Experts and Doctors on dna directed rna polymerases in United States


Locale: United States
Topic: dna directed rna polymerases

Top Publications

  1. Jin D, Burgess R, Richardson J, Gross C. Termination efficiency at rho-dependent terminators depends on kinetic coupling between RNA polymerase and rho. Proc Natl Acad Sci U S A. 1992;89:1453-7 pubmed
  2. Burgess R, Anthony L. How sigma docks to RNA polymerase and what sigma does. Curr Opin Microbiol. 2001;4:126-31 pubmed
    ..This region of beta' interacts with region 2.1-2.2 of sigma(70). Binding of this region of beta' to sigma(70) triggers a conformational change in sigma that allows it to bind to a -10 nontemplate promoter DNA strand oligonucleotide. ..
  3. Wu C, Yamaguchi Y, Benjamin L, Horvat Gordon M, Washinsky J, Enerly E, et al. NELF and DSIF cause promoter proximal pausing on the hsp70 promoter in Drosophila. Genes Dev. 2003;17:1402-14 pubmed
    ..The transcriptional activator, HSF, might cause NELF to dissociate from the elongation complex. DSIF continues to associate with the elongation complex and could serve a positive role in elongation. ..
  4. Kontur W, Saecker R, Capp M, Record M. Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments. J Mol Biol. 2008;376:1034-47 pubmed publisher
    ..The division of the large positive enthalpy change between the late steps of the mechanism suggests that an additional unstable intermediate (I(3)) may exist between I(2) and RP(o). ..
  5. He X, Hsu Y, Pontes O, Zhu J, Lu J, Bressan R, et al. NRPD4, a protein related to the RPB4 subunit of RNA polymerase II, is a component of RNA polymerases IV and V and is required for RNA-directed DNA methylation. Genes Dev. 2009;23:318-30 pubmed publisher
    ..Our results show that RDM2/NRPD4/NRPE4 is a new component of the RdDM pathway in Arabidopsis and that it functions as part of Pol IV and Pol V. ..
  6. Grundy F, Lehman S, Henkin T. The L box regulon: lysine sensing by leader RNAs of bacterial lysine biosynthesis genes. Proc Natl Acad Sci U S A. 2003;100:12057-62 pubmed
    ..The L box regulatory system represents an example of gene regulation using an RNA element that directly senses the intracellular concentration of a small molecule. ..
  7. Ghabrial S, Havens W. The Helminthosporium victoriae 190S mycovirus has two forms distinguishable by capsid protein composition and phosphorylation state. Virology. 1992;188:657-65 pubmed
    ..Radioiodination studies with intact Hv190S virions indicated that p88 and p83, but not the nonphosphorylated p78, were accessible to iodination, suggesting that capsid protein phosphorylation entailed conformational changes. ..
  8. Toulokhonov I, Shulgina I, Hernandez V. Binding of the transcription effector ppGpp to Escherichia coli RNA polymerase is allosteric, modular, and occurs near the N terminus of the beta'-subunit. J Biol Chem. 2001;276:1220-5 pubmed
    ..We propose that the N terminus of beta' together with the C terminus of beta constitute a modular ppGpp binding site. ..
  9. Becker M, Todd T, Moyer R. An Amsacta moorei entomopoxvirus ortholog of the poly(A) polymerase small subunit exhibits methyltransferase activity and is non-essential for virus growth. Virology. 2008;375:624-36 pubmed publisher
    ..No physical association was found between any of the putative AMEV PAP subunits. We therefore propose that mRNA polyadenylation does not require interactions between these three proteins...

More Information

Publications123 found, 100 shown here

  1. Strainic M, Sullivan J, Velevis A, deHaseth P. Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance. Biochemistry. 1998;37:18074-80 pubmed
    ..Finally, we provide evidence in support of models which describe the DNA melting process accompanying open complex formation as initiating in the -10 promoter region and progressing in the downstream direction. ..
  2. Shirako Y, Strauss E, Strauss J. Suppressor mutations that allow sindbis virus RNA polymerase to function with nonaromatic amino acids at the N-terminus: evidence for interaction between nsP1 and nsP4 in minus-strand RNA synthesis. Virology. 2000;276:148-60 pubmed
  3. Floss H, Yu T. Rifamycin-mode of action, resistance, and biosynthesis. Chem Rev. 2005;105:621-32 pubmed
  4. Vassylyev D, Svetlov V, Vassylyeva M, Perederina A, Igarashi N, Matsugaki N, et al. Structural basis for transcription inhibition by tagetitoxin. Nat Struct Mol Biol. 2005;12:1086-93 pubmed publisher
    ..Remodeling of the active site by metal ions could be a common theme in the regulation of catalysis by nucleic acid enzymes...
  5. Yawn B, Zhang L, Mura C, Sukhodolets M. RapA, the SWI/SNF subunit of Escherichia coli RNA polymerase, promotes the release of nascent RNA from transcription complexes. Biochemistry. 2009;48:7794-806 pubmed publisher
    ..This work further refines our models for RapA function in vivo and establishes a new role in RNA management for a representative of the SWI/SNF protein superfamily. ..
  6. Dicker I, Seetharam S. Cloning and nucleotide sequence of the firA gene and the firA200(Ts) allele from Escherichia coli. J Bacteriol. 1991;173:334-44 pubmed
    ..High-level expression of mutant FirA did not suppress this rifampin sensitivity. ..
  7. Krásný L, Gourse R. An alternative strategy for bacterial ribosome synthesis: Bacillus subtilis rRNA transcription regulation. EMBO J. 2004;23:4473-83 pubmed
    ..subtilis RNA polymerase directly. Rather, increases in the ppGpp concentration might reduce the available GTP pools, thereby modulating rRNA promoter activity indirectly. ..
  8. Weber K, Vincent O, Kiley P. Additional determinants within Escherichia coli FNR activating region 1 and RNA polymerase alpha subunit required for transcription activation. J Bacteriol. 2005;187:1724-31 pubmed
    ..In conclusion, this study demonstrates that multiple side chains within region 181 to 192 are required for FNR activation and the surface of alphaCTD required for FNR activation is more extensive than previously observed. ..
  9. Browning D, Beatty C, Sanstad E, Gunn K, Busby S, Wolfe A. Modulation of CRP-dependent transcription at the Escherichia coli acsP2 promoter by nucleoprotein complexes: anti-activation by the nucleoid proteins FIS and IHF. Mol Microbiol. 2004;51:241-54 pubmed
    ..We propose that FIS and IHF each function directly as anti-activators of CRP, each working independently at different times during growth to set the levels of CRP-dependent acs transcription. ..
  10. Dombroski A, Walter W, Record M, Siegele D, Gross C. Polypeptides containing highly conserved regions of transcription initiation factor sigma 70 exhibit specificity of binding to promoter DNA. Cell. 1992;70:501-12 pubmed
    ..Thus, we propose that sigma 70 is a sequence-specific DNA-binding protein that normally functions through an allosteric interaction with the core subunits of RNA polymerase. ..
  11. You S, Falgout B, Markoff L, Padmanabhan R. In vitro RNA synthesis from exogenous dengue viral RNA templates requires long range interactions between 5'- and 3'-terminal regions that influence RNA structure. J Biol Chem. 2001;276:15581-91 pubmed publisher
    ..RNA synthesis at the 3'-UTR, however, requires long range interactions involving the 5'-UTR, CYC motifs, and the 3'-stem-loop region that includes the tertiary pseudoknot structure...
  12. Artsimovitch I, Chu C, Lynch A, Landick R. A new class of bacterial RNA polymerase inhibitor affects nucleotide addition. Science. 2003;302:650-4 pubmed
    ..We propose that CBR703 compounds inhibit nucleotide addition allosterically by hindering movements of active site structures that are linked to the CBR703 binding site through a bridge helix. ..
  13. Trotochaud A, Wassarman K. A highly conserved 6S RNA structure is required for regulation of transcription. Nat Struct Mol Biol. 2005;12:313-9 pubmed
    ..These data highlight the critical importance of structural characteristics for 6S RNA activity. ..
  14. McKinley B, Sukhodolets M. Escherichia coli RNA polymerase-associated SWI/SNF protein RapA: evidence for RNA-directed binding and remodeling activity. Nucleic Acids Res. 2007;35:7044-60 pubmed
    ..Taken together, our data indicate a novel RNA remodeling activity for RapA, a representative of the SWI/SNF protein superfamily. ..
  15. Vassylyeva M, Svetlov V, Dearborn A, Klyuyev S, Artsimovitch I, Vassylyev D. The carboxy-terminal coiled-coil of the RNA polymerase beta'-subunit is the main binding site for Gre factors. EMBO Rep. 2007;8:1038-43 pubmed
    ..We show that substitutions of these residues and those in the GreB C-terminal domain cavity confer defects in GreB activity and binding to RNAP, and present a plausible model for the RNAP-GreB complex. ..
  16. Jia Y, Kumar A, Patel S. Equilibrium and stopped-flow kinetic studies of interaction between T7 RNA polymerase and its promoters measured by protein and 2-aminopurine fluorescence changes. J Biol Chem. 1996;271:30451-8 pubmed
    ..Thus, the 2-fold lower kon, the 4-fold higher koff, and the 2-5-fold weaker equilibrium interactions together make Phi3.8 a weaker promoter relative to Phi10. ..
  17. Arthur T, Burgess R. Localization of a sigma70 binding site on the N terminus of the Escherichia coli RNA polymerase beta' subunit. J Biol Chem. 1998;273:31381-7 pubmed
    ..We were able to more precisely map the interaction domain to amino acid residues 260-309 of beta' using nickel nitrilotriacetic acid co-immobilization assays. ..
  18. Rutherford S, Lemke J, Vrentas C, Gaal T, Ross W, Gourse R. Effects of DksA, GreA, and GreB on transcription initiation: insights into the mechanisms of factors that bind in the secondary channel of RNA polymerase. J Mol Biol. 2007;366:1243-57 pubmed
    ..Our results provide important clues to the mechanisms of both negative and positive control of transcription initiation by DksA. ..
  19. Gilmour D, Fan R. Derailing the locomotive: transcription termination. J Biol Chem. 2008;283:661-4 pubmed
  20. Qanungo K, Shaji D, Mathur M, Banerjee A. Two RNA polymerase complexes from vesicular stomatitis virus-infected cells that carry out transcription and replication of genome RNA. Proc Natl Acad Sci U S A. 2004;101:5952-7 pubmed
    ..We propose that two RNA polymerase complexes that differ in their content of virally and host-encoded proteins are separately responsible for transcription and replication of vesicular stomatitis virus genome RNA. ..
  21. MARTINEZ CALVILLO S, Nguyen D, Stuart K, Myler P. Transcription initiation and termination on Leishmania major chromosome 3. Eukaryot Cell. 2004;3:506-17 pubmed
    ..Transcription on both strands terminates within the tRNA-gene region. Transient-transfection studies support the role of the tRNA-gene region as a transcription terminator for RNA polymerase II (Pol II) and Pol III, and also for Pol I. ..
  22. Schwartz M, Chen J, Lee W, Janda M, Ahlquist P. Alternate, virus-induced membrane rearrangements support positive-strand RNA virus genome replication. Proc Natl Acad Sci U S A. 2004;101:11263-8 pubmed
  23. Curaba J, Chen X. Biochemical activities of Arabidopsis RNA-dependent RNA polymerase 6. J Biol Chem. 2008;283:3059-66 pubmed
    ..Our findings have important implications on the processes involving RDR6 in vivo and provide new biochemical insights into the mechanisms of RNA silencing in Arabidopsis. ..
  24. Ayers D, Auble D, deHaseth P. Promoter recognition by Escherichia coli RNA polymerase. Role of the spacer DNA in functional complex formation. J Mol Biol. 1989;207:749-56 pubmed
    ..As not all observations with the spacer length series of gapped and ungapped promoters can be interpreted in terms of an active role of the spacer DNA without additional assumptions, such a role must still be considered tentative. ..
  25. Malakooti J, Ely B. Principal sigma subunit of the Caulobacter crescentus RNA polymerase. J Bacteriol. 1995;177:6854-60 pubmed
    ..coli RNA polymerase, allowing the expression of C. crescentus promoters in E. coli. Thus, the C. crescentus sigma 73 appears to have a broader specificity than does the sigma 70 of the enteric bacteria...
  26. Shirako Y, Strauss J. Requirement for an aromatic amino acid or histidine at the N terminus of Sindbis virus RNA polymerase. J Virol. 1998;72:2310-5 pubmed
    ..However, suppressor mutations can arise that enable most such nsP4s to regain significant but still suboptimal activity. ..
  27. Condit R, Niles E. Regulation of viral transcription elongation and termination during vaccinia virus infection. Biochim Biophys Acta. 2002;1577:325-36 pubmed
    ..Control of transcription elongation and termination in vaccinia virus bears some similarity to the same process in other prokaryotic and eukaryotic systems, yet features some novel mechanisms as well. ..
  28. Walker K, Mallik P, Pratt T, Osuna R. The Escherichia coli Fis promoter is regulated by changes in the levels of its transcription initiation nucleotide CTP. J Biol Chem. 2004;279:50818-28 pubmed
    ..In particular, CTP pools fluctuate in a manner consistent with a role in regulating fis expression. These observations support a model whereby fis expression is subject to regulation by the availability of its initiating NTP. ..
  29. Wassarman K, Saecker R. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science. 2006;314:1601-3 pubmed
    ..In vivo, 6S RNA-directed RNA synthesis occurs during outgrowth from the stationary phase and likely is responsible for liberating RNAP from 6S RNA in response to nutrient availability. ..
  30. Kore A, Shanmugasundaram M, Vlassov A. Synthesis and application of a new 2',3'-isopropylidene guanosine substituted cap analog. Bioorg Med Chem Lett. 2008;18:4828-32 pubmed publisher
    ..The observed increase in the level of protein synthesis is likely resulted as a consequence of exclusively forward capped transcripts and increased cellular stability of the 5'-modified capped mRNA (Poly A). ..
  31. Zhang J, Palangat M, Landick R. Role of the RNA polymerase trigger loop in catalysis and pausing. Nat Struct Mol Biol. 2010;17:99-104 pubmed publisher
    ..The similar effects of TL/TH substitutions on pausing and nucleotide addition provide additional support for the view that TH formation is rate-limiting for escape from nonbacktracked pauses. ..
  32. Newlands J, Josaitis C, Ross W, Gourse R. Both fis-dependent and factor-independent upstream activation of the rrnB P1 promoter are face of the helix dependent. Nucleic Acids Res. 1992;20:719-26 pubmed
    ..We also demonstrate that RNAP interacts with the -53 region of the rrnB P1 UAR even when these sequences are displaced upstream of the RNAP binding site, and that these interactions correlate with factor-independent activation. ..
  33. Alarcon Chaidez F, Keith L, Zhao Y, Bender C. RpoN (sigma(54)) is required for plasmid-encoded coronatine biosynthesis in Pseudomonas syringae. Plasmid. 2003;49:106-17 pubmed
    ..Our results indicate that rpoN is required for growth and the expression of both chromosomal and plasmid-encoded virulence factors in P. syringae pv. glycinea PG4180. ..
  34. Losick V, Schlax P, Emmons R, Lawson T. Signals in hepatitis A virus P3 region proteins recognized by the ubiquitin-mediated proteolytic system. Virology. 2003;309:306-19 pubmed
  35. Toulokhonov I, Landick R. The role of the lid element in transcription by E. coli RNA polymerase. J Mol Biol. 2006;361:644-58 pubmed
    ..Importantly, Deltalid RNAP behaved differently from wild-type RNAP when transcribing single-stranded DNA templates where it synthesized long, persistent RNA:DNA hybrids, in contrast to efficient transcriptional arrest by wild-type RNAP. ..
  36. Gaal T, Mandel M, Silhavy T, Gourse R. Crl facilitates RNA polymerase holoenzyme formation. J Bacteriol. 2006;188:7966-70 pubmed
    ..Our results suggest that Crl facilitates holoenzyme formation, the first positive regulator identified with this mechanism of action. ..
  37. Vassylyev D, Vassylyeva M, Perederina A, Tahirov T, Artsimovitch I. Structural basis for transcription elongation by bacterial RNA polymerase. Nature. 2007;448:157-62 pubmed publisher
    ..The RNA is threaded through the RNA exit channel, where it adopts a conformation mimicking that of a single strand within a double helix, providing insight into a mechanism for hairpin-dependent pausing and termination...
  38. Peters J, Mooney R, Kuan P, Rowland J, Keles S, Landick R. Rho directs widespread termination of intragenic and stable RNA transcription. Proc Natl Acad Sci U S A. 2009;106:15406-11 pubmed publisher
    ..These Rho-terminated antisense transcripts point to a role of noncoding transcription in E. coli gene regulation that may resemble the ubiquitous noncoding transcription recently found to play myriad roles in eukaryotic gene regulation. ..
  39. Lodeiro M, Uchida A, Arnold J, Reynolds S, Moustafa I, Cameron C. Identification of multiple rate-limiting steps during the human mitochondrial transcription cycle in vitro. J Biol Chem. 2010;285:16387-402 pubmed publisher
  40. Flowers S, Beck G, Moran E. Transcriptional activation by pRB and its coordination with SWI/SNF recruitment. Cancer Res. 2010;70:8282-7 pubmed publisher
    ..Dissociation of BRM-containing SWI/SNF depends on p300, and association of BRG1-containing SWI/SNF depends on pRB. ..
  41. Artsimovitch I, Vassylyeva M, Svetlov D, Svetlov V, Perederina A, Igarashi N, et al. Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins. Cell. 2005;122:351-63 pubmed publisher
    ..Based on structural predictions, we designed enzyme substitutions that apparently interrupt this allosteric signal...
  42. Grdzelishvili V, Smallwood S, Tower D, Hall R, Hunt D, Moyer S. Identification of a new region in the vesicular stomatitis virus L polymerase protein which is essential for mRNA cap methylation. Virology. 2006;350:394-405 pubmed
    ..J. Virol. 79, 13373-13384], a new region between L amino acids 1450-1481 was identified which is critical for mRNA cap methylation. ..
  43. Duckworth D, Pinkerton T. ColIb plasmid genes that inhibit the replication of T5 and T7 bacteriophage. Plasmid. 1988;20:182-93 pubmed
    ..Promoters for pic have been mapped and hypotheses to explain the inhibition of T7 by a cloned gene but not the whole ColIb plasmid are presented...
  44. Wickstrum J, Egan S. Amino acid contacts between sigma 70 domain 4 and the transcription activators RhaS and RhaR. J Bacteriol. 2004;186:6277-85 pubmed
    ..Our genetic loss-of-contact analysis of these residues indicates that they identify a second site of contact between RhaS and sigma70. ..
  45. Van Wynsberghe A, Li G, Cui Q. Normal-mode analysis suggests protein flexibility modulation throughout RNA polymerase's functional cycle. Biochemistry. 2004;43:13083-96 pubmed
    ..These two observations validate that both of the RNAP crab claw's pincers are mobile, as both beta and beta' have substantial flexibility. ..
  46. Kim J, Yang Y, Chambliss G. Evidence that Bacillus catabolite control protein CcpA interacts with RNA polymerase to inhibit transcription. Mol Microbiol. 2005;56:155-62 pubmed
    ..5), CcpA blocked transcription initiation, not elongation (roadblock) at the site of the cre. Taken together, our results strongly suggest that CcpA requires interactions with RNAP to inhibit transcription...
  47. Mooney R, Davis S, Peters J, Rowland J, Ansari A, Landick R. Regulator trafficking on bacterial transcription units in vivo. Mol Cell. 2009;33:97-108 pubmed publisher
    ..However, inhibition of rho did not increase RNAP levels within genes downstream from the RNAP peaks, suggesting the peaks are caused by a mechanism other than rho-dependent attenuation. ..
  48. Chen Y, Livingston C, Carrington Lawrence S, Bai P, Weller S. A mutation in the human herpes simplex virus type 1 UL52 zinc finger motif results in defective primase activity but can recruit viral polymerase and support viral replication efficiently. J Virol. 2007;81:8742-51 pubmed publisher
    ..We showed that UL30 was extracted from replication compartments while UL42 remained bound, suggesting that UL30 may be tethered to the replication fork by protein-protein interactions...
  49. Hirata A, Klein B, Murakami K. The X-ray crystal structure of RNA polymerase from Archaea. Nature. 2008;451:851-4 pubmed publisher
    ..The striking structural similarity between archaeal RNAP and eukaryotic RNAPII highlights the simpler archaeal RNAP as an ideal model system for dissecting the molecular basis of eukaryotic transcription...
  50. Vrentas C, Gaal T, Berkmen M, Rutherford S, Haugen S, Vassylyev D, et al. Still looking for the magic spot: the crystallographically defined binding site for ppGpp on RNA polymerase is unlikely to be responsible for rRNA transcription regulation. J Mol Biol. 2008;377:551-64 pubmed publisher
    ..coli ribosomal RNA transcription initiation and highlight the importance of inclusion of omega in bacterial RNAP preparations. ..
  51. Belogurov G, Vassylyeva M, Sevostyanova A, Appleman J, Xiang A, Lira R, et al. Transcription inactivation through local refolding of the RNA polymerase structure. Nature. 2009;457:332-5 pubmed publisher
    ..The universally conserved switch-2 may have the same role in all multisubunit RNAPs. ..
  52. Lennon C, Gaal T, Ross W, Gourse R. Escherichia coli DksA binds to Free RNA polymerase with higher affinity than to RNA polymerase in an open complex. J Bacteriol. 2009;191:5854-8 pubmed publisher
    ..These results suggest that the conformation of RNAP present in an open complex is not optimal for DksA binding and that DNA directly or indirectly alters the interface between the two proteins. ..
  53. Toulokhonov I, Artsimovitch I, Landick R. Allosteric control of RNA polymerase by a site that contacts nascent RNA hairpins. Science. 2001;292:730-3 pubmed
    ..These findings favor an allosteric model for regulation of transcript elongation. ..
  54. Simeonov M, Bieber Urbauer R, Gilmore J, Adelman K, Brody E, Niedziela Majka A, et al. Characterization of the interactions between the bacteriophage T4 AsiA protein and RNA polymerase. Biochemistry. 2003;42:7717-26 pubmed
  55. Roy H, Ling J, Alfonzo J, Ibba M. Loss of editing activity during the evolution of mitochondrial phenylalanyl-tRNA synthetase. J Biol Chem. 2005;280:38186-92 pubmed
  56. Wickstrum J, Santangelo T, Egan S. Cyclic AMP receptor protein and RhaR synergistically activate transcription from the L-rhamnose-responsive rhaSR promoter in Escherichia coli. J Bacteriol. 2005;187:6708-18 pubmed
    ..It therefore appears that CRP activates transcription from rhaSR as it would at simple class I promoters, albeit from a relatively distant position. ..
  57. Sukhodolets M, Garges S, Adhya S. Ribosomal protein S1 promotes transcriptional cycling. RNA. 2006;12:1505-13 pubmed
  58. Cresawn S, Prins C, Latner D, Condit R. Mapping and phenotypic analysis of spontaneous isatin-beta-thiosemicarbazone resistant mutants of vaccinia virus. Virology. 2007;363:319-32 pubmed
    ..The results implicate the largest subunit of the RNA polymerase (rpo147) in the control of elongation, and suggest that there exist additional gene products which mediate intermediate and late transcription elongation in vaccinia virus. ..
  59. Svetlov V, Belogurov G, Shabrova E, Vassylyev D, Artsimovitch I. Allosteric control of the RNA polymerase by the elongation factor RfaH. Nucleic Acids Res. 2007;35:5694-705 pubmed
  60. Haugen S, Ross W, Manrique M, Gourse R. Fine structure of the promoter-sigma region 1.2 interaction. Proc Natl Acad Sci U S A. 2008;105:3292-7 pubmed publisher
    ..2. Our results refine models of RNAP-DNA interactions in the promoter complex that are crucial for regulation of transcription initiation. ..
  61. Dhakal S, Schonhoft J, Koirala D, Yu Z, Basu S, Mao H. Coexistence of an ILPR i-motif and a partially folded structure with comparable mechanical stability revealed at the single-molecule level. J Am Chem Soc. 2010;132:8991-7 pubmed publisher
    ..This suggests, from a mechanical perspective alone, that either of the structures can stop RNA transcription. ..
  62. Meijer W, Tabita F. Isolation and characterization of the nifUSVW-rpoN gene cluster from Rhodobacter sphaeroides. J Bacteriol. 1992;174:3855-66 pubmed
    ..Similar regions were found in pyruvate carboxylase and oxaloacetate decarboxylase. It is proposed that these conserved regions represent keto acid-binding sites. ..
  63. Rao L, Ross W, Appleman J, Gaal T, Leirmo S, Schlax P, et al. Factor independent activation of rrnB P1. An "extended" promoter with an upstream element that dramatically increases promoter strength. J Mol Biol. 1994;235:1421-35 pubmed
    ..A functional UP element is not absolutely essential for stimulation of rrnB P1 by the Fis protein. ..
  64. Arthur T, Anthony L, Burgess R. Mutational analysis of beta '260-309, a sigma 70 binding site located on Escherichia coli core RNA polymerase. J Biol Chem. 2000;275:23113-9 pubmed
    ..A. (1999) Cell 98, 811-824), the region homologous to beta'(260-309) of Escherichia coli forms a coiled coil. Modeling of our mutations onto that coiled coil places the most defective mutations on one face of the coiled coil. ..
  65. Xie Y, Reeve J. Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J Bacteriol. 2004;186:3492-8 pubmed
    ..This inhibited transcription presumably by preventing archaeal TATA-box binding protein, general transcription factor TFB, and RNAP access and thus inhibiting transcription initiation...
  66. Lawrence P. Purification and partial characterization of an entomopoxvirus (DLEPV) from a parasitic wasp of tephritid fruit flies. J Insect Sci. 2002;2:10 pubmed
    ..Unlike other EPVs, DlEPV does not express the spheroidin protein. Since it also replicates in both the wasp and fly, members of two different insect Orders, DlEPV may represent a new EPV Group, or a subgroup of the Group C viruses...
  67. Kulbachinskiy A, Feklistov A, Krasheninnikov I, Goldfarb A, Nikiforov V. Aptamers to Escherichia coli core RNA polymerase that sense its interaction with rifampicin, sigma-subunit and GreB. Eur J Biochem. 2004;271:4921-31 pubmed
    ..We propose that the aptamers obtained in this work will be useful for studying the interactions of RNAP with various ligands and regulatory factors and for investigating the conformational flexibility of the enzyme. ..
  68. Farris S, Rubio E, Moon J, Gombert W, Nelson B, Krumm A. Transcription-induced chromatin remodeling at the c-myc gene involves the local exchange of histone H2A.Z. J Biol Chem. 2005;280:25298-303 pubmed
    ..In combination, these results suggest a new model in which the incorporation of H2A.Z into nucleosomes down-regulates transcription; at the same time it may act as a cellular memory for transcriptionally poised gene domains. ..
  69. Singh K, Srivastava A, Patel S, Modak M. Participation of the fingers subdomain of Escherichia coli DNA polymerase I in the strand displacement synthesis of DNA. J Biol Chem. 2007;282:10594-604 pubmed
    ..We note that this 3-helix bundle motif also exists in prokaryotic RNA polymerase. Thus in both DNA and RNA polymerases, this motif may have been adopted to achieve the strand separation function. ..
  70. Davis C, Bingman C, Landick R, Record M, Saecker R. Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase. Proc Natl Acad Sci U S A. 2007;104:7833-8 pubmed
  71. Schroeder L, Gries T, Saecker R, Record M, Harris M, deHaseth P. Evidence for a tyrosine-adenine stacking interaction and for a short-lived open intermediate subsequent to initial binding of Escherichia coli RNA polymerase to promoter DNA. J Mol Biol. 2009;385:339-49 pubmed publisher
    ..These data refine the structural model for open complex formation and reveal a novel interaction involved in DNA melting by RNA polymerase. ..
  72. Belogurov G, Mooney R, Svetlov V, Landick R, Artsimovitch I. Functional specialization of transcription elongation factors. EMBO J. 2009;28:112-22 pubmed publisher
    ..We propose that RfaH and NusG may have opposite regulatory functions: although NusG appears to function in concert with Rho, RfaH inhibits Rho action and activates the expression of poorly translated, frequently foreign genes. ..
  73. Mooney R, Schweimer K, Rosch P, Gottesman M, Landick R. Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators. J Mol Biol. 2009;391:341-58 pubmed publisher
  74. Klocko A, Wassarman K. 6S RNA binding to Esigma(70) requires a positively charged surface of sigma(70) region 4.2. Mol Microbiol. 2009;73:152-64 pubmed publisher
    ..2 of sigma(70) are overlapping but distinct, raising interesting possibilities for how core promoter elements contribute to defining promoters that are sensitive to 6S RNA regulation. ..
  75. Wilcoxen S, Peterson C, Winkley C, Keller M, Jaehning J. Two forms of RPO41-dependent RNA polymerase. Regulation of the RNA polymerase by glucose repression may control yeast mitochondrial gene expression. J Biol Chem. 1988;263:12346-51 pubmed
    ..These results suggest that the mitochondrial RNA polymerase and, in consequence, mitochondrial transcription are regulated by carbon catabolite control. ..
  76. Erickson J, Vaughn V, Walter W, Neidhardt F, Gross C. Regulation of the promoters and transcripts of rpoH, the Escherichia coli heat shock regulatory gene. Genes Dev. 1987;1:419-32 pubmed
    ..5 degrees C but rpoH mRNA synthesis increases by less than twofold, indicating that there is post-transcriptional control of the level of rpoH mRNA and presumably of sigma 32. ..
  77. Mangus D, Jang S, Jaehning J. Release of the yeast mitochondrial RNA polymerase specificity factor from transcription complexes. J Biol Chem. 1994;269:26568-74 pubmed
    ..After the formation of a 13-nucleotide transcript, Mtf1p is no longer associated with Rpo41p on the DNA. These data establish that Mtf1p is functionally as well as structurally similar to eubacterial sigma factors. ..
  78. Frustaci J, O Brian M. The Escherichia coli visA gene encodes ferrochelatase, the final enzyme of the heme biosynthetic pathway. J Bacteriol. 1993;175:2154-6 pubmed
    ..The overexpressed protein was purified to near homogeneity and was found to contain ferrochelatase activity. The data show that the visA gene encodes ferrochelatase, and we propose that it be renamed hemH to reflect that conclusion. ..
  79. Artsimovitch I, Landick R. Interaction of a nascent RNA structure with RNA polymerase is required for hairpin-dependent transcriptional pausing but not for transcript release. Genes Dev. 1998;12:3110-22 pubmed
    ..Resistance of the paused complex to pyrophosphorolysis and its reversal by antisense oligonucleotides further suggest that interaction of the pause hairpin with RNA polymerase disengages the RNA 3' end from the active site. ..
  80. Kumari S, Simel E, Wolfe A. sigma(70) is the principal sigma factor responsible for transcription of acs, which encodes acetyl coenzyme A synthetase in Escherichia coli. J Bacteriol. 2000;182:551-4 pubmed
    ..In contrast, sigma(S) partially inhibits that transcription as cells enter stationary phase. ..
  81. Bhende P, Egan S. Genetic evidence that transcription activation by RhaS involves specific amino acid contacts with sigma 70. J Bacteriol. 2000;182:4959-69 pubmed
    ..More than 50% of AraC/XylS family members have Asp or Glu at the position of RhaS D241, suggesting that this interaction with sigma(70) may be conserved. ..
  82. Holcroft C, Egan S. Interdependence of activation at rhaSR by cyclic AMP receptor protein, the RNA polymerase alpha subunit C-terminal domain, and rhaR. J Bacteriol. 2000;182:6774-82 pubmed
    ..The magnitude of the synergistic effects was usually greater with just two activators than with all three, suggesting possible redundancies in the mechanisms of activation by CRP, alpha-CTD, and RhaR. ..
  83. Beatty C, Browning D, Busby S, Wolfe A. Cyclic AMP receptor protein-dependent activation of the Escherichia coli acsP2 promoter by a synergistic class III mechanism. J Bacteriol. 2003;185:5148-57 pubmed
    ..Other surface-exposed residues in the alpha-CTD contributed to acs transcription, suggesting that the alpha-CTD may interact with at least one protein other than CRP. ..
  84. Ross W, Gourse R. Sequence-independent upstream DNA-alphaCTD interactions strongly stimulate Escherichia coli RNA polymerase-lacUV5 promoter association. Proc Natl Acad Sci U S A. 2005;102:291-6 pubmed
  85. Paul B, Berkmen M, Gourse R. DksA potentiates direct activation of amino acid promoters by ppGpp. Proc Natl Acad Sci U S A. 2005;102:7823-8 pubmed
  86. Zheng B, Wang Z, Li S, Yu B, Liu J, Chen X. Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev. 2009;23:2850-60 pubmed publisher
    ..This study establishes that intergenic transcription by Pol II is required for siRNA-mediated TGS, and reveals an intricate collaboration and division of labor among the three polymerases in gene silencing. ..
  87. Siegele D, Hu J, Walter W, Gross C. Altered promoter recognition by mutant forms of the sigma 70 subunit of Escherichia coli RNA polymerase. J Mol Biol. 1989;206:591-603 pubmed
  88. Jin D, Gross C. Mapping and sequencing of mutations in the Escherichia coli rpoB gene that lead to rifampicin resistance. J Mol Biol. 1988;202:45-58 pubmed
    ..These alleles are located in three distinct clusters in the center of the rpoB gene. We discuss the implications of our results with regards to the structure of the rifampicin binding site. ..
  89. Janakiraman R, Brun Y. Transcriptional and mutational analyses of the rpoN operon in Caulobacter crescentus. J Bacteriol. 1997;179:5138-47 pubmed
    ..The mutations have no effect on the transcription of previously known sigma54-dependent flagellar promoters except for a slight effect of an ORF159 mutation on transcription of fljK. ..
  90. Ross W, Aiyar S, Salomon J, Gourse R. Escherichia coli promoters with UP elements of different strengths: modular structure of bacterial promoters. J Bacteriol. 1998;180:5375-83 pubmed
  91. Mooney R, Landick R. Tethering sigma70 to RNA polymerase reveals high in vivo activity of sigma factors and sigma70-dependent pausing at promoter-distal locations. Genes Dev. 2003;17:2839-51 pubmed
    ..coli (i.e., its thermodynamic activity) is close to its bulk concentration. At this level, sigma70 would be a bona fide elongation factor able to direct transcriptional pausing even after its release from RNAP during promoter escape. ..
  92. Trotochaud A, Wassarman K. 6S RNA function enhances long-term cell survival. J Bacteriol. 2004;186:4978-85 pubmed
    ..We conclude that 6S RNA regulation of both sigma(70) and sigma(S) activities contributes to increased cell persistence during nutrient deprivation. ..