M. J. Duncan. 2004. A regulation cascade controls expression of Porphyromonas gingivalis fimbriae via the FimR response regulator. Mol. Microbiol. 54:546-560.
44. Patek, M., B. J. Eikmanns, J. Patek, and H. Sahm. 1996. Promoters from Corynebacterium glutamicum: cloning, molecular analysis and search for a consensus motif. Microbiology 142:1297-1309.
45. 28-dependent flagellar gene transcription hierarchy of Vibrio cholerae. Mol. Microbiol. 39:1595-1609.
46. Ross, W., and R. L. Gourse. 2005. Sequence-independent upstream DNA-αCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc. Natl. Acad. Sci. USA 102:291-296.
47. Ross, W., D. A. Schneider, B. J. Paul, A. Mertens, and R. L. Gourse. 2003. An intersubunit contact stimulating transcription initiation by E. coli RNA polymerase: interaction of the alpha C-terminal domain and sigma region 4. Genes Dev. 17:1293-1307.
48. Sambrook, J., E. F. Fritsch, and T. Maniatis. 1989. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
49. Smith, C. J., M. B. Rogers, and M. L. McKee. 1992. Heterologous gene expression in Bacteroides fragilis. Plasmid 27:141-154.
50. Strohl, W. R. 1992. Compilation and analysis of DNA sequences associated with apparent Streptomycete promoters. Nucleic Acids Res. 20:961-974.
51. Su, H. S., Z. Q. Shao, L. Tkalec, F. Blain, and J. Zimmermann. 2001. Development of a genetic system for the transfer of DNA into Flavobacterium heparinum. Microbiology 147:581-589.
52. s promoter selectivity in Escherichia coli. Mol. Microbiol. 59:1037-1051.
53. van Helden, J. 2003. Regulatory sequence analysis tools. Nucleic Acids Res. 31:3593-3596.
54. van Veen, L., J. Nieuwenhuizen, D. Mekkes, M. Vrljenhoek, and P. van Empel. 2005. Diagnosis and incidence of Ornithobacterium rhinotracheale infections in commercial broiler chickens at slaughter. Vet. Rec. 156:315-317.
55. Vingadassalom, D., A. Kolb, C. Mayer, T. Rybkine, E. Collatz, and I. Podglajen. 2005. An unusual primary sigma factor in the Bacteroidetes phylum. Mol. Microbiol. 56:888-902.
56. Warne, S. E., and P. L. deHaseth. 1993. Promoter recognition by Escherichia coil RNA polymerase. Effects of single base pair deletions and insertions in the spacer DNA separating the -10 and -35 regions are dependent on spacer DNA sequence. Biochemistry 32:6134-6140.
57. Whitehead, T. R. 1997. Development of a bifunctional xylosidase/arabinosidase gene as a reporter gene for the gram-negative anaerobes Bacteroides and Porphyromonas, and Escherichia coli. Curr. Microbiol. 35:282-286.
58. Wösten, M., M. Boeve, M. G. A. Koot, A. C. van Nuenen, and B. A. M. van der Zeijst. 1998. Identification of Campylobacter jejuni promoter sequences. J. Bacteriol. 180:594-599.
59. Wösten, M. M. S. M. 1998. Eubacterial sigma-factors. FEMS Microbiol. Rev. 22:127-150.
60. Xie, H., W. O. Chung, Y. Park, and R. J. Lamont. 2000. Regulation of the Porphyromonas gingivalis fimA (fimbrillin) gene. Infect. Immun. 68:6574-6579.