Crystal Structure of the Escherichia coli Regulator of σ70, Rsd, in Complex with σ70 Domain 4

Journal of Molecular Biology

Volumn 372, Issue 3, 2007, Pages 649-659

  Patikoglou, Georgia A ^a   Westblade, Lars F ^a   Campbell, Elizabeth A ^a   Lamour, Valérie ^a   Lane, William J ^a   Darst, Seth A ^a  

^a ROCKEFELLER UNIVERSITY   (United States)

Author keywords

RNA polymerase; Rsd; sigma factor; transcription regulation; X ray crystallography

Indexed keywords

PROTEIN ALGQ; PROTEIN OMEGA 70; PROTEIN RSD; REGULATOR PROTEIN; RNA POLYMERASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL VIRULENCE; BINDING SITE; COMPLEX FORMATION; CRYSTAL STRUCTURE; ESCHERICHIA COLI; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN BINDING; PROTEIN DOMAIN; PROTEIN INTERACTION; PSEUDOMONAS AERUGINOSA; RESIDUE ANALYSIS; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI; PSEUDOMONAS AERUGINOSA;

EID: 34548153206     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2007.06.081     Document Type: Article

References (47)

1. Murakami K., and Darst S.A. Bacterial RNA polymerases: the wholo story. Curr. Opin. Struct. Biol. 13 (2003) 31-39
2. 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 Harbor Symp. Quant. Biol. 63 (1998) 141-155
3. Maeda H., Fujita N., and Ishihama A. Competition among seven Escherichia coli sigma subunits: relative binding affinities to the core RNA polymerase. Nucl. Acids Res. 28 (2000) 3497-3503
4. Jishage M., and Ishihama A. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of sigma 70 and sigma 38. J. Bacteriol. 177 (1995) 6832-6835
5. Jishage M., and Ishihama A. A stationary phase protein in Escherichia coli with binding activity to the major sigma subunit of RNA polymerase. Proc. Natl Acad. Sci. USA 95 (1998) 4953-4958
6. Jishage M., and Ishihama A. Transcriptional organization and in vivo role of the Escherichia coli rsd gene, encoding the regulator of RNA polymerase sigma D. J. Bacteriol. 181 (1999) 3768-3776
7. Jishage M., Kvint K., Shingler V., and Nystrom T. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev. 16 (2002) 1260-1270
8. Laurie A.D., Bernardo L.M., Sze C.C., Skarfstad E., Szalewska-Palasz A., Nystrom T., and Shingler V. The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase. J. Biol. Chem. 278 (2003) 1494-1503
9. Mitchell J.E., Oshima T., Piper S.E., Webster C.L., Westblade L.F., Karimova G., et al. The Escherichia coli regulator of sigma 70 protein, Rsd, can up-regulate some stress-dependent promoters by sequestering sigma 70. J. Bacteriol. 189 (2007) 3489-3495
10. Westblade L.F., Ilag L.L., Powell A.K., Kolb A., Robinson C.V., and Busby S.J.W. Studies of the Escherichia coli Rsd-sigma 70 complex. J. Mol. Biol. 335 (2004) 685-692
11. Dove S.L., and Hochschild A. Bacterial two-hybrid analysis of interactions between region 4 of the sigma 70 subunit of RNA polymerase and transcriptional regulators Rsd from Escherichia coli and AlgQ from Pseudomonas aeruginosa. J. Bacteriol. 183 (2001) 6413-6421
12. Jishage M., Dasgupta D., and Ishihama A. Mapping of the Rsd contact site on the sigma 70 subunit of Escherichia coli RNA polymerase. J. Bacteriol. 183 (2001) 2952-2956
13. Campbell E.A., Muzzin O., Chlenov M., Sun J.L., Olson C.A., Weinman O., et al. Structure of the bacterial RNA polymerase promoter specificity sigma factor. Mol. Cell 9 (2002) 527-539
14. Geszvain K., Gruber T.M., Mooney R.A., Gross C. A., and Landick R. A hydrophobic patch on the flap-tip helix of E. coli RNA polymerase mediates sigma 70 region 4 function. J. Mol. Biol. 343 (2004) 569-587
15. Kuznedelov K., Minakhin L., Niedziela-Majka A., Dove S.L., Rogulja D., Nickels B.E., et al. A role for interaction of the RNA polymerase flap domain with the sigma subunit in promoter recognition. Science 295 (2002) 855-857
16. Murakami K., Masuda S., and Darst S.A. Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 Å resolution. Science 296 (2002) 1280-1284
17. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., and Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 Å resolution. Nature 417 (2002) 712-719
18. Ambrosi C., Tiburzi F., Imperi F., Putignani L., and Visca P. Involvement of AlgQ in transcriptional regulation of pyoverdine genes in Pseudomonas aeruginosa PAO1. J. Bacteriol. 187 (2005) 5097-5107
19. Deretic K., and Konyecsni W.M. Control of mucoidy in Pseudomonas aeruginosa: transcriptional regulation of algR and identification of the second regulatory gene, algQ. J. Bacteriol. 171 (1989) 3680-3688
20. Kato J.L., Chiu L., Kitano K., DeVault J.D., Kimbara K., Chakrabarty A.M., and Misra T.K. Nucleotide sequence of a regulatory region controlling alginate synthesis in Pseudomonas aeruginosa: characterization of the algR2 gene. Gene 84 (1989) 31-38
21. Cacalano G., Kays M., Saiman L., and Prince A. Production of the Pseudomonas aeruginosa neuraminidase is increased under hyperosmolar conditions and is regulated by genes involved in alginate expression. J. Clin. Invest. 89 (1992) 1866-1874
22. Schlictman D., Kubo M., Shankar S., and Chakrabarty A.M. Regulation of nucleoside diphosphate kinase and secretable virulence factors in Pseudomonas aeruginosa: roles of algR2 and algH. J. Bacteriol. 177 (1995) 2469-2474
23. Severinova E., Severinov K., Fenyö D., Marr M., Brody E.N., Roberts J.W., et al. Domain organization of the Escherichia coli RNA polymerase sigma 70 subunit. J. Mol. Biol. 263 (1996) 637-647
24. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science 254 (1991) 51-58
25. Bakolitsa C., Cohen D.M., Bankston L.A., Bobkov A.A., Cadwell G.W., Jennings L., et al. Structural basis for vinculin activation at sites of cell adhesion. Nature 430 (2004) 583-586
26. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
27. Campbell E.A., Tupy J.L., Gruber T.M., Wang S., Sharp M.M., Gross C.A., and Darst S.A. Crystal structure of Escherichia coli sigma E with the cytoplasmic domain of its anti-sigma RseA. Mol. Cell 11 (2003) 1067-1078
28. 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 factor in an inactive conformation. Mol. Cell 14 (2004) 127-138
29. Lambert L.J., Wei Y., Schirf V., Demeler B., and Werner M.H. T4 AsiA blocks DNA recognition by remodeling sigma 70 region 4. EMBO J. 23 (2004) 2952-292
30. Pineda M., Gregory B.D., Szczypinski B., Baxter K. R., Hochschild A., Miller E.S., and Hinton D.M. A family of anti-sigma70 proteins in T4-type phages and bacteria that are similar to AsiA, a transcription inhibitor and co-activator of bacteriophage T4. J. Mol. Biol. 344 (2004) 1183-1197
31. Urbauer J.L., Simeonov M.F., Urbauer R.J., Adelman K., Gilmore J.M., and Brody E.N. Solution structure and stability of the anti-sigma factor AsiA: implications for novel functions. Proc. Natl Acad. Sci. USA 99 (2002) 1831-1835
32. Sharp M.M., Chan C.L., Lu C.Z., Marr M.T., Nechaev S., Merritt E.W., et al. The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes Dev. 13 (1999) 3015-3026
33. Gregory B.D., Nickels B.E., Garrity S.J., Severinova E., Minakhin L., Urbauer R.J., et al. A regulator that inhibits transcription by targeting a intersubunit interaction of the RNA polymerase holoenzyme. Proc. Natl Acad. Sci. USA 101 (2004) 4554-4559
34. 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
35. Gardella T., Moyle T., 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
36. Gregory B.D., Nickels B.E., Darst S.A., and Hochschild A. An altered-specificity DNA-binding mutant of Escherichia coli sigma 70 facilitates the analysis of sigma 70 function in vivo. J. Mol. Biol. 56 (2005) 1208-1219
37. Arifuzzaman M., Maeda M., Itoh A., Nishikata K., Takit C., Saito R., et al. Large-scale identification of protein-protein interactions of Escherichia coli K-12. Genome Res. 16 (2006) 686-691
38. Ilag L.L., Westblade L.F., Deshayes C., Kolb A., Busby S.J.W., and Robinson C.V. Mass spectrometry of Escherichia coli RNA polymerase: interactions of the core enzyme with sigma 70 and Rsd protein. Structure 12 (2004) 269-275
39. Campbell E.A., and Darst S.A. The anti-sigma factor SpoIIAB forms a 2:1 complex with sigma F, contacting multiple conserved regions of the sigma factor. J. Mol. Biol. 300 (2000) 17-28
40. Doublie S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276 (1997) 523-530
41. Weeks C.M., and Miller R. The design and implementation of SnB v2.0. J. Appl. Crystallog. 32 (1999) 120-124
42. de La Fortelle E., Irwin J.J., and Bricogne G. SHARP: a maximum-likelihood heavy-atom parameter refinement and phasing program for the MIR and MAD methods. In: Bourne P., and Watenpaugh K. (Eds). Crystallographic Computing vol. 7 (1997), Oxford University Press, Oxford, U.K 1-9
43. Abrahams J.P., and Leslie A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallog. sect. D 52 (1996) 30-42
44. Jones T.A., Zou J.-Y., Cowan S., and Kjeldgaard M. Improved methods for building protein models in electron denstiy maps and the location of errors in these models. Acta Crystallog. sect. A 47 (1991) 110-119
45. Adams P.D., Pannu N.S., Read R.J., and Brunger A.T. Cross-validated maximum likelihood enhances crystallographic simulated annealing refinement. Proc. Natl Acad. Sci. USA 94 (1997) 5018-5023
46. Laskowski R.A., MacArthur M.W., Moss D.S., and Thornton J.M. PROCHECK - A program to check the stereochemical quality of protein structures. J. Appl. Crystallog. 26 (1993) 283-291
47. Wallace A.C., Laskowski R.A., and Thornton J.M. LIGPLOT: a program to generate schematic diagrams of protein-ligand interactions. Protein Eng. 8 (1995) 127-134