Summary
We have determined the DNA sequence for the genes nifR1, nifR2 and nifR4 in the photosynthetic bacterium Rhodobacter capsulatus. These genes regulate transcription of the nifHDK operon and so limit the expression of nitrogen fixation activity to periods of low environmental concentrations of both oxygen and fixed nitrogen. The sequences of these three genes are similar to components of the ntr regulation system in Escherichia coli and Klebsiella pneumoniae. The two-component regulatory system of ntrB and ntrC in E. coli is represented by nifR2 and nifR1 in R. capsulatus and nifR4 in R. capsulatus is the equivalent of the E. coli ntr-related sigma factor ntrA.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
Ahombo G, Willison JC, Vignais PM (1986) The nifHDK genes are contiguous with a nifA-like regulatory gene in Rhodobacter capsulatus. Mol Gen Genet 205:442–445
Avtges P, Scolnik PA, Haselkorn R (1983) Genetic and physical map of the structural genes (nifHDK) coding for the nitrogenase complex of Rhodopseudomonas capsulata. J Bacteriol 156:251–256
Avtges P, Kranz RG, Haselkorn R (1985) Isolation and organization of genes for nitrogen fixation in Rhodopseudomonas capsulata. Mol Gen Genet 201:363–369
Berg DE, Weiss A, Crossland L (1980) Polarity of Tn5 insertion mutations in Escherichia coli. J Bacteriol 142:439–446
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
Buikema WJ, Szeto WW, Lemley P, Orme-Johnson WH, Ausubel FM (1985) Nitrogen fixation specific regulatory genes of Klebsiella pneumoniae and Rhizobium meliloti share homology with the general nitrogen regulatory gene ntrC of K. pneumoniae. Nucleic Acids Res 13:4539–4555
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
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
Dente L, Cesareni G, Cortese R (1983) pEMBL: a new family of single-stranded plasmids. Nucleic Acids Res 11:1645–1655
Drummond MH, Wootton JC (1987) Sequence of nifL from Klebsiella pneumoniae: mode of action and relationship to two families of regulatory proteins. Mol Microbiol 1:37–44
Drummond M, Whitty P, Wootton J (1986) Sequence and domain relationships of ntrC and nifA from Klebsiella pneumoniae: homologies to other regulatory proteins. EMBO J 5:441–447
Haselkorn R (1986) Organization of the genes for nitrogen fixation in photosynthetic bacteria and cyanobacteria. Annu Rev Microbiol 40:525–547
Hirschman J, Wong PK, 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
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
Imhoff JF, Truper HG, Pfennig N (1984) Rearrangement of the species and genera of the photosynthetic purple non-sulfur bacteria. Int J Syst Bacteriol 34:340–343
Jones R, Haselkorn R (1988) Sequence of Rhodobacter capsulatus nifH. Nucleic Acids Res 16:8135
Klipp W, Masepohl B, Puhler A (1988) Identification and mapping of nitrogen fixation genes of Rhodobacter capsulatus: Duplication of a nifA-nifB region. J Bacteriol 170:693–699
Kranz RG, Haselkorn R (1985) Characterization of the nif regulatory genes in Rhodopseudomonas capsulata using lac gene fusions. Gene 40:203–215
Kranz RG, Haselkorn R (1986) Anaerobic regulation of nitrogen fixation genes in Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 83:6805–6809
MacFarlane SA, Merrick M (1985) The nucleotide sequence of the nitrogen regulation gene ntrB and the glnA-ntrBC intergenic region of Klebsiella pneumoniae. Nucleic Acids Res 13:7591–7606
Masepohl B, Klipp W, Puhler A (1988) Genetic characterization and sequence analysis of the duplicated nifA/nifB region of Rhodobacter capsulatus. Mol Gen Genet 212:27–37
Merrick M, Gibbins JR (1985) The nucleotide sequence of the nitrogen regulation gene ntrA of Klebsiella pneumoniae and comparison with structural features in bacterial sigma factors. Nucleic Acids Res 13:7607–7620
Merrick M, Stewart WDP (1985) Studies on the regulation of the Klebsiella pneumoniae ntrA gene. Gene 35:297–303
Merrick M, Gibbins JR, Toukdarian A (1987) The nucleotide sequence of the sigma factor gene ntrA (rpoN) of Azotobacter vinelandii: Analysis of conserved sequences in ntrA proteins. Mol Gen Genet 210:323–330
Miranda-Rios J, Sanchez-Pescador R, Urdea M, Covarrubias AA (1987) The complete nucleotide sequence of the glnALG operon of Escherichia coli K12. Nucleic Acids Res 15:2757–2770
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
Nixon T, Ronson CW, Ausubel FM (1986) Two-component regulatory systems responsive to environmental stimuli share strongly conserved domains with the nitrogen assimilation regulatory genes ntrB and ntrC. Proc Natl Acad Sci USA 83:7850–7854
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
Sanger F, Nicklen S, Coulson A (1977) DNA sequencing with chain terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467
Scolnik PA, Virosco J, Haselkorn R (1983) The wild-type gene for glutamine synthetase restores ammonia control of nitrogen fixation to Gln- (glnA) mutants of Rhodopseudomonas capsulata. J Bacteriol 155:180–185
Szeto WW, Nixon BT, Ronson CW, Ausubel FM (1987) Identification and characterization of the Rhizobium meliloti ntrC gene: R. meliloti has separate regulatory pathways for activating nitrogen fixation genes in free-living and symbiotic cells. J Bacteriol 169:1423–1432
Walker JE, Saraste M, Runswick MJ, Gay NJ (1982) Distantly related sequences in the alpha and beta subunits of ATP synthase, myosin, kinases and other ATP-requiring enzymes and a common nucleotide binding fold. EMBO J 1:945–952
Wall JD, Braddock K (1984) Mapping of Rhodopseudomonas capsulata nif genes. J Bacteriol 158:404–410
Wall JD, Love J, Quinn SP (1984) Spontaneous Nif- mutants of Rhodopseudomonas capsulata. J Bacteriol 159:652–657
Wall JD, Goldenberg A, Figueredo A, Rapp BJ, Landrum DC (1985) Genetics of nitrogen fixation in photosynthetic bacteria. In: Evans HJ, Bottomley PJ, Newton WE (eds) Nitrogen fixation research progress. Nijhoff, Dordrecht Holland, pp 497–503
Waterman MS, Eggert M (1987) A new algorithm for best subsequence alignments with application to tRNA-rRNA comparisons. J Mol Biol 197:723–728
Willison JC, Ahombo G, Chabert J, Magnin J-P, Vignais PM (1985) Genetic mapping of the Rhodopseudomonas capsulata chromosome shows non-clustering of genes involved in nitrogen fixation. J Gen Microbiol 131:3001–3015
Yudkin MD (1988) The prediction of helix-turn-helix DNA-binding regions in proteins. Protein Eng 2:371–372
Author information
Authors and Affiliations
Additional information
Communicated by H. Hennecke
Rights and permissions
About this article
Cite this article
Jones, R., Haselkorn, R. The DNA sequence of the Rhodobacter capsulatus ntrA, ntrB and ntrC gene analogues required for nitrogen fixation. Molec. Gen. Genet. 215, 507–516 (1989). https://doi.org/10.1007/BF00427050
Received:
Issue Date:
DOI: https://doi.org/10.1007/BF00427050