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. 1981 Jun 25;9(12):2889–2903. doi: 10.1093/nar/9.12.2889

The nucleotide sequence of the cloned rpoD gene for the RNA polymerase sigma subunit from E coli K12.

Z Burton, R R Burgess, J Lin, D Moore, S Holder, C A Gross
PMCID: PMC326900  PMID: 6269063

Abstract

We have determined the nucleotide sequence of the rpoD gene which codes for the sigma subunit of RNA polymerase from E. coli K12. The gene, which we formerly cloned as a HindIII restriction fragment in the transducing phage, charon 25, was recloned into several plasmids. We have determined a 2600 base pair DNA sequence which includes the entire structural gene for sigma. The resulting amino acid sequence agrees with previous information obtained about sigma including the amino acid composition, partial sequence data for the N-terminus, the highly acidic nature of the polypeptide, and the cleavage pattern at cysteines. The molecular weight of 70,263 daltons calculated for the 613 amino acid polypeptides is significantly lower than had been determined previously by SDS polyacrylamide gel analysis.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. An G., Friesen J. D. The nucleotide sequence of tufB and four nearby tRNA structural genes of Escherichia coli. Gene. 1980 Dec;12(1-2):33–39. doi: 10.1016/0378-1119(80)90013-x. [DOI] [PubMed] [Google Scholar]
  2. Birnboim H. C., Doly J. A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res. 1979 Nov 24;7(6):1513–1523. doi: 10.1093/nar/7.6.1513. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Burgess R. R., Gross C. A., Walter W., Lowe P. A. Altered chemical properties in three mutants of E. coli RNA polymerase sigma subunit. Mol Gen Genet. 1979 Oct 1;175(3):251–257. doi: 10.1007/BF00397224. [DOI] [PubMed] [Google Scholar]
  4. Burgess R. R., Gross C., Engbaek F. Cysteine and methionine content of the Escherichia coli ribonucleic acid polymerase subunits. J Bacteriol. 1976 Oct;128(1):390–393. doi: 10.1128/jb.128.1.390-393.1976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Burgess R. R., Travers A. A., Dunn J. J., Bautz E. K. Factor stimulating transcription by RNA polymerase. Nature. 1969 Jan 4;221(5175):43–46. doi: 10.1038/221043a0. [DOI] [PubMed] [Google Scholar]
  6. Chamberlin M. J. The selectivity of transcription. Annu Rev Biochem. 1974;43(0):721–775. doi: 10.1146/annurev.bi.43.070174.003445. [DOI] [PubMed] [Google Scholar]
  7. Chou P. Y., Fasman G. D. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148. doi: 10.1002/9780470122921.ch2. [DOI] [PubMed] [Google Scholar]
  8. Coggins J. R., Lumsden J., Malcolm A. D. A study of the quaternary structure of Escherichia coli RNA polymerase using bis(imido esters). Biochemistry. 1977 Mar 22;16(6):1111–1116. doi: 10.1021/bi00625a013. [DOI] [PubMed] [Google Scholar]
  9. Crawford I. P., Nichols B. P., Yanofsky C. Nucleotide sequence of the trpB gene in Escherichia coli and Salmonella typhimurium. J Mol Biol. 1980 Oct 5;142(4):489–502. doi: 10.1016/0022-2836(80)90259-4. [DOI] [PubMed] [Google Scholar]
  10. Fujiki H., Zurek G. The subunits of DNA-dependent RNA polymerase from E. coli: I. Amino acid analysis and primary structure of the N-terminal regions. FEBS Lett. 1975 Jul 15;55(1):242–244. doi: 10.1016/0014-5793(75)81001-5. [DOI] [PubMed] [Google Scholar]
  11. Grantham R., Gautier C., Gouy M. Codon frequencies in 119 individual genes confirm consistent choices of degenerate bases according to genome type. Nucleic Acids Res. 1980 May 10;8(9):1893–1912. doi: 10.1093/nar/8.9.1893. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Gross C. A., Blattner F. R., Taylor W. E., Lowe P. A., Burgess R. R. Isolation and characterization of transducing phage coding for sigma subunit of Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 1979 Nov;76(11):5789–5793. doi: 10.1073/pnas.76.11.5789. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Gross C., Hoffman J., Ward C., Hager D., Burdick G., Berger H., Burgess R. Mutation affecting thermostability of sigma subunit of Escherichia coli RNA polymerase lies near the dnaG locus at about 66 min on the E. coli genetic map. Proc Natl Acad Sci U S A. 1978 Jan;75(1):427–431. doi: 10.1073/pnas.75.1.427. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Harris J. D., Heilig J. S., Martinez I. I., Calendar R., Isaksson L. A. Temperature-sensitive Escherichia coli mutant producing a temperature-sensitive sigma subunit of DNA-dependent RNA polymerase. Proc Natl Acad Sci U S A. 1978 Dec;75(12):6177–6181. doi: 10.1073/pnas.75.12.6177. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Harris J. D., Martinez I. I., Calendar R. A gene from Escherichia coli affecting the sigma subunit of RNA polymerase. Proc Natl Acad Sci U S A. 1977 May;74(5):1836–1840. doi: 10.1073/pnas.74.5.1836. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Hillel Z., Wu C. W. Photochemical cross-linking studies on the interaction of Escherichia coli RNA polymerase with T7 DNA. Biochemistry. 1978 Jul 25;17(15):2954–2961. doi: 10.1021/bi00608a003. [DOI] [PubMed] [Google Scholar]
  17. Hillel Z., Wu C. W. Subunit topography of RNA polymerase from Escherichia coli. A cross-linking study with bifunctional reagents. Biochemistry. 1977 Jul 26;16(15):3334–3342. doi: 10.1021/bi00634a008. [DOI] [PubMed] [Google Scholar]
  18. Ikemura T. Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J Mol Biol. 1981 Feb 15;146(1):1–21. doi: 10.1016/0022-2836(81)90363-6. [DOI] [PubMed] [Google Scholar]
  19. Levine B. J., Orphanos P. D., Fischmann B. S., Beychok S. Physicochemical properties and interactions of Escherichia coli ribonucleic acid polymerase holoenzyme, core enzyme, subunits, and subassembly alpha 2 beta. Biochemistry. 1980 Oct 14;19(21):4808–4814. doi: 10.1021/bi00562a015. [DOI] [PubMed] [Google Scholar]
  20. Liebke H., Gross C., Walter W., Burgess R. A new mutation rpoD800, affecting the sigma subunit of E. coli RNA polymerase is allelic to two other sigma mutants. Mol Gen Genet. 1980 Jan;177(2):277–282. doi: 10.1007/BF00267439. [DOI] [PubMed] [Google Scholar]
  21. Lowe P. A., Aebi U., Gross C., Burgess R. R. In vitro thermal inactivation of a temperature-sensitive sigma subunit mutant (rpoD800) of Escherichia coli RNA polymerase proceeds by aggregation. J Biol Chem. 1981 Feb 25;256(4):2010–2015. [PubMed] [Google Scholar]
  22. Lowe P. A., Hager D. A., Burgess R. R. Purification and properties of the sigma subunit of Escherichia coli DNA-dependent RNA polymerase. Biochemistry. 1979 Apr 3;18(7):1344–1352. doi: 10.1021/bi00574a034. [DOI] [PubMed] [Google Scholar]
  23. Maniatis T., Jeffrey A., Kleid D. G. Nucleotide sequence of the rightward operator of phage lambda. Proc Natl Acad Sci U S A. 1975 Mar;72(3):1184–1188. doi: 10.1073/pnas.72.3.1184. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  25. Meisenberger O., Pilz I., Heumann H. Small-angle X-ray study of DNA-dependent RNA polymerase subunit sigma from Escherichia coli. FEBS Lett. 1980 Mar 24;112(1):39–41. doi: 10.1016/0014-5793(80)80121-9. [DOI] [PubMed] [Google Scholar]
  26. Nakamura Y. Hybrid plasmid carrying Escherichia coli genes for the primase (dnaG) and RNA polymerase sigma factor (rpoD); gene organization and control of their expression. Mol Gen Genet. 1980;178(3):487–497. doi: 10.1007/BF00337853. [DOI] [PubMed] [Google Scholar]
  27. Nakamura Y., Kurihara T., Saito H., Uchida H. Sigma subunit of Escherichia coli RNA polymerase affects the function of lambda N gene. Proc Natl Acad Sci U S A. 1979 Sep;76(9):4593–4597. doi: 10.1073/pnas.76.9.4593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  28. Nakamura Y., Osawa T., Yura T. Chromosomal location of a structural gene for the RNA polymerase sigma factor in Escherichia coli. Proc Natl Acad Sci U S A. 1977 May;74(5):1831–1835. doi: 10.1073/pnas.74.5.1831. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Nakamura Y. RNA polymerase mutant with altered sigma factor in Escherichia coli. Mol Gen Genet. 1978 Sep 20;165(1):1–6. doi: 10.1007/BF00270369. [DOI] [PubMed] [Google Scholar]
  30. Ovchinnikov Y. A., Lipkin V. M., Modyanov N. N., Chertov O. Y., Smirnov Y. V. Primary structure of alpha-subunit of DNA-dependent RNA polymerase from Escherichia coli. FEBS Lett. 1977 Apr 1;76(1):108–111. doi: 10.1016/0014-5793(77)80131-2. [DOI] [PubMed] [Google Scholar]
  31. Post L. E., Nomura M. DNA sequences from the str operon of Escherichia coli. J Biol Chem. 1980 May 25;255(10):4660–4666. [PubMed] [Google Scholar]
  32. Post L. E., Nomura M. Nucleotide sequence of the intercistronic region preceding the gene for RNA polymerase subunit alpha in Escherichia coli. J Biol Chem. 1979 Nov 10;254(21):10604–10606. [PubMed] [Google Scholar]
  33. Scaife J. G., Heilig J. S., Rowen L., Calendar R. Gene for the RNA polymerase sigma subunit mapped in Salmonella typhimurium and Escherichia coli by cloning and deletion. Proc Natl Acad Sci U S A. 1979 Dec;76(12):6510–6514. doi: 10.1073/pnas.76.12.6510. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Shine J., Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci U S A. 1974 Apr;71(4):1342–1346. doi: 10.1073/pnas.71.4.1342. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Simpson R. B. The molecular topography of RNA polymerase-promoter interaction. Cell. 1979 Oct;18(2):277–285. doi: 10.1016/0092-8674(79)90047-3. [DOI] [PubMed] [Google Scholar]
  36. Stark G. R. Cleavage at cysteine after cyanylation. Methods Enzymol. 1977;47:129–132. doi: 10.1016/0076-6879(77)47015-0. [DOI] [PubMed] [Google Scholar]
  37. Stender W., Stütz A. A., Scheit K. H. The modification of DNA-dependent RNA polymerase from Escherichia coli by an alkylating derivative of rifamycin SV. Eur J Biochem. 1975 Aug 1;56(1):129–136. doi: 10.1111/j.1432-1033.1975.tb02215.x. [DOI] [PubMed] [Google Scholar]
  38. Sutcliffe J. G. Complete nucleotide sequence of the Escherichia coli plasmid pBR322. Cold Spring Harb Symp Quant Biol. 1979;43(Pt 1):77–90. doi: 10.1101/sqb.1979.043.01.013. [DOI] [PubMed] [Google Scholar]
  39. Sverdlov E. D., Tsarev S. A., Begar V. A. Subunits of E. coli RNA polymerase forming 3'-OH binding site at initial stages of transcription process: possible role of delta-subunit. FEBS Lett. 1980 May 19;114(1):111–114. doi: 10.1016/0014-5793(80)80871-4. [DOI] [PubMed] [Google Scholar]
  40. Travers A. A., Buckland R., Goman M., Le Grice S. S., Scaife J. G. A mutation affecting the sigma subunit of RNA polymerase changes transcriptional specificity. Nature. 1978 Jun 1;273(5661):354–358. doi: 10.1038/273354a0. [DOI] [PubMed] [Google Scholar]
  41. Yokota T., Sugisaki H., Takanami M., Kaziro Y. The nucleotide sequence of the cloned tufA gene of Escherichia coli. Gene. 1980 Dec;12(1-2):25–31. doi: 10.1016/0378-1119(80)90012-8. [DOI] [PubMed] [Google Scholar]

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