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The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: Analysis of conserved sequences in NtrA proteins

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Summary

The nucleotide sequence of the Azotobacter vinelandii ntrA gene has been determined. It encodes a 56916 Dalton acidic polypeptide (AvNtrA) with substantial homology to NtrA from Klebsiella pneumoniae (KpNtrA) and Rhizobium meliloti (RmNtrA). NtrA has been shown to act as a novel RNA polymerase sigma factor but the predicted sequence of AvNtrA substantiates our previous analysis of KpNtrA in showing no substantial homology to other known sigma factors. Alignment of the predicted amino acid sequences of AvNtrA, KpNtrA and RmNtrA identified three regions; two showing>50% homology and an intervening sequence of <10% homology. The predicted protein contains a short sequence near the centre with homology to a conserved region in other sigma factors. The C-terminal region contains a region of homology to the β′ subunit of RNA polymerase (RpoC) and two highly conserved regions one of which is significantly homologous to known DNA-binding motifs. In A. vinelandii, ntrA is followed by another open reading frame (ORF) which is highly homologous to a comparable ORF downstream of ntrA in K. pneumoniae and R. meliloti.

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References

  • Alvarez-Morales A, Hennecke H (1985) Expression of Rhizobium japonicum nifH and nifDK operons can be activated by the Klebsiella pneumoniae nifA protein but not by the product of ntrC. Mol Gen Genet 199:306–314

    Google Scholar 

  • Alvarez-Morales A, Dixon R, Merrick M (1984) Positive and negative control of the glnA ntrBC regulon in Klebsiella pneumoniae. EMBO J 3:501–507

    Google Scholar 

  • Ausubel FM (1984) Regulation of nitrogen fixation genes. Cell 37:5–6

    Google Scholar 

  • Beynon J, Cannon M, Buchanan-Wollaston V, Cannon F (1983) The nif promoters of Klebsiella pneumoniae have a characteristic primary structure. Cell 34:665–671

    Google Scholar 

  • Binnie C, Lampe M, Losick R (1986) Gene encoding the σ37 species of RNA polymerase σ factor from Bacillus subtilis. Proc Natl Acad Sci USA 83:5943–5947

    Google Scholar 

  • Brigle KE, Newton WE, Dean DR (1985) Complete nucleotide sequence of Azotobacter vinelandii nitrogenase structural gene cluster. Gene 37:37–44

    Google Scholar 

  • Buck M (1986) Deletion analysis of the Klebsiella pneumoniae nitro genase promoter: Importance of spacing between conservec sequences around positions-12 and-24 for activation by the nifA and ntrC (glnG) products. J Bacteriol 166:545–551

    Google Scholar 

  • Buck M, Khan H, Dixon R (1985) Site-directed mutagenesis of the Klebsiella pneumoniae nifL and nifH promoters and in vivo analysis of promoter activity. Nucleic Acids Res 13:7621–7638

    Google Scholar 

  • Castano I, Bastarrachea F (1984) glnF-lacZ fusions in Escherichia coli: studies on glnF expression and its chromosomal orientation. Mol Gen Genet 195:228–233

    Google Scholar 

  • Dayhoff MO, Hunt LT, Hurst-Calderone S (1978) In: Dayhoff MO (ed) Atlas of Protein Sequence and Structure, vol 5. pp 363–369

  • Dean DR, Brigle KE (1985) Azotobacter vinelandii nifD-and nifE-encoded polypeptides share structural homology. Proc Natl Acad Sci USA 82:5720–5723

    Google Scholar 

  • De Bruijn FJ, Ausubel FM (1983) The cloning and characterization of the glnF (ntrA) gene of Klebsiella pneumoniae: Role of glnF (ntrA) in the regulation of nitrogen fixation (nif) and other nitrogen assimilation genes. Mol Gen Genet 192:342–353

    Google Scholar 

  • Dixon RA (1984) The genetic complexity of nitrogen fixation. J Gen Microbiol 130:2745–2755

    Google Scholar 

  • Dixon R (1986) The xylABC promoter from the Pseudomonas putida TOL plasmid is activated by nitrogen regulatory genes in Escherichia coli. Mol Gen Genet 203:129–136

    Google Scholar 

  • Ferro-Luzzi Ames G, Nikaido K (1985) Nitrogen regulation in Salmonella typhimurium. Identification of a ntrC protein-binding site and definition of a consensus binding sequence. EMBO J 4:539–547

    Google Scholar 

  • Fischer M, Levy E, Geller T (1986) Regulatory mutation that controls nif expression and histidine transport in Azospirillum brasilense. J Bacteriol 167:423–426

    Google Scholar 

  • Gribskov M, Burgess RR (1986) Sigma factors from E. coli, B. subtilis, phage SPO1, and phage T4 are homologous proteins. Nucleic Acids Res 14:6745–6763

    Google Scholar 

  • Grosjean H, Fiers W (1982) Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes. Gene 18:199–209

    Google Scholar 

  • Henikoff S (1984) Unidirectional digestion with Exonuclease III creates targeted break points for DNA sequencing. Gene 28:351–359

    Google Scholar 

  • Hirschman J, Wong P-K, Sei K, Keener J, Kustu S (1985) Products of nitrogen regulatory genes ntrA and ntrC of enteric bacteria activate glnA transcription in vitro: evidence that the ntrA product is a sigma factor. Proc Natl Acad Sci USA 82:7525–7529

    Google Scholar 

  • Hochschild A, Irwin N, Ptashne M (1983) Repressor structure and the mechanism of positive control. Cell 32:319–325

    Google Scholar 

  • Hu J, Gross C (1983) Marker rescue with plasmids bearing deletions in rpoD identifies a dispensable part of E. coli sigma factor. Mol Gen Genet 191:492–498

    Google Scholar 

  • Hunt TP, Magasanik B (1985) Transcription of glnA by purified Escherichia coli components: Core RNA polymerase and the products of glnF, glnG, and glnL. Proc Natl Acad Sci USA 82:8453–8457

    Google Scholar 

  • Janssen DB, Habets WJA, Marugg JT, van der Drift C (1982) Nitrogen control in Pseudomonas aeruginosa: Mutants affected in the synthesis of glutamine synthetase, urease, and NADP-dependent glutamate dehydrogenase. J Bacteriol 151:22–28

    Google Scholar 

  • Kennedy C, Buck M, Evans D, Humphrey R, Jones R, Ramos J, Robson R, Santero E, Tibelius K, Toukdarian A, Woodley P, Yates G (1987) The genetic analysis of nitrogen fixation, oxygen tolerance, and hydrogen uptake in azotobacters. Philos Trans R Soc London [Biol] (in press)

  • Khan H, Buck M, Dixon R (1986) Deletion loop mutagenesis of the nifL promoter from Klebsiella pneumoniae: role of the-26 to-12 region in promoter function. Gene 45:281–288

    Google Scholar 

  • Krajewska-Grynkiewicz K, Kustu S (1984) Evidence that nitrogen regulatory gene ntrC of Salmonella typhimurium is transcribed from the glnA promoter as well as from a separate ntr promoter. Mol Gen Genet 193:135–142

    Google Scholar 

  • Magasanik B (1982) Genetic control of nitrogen assimilation in bacteria. Annu Rev Genet 16:135–168

    Google Scholar 

  • Merrick MJ, Gibbins JR (1985) The nucleotide sequence of the nitrogen regulation gene ntrA of Klebsiella pneumoniae and comparison with conserved features in bacterial sigma factors. Nucleic Acids Res 13:7607–7620

    Google Scholar 

  • Merrick MJ, Stewart WDP (1985) Studies on the regulation and function of the Klebsiella pneumoniae ntrA gene. Gene 35:297–303

    Google Scholar 

  • Merrick MJ, Austin S, Buck M, Dixon R, Drummond M, Holtel A, MacFarlane S (1987) Regulation of nitrogen assimilation in enteric bacteria. In: Torriani A, Silver S, Rothman F, Wright A, Yagil E (eds) Phosphate Metabolism and Cellular Regulation in Microorganisms, American Society for Microbiology, Washington DC, pp 277–283

    Google Scholar 

  • Ninfa AJ, Magasanik B (1986) Covalent modification of the glnG product, NRI, by the glnL product, NRII, regulates the transcription of the glnALG operon in Escherichia coli. Proc Natl Acad Sci USA 83:5909–5913

    Google Scholar 

  • Pabo CO, Sauer RT (1984) Protein-DNA recognition. Annu Rev Biochem 53:293–321

    Google Scholar 

  • Pahel G, Rothstein DM, Magasanik B (1982) Complex glnA-glnL-glnG operon of Escherichia coli. J Bacteriol 150:202–213

    Google Scholar 

  • Pedrosa FO, Yates MG (1984) Regulation of nitrogen fixation (nif) genes of Azospirillum brasilense by nifA and ntr (gln) type gene products. FEMS Microbiol Letts 23:95–101

    Google Scholar 

  • Ronson CW, Nixon BT, Albright LM, Ausubel FM (1987) The Rhizobium meliloti ntrA (rpoN) gene is required for diverse metabolic functions. J Bacteriol 169:2424–2431

    Google Scholar 

  • Santero E, Luque F, Medina JR, Tortolero M (1986) Isolation of ntrA-like mutants of Azotobacter vinelandii. J Bacteriol 166:541–544

    Google Scholar 

  • Staden R (1982) Automation of the computer handling of the gel reading data produced by the shotgun method of DNA sequencing. Nucleic Acids Res 10:4731–4751

    Google Scholar 

  • Staden R (1984) Graphic methods to determine the function of nucleic acid sequences. Nucleic Acids Res 10:521–538

    Google Scholar 

  • Stragier P, Parsot C, Bauvier J (1985) Two functional domains conserved in major and alternative bacterial sigma factors. FEBS Lett 187:11–15

    Google Scholar 

  • Toukdarian A, Kennedy C (1986) Regulation of nitrogen metabolism in Azotobacter vinelandii: isolation of ntr and glnA genes and construction of ntr mutants. EMBO J 5:399–407

    Google Scholar 

  • Valentin-Hansen P, Larsen JEL, Højrup P, Short SA, Barbier CS (1986) Nucleotide sequence of the CytR regulatory gene of E. coli K12. Nucleic Acids Res 14:2215–2228

    Google Scholar 

  • Yudkin MD (1987) Structure and function in a Bacillus subtilis sporulation-specific sigma factor: molecular nature of mutations in spoIIAC. J Gen Microbiol 133:475–481

    Google Scholar 

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Authors and Affiliations

  1. AFRC Unit of Nitrogen Fixation, University of Sussex, BN1 9RQ, Brighton, UK

    Mike Merrick, Jane Gibbins & Aresa Toukdarian

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  1. Mike Merrick
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  2. Jane Gibbins
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  3. Aresa Toukdarian
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Communicated by B.J. Kilbey

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Merrick, M., Gibbins, J. & Toukdarian, A. The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: Analysis of conserved sequences in NtrA proteins. Molec Gen Genet 210, 323–330 (1987). https://doi.org/10.1007/BF00325701

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  • DOI: https://doi.org/10.1007/BF00325701

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