A Full-Length Group 1 Bacterial Sigma Factor Adopts a Compact Structure Incompatible with DNA Binding

Chemistry and Biology

Volumn 15, Issue 10, 2008, Pages 1091-1103

  Schwartz, Edmund C ^a   Shekhtman, Alexander ^b   Dutta, Kaushik ^b   Pratt, Matthew R ^a   Cowburn, David ^b   Darst, Seth ^a   Muir, Tom W ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

^b NEW YORK STRUCTURAL BIOLOGY CENTER   (United States)

Author keywords

CHEMBIO; DNA

Indexed keywords

DNA; SIGMA FACTOR;

AMINO ACID SEQUENCE; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; METABOLISM; MOLECULAR GENETICS; NUCLEAR MAGNETIC RESONANCE; PROTEIN BINDING; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; THERMOTOGA MARITIMA;

AMINO ACID SEQUENCE; DNA; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SIGMA FACTOR; THERMOTOGA MARITIMA;

BACTERIA (MICROORGANISMS); THERMOTOGA MARITIMA;

EID: 53649093127     PISSN: 10745521     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chembiol.2008.09.008     Document Type: Article

References (46)

1. Barne K.A., Bown J.A., Busby S.J., and Minchin S.D. Region 2.5 of the Escherichia coli RNA polymerase sigma70 subunit is responsible for the recognition of the 'extended-10' motif at promoters. EMBO J. 16 (1997) 4034-4040
2. Borukhov S., and Nudler E. RNA polymerase holoenzyme: structure, function and biological implications. Curr. Opin. Microbiol. 6 (2003) 93-100
3. 70 affects promoter DNA binding by Escherichia coli RNA polymerase holoenzyme. EMBO J. 18 (1999) 709-716
4. Browning D.F., and Busby S.J. The regulation of bacterial transcription initiation. Nat. Rev. Microbiol. 2 (2004) 57-65
5. Burgess R.R., Travers A.A., Dunn J.J., and Bautz E.K. Factor stimulating transcription by RNA polymerase. Nature 221 (1969) 43-46
6. Callaci S., Heyduk E., and Heyduk T. Core RNA polymerase from E. coli induces a major change in the domain arrangement of the sigma 70 subunit. Mol. Cell 3 (1999) 229-238
7. Camarero J.A., Shekhtman A., Campbell E.A., Chlenov M., Gruber T.M., Bryant D.A., Darst S.A., Cowburn D., and Muir T.W. Autoregulation of a bacterial σ factor explored by using segmental isotopic labeling and NMR. Proc. Natl. Acad. Sci. USA 99 (2002) 8536-8541
8. Campbell E.A., and Darst S.A. Regulation of bacterial transcription by anti-s factors. In: Waksman G., Caparon M., and Hultgren S. (Eds). Structural Biology of Bacterial Pathogenesis (2005), ASM Press, Washington, DC 1-15
9. Campbell E.A., Masuda S., Sun J.L., Muzzin O., Olson C.A., Wang S., and Darst S.A. Crystal structure of the Bacillus stearothermophilus anti-sigma factor SpoIIAB with the sporulation sigma factor sigmaF. Cell 108 (2002) 795-807
10. Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O., Trester-Zedlitz M.L., and Darst S.A. Structure of the bacterial RNA polymerase promoter specificity sigma subunit. Mol. Cell 9 (2002) 527-539
11. E with the cytoplasmic domain of its anti-σ RseA. Mol. Cell 11 (2003) 1067-1078
12. Campbell E.A., Westblade L.F., and Darst S.A. Regulation of bacterial RNA polymerase sigma factor activity: a structural perspective. Curr. Opin. Microbiol. 11 (2008) 121-127
13. Cavanagh J., Fairbrother J.W., Palmer III A.G., and Skelton N.J. Protein NMR Spectroscopy; Principles and Practice. First Edition (1996), Academic Press, San Diego, CA
14. Cornilescu G., Delaglio F., and Bax A. Protein backbone angle restraints from searching a database for chemical shift and sequence homology. J. Biomol. NMR 13 (1999) 289-302
15. Darst S.A. Bacterial RNA polymerase. Curr. Opin. Struct. Biol. 11 (2001) 155-162
16. Dombroski A.J., Walter W.A., Record M.T.J., Siegele D.A., and Gross C.A. Polypeptides containing highly conserved regions of transcription initiation factor sigma-70 exhibit specificity of binding to promoter DNA. Cell 70 (1992) 501-512
17. Dombroski A.J., Walter W.A., and Gross C.A. Amino-terminal amino acids modulate sigma-factor DNA-binding activity. Genes Dev. 7 (1993) 2446-2455
18. Ebright R.H. RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II. J. Mol. Biol. 304 (2000) 687-698
19. Gardella T., Moyle H., and Susskind M.M. A mutant Escherichia coli sigma 70 subunit of RNA polymerase with altered promoter specificity. J. Mol. Biol. 206 (1989) 579-590
20. Gross C.A., Chan C., Dombroski A., Gruber T., Sharp M., Tupy J., and Young B. The functional and regulatory roles of sigma factors in transcription. Cold Spring Harb. Symp. Quant. Biol. 63 (1998) 141-155
21. Gruber T.M., and Gross C.A. Multiple sigma subunits and the partitioning of bacterial transcription space. Annu. Rev. Microbiol. 57 (2003) 441-466
22. Hinton D.M., Vuthoori S., and Mulamba R. The bacteriophage T4 inhibitor and coactivator AsiA inhibits Escherichia coli RNA polymerase more rapidly in the absence of sigma70 region 1.1: evidence that region 1.1 stabilizes the interaction between sigma70 and core. J. Bacteriol. 188 (2006) 1279-1285
23. Holm L., and Sander C. Mapping the protein universe. Science 273 (1996) 595-603
24. Johnson B.A. Using NMRView to visualize and analyze the NMR spectra of macromolecules. Methods Mol. Biol. 278 (2004) 313-352
25. Kobe B., and Kemp B.E. Active site-directed protein regulation. Nature 402 (1999) 373-376
26. Lane W.J., and Darst S.A. The structural basis for promoter -35 element recognition by the group IV sigma factors. PLoS Biol. 4 (2006) e269 10.1371/journal.pbio.0040269 Published online August 15, 2006
27. Laskowski R.A., Rullmannn J.A., MacArthur M.W., Kaptein R., and Thornton J.M. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 8 (1996) 477-486
28. Linge J.P., Habeck M., Rieping W., and Nilges M. ARIA: automated NOE assignment and NMR structure calculation. Bioinformatics 19 (2003) 315-316
29. Malhotra A., Severinova E., and Darst S.A. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87 (1996) 127-136
30. Mekler V., Kortkhonjia E., Mukhopadhyay J., Knight J., Revyakin A., Kapanidis A.N., Niu W., Ebright Y.W., Levy R., and Ebright R.H. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell 108 (2002) 599-614
31. Murakami K.S., and Darst S.A. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13 (2003) 31-39
32. Murakami K.S., Masuda S., Campbell E.A., Muzzin O., and Darst S.A. Structural Basis of Transcription Initiation: An RNA Polymerase Holoenzyme-DNA Complex. Science 296 (2002) 1285-1290
33. Murakami K.S., Masuda S., and Darst S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution. Science 296 (2002) 1280-1284
34. Muralidharan V., and Muir T.W. Protein ligation: an enabling technology for the biophysical analysis of proteins. Nat. Methods 3 (2006) 429-438
35. Nicholls A., Sharp K.A., and Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11 (1991) 281-296
36. Ottesen J.J., Blashke U.K., Cowburn D., and Muir T.W. In: Krishna N.R., and Berliner L.J. (Eds). Biological Magnetic Resonance (2003), Kluwer Academic, New York 35-51
37. Sattler M., Schleucher J., and Griesinger C. Heteronuclear multidimensional NMR experiments for the structure determination of proteins in solution employing pulse field gradients. Prog. Nucl. Magn. Reson. Spectrosc. 34 (1999) 93-158
38. Siegele D.A., Hu J.C., Walter W.A., and Gross C.A. Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J. Mol. Biol. 206 (1989) 591-603
39. Sorenson M.K., and Darst S.A. Disulfide cross-linking indicates that FlgM-bound and free σ28 adopt similar conformations. Proc. Natl. Acad. Sci. USA 103 (2006) 16722-16727
40. Sorenson M.K., Ray S.S., and Darst S.A. Crystal structure of the flagellar sigma/anti-sigma complex sigma-28/FlgM reveals an intact sigma factgor in an inactive conformation. Mol. Cell 14 (2004) 127-138
41. Travers A.A., and Burgess R.R. Cyclic re-use of the RNA polymerase sigma factor. Nature 222 (1969) 537-540
42. Vassylyev D.G., Sekine S.-i., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature 417 (2002) 712-719
43. Vuthoori S., Bowers C.W., McCracken A., Dombroski A.J., and Hinton D.M. Domain 1.1 of the sigma-70 subunit of Escherichia coli RNA polymerase modulates the formation of stable polymerase/promoter complexes. J. Mol. Biol. 309 (2001) 561-572
44. 70 is required for efficient isomerization and initiation of transcription by Escherichia coli RNA polymerase. J. Mol. Biol. 267 (1997) 60-74
45. Wishart D.S., and Sykes B.D. The 13C chemical-shift index: a simple method for the identification of protein secondary structure using 13C chemical-shift data. J. Biomol. NMR 4 (1994) 171-180
46. Yamazaki T., Forman-Kay J.D., and Kay L.E. Two-dimensional NMR experiments for correlating C-13b and H-1d/e chemical shifts of aromatic residues in 13C-labeled proteins via scalar couplings. J. Am. Chem. Soc. 115 (1993) 11054-11055