1887

Microbiology Society logo

Volume 140, Issue 5

Molecular analysis of the operon which encodes the RNA polymerase sigma factor of Free

Abstract

The gene (encoding the sigma factor σ) of was cloned and its nucleotide sequence determined. Promoter probe analysis confirmed the presence of a promoter in a 350 bp fragment covering the start of . The likely promoter was identified. The nucleotide sequence of the region extending 2·1 kb downstream of was also determined. This region contained four open reading frames encoding potential polypeptides of 10750, 17959, 32492 and 9810 Da; maxicell and T7 promoter studies showed that four polypeptides of similar molecular masses were expressed from this region. The amino acid sequence of the 17959 Da polypeptide showed homology to the enzyme IIA domains of several proteins of the bacterial sugar phosphotransferase system (PTS), and the 9810 Da polypeptide showed homology to the HPr proteins of the bacterial PTS. The proteins encoded downstream of are known to negatively regulate σ activity. The homologies therefore suggest that this effect on σ may be mediated by sequential protein phosphorylation and suggest that there is a link between signal transduction and transcription of σ-dependent genes.

  • Received:
  • Accepted:
  • Revised:
  • Published Online:
Keyword(s): Escherichia coli , rpoN , sigma factor , signal transduction and sugar phosphotransferase system
© Society for General Microbiology 1994
Loading

Article metrics loading...

/content/journal/micro/10.1099/13500872-140-5-1035
1994-05-01
2024-04-18
Loading full text...

Full text loading...

/deliver/fulltext/micro/140/5/mic-140-5-1035.html?itemId=/content/journal/micro/10.1099/13500872-140-5-1035&mimeType=html&fmt=ahah

References

  1. Albright L. M., Ronson C. W., Nixon B. T., Ausubel F. M. 1989; Identification of a gene linked to Rhizobium meliloti ntr A whose product is homologous to a family of ATP-binding proteins. J Bacteriol 171:1932–1941
     [Google Scholar]
  2. Alifano P., Rivellini F., Limanro D., Bruni C. B., Carlomagno M. S. 1991; A consensus motif common to all rho-dependent prokaryotic transcription terminators. Cell 64:553–563
     [Google Scholar]
  3. Berger D. K., Woods D. R., Rawlings D. E. 1990; Complementation of Escherichia coli abi (Ntr A)-dependent formate hydrogen lyase activity by a cloned Thiobacillus ferrooxidans ntr A gene. J Bacteriol 172:4399–4406
     [Google Scholar]
  4. Birkman A., Sawers R. G., Bock A. 1987; Factors affecting transcriptional regulation of the formate-hydrogen-lyase pathway of Escherichia coli.. Arch Microbiol 148:44–51
     [Google Scholar]
  5. Birnboim H.C., Doly J. 1979; A rapid alkaline extraction procedure for screening recombinant plasmid DNA. Nucleic Acids Res 7:1513–1523
     [Google Scholar]
  6. Brun Y.V., Shapiro L. 1992; A temporally controlled cr-factor is required for polar morphogenesis and normal cell division in Caulobacter.. Genes and Dev 6:2395–2408
     [Google Scholar]
  7. Byrne C. R., Monroe R. S., Ward K. A., Kredich N. M. 1988; DNA sequences of the cjs K regions of Salmonella typhimurium and Escherichia coli and linkage of the cjs K regions to pts H.. J Bacteriol 170:3150–3157
     [Google Scholar]
  8. Castano I., Bastarrachea F. 1984; gln F-lac Z fusions in Escherichia coli studies on gln F expression and its chromosomal orientation. Mol and Gen Genet 195:228–233
     [Google Scholar]
  9. Chen Y., Fairbrother W. J., Wright P. E. 1993; Three-dimensional structures of the central regulatory proteins of the bacterial phosphotransferase system, HPr and enzyme IIAgle. J Cell Biochem 51:75–82
     [Google Scholar]
  10. Debarbouille M., Martin-Verstraete I., Kunst F., Rapoport G. 1991; The Bacillus subtilis sig L gene encodes an equivalent of a5i from Gram-negative bacteria. Proc Natl Acad Sci USA 88:9092–9096
     [Google Scholar]
  11. De Bruijn F. J., Ausubel F. M. 1983; The cloning and characterisation of the gln F (ntr A) gene of Klebsiella pneumoniae: role of gln F (ntr A) in the regulation of nitrogen fixation (nif) and other nitrogen assimilation genes.. Mol and Gen Genet 192:342–353
     [Google Scholar]
  12. De Reuse H., Roy A., Danchin A. 1985; Analysis of the pts H ptsl crr region in Escherichia coli K12: nucleotide sequence of the pts H gene. Gene 35:199–207
     [Google Scholar]
  13. Deutscher J., Pevec B., Beyreuther K., Kiltz H., Hengstenberg W. 1986; Streptococcal phosphoenolpyruvate-sugar phospho-transferase system: amino acid sequence and site of ATP-dependent phosphorylation of HPr. Biochemistry 25:6543–6551
     [Google Scholar]
  14. Devereux J., Haeberli P., Smithies O. 1984; A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res 12:387–395
     [Google Scholar]
  15. Dixon R. 1986; The xyl ABC promoter from the Pseudomonas putida TOL plasmid is activated by nitrogen regulatory genes in Escherichia coli.. Mol and Gen Genet 203:129–136
     [Google Scholar]
  16. Eisermann R., Fischer R., Kessler U., Neubauer A., Hengstenberg W. 1991; Staphylococcal phosphoenolpyruvate - dependent phosphotransferase system. Purification and protein sequencing of the Staphylococcus carnosus histidine-containing protein, and cloning and DNA sequencing of the pts H gene. Fur J Biochem 197:9–14
     [Google Scholar]
  17. Fischer R., Eisermann R., Reiche B., Hengstenberg W. 1989; Cloning, sequencing and overexpression of the mannitol-specific enzyme-III-coding gene of Staphylococcus carnosus.. Gene 82:249–257
     [Google Scholar]
  18. Frey J., Bagdasarian M., Feiss D., Franklin F. C. H., Deshusses J. 1983; Stable cosmid vectors that enable the introduction of cloned fragments into a wide range of Gram-negative bacteria. Gene 24:299–308
     [Google Scholar]
  19. Frischauf A.-M., Lehrach H., Poustka A., Murray N. 1983; Lambda replacement vectors carrying polylinker sequences. J Mol Biol 170:827–842
     [Google Scholar]
  20. Gagnon G., Vadeboncoeur C., Levesque R. C., Frenette M. J. 1992; Cloning, sequencing and expression in Escherichia coli of the ptsl gene encoding enzyme I of the phosphoenolpyruvate: sugar phosphotransferase transport system from Streptococcus salivarius.. Gene 121:71–78
     [Google Scholar]
  21. Geerse R. H., Izzo F., Postma P. W. 1989; The PEP:fructose phosphotransferase system in Salmonella typhimurium: FPr combines Enzyme IIIFru and pseudo-HPr activities. Mol and Gen Genet 216:517–525
     [Google Scholar]
  22. Gonzy-Treboul G, Zagorec M., Rain-Guion M.-C., Steinmetz M. 1989; Phosphoenolpyruvate: sugar phosphotransferase system of Bacillus subtilis-. nucleotide sequence of pts X,pts H and the 5'-end of ptsl and evidence for a pts HI operon. Mol Microbiol 3:103–112
     [Google Scholar]
  23. Hirschman J., Wong P.-K., Sei K., Keener J., Kustu S. 1985; Products of nitrogen regulatory genes ntr A and ntr C of enteric bacteria activate gin A transcription in vitro: evidence that ntr A is a a factor. Proc Natl Acad Sci USA 82:7525–7529
     [Google Scholar]
  24. Hudson G.S., Davidson B. E. 1984; Nucleotide sequence and transcription of the phenylalanine and tyrosine operons of Escherichia coli K12. J Mol Biol 180:1023–1051
     [Google Scholar]
  25. Hunt T.P., Magasanik B. 1985; Transcription of gin A by purified Escherichia coli components: core RNA polymerase and the products of gln F, gln G and gln F.. Proc Natl Acad Sci USA 82:8453–8457
     [Google Scholar]
  26. Imaishi H., Gomada M., Inouye S., Nakazawa A. 1993; Physical map location of the rpo N gene of Escherichia coli.. J Bacteriol 175:1550–1551
     [Google Scholar]
  27. Inouye S., Yamada M., Nakazawa A., Nakazawa T. 1989; Cloning and sequence analysis of the ntr A (rpo N) gene of Pseudomonas putida.. Gene 85:145–152
     [Google Scholar]
  28. Ishimoto K.S., Lory S. 1989; Formation of pilin in Pseudomonas aeruginosa requires the alternative sigma factor (Rpo N) of RNA polymerase. Proc Natl Acad Sci USA 86:1954–1957
     [Google Scholar]
  29. Jagura-Burdzy G, Ibbotson J. P., Thomas C. M. 1991; The kor F region of broad-host-range plasmid RK2 encodes two polypeptides with transcriptional repressor activity. J Bacteriol 173:826–833
     [Google Scholar]
  30. Jones R., Haselkorn R. 1989; The DNA sequence of the Rhodobacter capsulatus ntr A, ntr B and ntr C gene analogues required for nitrogen fixation. Mol and Gen Genet 215:507–516
     [Google Scholar]
  31. Kahn M., Kolter R., Thomas C., Figurski D., Meyer R., Remaut E., Helinski D. R. 1979; Plasmid cloning vehicles derived from plasmids Col E1, R6K and RK2. Methods Enzymol 68:268–280
     [Google Scholar]
  32. Karin M., Smeal T. 1992; Control of transcription factors by signal transduction pathways: the beginning of the end. Trends Biochem Sci 17:418–422
     [Google Scholar]
  33. Karn J., Brenner S., Barnett L., Cesareni G. 1980; Novel bacteriophage 2 cloning vector. Proc Natl Acad Sci USA 77:5172–5176
     [Google Scholar]
  34. Kohler T., Cayrol J. M., Ramos J. L., Harayama S. 1989; Nucleotide and deduced amino acid sequence of the Rpo N σ-factor of Pseudomonas putida.. Nucleic Acids Res 17:10125
     [Google Scholar]
  35. Kullik I., Fritsche S., Knobel H., Sanjuan J., Hennecke H., Fischer H. 1991; Bradyrhigobium japonicum has two differentially regulated, functional homologs of the σ 54 gene (rpo N).. J Bacteriol 173:1125–1138
     [Google Scholar]
  36. Kustu S., Santero E., Keener J., Popham D., Weiss D. 1989; Expression of σ 54 (ntr A)-dependent genes is probably united by a common mechanism. Microbiol Rev 53:367–376
     [Google Scholar]
  37. Laemmli U.K. 1970; Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685
     [Google Scholar]
  38. Lee C.A., Saier M. H. 1983; Mannitol-specific Enzyme II of the bacterial phosphotransferase system.. J Biol Chem 258:10761–10767
     [Google Scholar]
  39. McKenny K., Shimatake H., Court D., Schmeissner U., Brady C., Rosenberg M. 1981; A system to study promoters and terminator signals recognised by Escherichia coli RNA polymerase.. In Gene Amplification and Analysis II pp. 383–415 Edited by Chirikjian J. C., Papas T. S. . Amsterdam: Elsevier;
     [Google Scholar]
  40. Meijer W.G., Tabita F. R. 1992; Isolation and characterization of the nit USW—rpo N gene cluster from Rhodobacter sphaeroides.. J Bacterial 174:3855–3866
     [Google Scholar]
  41. Merrick M.J., Coppard J. R. 1989; Mutations in genes downstream of the rpo N gene (encoding σ 54) of Klebsiella pneumoniae affect expression from σ 54-dependent promoters. Mol Microbiol 3:1765–1775
     [Google Scholar]
  42. Merrick M.J., Gibbins J. R. 1985; The nucleotide sequence of the nitrogen regulation gene ntr A of Klebsiella pneumoniae and comparison with conserved features in bacterial RNA polymerase sigma factors. Nucleic Acids Res 21:7607–7620
     [Google Scholar]
  43. Merrick M.J., Stewart W. D. P. 1985; Studies on the regulation and function of the Klebsiella pneumoniae ntr A gene. Gene 35:297–303
     [Google Scholar]
  44. Merrick M. J., Gibbins J., Toukdarian A. 1987; The nucleotide sequence of the sigma factor ntr A (rpo N) of Apotobacter vinelandii: analysis of conserved regions in Ntr A proteins. Mol and Gen Genet 210:323–330
     [Google Scholar]
  45. Merrick M., Jones D. H. A., Thomas C. M. 1993; Location of the rpo N gene on the physical map of Escherichia coli.. J Bacteriol 173:1548–1549
     [Google Scholar]
  46. Orchard L.M., Kornberg H. L. 1990; Sequence similarities between the gene specifying 1-phosphofructokinase (fru K), genes specifying other kinases in Escherichia coli K12, and lac C of Staphylococcus aureus.. Proc R Soc Eond B 242:87–90
     [Google Scholar]
  47. Popham D. L., Keener J., Kustu S. 1991; Purification of the alternate a factor, a54, from Salmonella typhimurium and characterization of the σ 54-holoenzyme. J Biol Chem 266:19510–19518
     [Google Scholar]
  48. Pries A., Priefert H., Kruger N., Steinbuchel A. 1991; Identification and characterization of two Alcaligenes eutrophus gene loci relevant to the poly(β-hydroxybutyric acid)-leaky phenotype which exhibit homology to pts H and ptsl of Escherichia coli.. J Bacteriol 173:5843–5853
     [Google Scholar]
  49. Reizer J., Deutscher J., Grenier F., Thompson J., Hengstenberg W., Saier W. H. 1988; The phosphoenolpyruvate: sugar phosphotransferase system in Gram-positive bacteria: properties, mechanism and regulation.. CRC Crit Rev Microbiol 15:297–338
     [Google Scholar]
  50. Reizer J., Reizer A., Saier M. H., Jacobsen G. R. 1992; A proposed link between nitrogen and carbon metabolism involving protein phosphorylation in bacteria. Protein Sci 1:722–726
     [Google Scholar]
  51. Reizer J., Romano A. H., Deutscher J. 1993; The role of phosphorylation of HPr, a phosphocarrier protein of the phospho-transferase system, in the regulation of carbon metabolism in Gram-positive bacteria. J Cell Biochem 51:19–24
     [Google Scholar]
  52. Ronson C. W., Nixon B. T., Albright L. M., Ausubel F. M. 1987; Rhizobium meliloti ntr A is required for diverse metabolic functions. J Bacteriol 169:2424–2431
     [Google Scholar]
  53. Sadaie Y., Takamatsu H., Nakamura K., Yamane K. 1991; Sequencing reveals similarity of the wild-type div+ gene of Bacillus subtilis to the Escherichia coli gene. Gene 98:101–105
     [Google Scholar]
  54. Saier M.H. 1993; Introduction: protein phosphorylation and signal transduction in bacteria. J Cell Biochem 51:1–6
     [Google Scholar]
  55. Saier M.H., Reizer J. 1992; Proposed uniform nomenclature for the proteins and protein domains of the bacterial phospho-enolpyruvate: sugar phosphotransferase system. J Bacteriol 174:1433–1438
     [Google Scholar]
  56. Sambrook J., Fritsch E. F., Maniatis T. 1989 Molecular Cloning. A Laboratory Manual, 2 nd edn.. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory;
     [Google Scholar]
  57. Sancar A., Hack A. M., Rupp W. D. 1978; Simple method for identification of plasmid-coded proteins. J Bacteriol 137:692–693
     [Google Scholar]
  58. Sanger F., Nicklen S., Coulsen A. R. 1977; DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
     [Google Scholar]
  59. Saraste M., Sibbaid P. R., Wittinghofer A. 1990; The P-loop - a common motif in ATP- and GTP-binding proteins. Trends Biol Sci 15:430–434
     [Google Scholar]
  60. Sasse-Dwight S, Gralla J. D. 1990; Role of eukaryotic-type functional domains found in the prokaryotic enhancer receptor factor σ 54 . Cell 62:945–954
     [Google Scholar]
  61. Shingler V., Thomas C. M. 1984; Analysis of the trf A region of broad host range plasmid RK2 by transposon mutagenesis and identification of polypeptide products. J Mol Biol 175:523–529
     [Google Scholar]
  62. van Slooten J. C., Cervantes E., Broughton W. J., Wong C. H., Stanley J. 1990; Sequence and analysis of the rpo N sigma factor gene of Rhizobium sp. strain NGR234, a primary coregulator of symbiosis. J Bacteriol 172:5563–5574
     [Google Scholar]
  63. Stewart V. J., Parales J., Merkel S. M. 1989; Structure of the genes nar E and nar X of the nar locus in Escherichia coli K12. J Bacteriol 171:2229–2234
     [Google Scholar]
  64. Titgemeyer F., Eisermann R., Hengstenberg W., Lengeler J. W. 1990; The nucleotide sequence of pts H from Klebsiella pneumoniae.. Nucleic Acids Res 18:1898
     [Google Scholar]
  65. Walker J. E., Saraste M., Runswick M. J., Gay N. J. 1982; Distantly related sequences in the α- and β-subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–951
     [Google Scholar]
  66. Warrelmann J., Eitinger M., Schwartz E., Romermann D, Friedrich B. 1992; Nucleotide sequence of the rpo N (hno) gene cluster of Alcaligenes eutrophus-. evidence for a conserved gene cluster. Arch Microbiol 158:107–114
     [Google Scholar]
  67. Wittekind M., Rajagopal P., Branchini B. R., Reizer J., Saier M. H., Klevit R. E. 1992; Solution structure of the phospho-carrier protein HPr from Bacillus subtilis by two-dimensional NMR spectroscopy. Protein Sci 1:1363–1376
     [Google Scholar]
  68. Wu L. F., Tomich J. M., Saier M. H. 1990; Structure and evolution of a multidomain multiphosphoryl transfer protein. Nucleotide sequence of the fru B(HP) gene in Rhodobacter capsulatus and comparisons with homologous genes from other organisms. J Mol Biol 213:687–703
     [Google Scholar]
  69. Yanisch-Perron C, Vieira J., Messing J. 1985; Improved M13 phage cloning vectors and host strains: nucleotide sequences of the M13mp18 and pUC19 vectors. Gene 33:103–119
     [Google Scholar]
  70. Yu G., Hong J. 1986; Identification and nucleotide sequence of the activator gene of the externally induced phosphoglycerate transport system of Salmonella typhimurium.. Gene 45:51–57
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/micro/10.1099/13500872-140-5-1035
Loading
Molecular analysis of the operon which encodes the RNA polymerase sigma factor σ54 of Escherichia coli
Microbiology 140, 1035 (1994); https://doi.org/10.1099/13500872-140-5-1035
/content/journal/micro/10.1099/13500872-140-5-1035
/content/journal/micro/10.1099/13500872-140-5-1035
Loading

Data & Media loading...

Most cited Most Cited RSS feed

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error