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PMID: 8552678 Published · ppublish English Journal Article Research Support, U.S. Gov't, P.H.S.

Binding of the sigma 70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting.

Proceedings of the National Academy of Sciences of the United States of America ·Vol. 93 ·No. 1 ·1996-01-09 ·Pages 71-5

Greiner DP, Hughes KA, Gunasekera AH, Meares CF

Abstract

We have used a nonspecific protein cleaving reagent to map the interactions between subunits of the multisubunit enzyme RNA polymerase (Escherichia coli). We developed suitable conditions for using an untethered Fe-EDTA reagent, which does not bind significantly to proteins. Comparison of the cleaved fragments of the subunits from the core enzyme (alpha 2 beta beta') and the holoenzyme (core+sigma 70) shows that absence of the sigma 70 subunit is associated with the appearance of several cleavage sites on the subunits beta (within 10 residues of sequence positions 745, 764, 795, and 812) and beta' (within 10 residues of sequence positions 581, 613, and 728). A cleavage site near beta residue 604 is present in the holoenzyme but absent in the core, demonstrating that a conformational change occurs when sigma 70 binds. No differences are observed for the alpha subunit.

MeSH Terms
Amino Acid Sequence Binding Sites DNA-Directed RNA Polymerases/chemistry Edetic Acid/chemistry Escherichia coli/enzymology Iron/chemistry Molecular Sequence Data Peptide Mapping Protein Binding Sigma Factor/chemistry
Chemicals
Sigma Factor Edetic Acid Iron DNA-Directed RNA Polymerases
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Greiner D P
Department of Chemistry, University of California, Davis 95616, USA.
Hughes K A
Gunasekera A H
Meares C F
References (33)
33 references, click to expand
  1. The primary structure of Escherichia coli RNA polymerase. Nucleotide sequence of the rpoB gene and amino-acid sequence of the beta-subunit.
    Eur J Biochem. 1981 Jun 1;116(3):621-9 PMID: 6266829
  2. Factor stimulating transcription by RNA polymerase.
    Nature. 1969 Jan 4;221(5175):43-6 PMID: 4882047
  3. Nonenzymatic cleavage of proteins by reactive oxygen species generated by dithiothreitol and iron.
    J Biol Chem. 1985 Dec 15;260(29):15394-7 PMID: 2866184
  4. Genetic studies on the beta subunit of Escherichia coli RNA polymerase. IX. The role of the carboxy-terminus in enzyme assembly.
    Mol Gen Genet. 1986 Jun;203(3):492-5 PMID: 3528752
  5. Synthetic peptide vaccine design: synthesis and properties of a high-density multiple antigenic peptide system.
    Proc Natl Acad Sci U S A. 1988 Aug;85(15):5409-13 PMID: 3399498
  6. Surface, subunit interfaces and interior of oligomeric proteins.
    J Mol Biol. 1988 Nov 5;204(1):155-64 PMID: 3216390
  7. Use of Mono Q high-resolution ion-exchange chromatography to obtain highly pure and active Escherichia coli RNA polymerase.
    Biochemistry. 1990 Aug 28;29(34):7890-4 PMID: 2261443
  8. A beta subunit mutation disrupting the catalytic function of Escherichia coli RNA polymerase.
    Proc Natl Acad Sci U S A. 1991 Jul 15;88(14):6018-22 PMID: 2068078
  9. Transfer of oxygen from an artificial protease to peptide carbon during proteolysis.
    Proc Natl Acad Sci U S A. 1991 Dec 1;88(23):10578-82 PMID: 1961724
  10. The isolated catalytic domain of NIFA, a bacterial enhancer-binding protein, activates transcription in vitro: activation is inhibited by NIFL.
    Proc Natl Acad Sci U S A. 1994 Jan 4;91(1):103-7 PMID: 8278350
  11. Mapping protein domains involved in macromolecular interactions: a novel protein footprinting approach.
    Biochemistry. 1994 Aug 16;33(32):9643-50 PMID: 8068641
  12. Mapping staphylococcal nuclease conformation using an EDTA-Fe derivative attached to genetically engineered cysteine residues.
    Biochemistry. 1994 Nov 22;33(46):13625-41 PMID: 7947771
  13. Pharmacokinetics of pretargeted monoclonal antibody 2D12.5 and 88Y-Janus-2-(p-nitrobenzyl)-1,4,7,10-tetraazacyclododecanetetraacetic acid (DOTA) in BALB/c mice with KHJJ mouse adenocarcinoma: a model for 90Y radioimmunotherapy.
    Cancer Res. 1994 Nov 15;54(22):5937-46 PMID: 7954426
  14. Protein footprinting by the combined use of reversible and irreversible lysine modifications.
    Proc Natl Acad Sci U S A. 1994 Dec 6;91(25):11904-8 PMID: 7991555
  15. Assembly of transcriptionally active RNA polymerase I initiation factor SL1 from recombinant subunits.
    Science. 1994 Dec 23;266(5193):2015-8 PMID: 7801130
  16. TFIIIB placement on a yeast U6 RNA gene in vivo is directed primarily by TFIIIC rather than by sequence-specific DNA contacts.
    Mol Cell Biol. 1995 Mar;15(3):1455-66 PMID: 7862139
  17. New models for the mechanism of transcription elongation and its regulation.
    Harvey Lect. 1992-1993;88:1-21 PMID: 1285418
  18. rpoE, the gene encoding the second heat-shock sigma factor, sigma E, in Escherichia coli.
    EMBO J. 1995 Mar 1;14(5):1032-42 PMID: 7889934
  19. Promoter determinants for Escherichia coli RNA polymerase holoenzyme containing sigma 38 (the rpoS gene product).
    Nucleic Acids Res. 1995 Mar 11;23(5):827-34 PMID: 7708499
  20. TATA-binding protein residues implicated in a functional interplay between negative cofactor NC2 (Dr1) and general factors TFIIA and TFIIB.
    J Biol Chem. 1995 May 5;270(18):10976-81 PMID: 7738039
  21. 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. 1995 Sep 12;34(36):11311-5 PMID: 7547857
  22. Contamination in trace element analysis and its control.
    Methods Biochem Anal. 1957;5:273-335 PMID: 13503678
  23. Cyclic re-use of the RNA polymerase sigma factor.
    Nature. 1969 May 10;222(5193):537-40 PMID: 5781654
  24. DNA-dependent RNA polymerase from E. coli: studies on the role of sigma in chain initiation.
    Biochem Biophys Res Commun. 1969 Sep 10;36(6):925-30 PMID: 4310148
  25. Oxidative modification of proteins in the presence of ferrous ion and air. Effect of ionic constituents of the reaction medium on the nature of the oxidation products.
    Biochemistry. 1973 Mar 27;12(7):1341-8 PMID: 4348833
  26. A study of the quaternary structure of Escherichia coli RNA polymerase using bis(imido esters).
    Biochemistry. 1977 Mar 22;16(6):1111-6 PMID: 321015
  27. Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli.
    FEBS Lett. 1977 Apr 1;76(1):108-11 PMID: 323055
  28. Subunit topography of RNA polymerase from Escherichia coli. A cross-linking study with bifunctional reagents.
    Biochemistry. 1977 Jul 26;16(15):3334-42 PMID: 329870
  29. Purification and properties of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase.
    Biochemistry. 1979 Apr 3;18(7):1344-52 PMID: 371677
  30. A centrifuged-column procedure for the measurement of ligand binding by beef heart F1.
    Methods Enzymol. 1979;56:527-30 PMID: 156867
  31. Diffusion-enhanced energy transfer shows accessibility of ribonucleic acid polymerase inhibitor binding sites.
    Biochemistry. 1981 Feb 3;20(3):610-7 PMID: 7011368
  32. Use of aryl azide cross-linkers to investigate protein-protein interactions: an optimization of important conditions as applied to Escherichia coli RNA polymerase and localization of a sigma 70-alpha cross-link to the C-terminal region of alpha.
    Biochemistry. 1994 Oct 11;33(40):12092-9 PMID: 7918430
  33. The primary structure of E. coli RNA polymerase, Nucleotide sequence of the rpoC gene and amino acid sequence of the beta'-subunit.
    Nucleic Acids Res. 1982 Jul 10;10(13):4035-44 PMID: 6287430
Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.93.1.71
Published
1996-01-09
Pages
71-5
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC40180
Subset
IM
Grants
NIGMS NIH HHS · GM 25909 · United States
External Links
PubMed source DOI: 10.1073/pnas.93.1.71 PMC Full Text View journal details
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