Comparison of Bacteroides thetaiotaomicron and Escherichia coli 16S rRNA gene expression signals

References

1. Amann E., Brosius J., Ptashne M. 1983; Vectors bearing a hybrid trp– lac promoter useful for regulated expression of cloned genes in Escherichia coli . Gene 25:167–178
   [Google Scholar]
2. Bayley D. P., Rocha E. R., Smith C. J. 2000; Analysis of cepA and other Bacteroides fragilis genes reveals a unique promoter structure. FEMS Microbiol Lett 193:149–154
   [Google Scholar]
3. Betermier M., Galas D. J., Chandler M. 1994; Interaction of Fis protein with DNA: bending and specificity of binding. Biochimie 76:958–967
   [Google Scholar]
4. Cashel M., Gentry D. R., Hernandez V. H., Vinella D. 1996; The stringent response. In Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology pp 1458–1496 Edited by Neidhardt F. C., Curtis R. III, Ingraham J. L., Lin E. C. C., Low K. B., Magasanik B., Reznikoff W. S., Riley M., Schaechter M., Umbarger H. E. Washington, DC: American Society for Microbiology;
   [Google Scholar]
5. Chatzidaki-Livanis M., Coyne M. J., Roche-Hakansson H., Comstock L. E. 2008; Expression of a uniquely regulated extracellular polysaccharide confers a large-capsule phenotype to Bacteroides fragilis . J Bacteriol 190:1020–1026
   [Google Scholar]
6. Chen S., Bagdasarian M., Kaufman M. G., Bates A. K., Walker E. D. 2007a; Mutational analysis of the ompA promoter from Flavobacterium johnsoniae . J Bacteriol 189:5108–5118
   [Google Scholar]
7. Chen S., Bagdasarian M., Kaufman M. G., Walker E. D. 2007b; Characterization of strong promoters from an environmental Flavobacterium hibernum strain by using a green fluorescent protein-based reporter system. Appl Environ Microbiol 73:1089–1100
   [Google Scholar]
8. Estrem S. T., Gaal T., Ross W., Gourse R. L. 1998; Identification of an UP element consensus sequence for bacterial promoters. Proc Natl Acad Sci U S A 95:9761–9766
   [Google Scholar]
9. Feldhaus M. J., Hwa V., Cheng Q., Salyers A. A. 1991; Use of an Escherichia coli β-glucuronidase gene as a reporter gene for investigation of Bacteroides promoters. J Bacteriol 173:4540–4543
   [Google Scholar]
10. Finney A. H., Blick R. J., Murakami K., Ishihama A., Stevens A. M. 2002; Role of the C-terminal domain of the alpha subunit of RNA polymerase in LuxR-dependent transcriptional activation of the lux operon during quorum sensing. J Bacteriol 184:4520–4528
    [Google Scholar]
11. Gafny R., Cohen S., Nachaliel N., Glaser G. 1994; Isolated P2 rRNA promoters of Escherichia coli are strong promoters that are subject to stringent control. J Mol Biol 243:152–156
    [Google Scholar]
12. Gourse R. L., Gaal T., Bartlett M. S., Appleman J. A., Ross W. 1996; rRNA transcription and growth rate-dependent regulation of ribosome synthesis in Escherichia coli . Annu Rev Microbiol 50:645–677
    [Google Scholar]
13. Graves M. C., Rabinowitz J. C. 1986; In vivo and in vitro transcription of the Clostridium pasteurianum ferredoxin gene. Evidence for “extended” promoter elements in Gram-positive organisms. J Biol Chem 261:11409–11415
    [Google Scholar]
14. Hanahan D. 1983; Studies on transformation of Escherichia coli with plasmids. J Mol Biol 166:557–580
    [Google Scholar]
15. Hawley D. K., McClure W. R. 1983; Compilation and analysis of Escherichia coli promoter DNA sequences. Nucleic Acids Res 11:2237–2255
    [Google Scholar]
16. Helmann J. D. 1995; Compilation and analysis of Bacillus subtilis σ ^A-dependent promoter sequences: evidence for extended contact between RNA polymerase and upstream promoter DNA. Nucleic Acids Res 23:2351–2360
    [Google Scholar]
17. Holdeman L. V., Moore W. E. C. 1975 Anaerobe Laboratory Manual , 4th edn. Blacksburg, VA: Virginia Polytechnic Institute and State University;
    [Google Scholar]
18. Josaitis C. A., Gaal T., Gourse R. L. 1995; Stringent control and growth-rate-dependent control have nonidentical promoter sequence requirements. Proc Natl Acad Sci U S A 92:1117–1121
    [Google Scholar]
19. Krinos C. M., Coyne M. J., Weinacht K. G., Tzianabos A. O., Kasper D. L., Comstock L. E. 2001; Extensive surface diversity of a commensal microorganism by multiple DNA inversions. Nature 414:555–558
    [Google Scholar]
20. Lane D. J. 1991 16S/23S rRNA sequencing, In Nucleic Acid Techniques in Bacterial Systematics pp 115–175 Edited by Stackebrandt E., Goodfellow M. Chichester, New York: Wiley;
    [Google Scholar]
21. Lutz R., Bujard H. 1997; Independent and tight regulation of transcriptional units in Escherichia coli via the LacR/O, the TetR/O and AraC/I₁–I₂ regulatory elements. Nucleic Acids Res 25:1203–1210
    [Google Scholar]
22. Murray H. D., Appleman J. A., Gourse R. L. 2003; Regulation of the Escherichia coli rrnB P2 promoter. J Bacteriol 185:28–34
    [Google Scholar]
23. Ninnemann O., Koch C., Kahmann R. 1992; The E. coli fis promoter is subject to stringent control and autoregulation. EMBO J 11:1075–1083
    [Google Scholar]
24. Pan N., Imlay J. A. 2001; How does oxygen inhibit central metabolism in the obligate anaerobe Bacteroides thetaiotaomicron . Mol Microbiol 39:1562–1571
    [Google Scholar]
25. Phillips-Jones M. K. 1993; Bioluminescence ( lux) expression in the anaerobe Clostridium perfringens . FEMS Microbiol Lett 106:265–270
    [Google Scholar]
26. Rao L., Ross W., Appleman J. A., Gaal T., Leirmo S., Schlax P. J., Record M. T. Jr, Gourse R. L. 1994; Factor independent activation of rrnB P1. An “extended” promoter with an upstream element that dramatically increases promoter strength. J Mol Biol 235:1421–1435
    [Google Scholar]
27. Ringquist S., Shinedling S., Barrick D., Green L., Binkley J., Stormo G. D., Gold L. 1992; Translation initiation in Escherichia coli: sequences within the ribosome-binding site. Mol Microbiol 6:1219–1229
    [Google Scholar]
28. Ross W., Gosink K. K., Salomon J., Igarashi K., Zou C., Ishihama A., Severinov K., Gourse R. L. 1993; A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science 262:1407–1413
    [Google Scholar]
29. Ross W., Aiyar S. E., Salomon J., Gourse R. L. 1998; Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol 180:5375–5383
    [Google Scholar]
30. Sarmientos P., Cashel M. 1983; Carbon starvation and growth rate-dependent regulation of the Escherichia coli ribosomal RNA promoters: differential control of dual promoters. Proc Natl Acad Sci U S A 80:7010–7013
    [Google Scholar]
31. Shoemaker N. B., Getty C., Gardner J. F., Salyers A. A. 1986; Tn 4351 transposes in Bacteroides spp. and mediates the integration of plasmid R751 into the Bacteroides chromosome. J Bacteriol 165:929–936
    [Google Scholar]
32. Shoemaker N. B., Wang G. R., Salyers A. A. 1996; The Bacteroides mobilizable insertion element, NBU1, integrates into the 3′ end of a Leu-tRNA gene and has an integrase that is a member of the lambda integrase family. J Bacteriol 178:3594–3600
    [Google Scholar]
33. Simon R., Priefer U., Puhler A. 1983; A broad host range mobilization system for in vivo genetic engineering: transposon mutagenesis in Gram negative bacteria. Biotechnology (N Y ) 1:784–791
    [Google Scholar]
34. Smith C. J., Rogers M. B., McKee M. L. 1992; Heterologous gene expression in Bacteroides fragilis . Plasmid 27:141–154
    [Google Scholar]
35. Szittner R., Meighen E. 1990; Nucleotide sequence, expression, and properties of luciferase coded by lux genes from a terrestrial bacterium. J Biol Chem 265:16581–16587
    [Google Scholar]
36. Travers A. A. 1984; Conserved features of coordinately regulated E. coli promoters. Nucleic Acids Res 12:2605–2618
    [Google Scholar]
37. Tribble G. D., Parker A. C., Smith C. J. 1999; Genetic structure and transcriptional analysis of a mobilizable, antibiotic resistance transposon from Bacteroides . Plasmid 42:1–12
    [Google Scholar]
38. Valentine P. J., Shoemaker N. B., Salyers A. A. 1988; Mobilization of Bacteroides plasmids by Bacteroides conjugal elements. J Bacteriol 170:1319–1324
    [Google Scholar]
39. Van Dyk T. K., Rosson R. A. 1998; Photorhabdus luminescens luxCDABE promoter probe vectors. Methods Mol Biol 102:85–95
    [Google Scholar]
40. Vingadassalom D., Kolb A., Mayer C., Rybkine T., Collatz E., Podglajen I. 2005; An unusual primary sigma factor in the Bacteroidetes phylum. Mol Microbiol 56:888–902
    [Google Scholar]
41. Vingadassalom D., Kolb A., Mayer C., Collatz E., Podglajen I. 2007; Probing the importance of selected phylum-specific amino acids in σ ^A of Bacteroides fragilis, a primary σ factor naturally devoid of an N-terminal acidic region 1.1. J Biol Chem 282:3442–3449
    [Google Scholar]
42. Weaver R. 1999; The mechanism of translation I: initiation. In Molecular Biology pp 531–564 Boston, MA: McGraw–Hill;
    [Google Scholar]
43. Werner H. 1974; Differentiation and medical importance of saccharolytic intestinal Bacteroides . Arzneimittelforschung 24:340–343
    [Google Scholar]
44. 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
    [Google Scholar]
45. Whittle G., Shoemaker N. B., Salyers A. A. 2002; Characterization of genes involved in modulation of conjugal transfer of the Bacteroides conjugative transposon CTnDOT. J Bacteriol 184:3839–3847
    [Google Scholar]
46. Xu J., Bjursell M. K., Himrod J., Deng S., Carmichael L. K., Chiang H. C., Hooper L. V., Gordon J. I. 2003; A genomic view of the human– Bacteroides thetaiotaomicron symbiosis. Science 299:2074–2076
    [Google Scholar]
47. Yanisch-Perron C., Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119
    [Google Scholar]