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Transcriptional Regulation

Identifying a Core RNA Polymerase Surface Critical for Interactions with a Sigma-Like Specificity Factor

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Pages 7013-7023 | Received 14 Apr 2000, Accepted 07 Jun 2000, Published online: 28 Mar 2023

REFERENCES

  • Arthur, T. M., and Burgess, R. R.. 1998. Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta′ subunit. J. Biol. Chem. 273:31381–31387
  • Bogenhagen, D. F., and Insdorf, N. F.. 1988. Purification of Xenopus laevis mitochondrial RNA polymerase and identification of a dissociable factor required for specific transcription. Mol. Cell. Biol. 8:2910–2916
  • Callaci, S., Heyduk, E., and Heyduk, T.. 1998. Conformational changes of Escherichia coli RNA polymerase sigma70 factor induced by binding to the core enzyme. J. Biol. Chem. 273:32995–33001
  • Callaci, S., Heyduk, E., and Heyduk, T.. 1999. Core RNA polymerase from E. coli induces a major change in the domain arrangement of the sigma 70 subunit. Mol. Cell 3:229–238
  • Carrodeguas, J. A., Yun, S., Shadel, G. S., Clayton, D. A., and Bogenhagen, D. F.. 1996. Functional conservation of yeast mtTFB despite extensive sequence divergence. Gene Expr. 6:219–230
  • Cermakian, N., Ikeda, T. M., Miramontes, P., Lang, B. F., Gray, M. W., and Cedergren, R.. 1997. On the evolution of the single-subunit RNA polymerases. J. Mol. Evol. 45:671–681
  • Cheetham, G. M., Jeruzalmi, D., and Steitz, T. A.. 1999. Structural basis for initiation of transcription from an RNA polymerase-promoter complex. Nature 399:80–83
  • Chen, B., Kubelik, A. R., Mohr, S., and Breitenberger, C. A.. 1996. Cloning and characterization of the Neurospora crassa cyt-5 gene. A nuclear-coded mitochondrial RNA polymerase with a polyglutamine repeat. J. Biol. Chem. 271:6537–6544
  • Cliften, P. F., and Jaehning, J. A.. 1999. DNA dependent RNA polymerases Encyclopedia of molecular biology. Creighton, T. E. 2218–2225 John Wiley & Sons, Inc., New York, N.Y
  • Cliften, P. F., Park, J. Y., Davis, B. P., Jang, S. H., and Jaehning, J. A.. 1997. Identification of three regions essential for interaction between a sigma-like factor and core RNA polymerase. Genes Dev. 11:2897–2909
  • Coggins, J. R., Lumsden, J., and Malcolm, A. D.. 1977. A study of the quaternary structure of Escherichia coli RNA polymerase using bis(imido esters). Biochemistry 16:1111–1116
  • Delarue, M., Poch, O., Tordo, N., Moras, D., and Argos, P.. 1990. An attempt to unify the structure of polymerases. Protein Eng. 3:461–467
  • Dombroski, A. J., Walter, W. A., Record, M. T.Jr., Siegele, D. A., and Gross, C. A.. 1992. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell 70:501–512
  • Fu, J., Gnatt, A. L., Bushnell, D. A., Jensen, G. J., Thompson, N. E., Burgess, R. R., David, P. R., and Kornberg, R. D.. 1999. Yeast RNA polymerase II at 5 Å resolution. Cell 98:799–810
  • Gao, G., Orlova, M., Georgiadis, M. M., Hendrickson, W. A., and Goff, S. P.. 1997. Conferring RNA polymerase activity to a DNA polymerase: a single residue in reverse transcriptase controls substrate selection. Proc. Natl. Acad. Sci. USA 94:407–411
  • Gardner, L. P., Mookhtiar, K. A., and Coleman, J. E.. 1997. Initiation, elongation, and processivity of carboxyl-terminal mutants of T7 RNA polymerase. Biochemistry 36:2908–2918
  • Gietz, R. D., and Sugino, A.. 1988. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene 74:527–534
  • Greenleaf, A. L., Kelly, J. L., and Lehman, I. R.. 1986. Yeast RPO41 gene product is required for transcription and maintenance of the mitochondrial genome. Proc. Natl. Acad. Sci. USA 83:3391–3394
  • Greiner, D. P., Hughes, K. A., Gunasekera, A. H., and Meares, C. F.. 1996. Binding of the sigma 70 protein to the core subunits of Escherichia coli RNA polymerase, studied by iron-EDTA protein footprinting. Proc. Natl. Acad. Sci. USA 93:71–75
  • Guthrie, C., and Fink, G. R.. 1991. Guide to yeast genetics and molecular biology. Methods Enzymol. 194:1–931
  • 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
  • Inoue, H., Nojima, H., and Okayama, H.. 1990. High efficiency transformation of Escherichia coli with plasmids. Gene 96:23–28
  • Ito, H., Fukuda, Y., Murata, K., and Kimura, A.. 1983. Transformation of intact yeast cells treated with alkali cations. J. Bacteriol. 153:163–168
  • Jang, S.-H., and Jaehning, J. A.. 1991. The yeast mitochondrial RNA polymerase specificity factor, MTF1, is similar to bacterial sigma factors. J. Biol. Chem. 266:22671–22677
  • Jeruzalmi, D., and Steitz, T. A.. 1998. Structure of T7 RNA polymerase complexed to the transcriptional inhibitor T7 lysozyme. EMBO J. 17:4101–4113
  • Joo, D. M., Ng, N., and Calendar, R.. 1997. A sigma32 mutant with a single amino acid change in the highly conserved region 2.2 exhibits reduced core RNA polymerase affinity. Proc. Natl. Acad. Sci. USA 94:4907–4912
  • Joo, D. M., Nolte, A., Calendar, R., Zhou, Y. N., and Jin, D. J.. 1998. Multiple regions on the Escherichia coli heat shock transcription factor sigma 32 determine core RNA polymerase binding specificity. J. Bacteriol. 180:1095–1102
  • Kulbachinskiy, A., Mustaev, A., Goldfarb, A., and Nikiforov, V.. 1999. Interaction with free beta′ subunit unmasks DNA-binding domain of RNA polymerase sigma subunit. FEBS Lett. 454:71–74
  • Lang, B. F., Burger, G., O'Kelly, C. J., Cedergren, R., Golding, G. B., Lemieux, C., Sankoff, D., Turmel, M., and Gray, M. W.. 1997. An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493–497
  • Leonetti, J. P., Wong, K., and Geiduschek, E. P.. 1998. Core-sigma interaction: probing the interaction of the bacteriophage T4 gene 55 promoter recognition protein with E. coli RNA polymerase core. EMBO J. 17:1467–1475
  • Malhotra, A., Severinova, E., and Darst, S. A.. 1996. Crystal structure of a sigma 70 subunit fragment from E. coli RNA polymerase. Cell 87:127–136
  • Mangus, D. A., Jang, S. H., and Jaehning, J. A.. 1994. Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J. Biol. Chem. 269:26568–26574
  • Masters, B. S., Stohl, L. L., and Clayton, D. A.. 1987. Yeast mitochondrial RNA polymerase is homologous to those encoded by bacteriophages T3 and T7. Cell 51:89–99
  • Miller, J. H.. 1972. Experiments in molecular genetics. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
  • Mookhtiar, K. A., Peluso, P. S., Muller, D. K., Dunn, J. J., and Coleman, J. E.. 1991. Processivity of T7 RNA polymerase requires the C-terminal Phe882-Ala883-COO- or “foot.” Biochemistry 30:6305–6313
  • Nagai, H., and Shimamoto, N.. 1997. Regions of the Escherichia coli primary sigma factor sigma70 that are involved in interaction with RNA polymerase core enzyme. Genes Cells 2:725–734
  • Nomura, T., Fujita, N., and Ishihama, A.. 1999. Mapping of subunit-subunit contact surfaces on the beta subunit of Escherichia coli RNA polymerase. Biochemistry 38:1346–1355
  • Owens, J. T., Miyake, R., Murakami, K., Chmura, A. J., Fujita, N., Ishihama, A., and Meares, C. F.. 1998. Mapping the sigma70 subunit contact sites on Escherichia coli RNA polymerase with a sigma70-conjugated chemical protease. Proc. Natl. Acad. Sci. USA 95:6021–6026
  • Patra, D., Lafer, E. M., and Sousa, R.. 1992. Isolation and characterization of mutant bacteriophage T7 RNA polymerases. J. Mol. Biol. 224:307–318
  • Polyakov, A., Severinova, E., and Darst, S. A.. 1995. Three-dimensional structure of E. coli core RNA polymerase: promoter binding and elongation conformations of the enzyme. Cell 83:365–373
  • Raskin, C. A., Diaz, G., Joho, K., and McAllister, W. T.. 1992. Substitution of a single bacteriophage T3 residue in bacteriophage T7 RNA polymerase at position 748 results in a switch in promoter specificity. J. Mol. Biol. 228:506–515
  • Raskin, C. A., Diaz, G. A., and McAllister, W. T.. 1993. T7 RNA polymerase mutants with altered promoter specificities. Proc. Natl. Acad. Sci. USA 90:3147–3151
  • Rong, M., He, B., McAllister, W. T., and Durbin, R. K.. 1998. Promoter specificity determinants of T7 RNA polymerase. Proc. Natl. Acad. Sci. USA 95:515–519
  • Rousvoal, S., Oudot, M., Fontaine, J., Kloareg, B., and Goer, S. L.. 1998. Witnessing the evolution of transcription in mitochondria: the mitochondrial genome of the primitive brown alga Pylaiella littoralis (L.) Kjellm. Encodes a T7-like RNA polymerase. J. Mol. Biol. 277:1047–1057
  • Sambrook, J., Fritsch, E. F., and Maniatis, T.. Molecular cloning: a laboratory manual, 2nd ed. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y
  • Shadel, G. S., and Clayton, D. A.. 1989. 1995. A Saccharomyces cerevisiae mitochondrial transcription factor, sc-mtTFB, shares features with sigma factors but is functionally distinct. Mol. Cell. Biol. 15:2101–2108
  • Sharp, M. M., Chan, C. L., Lu, C. Z., Marr, M. T., Nechaev, S., Merritt, E. W., Severinov, K., Roberts, J. W., and Gross, C. A.. 1999. The interface of sigma with core RNA polymerase is extensive, conserved, and functionally specialized. Genes Dev. 13:3015–3026
  • Shuler, M. F., Tatti, K. M., Wade, K. H., Moran, C. P.Jr.. 1995. A single amino acid substitution in sigma E affects its ability to bind core RNA polymerase. J. Bacteriol. 177:3687–3694
  • Sousa, R.. 1996. Structural and mechanistic relationships between nucleic acid polymerases. Trends Biochem. Sci. 21:186–190
  • Sousa, R., and Padilla, R.. 1995. A mutant T7 RNA polymerase as a DNA polymerase. EMBO J. 14:4609–4621
  • Sousa, R., Patra, D., and Lafer, E. M.. 1992. Model for the mechanism of bacteriophage T7 RNAP transcription initiation and termination. J. Mol. Biol. 224:319–334
  • Tintut, Y., and Gralla, J. D.. 1995. PCR mutagenesis identifies a polymerase-binding sequence of sigma 54 that includes a sigma 70 homology region. J. Bacteriol. 177:5818–5825
  • Vallejo, M., Gosse, M. E., Beckman, W., and Habener, J. F.. 1995. Impaired cyclic AMP-dependent phosphorylation renders CREB a repressor of C/EBP-induced transcription of the somatostatin gene in an insulinoma cell line. Mol. Cell. Biol. 15:415–424
  • Wach, A., Brachat, A., Pohlmann, R., and Philippsen, P.. 1994. New heterologous modules for classical or PCR-based gene disruptions in Saccharomyces cerevisiae. Yeast 10:1793–1808
  • Wang, Y., and Shadel, G. S.. 1999. Stability of the mitochondrial genome requires an amino-terminal domain of yeast mitochondrial RNA polymerase. Proc. Natl. Acad. Sci. USA 96:8046–8051
  • Winkley, C. S., Keller, M. J., and Jaehning, J. A.. 1985. A multicomponent mitochondrial RNA polymerase from Saccharomyces cerevisiae. J. Biol. Chem. 260:14214–14223
  • Zhang, G., Campbell, E. A., Minakhin, L., Richter, C., Severinov, K., and Darst, S. A.. 1999. Crystal structure of Thermus aquaticus core RNA polymerase at 3.3 Å resolution. Cell 98:811–824

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