Activation and repression of E. coli promoters

Current Opinion in Genetics and Development

Volumn 6, Issue 5, 1996, Pages 526-530

  Gralla, Jay D ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIAL DNA; RNA POLYMERASE;

BIOCHEMISTRY; ENHANCER REGION; ENZYME SUBUNIT; ESCHERICHIA COLI; GENE ACTIVATION; GENE REPRESSION; GENETICS; NONHUMAN; PRIORITY JOURNAL; PROMOTER REGION; PROTEIN DNA BINDING; SHORT SURVEY; TRANSCRIPTION INITIATION;

BACTERIA (MICROORGANISMS); ESCHERICHIA COLI;

EID: 0030271631     PISSN: 0959437X     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0959-437X(96)80079-7     Document Type: Article

References (41)

1. Gralla JD, Collado-Vides J. Organization and function of transcription regulatory elements. of outstanding interest Neidhardt F. Escherichia coli and Salmonella. 1996;1232-1246 American Society for Microbiology, Washington.
2. Zhang L, Gralla JD. Micrococcal nuclease as a probe for bound and distorted DNA in lac transcription and repression complexes. Nucleic Acids Res. 17:1989;5017-5028.
3. 70 exhibit specificity of binding to promoter DNA. Cell. 1992;501-512.
4. Ross W, Gosink KK, Salomon J, Igarashi K, Zou C, Ishihama A, Severinov K, Gourse RL. A third recognition element in bacterial promoters: DNA binding by the alpha subunit of RNA polymerase. Science. 262:1993;1407-1413.
5. Ebright RH, Busby S. The Escherichia coli RNA polymerase alpha subunit: structure and function. Curr Opin Genet Dev. 5:1995;197-203.
6. Ishihama A. Protein-protein communication within the transcription apparatus. J Bacteriol. 175:1993;2483-2489.
7. Tao K, Zou C, Fujita N, Ishihama A. Mapping of the OxyR protein contact site in the C-terminal region of RNA polymerase alpha subunit. J Bacteriol. 177:1995;6740-6744.
8. Jeon YH, Negishi T, Shirakawa M, Yamazaki t, Fujita N, Ishihama A, Kyogoku Y. Solution structure of the activator contact domain of the polymerase alpha subunit. of outstanding interest Science. 270:1995;1495-1497 The structure of the polymerase alpha subunit is determined and surfaces that bind CRP and DNA are mapped. The activation and DNA-binding surfaces appear to overlap.
9. Gaal T, Ross W, Blatter EE, Tang H, Jia X, Krishnan VV, Assa-Munt N, Ebright RH, Gourse RL. DNA-binding determinants of the alpha subunit of RNA polymerase: novel DNA-binding domain architecture. of outstanding interest Genes Dev. 10:1996;16-26 The authors detail the structure of the isolated polymerase alpha subunit by NMR and integration with genetics.
10. Chen Y, Ebright YW, Ebright RH. Identification of the target of a transcription activator protein by protein-protein photocrosslinking. Science. 265:1994;90-92.
11. Zhou Y, Merkel TJ, Ebright RH. 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. 243:1994;603-610.
12. Gaston K, Bell A, Kolb A, Buc H, Busby S. Stringent spacing requirements for transcription activation by CRP. Cell. 62:1990;733-743.
13. Tagami H, Aiba H. Role of CRP in transcription activation at Escherichia coli lac promoter: CRP is dispensable after the formation of open complex. of special interest Nucleic Acids Res. 23:1995;599-605 After CRP helps polymerase bind and open the DNA it appears that it is no longer needed for the subsequent steps.
14. Li M, Moyle H, Susskind MM. Target of the transcriptional activation function of phage lambda CI protein. Science. 263:1994;75-77.
15. Makino K, Amemura M, Kim S-K, Nakata A, Shinagawa H. Role of the sigma 70 subunit of RNA polymerase in transcriptional activation by activator protein PhoB in Escherichia coli. Genes Dev. 7:1993;149-160.
16. Kuldell N, Hochschild A. Amino acid substitutions in the -35 recognition motif of sigma 70 that result in defects in phage lambda repressor-stimulated transcription. J Bacteriol. 176:1994;2991-2998.
17. 70 subunit region 4 of Escherichia coli RNA polymerase in transcription initiation and activation. J Mol Biol. 235:1994;405-413.
18. Jin R, Sharif KA, Krakow JS. Evidence for contact between the cyclic AMP receptor protein and the sigma 70 subunit of Escherichia coli RNA polymerase. of outstanding interest J Biol Chem. 270:1995;19213-19216 This shows that CRP protein can crosslink to both the alpha and the sigma 70 subunits of the polymerase, depending on where CRP binds. More than one determinant on CRP is involved.
19. Joung JK, Koepp DM, Hochschild A. Synergistic activation of transcription by bacteriophage lambda cl protein and E. coli cAMP receptor protein. Science. 265:1994;1863-1866.
20. Brody EN, Kassavetis GA, Ouhammouch M, Sanders GM, Tinker RL, Geiduschek EP. Old phage, new insights: two recently recognized mechanisms of transcriptional regulation in bacteriophage T4 development. of outstanding interest FEMS Microbiol Lett. 128:1995;1-8 Contains an overview of the remarkable T4 late transcription system, involving replication-dependent and enhancer-dependent transcription.
21. Wang JT, Syed A, Hsieh M-L, Gralla JD. Converting Escherichia coli RNA polymerase into an enhancer-responsive enzyme - role of an NH2-terminal leucine patch in sigma 54. of outstanding interest Science. 270:1995;992-994 This paper illustrates how a small is essential in allowing sigma 54 to change RNA polymerase into an enzyme that can respond to enhancers. The domain, when mutated, causes polymerase to bypass the need for enhancer in vitro.
22. Hsieh M, Tintut Y, Gralla JD. Functional roles for the glutamines within the glutamine-rich region of the transcription factor sigma 54. J Biol Chem. 269:1994;373-378.
23. Porter SC, North AK, Wedel AB, Kustu S. Oligomerization of NTRC at the glnA enhancer is required for transcriptional activation. Genes Dev. 7:1993;2258-2273.
24. Weiss V, Claverie MF, Magasanik B. Phosphorylation of nitrogen regulator I of Escherichia coli induces strong cooperative binding to DNA essential for activation of transcription. Proc Natl Acad Sci USA. 89:1992;5088-5092.
25. Wedel A, Kustu S. The bacterial enhancer-binding protein NTRC is a molecular machine: ATP hydrolysis is coupled to transcriptional activation. of special interest Genes Dev. 9:1995;2042-2052 A detailed analysis of how NtrC uses ATP hydrolysis to drive melting and activation by the sigma 54 form of polymerase.
26. Hopper S, Bock A. Effector-mediated stimulation of ATPase activity by the sigma 54-dependent transcriptional activator FHLA from Escherichia coli. of special interest J Bacteriol. 177:1995;2798-2803 This paper demonstrates that a sigma 54 enhancer protein assembles into an ATPase as part of its activation function. The signal transduction involves small molecule binding.
27. Su W, Porter S, Kustu S, Echols H. DNA-looping and enhancer activity: association between DNA-bound NTRC activator and RNA polymerase at the bacterial glna promoter. Proc Natl Acad Sci USA. 87:1990;5504-5508.
28. Lee JH, Hoover TR. Protein crosslinking studies suggest that Rhizobium meliloti C4-dicarboxylic acid transport protein D, a sigma 54-dependent transcriptional activator, interacts with sigma 54 and the beta subunit of RNA polymerase. of special interest Proc Natl Acad Sci USA. 92:1995;9702-9706 The only example of crosslinking between sigma 54 polymerase and one of its activators.
29. 54 holoenzyme. J Bacteriol. 175:1993;2479-2482.
30. Sanders GM, Kassavetis GA, Geiduschek EP. Rules governing the efficiency and polarity of loading a tracking clamp protein onto DNA: determinants of enhancement in bacteriophage T4 late transcription. of special interest EMBO J. 14:1995;3966-3976 How enhancer protein is loaded onto DNA in a tracking system.
31. Tinker RL, Kassavetis GA, Geiduschek EP. Detecting the ability of viral, bacterial and eukaryotic replication proteins to track along DNA. EMBO J. 13:1994;5330-5337.
32. Herendeen DR, Kassavetis GA, Geiduschek EP. A transcriptional enhancer whose function imposes a requirement that proteins track along DNA. Science. 256:1992;1298-1303.
33. Sanders GM, Kassavetis GA, Geiduschek EP. Use of a macromolecular crowding agent to dissect interactions and define functions in transcriptional activation by a DNA-tracking protein: bacteriophage T4 gene 45 protein and late transcription. Proc Natl Acad Sci USA. 91:1994;7703-7707.
34. Lee J, Goldfarb A. Lac repressor acts by modifying the initial transcribing complex so that it cannot leave the promoter. Cell. 66:1991;793-798.
35. Schlax PJ, Capp MW, Record MT Jr. Inhibition of transcription initiation by lac repressor. of special interest J Mol Biol. 245:1995;331-350 A detailed and systematic study of the mechanism of lac repressor action. The repressor is found to block functional binding by polymerase.
36. Chuprina VP, Rullmann JA, Lamerichs RM, Van Boom JH, Boelens R, Kaptein R. Structure of the complex of lac repressor headpiece and an 11 base-pair half-operator determined by nuclear magnetic resonance spectroscopy and restrained molecular dynamics. J Mol Biol. 234:1993;446-462.
37. Lewis M, Chang G, Horton NC, Kercher MA, Pace HC, Schumacher MA, Brenna RG, Lu P. Crystal structure of the lactose operon repressor and its complexes with DNA and inducer. of outstanding interest Science. 271:1996;1247-1254 Finally, the full lac repressor - operator structure.
38. Choy HE, Park SW, Aki T, Parrack P, Fujita N, Ishihama A, Adhya S. Repression and activation of transcription by gal and lac repressors: involvement of alpha subunit of RNA polymerase. EMBO J. 14:1995;4523-4529.
39. Friedman AM, Fischmann TO, Steitz TA. Crystal structure of lac repressor core tetramer and its implications for DNA looping. of special interest Science. 268:1995;1721-1727 The lac repressor structure devoid of the DNA recognition determinants.
40. Gralla JD. Lac repressor. McKnight SL, Yamamoto K. Transcriptional Regulation. 1992;629-642 Cold Spring Harbor Laboratory Press, New York.
41. Markiewicz P, Kleina LG, Cruz C, Ehret S, Miller JH. Genetic studies of the lac repressor. XIV. Analysis of 4000 altered Escherichia coli lac repressors reveals essential and non-essential residues, as well as `spacers' which do not require a specific sequence. J Mol Biol. 240:1994;421-433.