Structural basis for transcription regulation by alarmone ppGpp

Cell

Volumn 117, Issue 3, 2004, Pages 299-310

  Artsimovitch, Irina ^a   Patlan, Vsevolod ^b   Sekine, Shun Ichi ^b   Vassylyeva, Marina N ^b,c   Hosaka, Takeshi ^d   Ochi, Kozo ^d   Yokoyama, Shigeyuki ^b,c,e   Vassylyev, Dmitry G ^b  

^a OHIO STATE UNIVERSITY   (United States)

^b RIKEN HARIMA INSTITUTE   (Japan)

^c RIKEN YOKOHAMA INSTITUTE   (Japan)

^d NATIONAL FOOD RESEARCH INSTITUTE   (Japan)

^e UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

GUANOSINE 3' DIPHOSPHATE 5' DIPHOSPHATE; RNA POLYMERASE;

ARTICLE; CONTROLLED STUDY; ENZYME BINDING; GENE CONTROL; GENETIC TRANSCRIPTION; MOLECULAR DYNAMICS; NONHUMAN; PRIORITY JOURNAL; THERMUS THERMOPHILUS;

BACTERIA (MICROORGANISMS); NEGIBACTERIA; THERMUS; THERMUS THERMOPHILUS;

EID: 2042475439     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0092-8674(04)00401-5     Document Type: Article

References (50)

1. Aivazashvili V.A., Bibilashvili R.S., Vartikian R.M., Kutateladze T.V. Mol. Biol. (Mosk.). 15:1981;653-667
2. Artsimovitch I., Landick R. Pausing by bacterial RNA polymerase is mediated by mechanistically distinct classes of signals. Proc. Natl. Acad. Sci. USA. 97:2000;7090-7095
3. Artsimovitch I., Landick R. The transcriptional regulator RfaH stimulates RNA chain synthesis after recruitment to elongation complexes by the exposed nontemplate DNA strand. Cell. 109:2002;193-203
4. Artsimovitch I., Svetlov V., Murakami K.S., Landick R. Co-overexpression of Escherichia coli RNA polymerase subunits allows isolation and analysis of mutant enzymes lacking lineage-specific sequence insertions. J. Biol. Chem. 278:2003;12344-12355
5. Barker M.M., Gaal T., Gourse R.L. Mechanism of regulation of transcription initiation by ppGpp. II. Models for positive control based on properties of RNAP mutants and competition for RNAP. J. Mol. Biol. 305:2001;689-702. a
6. Barker M.M., Gaal T., Josaitis C.A., Gourse R.L. Mechanism of regulation of transcription initiation by ppGpp. I. Effects of ppGpp on transcription initiation in vivo and in vitro. J. Mol. Biol. 305:2001;673-688. b
7. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S., et al. Crystallography & NMR system. A new software suite for macromolecular structure determination Acta Crystallogr. D. 54:1998;905-921
8. Cashel M., Gentry D.R., Hernandez V.H., Vinella D. The stringent response. Neidhart F.C. Escherichia coli and Salmonella. 1996;1458-1496 ASM Press, Washington, D.C.
9. Chatterji D., Fujita N., Ishihama A. The mediator for stringent control, ppGpp, binds to the beta-subunit of Escherichia coli RNA polymerase. Genes Cells. 3:1998;279-287
10. Choy H.E. The study of guanosine 5′-diphosphate 3′-diphosphate-mediated transcription regulation in vitro using a coupled transcription-translation system. J. Biol. Chem. 275:2000;6783-6789
11. Cramer P., Bushnell D.A., Kornberg R.D. Structural basis of transcription. RNA polymerase II at 2.8 angstrom resolution Science. 292:2001;1863-1876
12. Da Costa X.J., Artz S.W. Mutations that render the promoter of the histidine operon of Salmonella typhimurium insensitive to nutrient-rich medium repression and amino acid downshift. J. Bacteriol. 179:1997;5211-5217
13. Doublie S., Tabor S., Long A.M., Richardson C.C., Ellenberger T. Crystal structure of a bacteriophage T7 DNA replication complex at 2.2 A resolution. Nature. 391:1998;251-258
14. Esnouf R.M. Further additions to MolScript version 1.4, including reading and contouring of electron-density maps. Acta Crystallogr. D. 55:1999;938-940
15. Figueroa-Bossi N., Guerin M., Rahmouni R., Leng M., Bossi L. The supercoiling sensitivity of a bacterial tRNA promoter parallels its responsiveness to stringent control. EMBO J. 17:1998;2359-2367
16. Gentry D.R., Hernandez V.J., Nguyen L.H., Jensen D.B., Cashel M. Synthesis of the stationary-phase sigma factor sigma s is positively regulated by ppGpp. J. Bacteriol. 175:1993;7982-7989
17. Gnatt A.L., Cramer P., Fu J., Bushnell D.A., Kornberg R.D. Structural basis of transcription. an RNA polymerase II elongation complex at 3.3 A resolution Science. 292:2001;1876-1882
18. Jishage M., Kvint K., Shingler V., Nystrom T. Regulation of sigma factor competition by the alarmone ppGpp. Genes Dev. 16:2002;1260-1270
19. Jones T.A., Zou J.Y., Cowan S.W., Kjeldgaard Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr. A. 47:1991;110-119
20. Jores L., Wagner R. Essential steps in the ppGpp-dependent regulation of bacterial ribosomal RNA promoters can be explained by substrate competition. J. Biol. Chem. 278:2003;16834-16843
21. Kaplan W., Littlejohn T.G. Swiss-PDB viewer (deep view). Brief. Bioinform. 2:2001;195-197
22. Kraulis P.J. Molscript. a program to produce both detailed and schematic plots of protein structures J. Appl. Crystallogr. 24:1991;946-950
23. Krohn M., Wagner R. Transcriptional pausing of RNA polymerase in the presence of guanosine tetraphosphate depends on the promoter and gene sequence. J. Biol. Chem. 271:1996;23884-23894
24. Lamond A.I., Travers A.A. Genetically separable functional elements mediate the optimal expression and stringent regulation of a bacterial tRNA gene. Cell. 40:1985;319-326
25. Laurie A.D., Bernardo L.M., Sze C.C., Skarfstad E., Szalewska-Palasz A., Nystrom T., Shingler V. The role of the alarmone (p)ppGpp in sigma N competition for core RNA polymerase. J. Biol. Chem. 278:2003;1494-1503
26. McGlynn P., Lloyd R.G. Modulation of RNA polymerase by (p)ppGpp reveals a RecG-dependent mechanism for replication fork progression. Cell. 101:2000;35-45
27. Mekler V., Kortkhonjia E., Mukhopadhyay J., Knight J., Revyakin A., Kapanidis A.N., Niu W., Ebright Y.W., Levy R., Ebright R.H. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108:2002;599-614
28. Merrit E.A., Bacon D.J. Raster3D. photorealistic molecular graphics Methods Enzymol. 277:1997;505-524
29. Mizushima-Sugano J., Kaziro Y. Regulation of the expression of the tufB operon. DNA sequences directly involved in the stringent control EMBO J. 4:1985;1053-1058
30. Oki T., Yoshimoto A., Sato S., Takamatsu A. Purine nucleotide pyrophosphotransferase from Streptomyces morookaensis, capable of synthesizing pppApp and pppGpp. Biochim. Biophys. Acta. 410:1975;262-272
31. Otwinowski Z., Minor W. Processing X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326
32. Park J.W., Jung Y., Lee S.J., Jin D.J., Lee Y. Alteration of stringent response of the Escherichia coli rnpB promoter by mutations in the -35 region. Biochem. Biophys. Res. Commun. 290:2002;1183-1187
33. Potrykus K., Wegrzyn G., Hernandez V.J. Multiple mechanisms of transcription inhibition by ppGpp at the lambdap(R) promoter. J. Biol. Chem. 277:2002;43785-43791. a
34. Potrykus K., Wegrzyn G., Hernandez V.J. Multiple mechanisms of transcription inhibition by ppGpp at the lambdap(R) promoter. J. Biol. Chem. 277:2002;43785-43791. b
35. Sosunov V., Sosunova E., Mustaev A., Bass I., Nikiforov V., Goldfarb A. Unified two-metal mechanism of RNA synthesis and degradation by RNA polymerase. EMBO J. 22:2003;2234-2244
36. Steitz T.A. A mechanism for all polymerases. Nature. 391:1998;231-232
37. Steitz T.A., Steitz J.A. A general two-metal-ion mechanism for catalytic RNA. Proc. Natl. Acad. Sci. USA. 90:1993;6498-6502
38. Tahirov T.H., Temiakov D., Anikin M., Patlan V., McAllister W.T., Vassylyev D.G., Yokoyama S. Structure of a T7 RNA polymerase elongation complex at 2.9 A resolution. Nature. 420:2002;43-50
39. Toulokhonov I.I., Shulgina I., Hernandez V.J. Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta′-subunit. J. Biol. Chem. 276:2001;1220-1225
40. Travers A.A. ppApp alters transcriptional selectivity of Escherichia coli RNA polymerase. FEBS Lett. 94:1978;345-348
41. Travers A.A. Conserved features of coordinately regulated E. coli promoters. Nucleic Acids Res. 12:1984;2605-2618
42. Vassylyev D.G., Sekine S., Laptenko O., Lee J., Vassylyeva M.N., Borukhov S., Yokoyama S. Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution. Nature. 417:2002;712-719
43. Vassylyeva M.N., Lee J., Sekine S.I., Laptenko O., Kuramitsu S., Shibata T., Inoue Y., Borukhov S., Vassylyev D.G., Yokoyama S. Purification, crystallization and initial crystallographic analysis of RNA polymerase holoenzyme from Thermus thermophilus. Acta Crystallogr. D. 58:2002;1497-1500
44. Vogel U., Jensen K.F. Effects of guanosine 3′, 5′- bisdiphosphate (ppGpp) on rate of transcription elongation in isoleucine-starved Escherichia coli. J. Biol. Chem. 269:1994;16236-16241
45. Wagner R. Regulation of ribosomal RNA synthesis in E. coli. effects of the global regulator guanosine tetraphosphate (ppGpp) J. Mol. Microbiol. Biotechnol. 4:2002;331-340
46. Werner F., Weinzierl R.O. A recombinant RNA polymerase II-like enzyme capable of promoter-specific transcription. Mol. Cell. 10:2002;635-646
47. Yin Y.W., Steitz T.A. Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase. Science. 298:2002;1387-1395
48. Zacharias M., Goringer H.U., Wagner R. Influence of the GCGC discriminator motif introduced into the ribosomal RNA P2- and tac promoter on growth-rate control and stringent sensitivity. EMBO J. 8:1989;3357-3363
49. Zacharias M., Goringer H.U., Wagner R. The signal for growth rate control and stringent sensitivity in E. coli is not restricted to a particular sequence motif within the promoter region. Nucleic Acids Res. 18:1990;6271-6275
50. Zhang G., Campbell E.A., Minakhin L., Richter C., Severinov K., Darst S.A. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 A resolution. Cell. 98:1999;811-824