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The Mo-Fe protein of nitrogenase from both Azotobacter vinelandii and Klebsiella pneumoniae (Av1 and Kp1, respectively) consists of four subunits of similar, but not identical, relative molecular mass. The hydrodynamic properties of Av1 (sedimentation and diffusion coefficient) and its total relative molecular mass are very similar to those of Kp1 and catalase from bovine liver, a tetramer of four identical subunits. By electron microscopy the Av1, Kp1 and catalase tetramers are seen as protein particles of diameter 9.0-10.0 nm; no details of the subunit structure can be observed. Av1 (but not Kp1) forms regular polymers of variable length at low ionic strength in the presence of MgCl2. The structure of these polymers, of diameter 21.2 nm, is complex. Optical diffraction studies give a smallest repeating distance of 8.4 nm (corresponding to the diameter of the Av1 tetramer) and indicate a four-start helix. The latter structure is incompatible with a flat, square subunit arrangement of the Av1 tetramer as proposed by Stasny et al. [(1974) J. Cell. Biol. 60, 311-316]. We propose, therefore, that the subunit arrangement of the Av1 tetramer is of the tetrahedral type. This has also been proposed for the catalase tetramer from optical diffraction studies of electron micrographs of catalase tubes indicating a 222 symmetry [Kiselev, D. A., De Rosier, N. J. and Klug, A. (1968) J. Mol. Biol. 35, 561-566]. Our proposal is in agreement with the recent finding that Av1 protein crystals belong to the P2(1) space group [Weiniger, M. S. and Mortenson, L. E. (1982) Proc. Natl Acad Sci. USA, 79, 378-380].
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PMID:Structure of the Mo-Fe protein component of Azotobacter vinelandii nitrogenase. Analytical ultracentrifugation and electron microscopy studies. 657 28

In several species of Rhizobium the three genes which encode the nitrogenase complex are separated into two operons, nifH and nifDK. We have mapped the transcriptional promoter sites for these two operons from R. japonicum USDA strain 110 by S1 protection analyses using bacterial RNA isolated from soybean nodules. Transcription of the nifDK operon is initiated at a site located 46 nucleotides upstream of the proposed translation initiation codon. nifH transcription initiates predominantly at a site 152 nucleotides upstream of the proposed translation initiation codon. An additional minor start for nifH is found 35 nucleotides downstream of the major initiation site. The nucleotide sequences of these promoter sites are presented. Comparison of the major R. japonicum nif promoter sequences reveals a high degree of sequence homology with the conserved sequences clustered in the -11 to -15, -21 to -25, -27 to -31, and -38 to -41 regions. Conservation is also observed for the -11 to -15 and -21 to -25 regions with the R. meliloti nifHDK, a cowpea Rhizobium nifH, and even Klebsiella pneumoniae nif promoters. The -27 to -31 and -38 to -42 region homologies are not conserved with the other known nif promoters. These results are discussed in light of models for nif promoter activation.
J Mol Appl Genet 1984
PMID:The nifH and nifDK promoter regions from Rhizobium japonicum share structural homologies with each other and with nitrogen-regulated promoters from other organisms. 658 33

The review of the contemporary state of bioinorganic chemistry is presented, illustrated by a series of examples. A short presentation of the chemistry of the complexes of transient metals is given, the importance of the distorsion isomerism is emphasized. The roles of the alkaline and alkaline-earth metals in biology is considered as also the role of Zn, Co, Mo, Cu. The function of iron is presented and the influence of magnetic fields on organisms is discussed. The mechanisms of action of carboxypeptidase A and of nitrogenase are considered. The general properties of metalloenzymes are discussed--the entatic state of the active site, the role of the distorsion isomerism and of the trans-effect as also the electronic-conformational interactions. The physical properties of the biometallic compounds are formulated. The importance of these compounds for medicine is illustrated by the Podymov's theory of lupus, by the cancerogenic role of metals and by the use of the platinum complexes in oncological therapy. The importance of biometallic compounds for enzymology and other branches of molecular biology is emphasized.
Mol Biol (Mosk)
PMID:[Bioinorganic chemistry and molecular biology]. 675 21

A DNA fragment carrying the Klebsiella pneumoniae nifK, D, and H genes was isolated from the nif- strain UNF841 (Tn5::nifK) by molecular cloning into the Escherichia coli plasmid pBR325. The nucleotide sequences of both the nifH gene, which encodes the Fe protein of the nitrogenase enzyme complex, and 622 nucleotides of the nifD gene, which encodes the alpha-subunit of the Mo-Fe protein, were determined by direct DNA sequencing by both the chemical and chain termination methods. A comparison of the primary structure of the Klebsiella nifH gene and its product with that recently determined for the blue-green alga Anabaena demonstrates that the gene sequences are more divergent than the protein sequence data would suggest. This implies that despite the strong, presumably functional, constraints that act at the protein structure level, the nucleotide sequence of the gene and its mRNA are only restrained by the coding requirements, allowing substantial drift in codon usage.
J Mol Appl Genet 1981
PMID:Biological nitrogen fixation: primary structure of the Klebsiella pneumoniae nifH and nifD genes. 680 76

Large plasmids of molecular weight varying from 90 to around 200 x 10(6) have earlier been detected in most Rhizobium meliloti strains using an alkaline denaturation - phenol extraction procedure. With a less destructive method (Eckardt 1978) it was possible additionally to detect one plasmid of molecular weight clearly greater than 300 x 10(6) (= megaplasmid) in all of twenty-seven R. meliloti strains of various geographical origins and nodulation groupings investigated. Four strains (RCR 2011, A145, S26 and CC2013) were found to carry one megaplasmid and no smaller plasmids. Hybridization experiments with Klebsiella pneumoniae and R. meliloti cloned nitrogenase structural genes D and H showed that these genes are located on the megaplasmid and not on the smaller plasmids. All of the ten independent spontaneous non-nodulating derivatives of three strains of R. meliloti were shown to have suffered a deletion in the nifDH region of the megaplasmid. These results indicate that a gene controlling an early step in nodule formation is located in the nifDH region of the megaplasmid. This indicates that the same replicon carries genes controlling early and late functions in symbiosis.
Mol Gen Genet 1981
PMID:Genes controlling early and late functions in symbiosis are located on a megaplasmid in Rhizobium meliloti. 694 1

The kinetics of derepression of the enzyme nitrogenase were investigated, after exhaustion of a limiting amount of ammonium from the culture medium, in a prototrophic stringent-relaxed pair of Klebsiella pneumoniae strains and in their F relA+-F relA derivatives. The results indicate that ppGpp (guanosine 3'-5' diphosphate) increases the nitrogen fixation capability of K. pneumoniae by at least three different mechanisms. (1) It prevents exhaustion of the ATP pool when nitrogen starvation is imposed. (2) The translational defects in relaxed mutants are suppressed by ppGpp during nif derepression. (3) The synthesis of nitrogenase components is at least five times higher in the presence of ppGpp than in its absence. This latter conclusion was based on experimental results obtained when following the incorporation of (35S)-methionine into nitrogenase components after pulse labelling at various time intervals during nif derepression. The nitrogenase components were separated by solid phase radioimmunoassay as well as by two-dimensional gel electrophoresis.
Mol Gen Genet 1982
PMID:Positive involvement of ppGpp in derepression of the nif operon in Klebsiella pneumoniae. 704 80

The cyanobacterial ntcA gene encodes a DNA-binding protein that belongs to the Crp family of bacterial transcriptional regulators. In this work, we describe the isolation of an ntcA insertional mutant of the dinitrogen-fixing, heterocyst-forming cyanobacterium Anabaena sp. PCC 7120. The Anabaena ntcA mutant was able to use ammonium as a source of nitrogen for growth, but was unable to assimilate atmospheric nitrogen (dinitrogen) or nitrate. Nitrogenase and enzymes of the nitrate reduction system were not synthesized in the ntcA mutant under derepressing conditions, and glutamine synthetase levels were lower in the mutant than in the wild-type strain. In the ntcA mutant, in response to removal of ammonium, accumulation of mRNA of the genes encoding nitrogenase (nifHDK), nitrite reductase (nir, the first gene of the nitrate assimilation operon), and glutamine synthetase (glnA) was not observed. A transcription start point of the Anabaena glnA gene (corresponding to RNAl), that has been shown to be used preferentially after nitrogen step-down, was not used in the ntcA insertional mutant. Heterocyst development (which is necessary for the aerobic fixation of dinitrogen) and induction of hetR (a regulatory gene that is required for heterocyst development) were also impaired in the ntcA mutant. These results showed that the ntcA gene product, NtcA, is required in Anabaena sp. PCC 7120 for the expression of genes encoding proteins involved in the assimilation of nitrogen sources alternative to ammonium including dinitrogen and nitrate, and that the process of heterocyst development is also controlled by NtcA.
Mol Microbiol 1994 Nov
PMID:Requirement of the regulatory protein NtcA for the expression of nitrogen assimilation and heterocyst development genes in the cyanobacterium Anabaena sp. PCC 7120. 753 71

The mutant E135 (sym 13) of pea (Pisum sativum L.) forms a normal number of small white nodules that contain bacteroids, but these bacteroids lack nitrogenase activity. To evaluate the effects of the sym 13 gene on the expression of nodulin genes, cDNA clones for nodulins were isolated from pea nodules and the expression of nodulin genes in ineffective E135 nodules was compared with that in nitrogen-fixing nodules on the wild-type parent, cv. Sparkle. Nineteen cDNA clones for nodulins, including ENOD2 and cDNAs for two distinct leghemoglobins (Lbs), were isolated from Sparkle nodules by a subtractive hybridization procedure. All the nodulin genes examined were expressed in nodules on both E135 and Sparkle plants. However, the level of expression of seven genes, one of which was an Lb gene that corresponded to PsN5, was significantly lower in E135 nodules. The levels of Lb apo-proteins, with the exception of Lb-III and Lb-IV, in E135 nodules resembled those in Sparkle nodules, but the level of heme in E135 nodules was lower than that in Sparkle nodules. Although the expression of the two Lb genes that corresponded to PsN5 and PsN120 in E135 nodules was slightly depressed by exogenous ammonia, the level of the PsN5 transcript was still lower than the control level in Sparkle nodules. Our results indicate that the plant gene sym 13 does not influence the induction of nodulin genes but does influence the level of the expression of some genes, one of which is a gene for Lb, as well as the level of heme.
Plant Mol Biol 1995 Sep
PMID:Expression of nodulin genes in plant-determined ineffective nodules of pea. 754 21

The FeSII protein of Azotobacter vinelandii has been proposed to mediate the 'conformational protection' of the molybdenum-dependent nitrogenase components against oxygen inactivation. We have cloned and characterized the structural gene for the FeSII protein (the fesII locus). Hybridization studies did not reveal the presence of fesII-like genes in a number of diverse species of well-studied nitrogen-fixing bacteria, with the exception of Azotobacter chroococcum. The fesII locus is transcriptionally expressed during both nitrogen fixing and non-nitrogen fixing conditions, although the level of its message is upregulated by approximately 2.5-fold during nitrogen fixation. The promoter region was identified by primer extension analysis, and is similar to other sigma 70-type promoters. Mutants devoid of the FeSII protein were constructed. These mutants possessed growth characteristics on a variety of carbon substrates during non-diazotrophic as well as diazotrophic growth that were essentially indistinguishable from the wild-type strain. Nevertheless, the nitrogenase activity in cell-free extracts is significantly more sensitive to irreversible oxygen inactivation in the mutants as compared with the wild type. When treated with 250 mM NaCl (a condition known to dissociate FeSII from nitrogenase components), the wild-type and mutant extracts were equally hypersensitive to oxygen inactivation. Upon energy starvation, conditions in which 'respiratory protection' is inoperable, the MoFe and Fe proteins of nitrogenase are degraded much more rapidly in vivo in the deletion mutants, compared to the wild type. Strains relying on either the vanadium or the 'iron-only' alternative nitrogenases exhibited similar growth rates irrespective of the presence or absence of the FeSII protein, and the in vitro inactivation of the vanadium nitrogenase components was not affected by the lack of the FeSII protein. All in all, these results are consistent with a model whereby 'respiratory protection' is the major physiological mechanism responsible for the protection of all three nitrogenases during energy-supplemented growth. Upon energy starvation, however, 'conformational protection', mediated by the FeSII protein is capable of temporarily protecting the conventional molybdenum nitrogenase components from inactivation and subsequent degradation.
Mol Microbiol 1994 Oct
PMID:The FeSII protein of Azotobacter vinelandii is not essential for aerobic nitrogen fixation, but confers significant protection to oxygen-mediated inactivation of nitrogenase in vitro and in vivo. 783 May 48

The structural genes for nitrogenase, nifK, nifD, and nifH, are crucial for nitrogen fixation. Previous phylogenetic analysis of the amino acid sequence of nifH suggested that this gene had been horizontally transferred from a proteobacterium to the gram-positive/cyanobacterial clade, although the confounding effects of paralogous comparisons made interpretation of the data difficult. An additional test of nif gene horizontal transfer using nifD was made, but the NifD phylogeny lacked resolution. Here nif gene phylogeny is addressed with a phylogenetic analysis of a third and longer nif gene, nifK. As part of the study, the nifK gene of the key taxon Frankia was sequenced. Parsimony and some distance analyses of the nifK amino acid sequences provide support for vertical descent of nifK, but other distance trees provide support for the lateral transfer of the gene. Bootstrap support was found for both hypotheses in all trees; the nifK data do not definitively favor one or the other hypothesis. A parsimony analysis of NifH provides support for horizontal transfer in accord with previous reports, although bootstrap analysis also shows some support for vertical descent of the orthologous nifH genes. A wider sampling of taxa and more sophisticated methods of phylogenetic inference are needed to understand the evolution of nif genes. The nif genes may also be powerful phylogenetic tools. If nifK evolved by vertical descent, it provides strong evidence that the cyanobacteria and proteobacteria are sister groups to the exclusion of the firmicutes, whereas 16S rRNA sequences are unable to resolve the relationships of these three major eubacterial lineages.
Mol Biol Evol 1995 Jan
PMID:Assessing horizontal transfer of nifHDK genes in eubacteria: nucleotide sequence of nifK from Frankia strain HFPCcI3. 787 90


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