Abstract
Hierarchical clustering and similarity coefficients of pairwise alignments of the published nucleotide sequences of 27nifH genes suggest thatnif genes are as ancient as the archaebacteria and clostridia. The positions ofnifHl ofMethanococcus thermolithotrophicus, nifH3 ofClostridium pasteurianum, nifH3 ofAzotobacter vinelandii andnifH ofFrankia suggest that a variety of lateral transfers may have occurred during evolution ofnifH gene. The genes for type 3 nitrogenase ofA. vinelandii may have diverged early from methanogens and clostridia. A high similarity coefficient with the derived amino acid sequence of type 3 nitrogenase suggests the presence of a functionally similar enzyme inC. pasteurianum. The type 2 nitrogenase genenifH2 of azotobacters seems to have originated recently from the genenifHl for conventional type I nitrogenase. RhizobialnifH genes comprise two closely related but discrete clusters that are in consonance with the plasmid or chromosomal location ofnif genes. The chromosomal and plasmid locatednifH of rhizobia seem to have evolved independently but contemporaneously.
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Adams T. H. and Chelm B. K. 1984 ThenifH andnifDK promoler regions forRhizobium japonicum share structural homologies with each other and with nitrogen-regulated promoters from other organisms.J. Mol. Appl. Genet. 2: 392–405
Arnold W., Rump A., Klipp W., Priefer U. B. and Puhler A. 1988 Nucleotide sequence of a 24, 206-base-pair DNA fragment carrying the entire nitrogen fixation gene cluster ofKlebsiella pneumoniae.J. Mol. Biol. 203: 715–738
Bisseling T., van den Bos R. C., Moen L., Hontelez J. G. J. and Kammen van A. 1982 An immunological comparison of nitrogenase proteins of fast and slow growing rhizobia.FEBS Lett. 145: 45–48
Brigle K. E., Newton W. E. and Dean D. R. 1985 Complete nucleotide sequence of theAzotobacter vinelandii nitrogenase structural gene cluster.Gene 37: 37–44
Broda E. 1971 Origins of bacterial respiration. InChemical evolution and the origins of life (eds) R. Buvet and C. Ponnamperumal (Amsterdam: North-Holland) pp. 446–452
Chakrabarti S. K., Mishra A. K. and Chakrabarti P. K. 1984 Genome size variation of rhizobia.Experientia. 40: 1290
Corpet F 1988 Multiple sequence alignment with hierarchical clustering.Nucleic Acids Res. 16: 10881–10890
Dams E., Yamada T., Baere R. D., Huysmans E., Vandenberghe A. and Wachter R. D. 1987 Structure of 5S rRNA in Actinomycetes and relatives and evolution of eubacteria.J. Mol. Evol. 25: 255–260
Dilworth M. J., Eady R. R., Robson R. L. and Miller R. W. 1987 Ethane formation from acetylene as a potential test for vanadium nitrogenase in vivo.Nature (London) 327: 167–168
Donald R. G. K., Nees D. W., Raymond C. K., Loroch A. I. and Ludwig R. A. 1986 Characterisation of three genomic loci encodingRhizobium Sp. strain ORS571 N fixation genes.J. Bacteriol. 165: 72–81
Eady R. R. and Smith B. E. 1979 Physico-chemical properties of nitrogenase and its components. InA treatise on dinitrogen fixation, sections I and II (eds) R. W. F. Hardy, F. Bottomley and R. C. Burns (London: Wiley and Sons) pp. 399–490
Fox G. E., Magrum L. J., Balch W. E., Wolfe R. S. and Woese C. R. 1977 Classification of methanogenic bacteria by 16S ribosomal RNA characterisation.Proc. Natl. Acad. Sci. USA 74: 4537–4541
Holland D., Zilberstein A., Zamir A. and Sussman J. L. 1987 A quantitative approach to sequence comparisions of nitrogenase MoFe protein α- and β-subunits including the newly sequencednifK gene fromKlebsiella pneumoniae.Biochem. J. 247: 277–285
Loannidis I. and Buck M. 1987 Nucleotide sequence of theKlebsiella pneumoniae nifD gene and predicted amino acid sequence of the alpha subunit of the Mo-Fe protein.Biochem. J. 247: 287–291
Jacobson M. R., Prernkumar R. and Bishop P. E. 1986 Transcriptional regulation of nitrogen fixation by molybdenum inAzotobacter vinelandii.J. Bacteriol. 170: 1475–1487
Joerger R. D., Jacobson M. R., Premkumar R., Wolfinger E. D. and Bishop P. E. 1989 Nucleotide sequence and mutational analysis of the structural genesanfHDGK for the second alternative nitrogenase fromAzotobacter vinelandii.J. Bacteriol. 171: 1079–1086
Jones J. B., Holton T. A., Morrison C. M., Scott K. F. and Shine J. 1989 Structural and functional analysis of nitrogenase genes from the broad-host-rangeRhizobium strain ANU240.Gene 77: 141–153
Jones R. and Haselkorn R. 1988 DNA sequence of theRhodobacter capsulatus nifH gene.Nucleic Acids Mes. 17: 8735
Kaluza K. and Hennecke H. 1984 Fine structure analysis of thenifDK operon encoding the alpha and beta subunits of dinitrogenase fromRhizobium japonicum.Mol. Gen. Genet. 196: 35–42
Lammers P. J. and Haselkorn R. 1983 Sequence of thenifD gene coding for the alpha subunit- of dinitrogenase from the cyanobacteriumAnabaena.Proc. Natl. Acad. Sci. USA 80: 4723–4727
Mathur M. and Tuli R. 1989aAnabaena and yeast genes well matched.Cyanonews 5: 3
Mathur M. and Tuli R. 1989b General codon usage analysis of functionally related genes from different species. InProc. Workshop on Mathematical Models in. Biology and Medicine (Calcutta: Indian Institute of Chemical Biology) p. 81
Mathur M. and Tuli R. 1990a Phylogenetic relationship and codon usage analysis in genes for nitrogen fixation. InProc. D.A.E. Symposium on Advances in Molecular Biology, B.A.R.C., Bombay, pp. 473–474
Mathur M. and Tuli R. 1990bnif gene comparison challenges conventional taxonomy.Cyanonews 6: 4–5
Mazur B. J. and Chui C. F. 1982 Sequence of the gene coding for the beta subunit of dinitrogenase from the blue-green algaAnabaena.Proc. Natl. Acad. Sci. USA 79: 6782–6786
Mevarech M., Rice D. and Haselkorn R. 1980 Nucleotide sequence of a cyanobacterialnifH gene coding for nitrogenase reductase.Proc. Natl. Acad. Sci. USA 77: 6476–6480
Norel F. and Elmerich C. 1987 Nucleotide sequence and functional analysis of twonifH copies ofRhizobium ORS571.J. Gen. Microbiol. 133: 1563–1576
Normand P. and Bousquet J. 1989 Phylogeny of nitrogenase sequences inFrankia and other nitrogen-fixing microorganisms.J. Mol. Evol. 29: 436–447
Normand P., Simonet P. and Bardin R. 1988 Conservation ofnif sequences inFrankia.Mol. Gen. Genet. 213: 238–246
Osawa S., Jukes T. H., Muto A., Yammo F., Ohama T. and Andachi Y. 1987 Role of directional mutation pressure in the evolution of the eubacterial genetic code.Cold Spring Harbor Symp. Quant. Biol. 52: 777–789
Pretorius I. M., Rawlings D. E., ONiell E. G., Jones W. A. and Woods D. R. 1987 Nucleotide sequences of the gene encoding the nitrogenase iron protein ofThiobacillus ferrooxidans.J. Bacteriol. 169: 367–370
Quinto C., de La Vega H., Flores M., Leemans J., Cevallos M. A., Pardo M. A., Azpiroz R., de Lourdes Girard M., Calva E. and Palacios R. 1985 Nitrogenase reductase: a functional multigene family inRhizobium phaseoli.Proc. Natl. Acad. Sci. USA 82: 1170–1174
Raina R., Reddy M. A., Ghosall D. and Das H. K. 1988 Characterization of the gene for the Fe-protein of the vanadium dependent alternative nitrogenase ofAzotobacter vinelandii and construction of a Tn5 mutant.Mol. Gen. Genet. 214: 121–127
Robson R., Woodley P. and Jones R. 1986 Second genenifH* coding for a nitrogenase iron protein inAzotobacter chroococcum is adjacent to a gene coding for a ferredoxin-like protein.EMBO J. 5: 1159–1163
Ruvkun G. B. and Ausubel F. M. 1980 Interspecies homology of nitrogenase genes.Proc. Natl. Acad. Sci. USA 77: 191–195
Schumann J. P., Waitehes G. M. and Scolnik P. A. 1986 A DNA fragment hybridizing to anif probe inRhodobacter capsulatus is homologous to a 16S rRNA gene.Gene 48: 81–92
Scolnik P. A. and Haselkorn R. 1984 Activation of extra copies of genes coding for nitrogenase inRhodopseudomonas capsulata.Nature (London) 307: 289–292
Scott K. F., Rolfe G. B. and Shine J. 1983a Nitrogenase structural genes are unlinked in the nonlegume symbioantParasponia rhizobium.DNA 2: 141–148
Scott K. F., Rolfe G. B. and Shine J. 1983b Biological nitrogen fixation: primary structure of theRhizobium trifoli iron protein gene.DNA 2: 149–155
Souillard N., Magot M., Possot O. and Sibold L. 1988 Nucleotide sequence of regions homologous tonifH nitrogenase Fe protein from the nitrogen-fixing archaebacteriaMethanococcus thermolitho-trophicus andMethanobacterium ivanovii: evolutionary implications.J. Mol. Evol. 27: 65–76
Souillard N. and Sibold L. 1986 Primary structure and expression of a gene homologous tonifH nitrogenase Fe protein from the archaebacteriumMethanococcus voltae.Mol. Gen. Genet. 203: 21–28
Souillard N. and Sibold L. 1989 Primary structure, functional organization and expression of nitrogenase structural genes of the thermophilic archaebacteriumMethanococcus thermolithotrophicus.Mol. Microbiol. 34: 541–551
Sundaresan V. K. and Ausubel F. M. 1981 Nucleotide sequence of the gene coding for nitrogenase iron protein fromKlebsiella pneumoniae.J. Biol. Chem. 256: 2808–2812
Toerock I. and Kondorosi A. 1981 Nucleotide sequence of theR. meliloti nitrogenase reductasenifH gene.Nucleic Acids Res. 9: 5711–5723
Wang S. Z., Chen J. S. and Johnson J. K. 1987 Nucleotide and deduced amino acid sequences ofnifD encoding the alpha-subunit of nitrogenase Mo-Fe protein ofClostridium pasteurianum.Nucleic Acids Res. 15: 3935
Wang S. Z., Chen J. S. and Johnson J. L. 1988 The presence of fivenifH-like sequences inClostridium pasteurianum sequence divergence and transcription properties.Nucleic Acids Res. 16: 439–454
Weinmann J. J., Fellows F. F., Gresshoff P. M., Shine J. and Scott K. F. 1984 Structural analysis of the genes encoding the molybdenum-riron protein of nitrogenase in theParasponia rhizobium strain ANU289.Nucleic Acids Res. 12: 8329–8344
Wilbur W. J. and Lipman D. J. 1983 Rapid similarity searches of nucleic acid and protein data banks.Proc. Natl. Acad. Sci. USA 80: 726–730
Woese C. R. 1987 Bacterial evolution.Microbiol. Rev. 221 – 271
Yunn A. C. and Szalay A. A. 1984 Structural genes of dinitrogenase and dinitrogenase reductase are transcribed from two separate promoters in the broad host range cowpeaRhizobium strainIrc78.Proc. Natl. Acad. Sci. USA 81: 7358–7362
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Mathur, M., Tuli, R. Cluster analysis of genes for nitrogen fixation from several diazotrophs. J. Genet. 69, 67–78 (1990). https://doi.org/10.1007/BF02927969
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DOI: https://doi.org/10.1007/BF02927969