Protein-protein interactions mapped by artificial proteases: Where σ factors bind to RNA polymerase

Trends in Biochemical Sciences

Volumn 25, Issue 9, 2000, Pages 408-414

  Datwyler, Saul A ^a   Meares, Claude F ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MUTANT PROTEIN; PROTEINASE; RNA POLYMERASE; SIGMA FACTOR;

ARTICLE; BINDING SITE; COMPLEX FORMATION; GENE EXPRESSION; IN VITRO STUDY; MOLECULAR CLONING; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; PROTEIN DEGRADATION; PROTEIN MODIFICATION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; TECHNIQUE;

EID: 0034284365     PISSN: 09680004     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0968-0004(00)01652-2     Document Type: Review

References (44)

1. 1 Gentry, D.R. and Burgess, R.R. (1993) Cross-linking of Escherichia coli RNA polymerase subunits: identification of β' as the binding site of ω. Biochemistry 32, 11224-11227
2. 2 Callaci, S. et al. (1999) Core RNA polymerase from E. coli induces a major change in the domain arrangement of the σ70 subunit. Mol. Cell 3, 229-238
3. 3 Sharp, M.M. et al. (1999) The interface of σ with core RNA polymerase is extensive, conserved, and functionally specialized. Genes Dev. 13, 3015-3026
4. 4 Lonetto, M.A. et al. (1998) Identification of a contact site for different transcription activators in region 4 of the Escherichia coli RNA polymerase σ70 subunit. J. Mol. Biol. 284, 1353-1365
5. 5 Lei, S. et al. (1999) Genetic analysis of nif regulatory genes by utilizing the yeast two-hybrid system detected formation of a NifL-NifA complex that is implicated in regulated expression of nif genes. J. Bacteriol. 181, 6535-6539
6. 6 Rana, T.M. and Meares, C.F. (1990) Specific cleavage of a protein by an attached iron chelate. J. Am. Chem. Soc. 112, 2457-2458
7. 7 Schepartz, A. and Cuenoud, B. (1990) Site-specific cleavage of the protein calmodulin using a trifluoperazine-based affinity reagent. J. Am. Chem. Soc. 112, 3247-3249
8. 8 Hoyer, D. et al. (1990) A new strategy for selective protein cleavage. J. Am. Chem. Soc. 112, 3249-3250
9. 9 Ghaim, J.B. et al. (1995) Proximity mapping the surface of a membrane protein using an artificial protease: demonstration that the quinone-binding domain of subunit I is near the N-terminal region of subunit II of cytochrome bd. Biochemistry 34, 11311-11315
10. 10 Ebright, Y.W. et al. (1992) Incorporation of an EDTA-metal complex at a rationally selected site within a protein: application to EDTA-iron DNA affinity cleaving with catabolite gene activator protein (CAP) and Cro. Biochemistry 31, 10664-10670
11. 11 Owens, J.T. et al. (1998) Mapping the σ70 subunit contact sites on Escherichia coli RNA polymerase with a σ70-conjugated chemical protease. Proc. Natl. Acad. Sci. U. S. A. 95, 6021-6026
12. 12 Owens, J.T. et al. (1998) Mapping the promoter DNA sites proximal to conserved regions of σ70 in an Escherichia coli RNA polymerase-lacUV5 open promoter complex. Biochemistry 37, 7670-7675
13. 13 Traviglia, S.L. et al. (1999) Mapping protein-protein interactions with a library of tethered cutting reagents: the binding site of σ70 on Escherichia coli RNA polymerase. Biochemistry 38, 4259-4265
14. 14 Traviglia, S.L. et al. (1999) Targeted protein footprinting: where different transcription factors bind to RNA polymerase. Biochemistry 38, 15774-15778
15. 15 Galas, D.J. and Schmitz, A. (1978) DNAse footprinting: a simple method for the detection of protein-DNA binding specificity. Nucleic Acids Res. 5, 3157-3170
16. 16 Dervan, P.B. (1991) Characterization of protein-DNA complexes by affinity cleaving. Methods Enzymol. 208, 497-515
17. 17 Tullius, T.D. et al. (1987) Hydroxyl radical footprinting: a high-resolution method for mapping protein-DNA contacts. Methods Enzymol. 155, 537-558
18. 18 Gallagher, J. et al. (1998) Protease activity of 1,10-phenanthroline-copper(I). Targeted scission of the catalytic site of carbonic anhydrase. Biochemistry 37, 2096-2104
19. 19 Ermácora, M.R. et al. (1992) Conformation-dependent cleavage of staphylococcal nuclease with a disulfide-linked iron chelate. Proc. Natl. Acad. Sci. U. S. A. 89, 6383-6387
20. 20 Heyduk, E. and Heyduk, T. (1994) Mapping protein domains involved in macromolecular interactions: a novel protein footprinting approach. Biochemistry 33, 9643-9650
21. 21 Greiner, D.P. et al. (1996) Binding of the σ70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting. Proc. Natl. Acad. Sci. U. S. A. 93, 71-75
22. 22 Greiner, D.P. et al. (1997) Synthesis of the protein cutting reagent iron (S)-1-(p-bromoacetamidobenzyl) ethylenediaminetetraacetate and conjugation to cysteine side chains. Bioconjugate Chem. 8, 44-48
23. 23 Rana, T.M. and Meares, C.F. (1991) Transfer of oxygen from an artificial protease to peptide carbon during proteolysis. Prac. Natl. Acad. Sci. U. S. A. 88, 10578-10582
24. 24 Platis, I.E. et al. (1993) Oxidative polypeptide cleavage mediated by EDTA-Fe covalently linked to cysteine residues. Biochemistry 32, 12761-12767
25. 25 Chen, C.H. and Sigman, D.S. (1987) Chemical conversion of a DNA-binding protein into a site-specific nuclease. Science 237, 1197-1201
26. 26 Aki, T. and Adhya, S. (1997) Repressor induced site-specific binding of HU for transcriptional regulation. EMBO J. 16, 3666-3674
27. 27 Young, R. (1991) RNA polymerase II. Annu. Rev. Biochem. 60, 689-715
28. 28 Chamberlin, M. (1976) RNA polymerase - an overview. In RNA Polymerase (Losick, R. and Chamberlin, M., eds), pp. 17-67, Cold Spring Harbor Laboratory Press
29. 29 Ishihama, A. (1997) Promoter selectivity control of RNA polymerase. In Nucleic Acids and Molecular Biology (Vol. 11) (Eckstein, F. and Lilley, D.M.J., eds), pp. 53-70, Springer-Verlag
30. 30 Gill, S.C. et al. (1991) Escherichia coli σ70 and NusA proteins, I. Binding interactions with core RNA polymerase in solution and within the transcription complex. J. Mol. Biol. 220, 307-324
31. 31 Hillel, Z. and Wu, C.W. (1977) Subunit topography of RNA polymerase from Escherichia coli. A cross-linking study with bifunctional reagents. Biochemistry 16, 3334-3342
32. 32 Arthur, T.M. and Burgess, R.R. (1998) Localization of a σ70 binding site on the N terminus of the Escherichia coli RNA polymerase β' subunit. J. Biol. Chem. 273, 31381-31387
33. 33 Malhotra, A. et al. (1996) Crystal structure of a σ70 subunit fragment from E. coli RNA polymerase. Cell 87, 127-136
34. 34 Zhang, G. et al. (1999) Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98, 811-824
35. 35 Polyakov, A. et al. (1995) Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83, 365-373
36. 70. Biochemistry 38, 12424-12431
37. 37 Naryshkin, N. et al. (2000) Structural organization of the RNA polymerase-promoter open complex. Cell 101, 601-611
38. 38 Ebright, R.H. (1998) RNA polymerase-DNA interaction: structures of intermediate, open, and elongation complexes. Cold Spring Harbor Symp. Quant. Biol. 63, 11-20
39. 39 Helmann, J.D. and deHaseth, P.L. (1999) Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners. Biochemistry 38, 5959-5967
40. 40 Allison, L.A. et al. (1985) Extensive homology among the largest subunits of eukaryotic and prokaryotic RNA polymerases. Cell 42, 599-610
41. 41 Helmann, J.D. (1994) Bacterial sigma factors. In Transcription: Mechanisms and Regulation (Conaway, R.C. and Conaway, J.W., eds), pp. 1-17, Raven Press, New York, NY, USA
42. 42 Wigneshweraraj, S.R. et al. (2000) Conservation of sigma-core RNA polymerase proximity relationships between the enhancer-independent and enhancer-dependent sigma classes. EMBO J. 19, 3038-3048
43. 43 Culver, G.M. et al. (1999) Identification of an RNA-protein bridge spanning the ribosomal subunit interface. Science 285, 2133-2136
44. 44 Newcomb, L.F. and Noller, H.F. (1999) Directed hydroxyl radical probing of 16S rRNA in the ribosome: spatial proximity of RNA elements of the 3′ and 5′ domains. RNA 5, 849-855