Additional determinants within Escherichia coli FNR activating region 1 and RNA polymerase α subunit required for transcription activation

Journal of Bacteriology

Volumn 187, Issue 5, 2005, Pages 1724-1731

  Weber, K Derek ^a   Vincent, Owen D ^a   Kiley, Patricia J ^a,b  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

^b NONE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALANINE; AMINO ACID; DNA BINDING PROTEIN; PROTEIN FNR; RNA POLYMERASE; SERINE; UNCLASSIFIED DRUG;

ALPHA CHAIN; ANAEROBIC METABOLISM; ARTICLE; CARBOXY TERMINAL SEQUENCE; CONTROLLED STUDY; ESCHERICHIA COLI; GENETIC TRANSCRIPTION; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DOMAIN; PROTEIN PROTEIN INTERACTION; SITE DIRECTED MUTAGENESIS; TRANSCRIPTION INITIATION;

ALANINE; AMINO ACID SEQUENCE; DNA-DIRECTED RNA POLYMERASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENE EXPRESSION REGULATION, BACTERIAL; IRON-SULFUR PROTEINS; MUTAGENESIS, SITE-DIRECTED; PROMOTER REGIONS (GENETICS); PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; SEQUENCE HOMOLOGY, AMINO ACID; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 14244253987     PISSN: 00219193     EISSN: None     Source Type: Journal    
DOI: 10.1128/JB.187.5.1724-1731.2005     Document Type: Article

References (36)

1. Aiyar, S. E., S. M. McLeod, W. Ross, C. A. Hirvonen, M. S. Thomas, R. C. Johnson, and R. L. Course. 2002. Architecture of Fis-activated transcription complexes at the Escherichia coli rrnB P1 and rrnE P1 promoters. J. Mol. Biol. 316:501-516.
2. Barnard, A. M., G. S. Lloyd, J. Green, S. J. Busby, and D. J. Lee. 2004. Location of the Escherichia coli RNA polymerase alpha subunit C-terminal domain at an FNR-dependent promoter: analysis using an artificial nuclease. FEBS Lett. 558:13-18.
3. Bell, A., and S. Busby. 1994. Location and orientation of an activating region in the Escherichia coli transcription factor, FNR. Mol. Microbiol. 11:383-390.
4. Benoff, B., H. Yang, C. L. Lawson, G. Parkinson, J. Liu, E. Blatter, Y. W. Ebright, H. M. Herman, and R. H. Ebright. 2002. Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science 297:1562-1566.
5. Blake, T., A. Barnard, S. J. Busby, and J. Green. 2002. Transcription activation by FNR: evidence for a functional activating region 2. J. Bacteriol. 184:5855-5861.
6. Browning, D., D. Lee, and S. Busby. 2002. Secrets of bacterial transcription initiation taught by the Escherichia coli FNR protein, p. 127-142. In D. Hodgson and C. Thomas (ed.), Signals, switches, regulons, and cascades. Cambridge University Press, Cambridge, United Kingdom.
7. Chang, A. C., and S. N. Cohen. 1978. Construction and characterization of amplifiable multicopy DNA cloning vehicles derived from the P15A cryptic miniplasmid. J. Bacteriol. 134:1141-1156.
8. Erickson, J. W., and C. A. Gross. 1989. Identification of the sigma E subunit of Escherichia coli RNA polymerase: a second alternate sigma factor involved in high-temperature gene expression. Genes Dev. 3:1462-1471.
9. Green, J., A. S. Irvine, W. Meng, and J. R. Guest. 1996. FNR-DNA interactions at natural and semi-synthetic promoters. Mol. Microbiol. 19:125-137.
10. Green, J., and F. A. Marshall. 1999. Identification of a surface of FNR overlapping activating region 1 that is required for repression of gene expression. J. Biol. Chem. 274:10244-10248.
11. He, Y., T. Gaal, R. Karls, T. J. Donohue, R. L. Course, and G. P. Roberts. 1999. Transcription activation by CooA, the CO-sensing factor from Rhodospirillum rubrum. The interaction between CooA and the C-terminal domain of the alpha subunit of RNA polymerase. J. Biol. Chem. 274:10840-10845.
12. Kang, Y., K. D. Weber, Y. Qui, P. J. Kiley, and F. R. Blattner. 2005. Genomewide expression analysis indicates that FNR of Escherichia coli K-12 regulates a large number of genes of unknown function. J. Bacteriol. 87: 1135-1160.
13. Korner, H., H. J. Sofia, and W. G. Zumft. 2003. Phytogeny of the bacterial superfamiiy of Crp-Fnr transcription regulators: exploiting the metabolic spectrum by controlling alternative gene programs. FEMS Microbiol. Rev. 27:559-592.
14. Lamberg, K. E., and P. J. Kiley. 2000. FNR-dependent activation of the class II dmsA and narG promoters of Escherichia coli requires FNR-activating regions 1 and 3. Mol. Microbiol. 38:817-827.
15. Lamberg, K. E., C. Luther, K. D. Weber, and P. J. Kiley. 2002. Characterization of activating region 3 from Escherichia coli FNR. J. Mol. Biol. 315: 275-283.
16. Lazazzera, B. A., D. M. Bates, and P. J. Kiley. 1993. The activity of the Escherichia coli transcription factor FNR is regulated by a change in oligomeric state. Genes Dev. 7:1993-2005.
17. Lazazzera, B. A., H. Beinert, N. Khoroshilova, M. C. Kennedy, and P. J. Kiley. 1996. DNA binding and dimerization of the Fe-S-containing FNR protein from Escherichia coli are regulated by oxygen. J. Biol. Chem. 271: 2762-2768.
18. Lee, D. J., S. J. Busby, and G. S. Lloyd. 2003. Exploitation of a chemical nuclease to investigate the location and orientation of the Escherichia coli RNA polymerase alpha subunit C-terminal domains at simple promoters that are activated by cyclic AMP receptor protein. J. Biol. Chem. 278:52944-52952.
19. Lee, D. J., H. J. Wing, N. J. Savery, and S. J. Busby. 2000. Analysis of interactions between Activating Region 1 of Escherichia coli FNR protein and the C-terminal domain of the RNA polymerase alpha subunit: use of alanine scanning and suppression genetics. Mol. Microbiol. 37:1032-1040.
20. Li, B., H. Wing, D. Lee, H. C. Wu, and S. Busby. 1998. Transcription activation by Escherichia coli FNR protein: similarities to, and differences from, the CRP paradigm. Nucleic Acids Res. 26:2075-2081.
21. Lloyd, G., P. Landini, and S. Busby. 2001. Activation and repression of transcription initiation in bacteria. Essays Biochem. 37:17-31.
22. Lombardo, M. J., D. Bagga, and C. G. Miller. 1991. Mutations in rpoA affect expression of anaerobically regulated genes in Salmonella lyphimurium. J. Bacteriol. 173:7511-7518.
23. Lonetto, M. A., V. Rhodius, K. Lamberg, P. Kiley, S. Busby, and C. Gross. 1998. Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase sigma70 subunit. J. Mol. Biol. 284:1353-1365.
24. Miller, J. 1972. Experiments in molecular genetics, p. 48. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
25. Niu, W., Y. Zhou, Q. Dong, Y. W. Ebright, and R. H. Ebright. 1994. Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). I. Saturation and alanine-scanning mutagenesis. J. Mol. Biol. 243:595-602.
26. Rhodius, V. A., D. M. West, C. L. Webster, S. J. Busby, and N. J. Savery. 1997. Transcription activation at class II CRP-dependent promoters: the role of different activating regions. Nucleic Acids Res. 25:326-332.
27. Savery, N. J., G. S. Lloyd, S. J. Busby, M. S. Thomas, R. H. Ebright, and R. L. Gourse. 2002. Determinants of the C-terminal domain of the Escherichia coli RNA polymerase alpha subunit important for transcription at class I cyclic AMP receptor protein-dependent promoters. J. Bacteriol. 184:2273-2280.
28. Savery, N. J., G. S. Lloyd, M. Kainz, T. Gaal, W. Ross, R. H. Ebright, R. L. Course, and S. J. Busby. 1998. Transcription activation at Class II CRP-dependent promoters: identification of determinants in the C-terminal domain of the RNA polymerase alpha subunit. EMBO J. 17:3439-3447.
29. Sutton, V. R., and P. J. Kiley. 2003. Techniques for studying the oxygen-sensitive transcription factor FNR from Escherichia coli. Methods Enzymol. 370:300-312.
30. Weber, I. T., and T. A. Steitz. 1987. Structure of a complex of catabolite gene activator protein and cyclic AMP refined at 2.5 A resolutioin. J. Mol. Biol. 198:311-326.
31. Williams, R., A. Bell, G. Sims, and S. Busby. 1991. The role of two surface exposed loops in transcription activation by the Escherichia coli CRP and FNR proteins. Nucleic Acids Res. 19:6705-6712.
32. Williams, S. M., N. J. Savery, S. J. Busby, and H. J. Wing. 1997. Transcription activation at class I FNR-dependent promoters: identification of the activating surface of FNR and the corresponding contact site in the C-terminal domain of the RNA polymerase alpha subunit. Nucleic Acids Res. 25:4028-4034.
33. Wing, H. J., J. Green, J. R. Guest, and S. J. Busby. 2000. Role of activating region 1 of Escherichia coli FNR protein in transcription activation at class II promoters. J. Biol. Chem. 275:29061-29065.
34. Wing, H. J., S. M. Williams, and S. J. Busby. 1995. Spacing requirements for transcription activation by Escherichia coli FNR protein. J. Bacteriol. 177: 6704-6710.
35. Zhou, Y., T. J. Merkel, and R. H. Ebright. 1994. Characterization of the activating region of Escherichia coli catabolite gene activator protein (CAP). II. Role at class I and class II CAP-dependent promoters. J. Mol. Biol. 243:603-610.
36. Ziegelhoffer, E. C., and P. J. Kiley. 1995. In vitro analysis of a constitutively active mutant form of the Escherichia coli global transcription factor FNR. J. Mol. Biol. 245:351-361.