rna polymerase sigma 54


Summary: A DNA-directed RNA polymerase found in BACTERIA. It is a holoenzyme that consists of multiple subunits including sigma factor 54.

Top Publications

  1. Doucleff M, Pelton J, Lee P, Nixon B, Wemmer D. Structural basis of DNA recognition by the alternative sigma-factor, sigma54. J Mol Biol. 2007;369:1070-8 pubmed publisher
    ..This structure elucidates the basis for sequence specific recognition of the -24 element, orients sigma(54) on the promoter, and suggests how the C-terminal domain of sigma(54) interacts with RNAP...
  2. Joly N, Rappas M, Buck M, Zhang X. Trapping of a transcription complex using a new nucleotide analogue: AMP aluminium fluoride. J Mol Biol. 2008;375:1206-11 pubmed
  3. Ouyang Z, Blevins J, Norgard M. Transcriptional interplay among the regulators Rrp2, RpoN and RpoS in Borrelia burgdorferi. Microbiology. 2008;154:2641-58 pubmed publisher
    ..Although several known B. burgdorferi virulence determinants were regulated by the RpoN-RpoS pathway, a defined function has yet to be ascribed to most of the genes substantially regulated by Rrp2, RpoN and RpoS. ..
  4. Bernardo L, Johansson L, Solera D, Skarfstad E, Shingler V. The guanosine tetraphosphate (ppGpp) alarmone, DksA and promoter affinity for RNA polymerase in regulation of sigma-dependent transcription. Mol Microbiol. 2006;60:749-64 pubmed
  5. Schumacher J, Joly N, Rappas M, Zhang X, Buck M. Structures and organisation of AAA+ enhancer binding proteins in transcriptional activation. J Struct Biol. 2006;156:190-9 pubmed
    ..Parallels with the substrate binding elements near the central pore of other AAA+ members are drawn. We propose a structural model of EBPs in complex with a sigma(54)-RNAP-promoter complex. ..
  6. Rappas M, Bose D, Zhang X. Bacterial enhancer-binding proteins: unlocking sigma54-dependent gene transcription. Curr Opin Struct Biol. 2007;17:110-6 pubmed
  7. Chaney M, Grande R, Wigneshweraraj S, Cannon W, Casaz P, Gallegos M, et al. Binding of transcriptional activators to sigma 54 in the presence of the transition state analog ADP-aluminum fluoride: insights into activator mechanochemical action. Genes Dev. 2001;15:2282-94 pubmed
    ..Energy transduction appears to occur through activator contacts to sigma(54) Region I. ADP-aluminum fluoride-dependent interactions and consideration of other AAA+ proteins provide insight into activator mechanochemical action. ..
  8. Jakobsen J, Jelsbak L, Jelsbak L, Welch R, Cummings C, Goldman B, et al. Sigma54 enhancer binding proteins and Myxococcus xanthus fruiting body development. J Bacteriol. 2004;186:4361-8 pubmed
    ..Three were previously unknown genes, and they were inactivated to look for effects on fruiting body development. One knockout mutant produced fruiting bodies of abnormal shape that depended on the composition of the medium. ..
  9. Cannon W, Wigneshweraraj S, Buck M. Interactions of regulated and deregulated forms of the sigma54 holoenzyme with heteroduplex promoter DNA. Nucleic Acids Res. 2002;30:886-93 pubmed
    ..DNA opening from -5 to -1 appears important for stable engagement of the holoenzyme following activation. The regulatory Region I of sigma54 was shown to be involved in interactions with the sequences in the -5 to -1 area. ..

More Information


  1. Tucker N, Ghosh T, Bush M, Zhang X, Dixon R. Essential roles of three enhancer sites in sigma54-dependent transcription by the nitric oxide sensing regulatory protein NorR. Nucleic Acids Res. 2010;38:1182-94 pubmed publisher
    ..We also find that site-specific DNA binding per se promotes oligomerisation but the DNA flanking the three sites is needed to further stabilise the functional higher order oligomer of NorR at the enhancers. ..
  2. Gardner A, Gessner C, Gardner P. Regulation of the nitric oxide reduction operon (norRVW) in Escherichia coli. Role of NorR and sigma54 in the nitric oxide stress response. J Biol Chem. 2003;278:10081-6 pubmed
    ..The results demonstrate the role of NorR as a sigma(54)-dependent regulator of norVW expression. A role for the NorR N-terminal domain as a transducer or sensor for NO is suggested. ..
  3. Ouyang Z, Deka R, Norgard M. BosR (BB0647) controls the RpoN-RpoS regulatory pathway and virulence expression in Borrelia burgdorferi by a novel DNA-binding mechanism. PLoS Pathog. 2011;7:e1001272 pubmed publisher
    ..Our findings also have broader implications regarding a previously unappreciated layer of control that can be involved in ???-dependent gene regulation in bacteria. ..
  4. Arous S, Buchrieser C, Folio P, Glaser P, Namane A, Hebraud M, et al. Global analysis of gene expression in an rpoN mutant of Listeria monocytogenes. Microbiology. 2004;150:1581-90 pubmed
    ..These results suggest that sigma(54) is mainly involved in the control of carbohydrate metabolism in L. monocytogenes via direct regulation of PTS activity, alteration of the pyruvate pool and modulation of carbon catabolite regulation. ..
  5. Yildiz F, Liu X, Heydorn A, Schoolnik G. Molecular analysis of rugosity in a Vibrio cholerae O1 El Tor phase variant. Mol Microbiol. 2004;53:497-515 pubmed
  6. Sallai L, Tucker P. Crystal structure of the central and C-terminal domain of the sigma(54)-activator ZraR. J Struct Biol. 2005;151:160-70 pubmed
    ..The dimerisation interface between DNA-binding domains observed in the crystal structure suggests that dodecamers, rather than hexamers, might be the functionally important oligomer. ..
  7. Kuczynska Wisnik D, Laskowska E, Taylor A. Transcription of the ibpB heat-shock gene is under control of sigma(32)- and sigma(54)-promoters, a third regulon of heat-shock response. Biochem Biophys Res Commun. 2001;284:57-64 pubmed
    ..coli besides pspA-E operon. Thus, heat-shock response involves three regulons controlled by sigma(32), sigma(24), and sigma(54) RNA polymerase subunits. ..
  8. Wigneshweraraj S, Casaz P, Buck M. Correlating protein footprinting with mutational analysis in the bacterial transcription factor sigma54 (sigmaN). Nucleic Acids Res. 2002;30:1016-28 pubmed
    ..Their properties support the view that the interface between sigma54 and core RNAP is functionally specialised. ..
  9. Studholme D, Buck M. The biology of enhancer-dependent transcriptional regulation in bacteria: insights from genome sequences. FEMS Microbiol Lett. 2000;186:1-9 pubmed
    ..By scanning their genome sequences, new functions have been predicted for enhancer-dependent transcription in A. aeolicus, Chlamydia trachomatis, Escherichia coli, Treponema pallidum and B. burgdorferi. ..
  10. Wigneshweraraj S, Savalia D, Severinov K, Buck M. Interplay between the beta' clamp and the beta' jaw domains during DNA opening by the bacterial RNA polymerase at sigma54-dependent promoters. J Mol Biol. 2006;359:1182-95 pubmed
    ..Clearly, regulated interplay between the mobile modules of the beta' and the sigma subunits of the RNAP appears to be necessary for stable OC formation. ..
  11. Poggio S, Osorio A, Dreyfus G, Camarena L. Transcriptional specificity of RpoN1 and RpoN2 involves differential recognition of the promoter sequences and specific interaction with the cognate activator proteins. J Biol Chem. 2006;281:27205-15 pubmed publisher
    ..In conclusion, two different molecular mechanisms underlie the transcriptional specialization of these sigma factors...
  12. Stigter J, Schneider M, de Bruijn F. Azorhizobium caulinodans nitrogen fixation (nif/fix) gene regulation: mutagenesis of the nifA -24/-12 promoter element, characterization of a ntrA(rpoN) gene, and derivation of a model. Mol Plant Microbe Interact. 1993;6:238-52 pubmed
    ..caulinodans nif genes, but not the central nif regulatory gene nifA. Based on these results, a new model for the regulation of nif/fix gene expression in A. caulinodans is proposed. ..
  13. Reichenbach B, Göpel Y, Görke B. Dual control by perfectly overlapping sigma 54- and sigma 70- promoters adjusts small RNA GlmY expression to different environmental signals. Mol Microbiol. 2009;74:1054-70 pubmed publisher
    ..Target genes regulated by YfhK and YfhA were unknown so far. We propose to rename these proteins to GlrK and GlrR, for glmY regulating kinase and response regulator respectively. ..
  14. Tintut Y, Wang J, Gralla J. A novel bacterial transcription cycle involving sigma 54. Genes Dev. 1995;9:2305-13 pubmed
    ..This unexpected pathway raises interesting possibilities for transcriptional regulation, especially with regard to control at the level of reinitiation. ..
  15. da Silva Neto J, Koide T, Abe C, Gomes S, Marques M. Role of sigma54 in the regulation of genes involved in type I and type IV pili biogenesis in Xylella fastidiosa. Arch Microbiol. 2008;189:249-61 pubmed
    ..These results indicate that sigma(54) differentially regulates genes involved in type IV and type I fimbrial biogenesis, and is involved in biofilm formation in X. fastidiosa. ..
  16. Bose D, Pape T, Burrows P, Rappas M, Wigneshweraraj S, Buck M, et al. Organization of an activator-bound RNA polymerase holoenzyme. Mol Cell. 2008;32:337-46 pubmed publisher
  17. Zhang N, Joly N, Burrows P, Jovanovic M, Wigneshweraraj S, Buck M. The role of the conserved phenylalanine in the sigma54-interacting GAFTGA motif of bacterial enhancer binding proteins. Nucleic Acids Res. 2009;37:5981-92 pubmed publisher
    ..The functionality of F85 is distinct from that of other GAFTGA residues, especially T86 where in contrast to F85 a clean uncoupling phenotype is observed. ..
  18. Schumacher J, Zhang X, Jones S, Bordes P, Buck M. ATP-dependent transcriptional activation by bacterial PspF AAA+protein. J Mol Biol. 2004;338:863-75 pubmed
  19. Bittner M, Saldías S, Altamirano F, Valvano M, Contreras I. RpoS and RpoN are involved in the growth-dependent regulation of rfaH transcription and O antigen expression in Salmonella enterica serovar Typhi. Microb Pathog. 2004;36:19-24 pubmed
    ..Thus, we conclude that both RpoS and RpoN control the rfaH promoter activity and concomitantly, the production of O-specific LPS in S. typhi. ..
  20. Gonz lez V, Bustos P, Ram rez Romero M, Medrano Soto A, Salgado H, Hern ndez Gonz lez I, et al. The mosaic structure of the symbiotic plasmid of Rhizobium etli CFN42 and its relation to other symbiotic genome compartments. Genome Biol. 2003;4:R36 pubmed publisher
    ..Our data support the notion that the symbiotic compartments of rhizobia genomes are mosaic structures that have been frequently tailored by recombination, horizontal transfer and transposition...
  21. Brun Y, Shapiro L. A temporally controlled sigma-factor is required for polar morphogenesis and normal cell division in Caulobacter. Genes Dev. 1992;6:2395-408 pubmed
    ..of many spatially and temporally controlled flagellar structural genes in Caulobacter requires the RNA polymerase sigma 54 subunit...
  22. Reitzer L. Nitrogen assimilation and global regulation in Escherichia coli. Annu Rev Microbiol. 2003;57:155-76 pubmed
    ..Guanosine tetraphosphate appears to control Lrp synthesis. In summary, a network of interacting global regulators that senses different aspects of metabolism integrates nitrogen assimilation with other metabolic processes. ..
  23. Studholme D, Dixon R. Domain architectures of sigma54-dependent transcriptional activators. J Bacteriol. 2003;185:1757-67 pubmed
  24. Kiupakis A, Reitzer L. ArgR-independent induction and ArgR-dependent superinduction of the astCADBE operon in Escherichia coli. J Bacteriol. 2002;184:2940-50 pubmed
    ..The transcriptional regulation of the ast operon in E. coli differs from that in Salmonella enterica serovar Typhimurium, in which ArgR is required for ast operon expression. ..
  25. Powell B, Court D, Inada T, Nakamura Y, Michotey V, Cui X, et al. Novel proteins of the phosphotransferase system encoded within the rpoN operon of Escherichia coli. Enzyme IIANtr affects growth on organic nitrogen and the conditional lethality of an erats mutant. J Biol Chem. 1995;270:4822-39 pubmed
    ..These results support our previous proposal of a novel mechanism linking carbon and nitrogen assimilation and relates IIANtr to the unknown process regulated by the essential GTPase Era...
  26. Hsieh M, Gralla J. Analysis of the N-terminal leucine heptad and hexad repeats of sigma 54. J Mol Biol. 1994;239:15-24 pubmed
    ..The collection of data suggests that the N-terminal region contains overlapping functional motifs, hydrophobic heptad and glutamine-rich, which together appear to constitute the activation domain of sigma 54. ..
  27. Jovanovic G, Weiner L, Model P. Identification, nucleotide sequence, and characterization of PspF, the transcriptional activator of the Escherichia coli stress-induced psp operon. J Bacteriol. 1996;178:1936-45 pubmed
    ..In the absence of inducing stimuli, multicopy-plasmid-borne PspF or PspF delta HTH overcomes repression of the psp operon mediated by the negative regulator PspA. ..
  28. Michiels J, Van Soom T, D hooghe I, Dombrecht B, Benhassine T, de Wilde P, et al. The Rhizobium etli rpoN locus: DNA sequence analysis and phenotypical characterization of rpoN, ptsN, and ptsA mutants. J Bacteriol. 1998;180:1729-40 pubmed
    ..These results suggest that ptsN and ptsA are part of the same regulatory cascade, the inactivation of which renders the cells sensitive to toxic effects of elevated concentrations of malate or succinate. ..
  29. Svergun D, Malfois M, Koch M, Wigneshweraraj S, Buck M. Low resolution structure of the sigma54 transcription factor revealed by X-ray solution scattering. J Biol Chem. 2000;275:4210-4 pubmed
    ..Potential DNA binding surfaces of sigma54 are also predicted by comparison with the sigma54 core binding fragment. ..
  30. Vogel S, Schulz A, Rippe K. Binding affinity of Escherichia coli RNA polymerase*sigma54 holoenzyme for the glnAp2, nifH and nifL promoters. Nucleic Acids Res. 2002;30:4094-101 pubmed
    ..1 +/- 0.5 for the glnAp2, 5.2 +/- 1.2 for the nifH and 2.1 +/- 0.1 for the nifL promoter. This suggests that the polymerase can form fewer ion pairs with the nifL promoter, which would account for its weaker binding affinity...
  31. Wong C, Gralla J. A role for the acidic trimer repeat region of transcription factor sigma 54 in setting the rate and temperature dependence of promoter melting in vivo. J Biol Chem. 1992;267:24762-8 pubmed
    ..The acid region is required for these changes to occur fully at physiological temperature and influences the rate at which they occur. ..
  32. Ramakrishnan G, Zhao J, Newton A. Multiple structural proteins are required for both transcriptional activation and negative autoregulation of Caulobacter crescentus flagellar genes. J Bacteriol. 1994;176:7587-600 pubmed
    ..We also discuss the requirement of multiple structural genes for regulation of levels II and III genes and suggest that fla gene expression in C. crescentus may be coupled to two checkpoints in flagellum assembly...
  33. Leang C, Krushkal J, Ueki T, Puljic M, Sun J, Ju rez K, et al. Genome-wide analysis of the RpoN regulon in Geobacter sulfurreducens. BMC Genomics. 2009;10:331 pubmed publisher
    ..The G. sulfurreducens RpoN is an essential sigma factor and a global regulator involved in a complex transcriptional network controlling a variety of cellular processes...
  34. Klose K, Mekalanos J. Distinct roles of an alternative sigma factor during both free-swimming and colonizing phases of the Vibrio cholerae pathogenic cycle. Mol Microbiol. 1998;28:501-20 pubmed
    ..cholerae life cycle, and some as yet unidentified gene(s) that aid colonization within the host...
  35. Pohlmann A, Cramm R, Schmelz K, Friedrich B. A novel NO-responding regulator controls the reduction of nitric oxide in Ralstonia eutropha. Mol Microbiol. 2000;38:626-38 pubmed
    ..eutropha. This reaction is not strictly co-ordinated on the regulatory level with the other nitrogen oxide-reducing steps of the denitrification chain that are independent of NorR. ..
  36. Huo Y, Tian Z, Rappas M, Wen J, Chen Y, You C, et al. Protein-induced DNA bending clarifies the architectural organization of the sigma54-dependent glnAp2 promoter. Mol Microbiol. 2006;59:168-80 pubmed
    ..This proposal is further supported by the modelling of activator-promoter DNA-Esigma54 complex. ..
  37. Zhang X, Chaney M, Wigneshweraraj S, Schumacher J, Bordes P, Cannon W, et al. Mechanochemical ATPases and transcriptional activation. Mol Microbiol. 2002;45:895-903 pubmed
    ..In particular, interprotomer ATP interactions rely upon the use of an arginine finger, a situation reminiscent of GTPase-activating proteins. ..
  38. Hubner A, Yang X, Nolen D, Popova T, Cabello F, Norgard M. Expression of Borrelia burgdorferi OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway. Proc Natl Acad Sci U S A. 2001;98:12724-9 pubmed
    ..burgdorferi. Our findings provide a foundation for elucidating further key regulatory networks that potentially impact many aspects of B. burgdorferi's parasitic strategy, host range, and virulence expression. ..
  39. Hutcheson S, Bretz J, Sussan T, Jin S, Pak K. Enhancer-binding proteins HrpR and HrpS interact to regulate hrp-encoded type III protein secretion in Pseudomonas syringae strains. J Bacteriol. 2001;183:5589-98 pubmed
    ..Physical interaction of HrpR and HrpS was confirmed by column-binding experiments. The results show that HrpR and HrpS physically interact to regulate the sigma(54)-dependent hrpL promoter in P. syringae strains. ..
  40. Clark S, Oresnik I, Hynes M. RpoN of Rhizobium leguminosarum bv. viciae strain VF39SM plays a central role in FnrN-dependent microaerobic regulation of genes involved in nitrogen fixation. Mol Gen Genet. 2001;264:623-33 pubmed
    ..This suggests that the reduced fixG::lacZ expression seen in the rpoN background is due to the dependence of fnrN expression on RpoN. ..
  41. Rappas M, Schumacher J, Beuron F, Niwa H, Bordes P, Wigneshweraraj S, et al. Structural insights into the activity of enhancer-binding proteins. Science. 2005;307:1972-5 pubmed
    ..Comparing enhancer-binding structures in different nucleotide states and mutational analysis led us to propose nucleotide-dependent conformational changes that free the loops for association with sigma54. ..
  42. Burrows P, Schumacher J, Amartey S, Ghosh T, Burgis T, Zhang X, et al. Functional roles of the pre-sensor I insertion sequence in an AAA+ bacterial enhancer binding protein. Mol Microbiol. 2009;73:519-33 pubmed publisher
  43. Bush M, Dixon R. The role of bacterial enhancer binding proteins as specialized activators of ?54-dependent transcription. Microbiol Mol Biol Rev. 2012;76:497-529 pubmed publisher
    ..Particular attention is paid to the importance of ?(54) to the bacterial cell and its unique role in regulating transcription. ..
  44. Zhang N, Joly N, Buck M. A common feature from different subunits of a homomeric AAA+ protein contacts three spatially distinct transcription elements. Nucleic Acids Res. 2012;40:9139-52 pubmed publisher
    ..The mechanistic implications for these multivalent L1 interactions are elaborated in the light of available structures for the bEBP and its target complexes. ..
  45. Bernard C, Brunet Y, Gavioli M, Lloubes R, Cascales E. Regulation of type VI secretion gene clusters by sigma54 and cognate enhancer binding proteins. J Bacteriol. 2011;193:2158-67 pubmed publisher
    ..Using in vitro binding experiments and in vivo reporter fusion assays, we showed that the expression of these clusters is dependent on both ?(54) and bEBPs. ..
  46. Reitzer L, Schneider B. Metabolic context and possible physiological themes of sigma(54)-dependent genes in Escherichia coli. Microbiol Mol Biol Rev. 2001;65:422-44, table of contents pubmed
    ..Such a relationship may limit the number of physiological themes of sigma(54)-dependent genes within a single organism and may partially account for the unique features of sigma(54) and sigma(54)-dependent gene expression. ..
  47. Gao M, D Haeze W, De Rycke R, Holsters M. Dual control of the nodA operon of Azorhizobium caulinodans ORS571 by a nod box and a NifA-sigma54-type promoter. Mol Genet Genomics. 2001;265:1050-9 pubmed
  48. Jishage M, Iwata A, Ueda S, Ishihama A. Regulation of RNA polymerase sigma subunit synthesis in Escherichia coli: intracellular levels of four species of sigma subunit under various growth conditions. J Bacteriol. 1996;178:5447-51 pubmed
  49. Keseler I, Kaiser D. sigma54, a vital protein for Myxococcus xanthus. Proc Natl Acad Sci U S A. 1997;94:1979-84 pubmed
    ..The product of the rpoN gene, sigma54, therefore appears to be essential for growth in M. xanthus. ..
  50. Wigneshweraraj S, Burrows P, Bordes P, Schumacher J, Rappas M, Finn R, et al. The second paradigm for activation of transcription. Prog Nucleic Acid Res Mol Biol. 2005;79:339-69 pubmed
  51. Dworkin J, Jovanovic G, Model P. The PspA protein of Escherichia coli is a negative regulator of sigma(54)-dependent transcription. J Bacteriol. 2000;182:311-9 pubmed
    ..We describe here the in vivo and in vitro properties of the PspA protein of Escherichia coli, which negatively regulates expression of the pspA promoter without binding DNA directly. ..
  52. Rappas M, Schumacher J, Niwa H, Buck M, Zhang X. Structural basis of the nucleotide driven conformational changes in the AAA+ domain of transcription activator PspF. J Mol Biol. 2006;357:481-92 pubmed
    ..Striking similarities in nucleotide-specific conformational changes and atomic switch exist between PspF and the large T antigen helicase, suggesting conservation in the origin of those events amongst AAA(+) proteins. ..
  53. Gallegos M, Buck M. Sequences in sigma(54) region I required for binding to early melted DNA and their involvement in sigma-DNA isomerisation. J Mol Biol. 2000;297:849-59 pubmed
    ..DNA-binding, sigma isomerisation and transcription activation assays allow formulation of a functional map of region I. ..