Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes

EMBO Journal

Volumn 19, Issue 12, 2000, Pages 3038-3048

  Wigneshweraraj, Siva R ^a   Fujita, Nobuyuki ^b   Ishihama, Akira ^b   Buck, Martin ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

^b NATIONAL INSTITUTE OF GENETICS   (Japan)

Author keywords

Enhancers; Protein footprinting; RNA polymerase; factors

Indexed keywords

AMINO ACID; HOLOENZYME; IRON CHELATE; PROTEIN SUBUNIT; RNA POLYMERASE;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENETIC TRANSCRIPTION; NONHUMAN; PRIORITY JOURNAL; PROTEIN QUATERNARY STRUCTURE; SEQUENCE ANALYSIS; SITE DIRECTED MUTAGENESIS; STRUCTURE ACTIVITY RELATION;

NEGIBACTERIA;

EID: 0034660249     PISSN: 02614189     EISSN: None     Source Type: Journal    
DOI: 10.1093/emboj/19.12.3038     Document Type: Article

References (53)

1. 70 binding site on the N-terminus of the Escherichia coli RNA polymerase β′ subunit. J. Biol. Chem., 273, 31381-31387.
2. Cannon, W., Claverie-Martin, F., Austin, S. and Buck, M. (1994) Identification of a DNA-contacting surface in the transcription factor σ-54. Mol. Microbiol., 11, 227-236.
3. Cannon, W., Missailidis, S., Smith, C., Cottier, A., Austin, S., Moore, M. and Buck, M. (1995) Core RNA polymerase and promoter DNA interactions of purified domains of sigma N: bipartite functions. J. Mol. Biol. 248, 781-803.
4. 54) cooperate for DNA binding. Proc. Natl Acad. Sci. USA, 94, 5006-5011.
5. 54) inhibit RNA polymerase isomerization. Genes Dev., 13, 357-370.
6. N protease sensitivity. Proc. Natl Acad. Sci. USA, 94, 12145-12150.
7. 54 within the holoenzyme. J. Mol. Biol., 285, 507-514.
8. 54 N-terminal sequences identifies regions involved in positive and negative regulation of transcription. J. Mol. Biol., 292, 229-239.
9. 54 DNA-binding domain includes a determinant of enhancer responsiveness. Mol. Microbiol., 33, 1200-1209.
10. Claverie-Martin, F. and Magasanik, B. (1992) Positive and negative effects of DNA berding on activation of transcription from a distant site. J. Mol. Biol., 227, 996-1008.
11. 54. Mol. Microbiol., 5, 1309-1317.
12. 54 from gram-negative bacteria. Proc. Natl Acad. Sci. USA, 88, 9092-9096.
13. Fujita, N., Nomura, T. and Ishihama, A. (1987) Promoter selectivity of Escherichia coli RNA polymerase. Purification and properties of holoenzyme containing the heat-shock σ subunit. J. Biol. Chem., 262, 1855-1859.
14. N determining holoenzyme formation and properties. J. Mol. Biol., 288, 539-553.
15. 54 region I required for binding to early melted DNA and their involvement in σ-DNA interactions. J. Mol. Biol., 297, 849-859.
16. 54 region I in trans and implications for transcription activation. J. Biol. Chem., 274, 25285-25290.
17. Grachev, M.A., Lukhtanov, E.A., Mustaev, A.A., Zaychikov, E.F., Abdukayumov, M.N., Rabinov, I.V., Richter, V.I., Skoblov, Y.S. and Chistyakov, P.G. (1989) Studies of the functional topography of Escherichia coli RNA polymerase. A method for localization of the sites of affinity labelling. Eur. J. Biochem., 180, 577-585.
18. 70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting. Proc. Natl Acad. Sci. USA. 93, 71-75.
19. Greiner, D.P., Miyake, R., Moran, J.K., Jones, A.D., Negishi, T., Ishihama, A. and Meares, C.F. (1997) Synthesis of the protein cutting reagent iron (S)-l(p-bromoacetamidobenzyl)-ethylenediaminetetra-acetate and conjugation to cysteine side chains. Bioconj. Chem., 8, 44-48.
20. Gross, C.A., Chan, C., Dombroski, A., Gruber, T., Sharp, M., Tupy, J. and Young, B. (1998) The functional and regulatory roles of σ factors in transcription. Cold Spring Harb. Symp. Quant. Biol., 63, 141-155.
21. 54 as deduced from libraries of mutations. J. Bacteriol., 179, 1239-1245.
22. Guo, Y., Wang, L. and Gralla, J.D. (1999) A fork junction DNA-binding switch that controls promoter melting by the bacterial enhancer-dependent σ factor. EMBO J., 18, 3736-3745.
23. 54. J. Mol. Biol., 239, 15-24.
24. 54. J. Biol. Chem., 269, 373-378.
25. Ishihama, A. (2000) Molecular anatomy of RNA polymerase using protein-conjugated metal probes with nuclease and protease activities. Chem. Commun., in press.
26. Jacobson, G.R., Schaffer, M.H., Stark, G.R. and Vanaman, T.C. (1973) Specific chemical cleavage in high yield at the amino peptide bonds of cysteine and cystine residues. J. Biol. Chem., 248, 6583-6591.
27. Jishage, M. and Ishihama, A. (1997) Variation in RNA polymerase σ subunit composition within different stocks of Escherichia coli W3110. J. Bacteriol., 179, 959-963.
28. Jovanovic, G., Weiner, L. and Model, P. (1996) Identification, nucleotide sequence and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J. Bacteriol., 178, 1936-1945.
29. Katayama, A., Fujita, N. and Ishihama, A. (2000) Mapping of subunit-subunit contact surfaces on the β′ subunit of Escherichia coli RNA polymerase. J. Biol. Chem., 275, 3583-3592.
30. 38 holoenzymes. Effect of DNA supercoiling. J. Biol. Chem., 271, 1998-2004.
31. Leary, B.A., Ward-Rainey, N. and Hoover, T.R. (1998) Cloning and characterization of Planctomyces limnophilus rpoN: complementation of a Salmonella typhimurium rpoN mutant strain. Gene, 221, 151-157.
32. Luo, J., Sharif, K.A., Jin, R., Fujita, N., Ishihama, A. and Krakow, J.S. (1996) Molecular anatomy of the β′ subunit of the E.coli RNA polymerase: identification of regions involved in polymerase assembly. Genes Cells, 1, 819-827.
33. N). Mol. Microbiol., 10, 903-909.
34. 54 is involved in recognition of the -13 promoter region. J. Bacteriol., 174, 7221-7226.
35. Miyake, R., Murakami, K., Owens, J.T., Greiner, D.P., Ozoline, O.N., Ishihama, A. and Meares, C.F. (1998) Dimeric association of Escherichia coli RNA polymerase α subunits, studied by cleavage of single-cysteine α subunits conjugated to iron-(S)-l-[p-(bromoacetamido)benzyl]ethylenediaminetetraacetate. Biochemistry, 37, 1344-1349.
36. Mustaev, A., Kozlov, M., Markovtsov, V., Zaychikov, E., Denissova, L. and Goldfarb, A. (1997) Modular organization of the catalytic center of RNA polymerase. Proc. Natl Acad. Sci. USA, 94, 6641-6645.
37. 70-conjugated chemical protease. Proc. Natl Acad. Sci. USA, 95, 6021-6026.
38. Parvari, R., Pecht, I. and Soreq, H. (1983) A microfluorometric assay for cholinesterases, suitable for multiple kinetic determinations of picomoles of released thiocholine. Anal. Biochem., 133, 450-456.
39. Rana, T.M. and Meares, C.F. (1991) Transfer of oxygen from an artificial protease to peptide carbon during proteolysis. Proc. Natl Acad. Sci. USA, 88, 10578-10582.
40. 54. Cell, 62, 945-954.
41. Sharp, M.M., Chan, C.L., Lu, C.Z., Marr, M.T., Nechaev, S., Merritt, E.W., Severinov, K., Roberts, J.W. and Gross, C.A. (1999) The interface of σ with core RNA polymerase is extensive, conserved and functionally specialized. Genes Dev., 13, 3015-3026.
42. 54 transcription factor revealed by X-ray solution scattering. J. Biol. Chem., 275, 4210-4214.
43. 54. Mol. Microbiol., 23, 987-995.
44. 54 required for enhancer responsiveness. J. Bacteriol., 180, 5619-5625.
45. N plays a role in promoter recognition. Mol. Microbiol., 22, 1045-1054.
46. 70 homology region. J. Bacteriol., 177, 5818-5825.
47. Traviglia, S.L., Datwyler, S.A., Van, D., Ishihama, A. and Meares, C.F. (1999) Targeted protein footprinting: where different transcription factors bind to RNA polymerase. Biochemistry, 38, 15774-15778.
48. 54. Science, 270, 992-994.
49. 54 RNA polymerase: roles for DNA and protein determinants. Proc. Natl Acad. Sci. USA, 94, 9538-9543.
50. Weiss, D.S., Batut, J., Klose, K.E., Keener, J. and Kustu, S. (1991) The phosphorylated form of the enhancer-binding protein NTRC has an ATPase activity that is essential for activation of transcription. Cell, 67, 155-167.
51. 54 as determined by analysis of a set of deletion mutants. J. Mol. Biol., 236, 81-90.
52. Zaychikov, E. et al. (1996) Mapping of catalytic residues in the RNA polymerase active center. Science, 273, 107-109.
53. Zhang, G., Campbell, E.A., Minakhin, L., Richter, C., Severinov, K. and Darst, S.A. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell, 98, 811-824.