Domain architectures of σ54-dependent transcriptional activators

Journal of Bacteriology

Volumn 185, Issue 6, 2003, Pages 1757-1767

  Studholme, David J ^a   Dixon, Ray ^b  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b JOHN INNES CENTRE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; BACTERIAL PROTEIN; RNA POLYMERASE; SIGMA FACTOR; SIGMA FACTOR RPON; UNCLASSIFIED DRUG; DNA BINDING PROTEIN; DNA DIRECTED RNA POLYMERASE; TRANSACTIVATOR PROTEIN;

AMINO ACID SEQUENCE; BACTERIAL GENETICS; BACTERIAL GENOME; GENETIC TRANSCRIPTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; SHORT SURVEY; SIGNAL TRANSDUCTION; TRANSCRIPTION INITIATION; TRANSCRIPTION REGULATION; BACTERIUM; CHEMISTRY; CLASSIFICATION; ENHANCER REGION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGY; REVIEW;

BACTERIA (MICROORGANISMS);

BACTERIA; BACTERIAL PROTEINS; DNA-BINDING PROTEINS; DNA-DIRECTED RNA POLYMERASES; ENHANCER ELEMENTS (GENETICS); GENE EXPRESSION REGULATION, BACTERIAL; PHYLOGENY; RNA POLYMERASE SIGMA 54; SIGMA FACTOR; SIGNAL TRANSDUCTION; TRANS-ACTIVATORS; TRANSCRIPTION, GENETIC;

EID: 0037332383     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.185.6.1757-1767.2003     Document Type: Short Survey

References (74)

1. Alm, R. A., L. S. Ling, D. T. Moir, B. L. King, E. D. Brown, P. C. Doig, D. R. Smith, B. Noonan, B. C. Guild, B. L. deJonge, G. Carmel, P. J. Tummino, A. Caruso, M. Uria-Nickelsen, D. M. Mills, C. Ives, R. Gibson, D. Merberg, S. D. Mills, Q. Jiang, D. E. Taylor, G. F. Vovis, and T. J. Trust. 1999. Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori. Nature 397:176-180.
2. Anantharaman, V., E. V. Koonin, and L. Aravind. 2001. Regulatory potential, phyletic distribution and evolution of ancient, intracellular small-molecule-binding domains. J. Mol. Biol. 307:1271-1292.
3. Aravind, L., and C. P. Ponting. 1997, The GAF domain: an evolutionary link between diverse phototransducing proteins. Trends Biochem. Sci. 22:458-459.
4. Aravind, L., and E. V. Koonin. 1999. Gleaning non-trivial structural, functional and evolutionary information about proteins by iterative database searches. J. Mol. Biol. 287:1023-1040.
5. Barrett, J., P. Ray, and A. Sobczyk, 2001. Concerted inhibition of the transcriptional activation functions of the enhancer-binding protein NIFA by the anti-activator NIFL. Mol. Microbiol. 39:480-494.
6. 54-dependent promoter sequences. Nucleic Acids Res. 27:4305-4313.
7. Bateman, A. 1997. The structure of a domain common to archaebacteria and the homocystinuria disease protein. Trends Biochem. Sci. 22:12-13.
8. Bateman, A., E. Birney, L. Cerruti, R. Durbin, L. Etwiller, S. R. Eddy, S. Griffiths-Jones, K. L. Howe, M. Marshall, and E. L. Sonnhammer. 2002. The Pfam protein families database. Nucleic Acids Res. 30:276-280.
9. Blattner, F. R., G. Plunkett III, C. A. Bloch, N. T. Perna, V. Burland, M. Riley, J. Collado-Vides, J. D. Glasner, C. K. Rode, G. F. Mayhew, J. Gregor, N. W. Davis, H. A. Kirkpatrick, M. A. Goeden, D. J. Rose, B. Mau, and Y. Shao. 1997. The complete genome sequence of Escherichia coil K-12. Science 277:1453-1474.
10. Bowman, W. C., and R. G. Kranz. 1998. A bacterial ATP-dependent, enhancer binding protein that activates the housekeeping RNA polymerase. Genes Dev. 12:1884-1893.
11. N) transcription factor. J. Bacteriol. 182:4129-4136.
12. Charbonneau, H., R. K. Prusti, H. LeTrong, W. K. Sonnenburg, P. J. Mullaney, K. A. Walsh, and J. A. Beavo. 1990. Identification of a noncatalytic cGMP-binding domain conserved in both the cGMP-stimulated and photoreceptor cyclic nucleotide phosphodiesterases. Proc. Natl. Acad. Sci. USA 87:288-292.
13. 54 dependent PTS permease of the mannose family is responsible for sensitivity of Listeria monocytogenes to mesentericin Y105. Microbiology 147:3263-3269.
14. Darwin, A. J., and V. L. Miller. 2001. The psp locus of Yersinia enterocolitica is required for virulence and for growth in vitro when the Ysc type III secretion system is produced. Mol. Microbiol. 39:429-444.
15. Debarbouille, M., R. Gardan, M. Arnaud, and G. Rapoport. 1999. Role of bkdR, a transcriptional activator of the sigL-dependent isoleucine and valine degradation pathway in Bacillus subtilis. J. Bacteriol. 181:2059-2066.
16. Deng, W., V. Burland, G. Plunkett III, A. Boutin, G. F. Mayhew, P. Liss, N. T. Perna, D. J. Rose, B. Mau, S. Zhou, D. C. Schwartz, J. D. Fetherston, L. E. Lindler, R. R. Brubaker, G. V. Piano, S. C. Straley, K. A. McDonough, M. L. Nilles, J. S. Matson, F. R. Blattner, and R. D. Perry. 2002. Genome sequence of Yersinia pestis KIM. J. Bacteriol. 184:4601-4611.
17. Devos, D., J. Garmendia, V. de Lorenzo, and A. Valencia. 2002. Deciphering the action of aromatic effectors on the prokaryotic enhancer-binding protein XylR: a structural model of its N-terminal domain. Environ. Microbiol. 4:29-41.
18. Dixon, M. P., R. N. Pau, G. J. Howlett, D. E. Dunstan, W. H. Sawyer, and B. E. Davidson. 2002. The central domain of Escherichia coli TyrR is responsible for hexamerization associated with tyrosine-mediated repression of gene expression. J. Biol. Chem. 277:23186-23192.
19. Elderkin, S., S. Jones, J. Schumacher, D. Studholme, and M. Buck. 2002. Mechanism of action of the Escherichia coli phage shock protein PspA in repression of the AAA family transcription factor PspF. J. Mol. Biol. 320: 23-37.
20. 54 subunit in Helicobacter pylori. J. Infect. Chemother. 7:148-155.
21. Gardner, A. M., R. A. Helmick, and, P. R. Gardner. 2002. Favorubredoxin, an inducible catalyst for nitric oxide reduction and detoxification in Escherichia coli. J. Biol. Chem. 277:8172-8177.
22. González, V., L Olvera, X. Soberon, and E. Morett. 1998. In vivo studies on the positive control function of NifA: a conserved hydrophobic amino acid patch at the central domain involved in transcriptional activation. Mol. Microbiol. 28:55-67.
23. Hayashi, T., K. Makino, M. Ohnishi, K. Kurokawa, K. Ishii, K. Yokoyama, C. G. Han, E. Ohtsubo, K. Nakayama, T. Murata, M. Tanaka, T. Tobe, T. Iida, H. Takami, T. Honda, C. Sasakawa, N. Ogasawara, T. Yasunaga, S. Kuhara, T. Shiba, M. Hattori, and H. Shinagawa. 2001. Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12. DNA Res. 8:11-22.
24. Ho, Y. S., L. M. Burden, and J. H. Hurley. 2000. Structure of the GAF domain, a ubiquitous signaling motif and a new class of cyclic GMP receptor. EMBO J. 19:5288-5299.
25. Hoch, J. A. 2000. Two-component and phosphorelay signal transduction. Curr. Opin. Microbiol. 3:165-170.
26. Hopper, S., and A. Bock. 1995. Effector-mediated stimulation of ATPase activity by the sigma 54-dependent transcriptional activator FHLA from Escherichia coli. J. Bacteriol. 177:2798-2803.
27. Hubner, A., X. Yang, D. M. Nolen, T. G. Popova, F. C. Cabello, and M. V. Norgard. 2001. Expression of Borrelia burgdorferi OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway. Proc. Natl. Acad. Sci. USA 98:12724-12729.
28. Hutchings, M. I., N. Mandhana, and S. Spiro. 2002. The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive nitrogen species. J. Bacteriol. 184:4640-4643.
29. Jin, Q., Z. Yuan, J. Xu, Y. Wang, Y. Shen, W. Lu, J. Wang, H. Liu, J. Yang, F. Yang, X. Zhang, J. Zhang, G. Yang, H. Wu, D. Qu, J. Dong, L Sun, Y. Xue, A. Zhao, Y. Gao, J. Zhu, B. Kan, K. Ding, S. Chen, H. Cheng, Z. Yao, B. He, R. Chen, D. Ma, B. Qiang, Y. Wen, Y. Hou, and J. Yu. 2002. Genome sequence of Shigella flexneri 2a: insights into pathogenicity through comparison with genomes of Escherichia coli K12 and O157. Nucleic Acids Res. 30:4432-4441.
30. Jyot, J., N. Dasgupta, and R. Ramphal. 2002. FleQ, the major flagellar gene regulator in Pseudomonas aeruginosa, binds to enhancer sites located either upstream or atypically downstream of the RpoN binding site. J. Bacteriol. 184:5251-5260.
31. Kabisch, U. C. 2001. Ph.D. thesis. Proteinchemische und molekularbiologische Charakterisierung der D-Prolin-Reduktase aus Clostridium sticklandii. Martin-Luther-Universität Halle-Wittenberg, Halle, Germany.
32. Kabisch, U. C., A. Grantzdorffer, A. Schierhorn, K. P. Rucknagel, J. R. Andreesen, and A. Pich. 1999. Identification of D-proline reductase from Clostridium sticklandii as a selenoenzyme and indications for a catalytically active pyruvoyl group derived from a cysteine residue by cleavage of a proprotein. J. Biol. Chem. 274:8445-8454.
33. Kalman, S., W. Mitchell, R. Marathe, C. Lammel, J. Fan, R. W. Hyman, L. Olinger, J. Grimwood, R. W. Davis, and R. S. Stephens. 1999. Comparative genomes of Chlamydia pneumoniae and C. trachomatis. Nat. Genet. 21:385-389.
34. Kapatral, V., I. Anderson, N. Ivanova, G. Reznik, T. Los, A. Lykidis, A. Bhattacharyya, W. Bartman, G. Gardner, G. Grechkin, L. Zhu, O. Vasieva, L. Chu, Y. Kogan, O. Chaga, E. Goltsman, A. Bernal, N. Larsen, M. D'Souza, T. Walunas, G. Pusch, R. Haselkorn, M. Fonstein, N. Kyrpides, and R. Overbeek. 2002. Genome sequence and analysis of the oral bacterium Fusobacterium nucleatum strain ATCC 25586. J. Bacteriol. 184:2005-2018.
35. 54. J. Bacteriol. 179:4647-4653.
36. Little, R., V. Colombo, A. Leech, and R. Dixon. 2002. Direct interaction of the NifL regulatory protein with the GlnK signal transducer enables the Azotobacter vinelandii NifL-NifA regulatory system to respond to conditions replete for nitrogen. J. Biol. Chem. 277:15472-15481.
37. Little, R., S. Perry, V. Colombo, et al. 2002. Integration of nitrogen, oxygen and redox status by the Azotobacter vinelandii regulatory complex, p. 238-242. In T. Finan, M. O'Brian, D. Layzell, et al. (ed.), Nitrogen fixation: global perspectives. CABI International, Wallingford, United Kingdom.
38. Little, R., F. Reyes-Ramirez, Y. Zhang, W. C. van Heeswijk, and R. Dixon. 2000. Signal transduction to the Azotobacter vinelandii NIFL-NIFA regulatory system is influenced directly by interaction with 2-oxoglutarate and the PII regulatory protein. EMBO J. 19:6041-6050.
39. Maloy, S. R., and W. D. Nunn. 1982. Genetic regulation of the glyoxylate shunt in Escherichia coli K-12. J. Bacteriol. 149:173-180.
40. Martin-Verstraete, I., V. Charrier, J. Stulke, A. Galinier, B. Erni, G. Rapoport, and J. Deutscher. 1998. Antagonistic effects of dual PTS-catalysed phosphorylation on the Bacillus subtilis transcriptional activator LevR. Mol. Microbiol. 28:293-303.
41. Mathews, S. A., and P. Timms. 2000. Identification and mapping of sigma-54 promoters in Chlamydia trachomatis. J. Bacteriol. 182:6239-6242.
42. N). Mol. Microbiol. 10:903-909.
43. Money, T., J. Barrett, R. Dixon, and S. Austin. 2001. Protein-protein interactions in the complex between the enhancer binding protein NIFA and the sensor NIFL from Azotobacter vinelandii. J. Bacteriol. 183:1359-1368.
44. Morett, E., and L. Segovia. 1993. The sigma 54 bacterial enhancer-binding protein family: mechanism of action and phylogenetic relationship of their functional domains. J. Bacteriol. 175:6067-6074.
45. Neuwald, A. F., L. Aravind, J. L. Spouge, and E. V. Koonin. 1999. AAA+: a class of chaperone-like ATPases associated with the assembly, operation, and disassembly of protein complexes. Genome Res. 9:27-43.
46. Parkhill, J., B. W. Wren, N. R. Thomson, R. W. Titball, M. T. Holden, M. B. Prentice, M. Sebaihia, K. D. James, C. Churcher, K. L. Mungall, S. Baker, D. Basham, S. D. Bentley, K. Brooks, A. M. Cerdeno-Tarraga, T. Chillingworth, A. Cronin, R. M. Davies, P. Davis, G. Dougan, T. Feltwell, N. Hamlin, S. Holroyd, K. Jagels, A. V. Karlyshev, S. Leather, S. Moule, P. C. Oyston, M. Quail, K. Rutherford, M. Simmonds, J. Skelton, K. Stevens, S. Whitehead, and B. G. Barrell. 2001. Genome sequence of Yersinia pestis, the causative agent of plague. Nature 413:523-527.
47. Pelton, J. G., S. Kustu, and D. E. Wemmer. 1999. Solution structure of the DNA-binding domain of NtrC with three alanine substitutions. J. Mol. Biol. 292:1095-1110.
48. Pittard, A. J., and B. E. Davidson. 1991. TyrR protein of Escherichia coli and its role as repressor and activator. Mol. Microbiol. 5:1585-1592.
49. Ponting, C. P., and L. Aravind. 1997. PAS: a multifunctional domain family comes to light. Curr. Biol. 7:R674-R677.
50. Postma, P. W., J. W. Lengeler, and G. R. Jacobson. 1993. Phosphoenolpyruvate:carbohydrate phosphotransferase systems of bacteria. Microbiol. Rev. 57:543-594.
51. Rabinovich, E., A. Kerem, K. U. Frohlich, N. Diamant, and S. Bar-Nun. 2002. AAA-ATPase p97/Cdc48p, a cytosolic chaperone required for endoplasmic reticulum-associated protein degradation. Mol. Cell. Biol. 22:626-634.
52. Ray, P., K. J. Smith, R. A. Parslow, R. Dixon, and E. I. Hyde. 2002. Secondary structure and DNA binding by the C-terminal domain of the transcriptional activator NifA from Klebsiella pneumoniae. Nucleic Acids Res. 30: 3972-3980.
53. 54-dependent genes in Escherichia coli. Microbiol. Mol. Biol. Rev. 65:422-444.
54. Reizer, J., and M. H. Saier, Jr. 1997. Modular multidomain phosphoryl transfer proteins of bacteria. Curr. Opin. Struct. Biol. 7:407-415.
55. Reyes-Ramirez, F., R. Little, and R. Dixon. 2001. Role of Escherichia coli nitrogen regulatory genes in the nitrogen response of the Azotobacter vinelandii NifL-NifA complex. J. Bacteriol. 183:3076-3082.
56. Rombel, I., A. North, I. Hwang, C. Wyman, and S. Kustu. 1998. The bacterial enhancer-binding protein NtrC as a molecular machine. Cold Spring Harbor Symp. Quant. Biol. 63:157-166.
57. Rudnick, P., C. Kunz, M. K. Gunatilaka, E. R. Hines, and C. Kennedy. 2002. Role of GlnK in NifL-mediated regulation of NifA activity in Azotobacter vinelandii. J. Bacteriol. 184:812-820.
58. Saier, M. H., Jr., and J. Reizer. 1994. The bacterial phosphotransferase system: new frontiers 30 years later. Mol. Microbiol. 13:755-764.
59. Song, J., and R. A. Jensen. 1996. PhhR, a divergently transcribed activator of the phenylalanine hydroxylase gene cluster of Pseudomonas aeruginosa. Mol. Microbiol. 22:497-507.
60. Souza, E. M., F. O. Pedrosa, M. Drummond, L. U. Rigo, and M. G. Yates. 1999. Control of Herbaspirillum seropedicae NifA activity by ammonium ions and oxygen. J. Bacteriol. 181:681-684.
61. Spohn, G., and V. Scarlato. 1999. Motility of Helicobacter pylori is coordinately regulated by the transcriptional activator FlgR, an NtrC homolog. J. Bacteriol. 181:593-599.
62. Stock, A. M., V. L. Robinson, and, P. N. Goudreau. 2000. Two-component signal transduction. Annu. Rev. Biochem. 69:183-215.
63. N regulon inferred from protein sequence homology and predicted promoter sites. J. Mol. Microbiol. Biotechnol. 4:367-374.
64. Studholme, D. J., and M. Buck. 2000. The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiol. Lett. 186:1-9.
65. 54) and a NifA-like protein from the hyperthermophile Aquifex aeolicus. J. Bacteriol. 182:1616-1623.
66. Taylor, B. L., and I. B. Zhulin. 1999. PAS domains: internal sensors of oxygen, redox potential, and light. Microbiol. Mol. Biol. Rev. 6:479-506.
67. Tchieu, J. H., V. Norris, J. S. Edwards, and M. H. Saier, Jr. 2001. The complete phosphotransferase system in Escherichia coli. J. Mol. Microbiol. Biotechnol. 3:329-346.
68. Tomb, J. F., O. White, A. R. Kerlavage, R. A. Clayton, G. G. Sutton, R. D. Fleischmann, K. A. Ketchum, H. P. Klenk, S. Gill, B. A. Dougherty, K. Nelson, J. Quackenbush, L. Zhou, E. F. Kirkness, S. Peterson, B. Loftus, D. Richardson, R. Dodson, H. G. Khalak, A. Glodek, K. McKenney, L. M. Fitzegerald, N. Lee, M. D. Adams, J. C. Venter, et al. 1997. The complete genome sequence of the gastric pathogen Helicobacter pylori. Nature 388: 539-547.
69. van Tilbeurgh, H., and N. Declerck. 2001. Structural insights into the regulation of bacterial signalling proteins containing PRDs. Curr. Opin. Struct. Biol. 11:685-693.
70. 54-dependent activator DctD is involved in both binding to RNA polymerase and coupling ATP hydrolysis to activation. Mol. Microbiol. 26:373-386.
71. Wilson, T. J., P. Maroudas, G. J. Howlett, and B. E. Davidson. 1994. Ligand-induced self-association of the Escherichia coli regulatory protein TyrR. J. Mol. Biol. 238:309-318.
72. Xu, H., and T. R. Hoover. 2001. Transcriptional regulation at a distance in bacteria. Curr. Opin. Microbiol. 4:138-144.
73. Zhang, X., M. Chaney, S. R. Wigneshweraraj, J. Schumacher, P. Bordes, W. Cannon, and M. Buck. 2002. Mechanochemical ATPases and transcriptional activation. Mol. Microbiol. 45:895-903.
74. Zhulin, I. B., B. L. Taylor, and R. Dixon. 1997. PAS domain S-boxes in Archaea, Bacteria and sensors for oxygen and redox. Trends Biochem. Sci. 22:331-333.