Identification of promoters recognized by RNA polymerase- σE holoenzyme from Thermus thermophilus HB8

Journal of Bacteriology

Volumn 189, Issue 23, 2007, Pages 8758-8764

  Shinkai, Akeo ^a   Ohbayashi, Naomi ^b   Terada, Takaho ^b   Shirouzu, Mikako ^b   Kuramitsu, Seiki ^a,c   Yokoyama, Shigeyuki ^a,b,d  

^a Harima Institute ^*  (Japan)

^b RIKEN YOKOHAMA INSTITUTE   (Japan)

^c OSAKA UNIVERSITY   (Japan)

^d UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

HOLOENZYME; RNA POLYMERASE; SIGMA FACTOR E; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; BACTERIAL CELL; ENZYME ACTIVITY; MOLECULAR CLONING; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN EXPRESSION; THERMUS THERMOPHILUS;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BASE SEQUENCE; DNA-DIRECTED RNA POLYMERASES; GENE EXPRESSION REGULATION, BACTERIAL; MOLECULAR SEQUENCE DATA; PROMOTER REGIONS (GENETICS); PROTEIN BINDING; SIGMA FACTOR; THERMUS THERMOPHILUS; TRANSCRIPTION FACTORS;

BACTERIA (MICROORGANISMS); THERMUS THERMOPHILUS;

EID: 36749028152     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.01076-07     Document Type: Article

References (32)

1. Bashyam, M. D., and S. E. Hasnain. 2004. The extracytoplasmic function sigma factors: role in bacterial pathogenesis. Infect. Genet. Evol. 4:301-308.
2. Braun, V., and S. Mahren. 2005. Transmembrane transcriptional control (surface signalling) of the Escherichia coli Fec type. FEMS Microbiol. Rev. 29:673-684.
3. Ebright, R. H. 2000. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304:687-698.
4. S RNA polymerase. Mol. Microbiol. 42:939-954.
5. Gross, C. A., C. Chan, A. Dombroski, T. Gruber, M. Sharp, J. Tupy, and B. Young. 1998. The functional and regulatory roles of sigma factors in transcription. Cold Spring Harbor Symp. Quant. Biol. 63:141-155.
6. Gruber, T. M., and C. A. Gross. 2003. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57:441-466.
7. Hashimoto, Y., T. Yano, S. Kuramitsu, and H. Kagamiyama. 2001. Disruption of Thermus thermophilus genes by homologous recombination using a thermostable kanamycin-resistant marker. FEBS Lett. 506:231-234.
8. Helmann, J. D. 1999. Anti-sigma factors. Curr. Opin. Microbiol. 2:135-141.
9. Helmann, J. D. 2002. The extracytoplasmic function (ECF) sigma factors. Adv. Microb. Physiol. 46:47-110.
10. Hughes, K. T., and K. Mathee. 1998. The anti-sigma factors. Annu. Rev. Microbiol. 52:231-286.
11. Kazmierczak, M. J., M. Wiedmann, and K. J. Boor. 2005. Alternative sigma factors and their roles in bacterial virulence. Microbiol. Mol. Biol. Rev. 69:527-543.
12. Kigawa, T., T. Yabuki, N. Matsuda, T. Matsuda, R. Nakajima, A. Tanaka, and S. Yokoyama. 2004. Preparation of Escherichia coli cell extract for highly productive cell-free protein expression. J. Struct. Funct. Genomics 5:63-68.
13. Laemmli, U. K. 1970. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680-685.
14. Lee, P. A., D. Tullman-Ercek, and G. Georgiou. 2006. The bacterial twin-arginine translocation pathway. Annu. Rev. Microbiol. 60:373-395.
15. 70 family: sequence conservation and evolutionary relationships. J. Bacteriol. 174:3843-3849.
16. Lonetto, M. A., K. L. Brown, K. E. Rudd, and M. J. Buttner. 1994. Analysis of the Streptomyces coelicolor sigE gene reveals the existence of a subfamily of eubacterial RNA polymerase sigma factors involved in the regulation of extracytoplasmic functions. Proc. Natl. Acad. Sci. USA 91:7573-7577.
17. Missiakas, D., and S. Raina. 1998. The extracytoplasmic function sigma factors: role and regulation. Mol. Microbiol. 28:1059-1066.
18. Mittenhuber, G. 2002. An inventory of genes encoding RNA polymerase sigma factors in 31 completely sequenced eubacterial genomes. J. Mol. Microbiol. Biotechnol. 4:77-91. (Erratum, 4:514.)
19. Omelchenko, M. V., Y. I. Wolf, E. K. Gaidamakova, V. Y. Matrosova, A. Vasilenko, M. Zhai, M. J. Daly, E. V. Koonin, and K. S. Makarova. 2005. Comparative genomics of Thermus thermophilus and Deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. BMC Evol. Biol. 5:57.
20. Oshima, T., and K. Imabori. 1974. Description of Thermus thermophilus (Yoshida and Oshima) com. nov., a non-sporulating thermophilic bacterium from a Japanese thermal spa. Int. J. Syst. Bacteriol. 24:102-112.
21. Raivio, T. L., and T. J. Silhavy. 2001. Periplasmic stress and ECF sigma factors. Annu. Rev. Microbiol. 55:591-624.
22. Sanger, F., S. Nicklen, and A. R. Coulson. 1977. DNA sequencing with chain-terminating inhibitors. Proc. Natl. Acad. Sci. USA 74:5463-5467.
23. Shinkai, A., S. Kira, N. Nakagawa, A. Kashihara, S. Kuramitsu, and S. Yokoyama. 2007. Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8. J. Bacteriol. 189:3891- 3901.
24. Storey, J. D. 2002. A direct approach to false discovery rates. J. R. Stat. Soc. B 64:479-498.
25. Storey, J. D., and R. Tibshirani. 2003. Statistical significance for genomewide studies. Proc. Natl. Acad. Sci. USA 100:9440-9445.
26. Sweetser, D., M. Nonet, and R. A. Young. 1987. Prokaryotic and eukaryotic RNA polymerases have homologous core subunits. Proc. Natl. Acad. Sci. USA 84:1192-1196.
27. Tatusov, R. L., N. D. Fedorova, J. D. Jackson, A. R. Jacobs, B. Kiryutin, E. V. Koonin, D. M. Krylov, R. Mazumder, S. L. Mekhedov, A. N. Nikolskaya, B. S. Rao, S. Smirnov, A. V. Sverdlov, S. Vasudevan, Y. I. Wolf, J. J. Yin, and D. A. Natale. 2003. The COG database: an updated version includes eukaryotes. BMC Bioinformatics 4:41.
28. Thompson, J. D., D. G. Higgins, and T. J. Gibson. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
29. Vassylyev, D. G., S. Sekine, O. Laptenko, J. Lee, M. N. Vassylyeva, S. Borukhov, and S. Yokoyama. 2002. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417:712-719.
30. Vassylyeva, M. N., J. Lee, S. I. Sekine, O. Laptenko, S. Kuramitsu, T. Shibata, Y. Inoue, S. Borukhov, D. G. Vassylyev, and S. Yokoyama. 2002. Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallogr. D 58: 1497-1500.
31. Wada, T., M. Shirouzu, T. Terada, Y. Ishizuka, T. Matsuda, T. Kigawa, S. Kuramitsu, S. Y. Park, J. R. Tame, and S. Yokoyama. 2003. Structure of a conserved CoA-binding protein synthesized by a cell-free system. Acta Crystallogr. D 59:1213-1218.
32. Wnendt, S., R. K. Hartmann, N. Ulbrich, and V. A. Erdmann. 1990. Isolation and physical properties of the DNA-directed RNA polymerase from Thermus thermophilus HB8. Eur. J. Biochem. 191:467-472.