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Fine structure analysis of the nifDK operon encoding the α and β subunits of dinitrogenase from Rhizobium japonicum

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Summary

In the nitrogen fixing soybean symbiont, Rhizobium japonicum, the genes nifD and nifK for the α and β subunits of dinitrogenase, respectively, and nifH for dinitrogenase reductase are located on separate operons (nifDK and nifH). We report here the transcription start point and the nucleotide sequence of the nifDK promoter and compare it with the nifH promoter. Furthermore, the nucleotide sequences of the complete nifD gene and the beginning of the adjacent nifK gene are presented. The promoter is located in a region from 10 to 31 nucleotides upstream from the transcription start point. It contains a sequence 5′-CTGG-8bp-TTGCA-3′ which has also been recognized as the consensus nif promoter sequence of other nitrogen fixing bacteria such as Klebsiella pneumoniae and Rhizobium meliloti (for refs. see text). On the 5′ side the consensus sequence is immediately preceded by the sequence 5′-GTGC-5bp-AGACC-3′ which appears to be unique to R. japonicum. The nifD gene is 1545 nucleotides long, coding for 515 amino acids which make up a dinitrogenase α subunit with a molecular weight of 57,918. The comparison with the nifD gene product from the cyanobacterium Anabaena (ref. in the text) makes it now possible to identify conserved (and, hence, functionally important) protein domains. Five conserved cysteine residues may be involved in the binding of FeS clusters and/or the MoFe cofactor. On the basis of sequence homologies we discuss the possible evolution of nif genes, and suggest that they may have evolved in parallel with the bacteria that harbor them.

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Abbreviations

nif :

nitrogen fixation gene

bp:

base pair(s)

kb:

kilobase pair(s)

References

  • Avtges P, Scolnick PA, Haselkorn R (1983) Genetic and physical map of the structural genes (nifH, D, K) coding for the nitrogenase complex of Rhodopseudomonas capsulata. J Bacteriol 156:251–256

    Google Scholar 

  • Berk AJ, Sharp PA (1977) Sizing and mapping of early adenovirus mRNA's by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 12:721–732

    Google Scholar 

  • Better M, Lewis B, Corbin D, Ditta G, Helinski DR (1983) Structural relationships among Rhizobium meliloti symbiotic promoters. Cell 35:479–485

    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 

  • Brosius J, Cate RL, Perlmutter A (1982) S1 mapping of pBR322 β-lactamase promoters. J Biol Chem 257:9205–9210

    Google Scholar 

  • Corbin D, Barran L, Ditta G (1983) Organization and expression of Rhizobium meliloti nitrogen fixation genes. Proc Natl Acad Sci USA 80:3005–3009

    Google Scholar 

  • Chou PY, Fasman GD (1978) Empirical predictions protein conformation. Annu Rev Biochem 47:251–276

    Google Scholar 

  • Drummond M, Clements J, Merrick M, Dixon R (1983) Positive control and autogenous regulation of the nifLA promoter in Klebsiella pneumoniae. Nature (London) 301:302–307

    Google Scholar 

  • Eady RR, Postgate JR (1974) Nitrogenase. Nature (London) 249:805–810

    Google Scholar 

  • Emerich DW, Burris RH (1978) Complementary functioning of the component proteins of nitrogenase from several bacteria. J Bacteriol 134:936–943

    Google Scholar 

  • Fox GE, Stackebrandt E, Hespell RB, Gibson J, Maniloff J, Dyer TA, Wolfe RS, Balch WE, Tanner RS, Magrum LJ, Zablen LB, Blakemore R, Gupta R, Bonnen L, Lewis BJ, Stahl DA, Luehrsen KR, Chen KN, Woese CR (1980) The phylogeny of prokaryotes. Science 209:457–463

    Google Scholar 

  • Fuhrmann M, Hennecke H (1982) Coding properties of clones nitrogenase structural genes from Rhizobium japonicum. Mol Gen Genet 187:419–425

    Google Scholar 

  • Fuhrmann M, Hennecke H (1984) Rhizobium japonicum nitrogenase Fe protein gene (nifH). J Bacteriol 158:in press

  • Gray CP, Sommer R, Polke C, Beck E, Schaller H (1978) Structure of the origin of DNA replication of bacteriophage fd. Proc Natl Acad Sci USA 75:50–53

    Google Scholar 

  • Hahn M, Hennecke H (1984) Localized mutagenesis in Rhizobium japonicum. Mol Gen Genet 193:46–52

    Google Scholar 

  • Hennecke H (1981a) Recombinant plasmids carrying nitrogen fixation genes from Rhizobium japonicum. Nature (London) 291:354–355

    Google Scholar 

  • Hennecke H (1981b) Regulation of nitrogenase biosynthesis in free-living and symbiotic N2-fixing bacteria: a comparison. In: Bothe H, Trebst A (eds) Biology of inorganic nitrogen and sulfur. Springer, Berlin Heidelberg New York, p 309

    Google Scholar 

  • Israel DW, Howard RL, Evans HJ, Russell SA (1974) Purification and characterization of the molybdenum-iron protein component of nitrogenase from soybean nodule bacteroids. J Biol Chem 249:500–508

    Google Scholar 

  • Jordan DC (1982) Transfer of Rhizobium japonicum Buchanan 1980 to Bradyrhizobium gen.nov., a genus of slow growing root nodule bacteria from leguminous plants. Int J Syst Bacteriol 32:136–139

    Google Scholar 

  • Kaluza K, Hennecke H (1981) Regulation of nitrogenase messenger RNA synthesis and stability in Klebsiella pneumoniae. Arch Microbiol 130:38–43

    Google Scholar 

  • Kaluza K, Fuhrmann M, Hahn M, Regensburger B, Hennecke H (1983) In Rhizobium japonicum the nitrogenase genes nifH and nifDK are separated. J Bacteriol 155:915–918

    Google Scholar 

  • Kennedy C, Cannon F, Cannon M, Dixon R, Hill S, Jensen J, Kumar S, McLean P, Merrick M, Robson R, Postgate JR (1981) Recent advances in the genetics and regulation of nitrogen fixation. In: Gibson AH, Newton WE (eds) Current perspectives in nitrogen fixation. Australian Academy of Science, Canberra, p 146

    Google Scholar 

  • Lammers PJ, Haselkorn R (1983) Sequence of the nifD gene coding for the α subunit of dinitrogenase from the cyanobacterium Anabaena. Proc Natl Acad Sci USA 80:4723–4727

    Google Scholar 

  • Larson R, Messing J (1982) Apple II software for M13 shotgun DNA sequencing. Nucl Acid Res 10:39–49

    Google Scholar 

  • Lundell DJ, Howard JB (1981) Isolation and sequences of the cysteinyl tryptic peptides from the MoFe-protein of Azotobacter vinelandii nitrogenase. J Biol Chem 256:6385–6391

    Google Scholar 

  • Maxam A, Gilbert W (1980) Sequencing end-labeled DNA with base-specific chemical cleavage. Methods Enzymol 65:499–561

    Google Scholar 

  • Mazur BJ, Chui CF (1982) Sequence of the gene coding for the β-subunit of dinitrogenase from the blue green alga Anabaena. Proc Natl Acad Sci USA 79:6782–6786

    Google Scholar 

  • Merrick MJ (1983) Nitrogen control of the nif regulation in Klebsiella pneumoniae: involvement of the ntrA gene and analogies between ntrC and nifA. EMBO J 2:39–44

    Google Scholar 

  • Messing J (1983) New M13 vectors for cloning. Methods Enzymol 101:20–78

    Google Scholar 

  • Mortensen LE, Thorneley RNF (1979) Structure and function of nitrogenase. Annu Rev Biochem 48:387–418

    Google Scholar 

  • Ow DW, Sundaresan V, Rothstein DM, Brown SE, Ausubel FM (1983) Promoters regulated by the glnG(ntrC) and the nifA gene products share a heptameric consensus sequence in the-15 region. Proc Natl Acad Sci USA 80:2524–2528

    Google Scholar 

  • Regensburger B, Hennecke H (1983) RNA polymerase from Rhizobium japonicum. Arch Microbiol 135:103–109

    Google Scholar 

  • Rice D, Mazur BJ, Haselkorn R (1982) Isolation and physical mapping of nitrogen fixation genes from the cyanobacterium Anabaena 7120. J Biol Chem 257:13157–13163

    Google Scholar 

  • Roberts GP, Brill WJ (1981) Genetics and regulation of nitrogen fixation. Annu Rev Microbiol 35:207–235

    Google Scholar 

  • Rosenberg M, Court D (1979) Regulatory sequences involved in promotion and termination of RNA transcription. Annu Rev Genet 13:319–353

    Google Scholar 

  • Ruvkun G, Ausubel FM (1980) Interspecies homology of nitrogenase genes. Proc Natl Acad Sci USA 77:191–195

    Google Scholar 

  • Ruvkun GB, Sundaresan V, Ausubel FM (1982) Directed transposon Tn5 mutagenesis and complementation analysis of Rhizobium meliloti symbiotic nitrogen fixation genes. Cell 29:551–559

    Google Scholar 

  • Sanger F, Nicklen S, Coulson AR (1977) DNA-sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 74:5463–5467

    Google Scholar 

  • Scott DB, Hennecke H, Lim ST (1979) The biosynthesis of nitrogenase MoFe protein polypeptides in free-living cultures of Rhizobium japonicum. Biochim Biophys Acta 565:365–378

    Google Scholar 

  • Scott KF, Rolfe GB, Shine J (1981) Biological nitrogen fixation: primary structure of the Klebsiella pneumoniae nifH and nifD genes. J Mol Appl Genet 1:71–81

    Google Scholar 

  • Scott KF, Rolfe GB, Shine J (1983) Nitrogenase structural genes are unlinked in the nonlegume symbiont Parasponia Rhizobium. DNA 2:141–148

    Google Scholar 

  • Shine, J, Dalgarno L (1974) The 3′-terminal sequence of Escherichia coli 16S ribosomal RNA: complementarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 71:1342–1346

    Google Scholar 

  • Smith BE (1983) Reactions and physicochemical properties of the nitrogenase MoFe proteins. In: Müller A, Newton WE (eds) Nitrogen fixation. Plenum Press, New York, p 23

    Google Scholar 

  • Stormo GD, Schneider TD, Gold LM (1982) Characterization of translational initiation sites in E. coli. Nucl Acid Res 10:2971–2996

    Google Scholar 

  • Sundaresan V, Jones JDG, Ow DW, Ausubel FM (1983) Klebsiella pneumoniae nifA product activates the Rhizobium meliloti nitrogenase promoter. Nature (London) 301:728–732

    Google Scholar 

  • Weaver RF, Weissmann C (1979) Mapping of RNA by a modification of the Berk-Sharp procedure: the 5′ termini of 15S β-globin mRNA precursor and mature 10S β-globin mRNA have identical map coordinates. Nucl Acid Res 7:1175–1192

    Google Scholar 

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Authors and Affiliations

  1. Mikrobiologisches Institut, Eidgenössische Technische Hochschule, ETH-Zentrum, CH-8092, Zürich, Switzerland

    Klaus Kaluza & Hauke Hennecke

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  1. Klaus Kaluza
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  2. Hauke Hennecke
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Additional information

Communicated by A. Böck

For uniformity with other authors' work we now designate the nifD gene product as α subunit and the nifK gene product as β subunit, despite the fact that the R. japonicum nifD gene product uniquely is the larger one of the two dinitrogenase subunits. This nomenclature replaces the one given previously (Fuhrmann and Hennecke 1982)

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Kaluza, K., Hennecke, H. Fine structure analysis of the nifDK operon encoding the α and β subunits of dinitrogenase from Rhizobium japonicum . Mol Gen Genet 196, 35–42 (1984). https://doi.org/10.1007/BF00334089

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  • DOI: https://doi.org/10.1007/BF00334089

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