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PubMed1991

Glycine 100 in the dinitrogenase reductase of Rhodospirillum rubrum is required for nitrogen fixation but not for ADP-ribosylation.

Dinitrogenase reductase (Rr2) is required for reduction of the molybdenum dinitrogenase in the nitrogen fixation reaction and is the target of posttranslational regulation in Rhodospirillum rubrum. This posttranslational regulation involves the ADP-ribosylation of Rr2. To study the structural requirements for these two functions of Rr2, i.e., activity and regulation, two site-directed mutations in nifH, the gene encoding Rr2, were constructed and analyzed. The mutations both affected a region of the protein known to be highly conserved in evolution and to be relevant to both of the above properties. These mutants were both Nif-, but one of the altered Rr2s was a substrate for ADP-ribosylation. This demonstrates that the ability of Rr2 to participate in nitrogen fixation can be separated from its ability to act as a substrate for ADP-ribosylation.

Adenosine Diphosphate Ribose↗

PubMed2005

Symbiotic leghemoglobins are crucial for nitrogen fixation in legume root nodules but not for general plant growth and development.

Hemoglobins are ubiquitous in nature and among the best-characterized proteins. Genetics has revealed crucial roles for human hemoglobins, but similar data are lacking for plants. Plants contain symbiotic and nonsymbiotic hemoglobins; the former are thought to be important for symbiotic nitrogen fixation (SNF). In legumes, SNF occurs in specialized organs, called nodules, which contain millions of nitrogen-fixing rhizobia, called bacteroids. The induction of nodule-specific plant genes, including those encoding symbiotic leghemoglobins (Lb), accompanies nodule development. Leghemoglobins accumulate to millimolar concentrations in the cytoplasm of infected plant cells prior to nitrogen fixation and are thought to buffer free oxygen in the nanomolar range, avoiding inactivation of oxygen-labile nitrogenase while maintaining high oxygen flux for respiration. Although widely accepted, this hypothesis has never been tested in planta. Using RNAi, we abolished symbiotic leghemoglobin synthesis in nodules of the model legume Lotus japonicus. This caused an increase in nodule free oxygen, a decrease in the ATP/ADP ratio, loss of bacterial nitrogenase protein, and absence of SNF. However, LbRNAi plants grew normally when fertilized with mineral nitrogen. These data indicate roles for leghemoglobins in oxygen transport and buffering and prove for the first time that plant hemoglobins are crucial for symbiotic nitrogen fixation.

Adenosine Triphosphate↗

PubMed1993

One member of a gro-ESL-like chaperonin multigene family in Bradyrhizobium japonicum is co-regulated with symbiotic nitrogen fixation genes.

This report is concerned with the structural characterization and genetic regulation of new bacterial groES and groEL chaperonin genes, and presents two novelties. The first is the discovery that the nitrogen fixing soybean root nodule bacterium, Bradyrhizobium japonicum, unlike all other prokaryotes investigated so far, possesses a multigene family consisting of five very similar, though not identical, groESL-like genes. The second novelty relates to the finding that these five homologues are expressed to different degrees and, in particular, that one family member (namely groESL3) is induced by a mechanism that does not involve the well-known heat shock response. By contrast, the groESL3 genes are co-regulated together with symbiotic nitrogen fixation genes, in that they are activated by the nitrogen fixation regulatory protein NifA at low oxygen conditions and transcribed from a -24/-12 promoter by the sigma 54 RNA polymerase. Two other members of the groESL gene family are apparently expressed constitutively at different levels, and yet another one is strongly induced by high temperature. As an attractive hypothesis it follows that B. japonicum may modulate its cellular contents of GroES- and GroEL-like chaperonins in response to specific environmental conditions and physiological needs.

Amino Acid Sequence↗

PubMed1989

fixK, a gene homologous with fnr and crp from Escherichia coli, regulates nitrogen fixation genes both positively and negatively in Rhizobium meliloti.

Nitrogen fixation genes are shown to undergo a complex positive and negative regulation in Rhizobium meliloti. Activation of fixN by fixLJ is shown to require a third regulatory gene, fixK. As fixK is activated by fixLJ, we propose a cascade model for fixN regulation such that fixLJ activates fixN via fixK. In addition fixK negatively regulates expression of the nif-specific activator nifA as well as its own expression by autoregulation. Thus nifA and fixK are subject to a mixed regulation, positive (by fixLJ) and negative (by fixK). The sequence of fixK shows homology with the Escherichia coli regulators fnr and crp, which makes fixK the third characterized member of this family of prokaryotic regulators.

Amino Acid Sequence↗

PubMed1985

Expression of a nitrogen-fixation gene encoding a nitrogenase subunit in yeast.

Biological nitrogen fixation is catalyzed by nitrogenase, an enzyme complex exclusive to prokaryotes. We used the yeast Saccharomyces cerevisiae to study the synthesis, and subsequently the assembly, of nitrogenase components in a eukaryote. Here, the Klebsiella pneumoniae nifH gene, encoding the subunit of the Fe protein (Kp2) component of nitrogenase, was expressed in S. cerevisiae from the yeast ADHI promoter. The nifH gene product, detected in yeast by immunoblot analysis with anti-Kp2 antibodies, exhibited the same electrophoretic mobility in SDS-polyacrylamide gels as that of the Kp2 subunit synthesized in K. pneumoniae. Estimates of Kp2 antigen and assays of beta-galactosidase activity specified by nifH'-'lacZ fusions showed that the level of nifH product was similar in anaerobically and aerobically grown yeast, but varied with different transforming plasmids and in various haploid and diploid yeast strains. A cistron located downstream to nifH in a transcript resembling the polycistronic mRNA of the nifHDKY operon in K. pneumoniae is not translated in yeast.

Gene Expression Regulation↗

PubMed1990

The integration host factor stimulates interaction of RNA polymerase with NIFA, the transcriptional activator for nitrogen fixation operons.

The regulatory protein NIFA activates transcription of nitrogen fixation (nif) operons by the sigma 54 holoenzyme form of RNA polymerase. NIFA from Klebsiella pneumoniae activates transcription from the nifH promoter in vitro; in addition, the integration host factor, IHF, binds between the nifH promoter and an upstream binding site for NIFA. We demonstrate here that IHF greatly stimulates NIFA-mediated activation of nifH transcription in vitro and thus that the two factors are functionally synergistic. Electron micrographs indicate that IHF bends the DNA in the nifH promoter regulatory region. Although IHF binds close to the nifH promoter, it does not directly stimulate binding of sigma 54 holoenzyme. Rather, the IHF-induced bend may facilitate productive contacts between NIFA and sigma 54 holoenzyme that lead to the formation of open complexes. IHF binds to nif promoter regulatory regions from a variety of organisms within the phylum "purple bacteria," suggesting a general ability to stimulate NIFA-mediated activation of nif transcription.

Bacterial Proteins↗

PubMed1986

Tight coupling of root-associated nitrogen fixation and plant photosynthesis in the salt marsh grass Spartina alterniflora and carbon dioxide enhancement of nitrogenase activity.

The coupling of root-associated nitrogen fixation and plant photosynthesis was examined in the salt marsh grass Spartina alterniflora. In both field experiments and hydroponic assay chambers, nitrogen fixation associated with the roots was rapidly enhanced by stimulating plant photosynthesis. A kinetic analysis of acetylene reduction activity (ARA) showed that a five-to sixfold stimulation occurred within 10 to 60 min after the plant leaves were exposed to light or increased CO2 concentrations (with the light held constant). In field experiments, CO2 enrichment increased plant-associated ARA by 27%. Further evidence of the dependence of ARA on plant photosynthate was obtained when activity in excised roots was shown to decrease after young greenhouse plants were placed in the dark. Seasonal variation in the ARA of excised plant roots from field cores appears to be related to the annual cycle of net photosynthesis in S. alterniflora.

Acetylene↗

PubMed2003

Nitrogen fixation genetics and regulation in a Pseudomonas stutzeri strain associated with rice.

The Pseudomonas stutzeri strain A1501 (formerly known as Alcaligenes faecalis) fixes nitrogen under microaerobic conditions in the free-living state and colonizes rice endophytically. The authors characterized a region in strain A1501, corresponding to most of the nif genes and the rnf genes, involved in electron transport to nitrogenase in Rhodobacter capsulatus. The region contained three groups of genes arranged in the same order as in Azotobacter vinelandii: (1) nifB fdx ORF3 nifQ ORF5 ORF6; (2) nifLA-rnfABCDGEF-nifY2/nafY; (3) ORF13 ORF12-nifHDK-nifTY ORF1 ORF2-nifEN. Unlike in A. vinelandii, where these genes are not contiguous on the chromosome, but broken into two regions of the genome, the genes characterized here in P. stutzeri are contiguous and present on a 30 kb region in the genome of this organism. Insertion mutagenesis confirmed that most of the nif and the rnf genes in A1501 were essential for nitrogen fixation. Using lacZ fusions it was found that nif and rnf gene expression was under the control of ntrBC, nifLA and rpoN and that the rnf gene products were involved in the regulation of the nitrogen fixation process.

Ammonia↗

PubMed2000

Molecular evolution of nitrogen fixation: the evolutionary history of the nifD, nifK, nifE, and nifN genes.

The pairs of nitrogen fixation genes nifDK and nifEN encode for the alpha and beta subunits of nitrogenase and for the two subunits of the NifNE protein complex, involved in the biosynthesis of the FeMo cofactor, respectively. Comparative analysis of the amino acid sequences of the four NifD, NifK, NifE, and NifN in several archaeal and bacterial diazotrophs showed extensive sequence similarity between them, suggesting that their encoding genes constitute a novel paralogous gene family. We propose a two-step model to reconstruct the possible evolutionary history of the four genes. Accordingly, an ancestor gene gave rise, by an in-tandem paralogous duplication event followed by divergence, to an ancestral bicistronic operon; the latter, in turn, underwent a paralogous operon duplication event followed by evolutionary divergence leading to the ancestors of the present-day nifDK and nifEN operons. Both these paralogous duplication events very likely predated the appearance of the last universal common ancestor. The possible role of the ancestral gene and operon in nitrogen fixation is also discussed.

Dinitrogenase Reductase↗

PubMed1962

Physiology of nitrogen fixation by Bacillus polymyxa.

Grau, F. H. (University of Wisconsin, Madison) and P. W. Wilson. Physiology of nitrogen fixation by Bacillus polymyxa. J. Bacteriol. 83:490-496. 1962.-Of 17 strains of Bacillus polymyxa tested for fixation of molecular nitrogen, 15 fixed considerable quantities (30 to 150 mug N/ml). Two strains of the closely related B. macerans did not use N(2), but possibly other members of this species may do so. Confirmation of fixation was obtained by showing incorporation of N(15) into cell material. Both iron and molybdenum are specifically required for fixation; without the addition of these metals to the nitrogen-free medium, the growth rate and the total nitrogen fixed were reduced about 30 to 50%. No requirement for added molybdenum could be shown when ammonia was the nitrogen source, and the absence of iron caused only a slight decrease in growth. Washed-cell suspensions of B. polymyxa containing an active hydrogenase readily incorporated N(15) into cell materials when provided with mannitol, glucose, or pyruvate but not when formate was the substrate. Hydrogen is a specific inhibitor of fixation, reducing both the rate and final amount of nitrogen fixed; it did not reduce growth on ammonia. Fixation was strictly anaerobic, 1% oxygen in the gas phase being sufficient to stop fixation. Arsenate is a powerful inhibitor of fixation of N(2) by washed-cell suspensions of B. polymyxa, indicating that high-energy phosphate may be significant for this process.

Bacillus↗

PubMed1980

Nitrate and Carbohydrate Effects on Nodulation and Nitrogen Fixation (Acetylene Reduction) Activity of Lentil (Lens esculenta Moench).

Lentils (Lens esculenta Moench, cv. Tekoas) grown in a nutrient solution containing 15 millimolar nitrate had 84% fewer nodules than lentils grown in nitrate-free nutrient solution. Nodules from the nitrate-grown plants weighed 71% less than nodules from the nitrate-free plants. Nitrate-grown plants also fixed much less nitrogen (measured by acetylene reduction) than the nitrate-free plants. When lentils were grown in a solution containing 15 millimolar nitrate and 75 millimolar fructose, glucose, or sucrose, however, the nitrogen fixation activity of their nodules was similar to that of nodules from nitrate-free plants. Leaves of lentils grown in the nitrate-sugar solutions had only about 7% as much nitrate reductase activity and accumulated only 10% as much nitrate as leaves from lentils grown in the nitrate solution alone. Roots of lentils grown in the nitrate-sugar solutions had similar nitrate reductase activity but accumulated only 17 to 25% as much nitrate as roots from lentils grown in the nitrate solution. The results indicate that the added sugars alleviated the inhibitory effects of nitrate on symbiotic nitrogen fixation not only by increasing the carbohydrate supply so lentils could support both nitrogen fixation and nitrate reduction but also by inhibiting the accumulation of nitrate and, hence, lowering nitrate reductase activity in the leaves.

Journal Article↗

PubMed1996

Control of nitrogen fixation by oxygen in purple nonsulfur bacteria

Some members of the facultatively phototrophic bacteria are able to grow diazotrophically in the presence of oxygen. As in other diazotrophs, the nitrogenase of the phototrophic bacteria is highly sensitive to oxygen; therefore, both the function and the expression of nitrogenase are strictly controlled by oxygen. This review focuses on the different levels of oxygen control in the two most extensively studied facultatively phototrophic bacteria, Rhodospirillum rubrum and Rhodobacter capsulatus. Current data show that oxygen controls nitrogen fixation at least at the levels of (1) transcription of nif genes, (2) the accumulation of the three different nitrogenase polypeptides, (3) the cellular activity of nitrogen fixation. In Rba. capsulatus, activation of the nifH promoter is the least oxygen-sensitive step, and nitrogen fixation is the most oxygen-sensitive step. ADP-Ribosylation of nitrogenase, occurring under conditions of ammonium-dependent inactivation of the enzyme, is not observed when Rba. capsulatus is exposed either suddenly or at a steady state to increased oxygen concentrations. Future research is required to understand the mechanisms of protection of nitrogenase against oxygen damage, and also the mechanisms by which oxygen controls the formation and activity of nitrogenase; this will add significantly to the biologically important question of how cells deal with the presence of toxic oxygen.

Journal Article↗

PubMed1977

Effect of nitrite upon leghemoglobin and interaction with nitrogen fixation.

Nitrite (0.4 mM) added to soybean bacteroid preparations strongly inhibited C2H2 reduction. In the presence of leghemoglobin (0.1mM), a 3-fold enhancement of nitrogen fixation occurred but the inhibitory effect of nitrite was delayed. Spectra of leghemoglobin showed a rapid disappearance of the 574 nm and 541 nm peaks of oxyleghemoglobin the presence of nitrite. Concomitant oxidation of this hemoprotein gave ferric leghemoglobin as the single final product. High nitrite levels could depress nitrogen fixation both by inactivation of nitrogenase and by conversion of leghemoglobin into an inactive form. Nitrite present at low concentrations reacts with this hemoprotein and is then no longer able to penetrate into bacteroids.

Hemeproteins↗

PubMed2006

Nitrogen fixation at 92 degrees C by a hydrothermal vent archaeon.

A methanogenic archaeon isolated from deep-sea hydrothermal vent fluid was found to reduce N(2) to NH(3) at up to 92 degrees C, which is 28 degrees C higher than the current upper temperature limit of biological nitrogen fixation. The 16S ribosomal RNA gene of the hyperthermophilic nitrogen fixer, designated FS406-22, was 99% similar to that of non-nitrogen fixing Methanocaldococcus jannaschii DSM 2661. At its optimal growth temperature of 90 degrees C, FS406-22 incorporated (15)N(2) and expressed nifH messenger RNA. This increase in the temperature limit of nitrogen fixation could reveal a broader range of conditions for life in the subseafloor biosphere and other nitrogen-limited ecosystems than previously estimated.

Amino Acid Sequence↗

PubMed1980

Carbohydrates in Soybean Nodules: II. DISTRIBUTION OF COMPOUNDS IN SEEDLINGS DURING THE ONSET OF NITROGEN FIXATION.

During the first few days of nitrogen fixation activity by soybean (Glycine max (L.) Merr) root nodules, d-chiro-inositol, myo-inositol, sucrose, alpha,alpha-trehalose, and maltose accumulate rapidly and reach concentrations several fold greater than concentrations in other plant organs. Concentrations of d-pinitol in nodules (>/=1.0 milligrams per gram fresh weight) were similar to concentrations in leaf blades. The concentration of fructose in nodules was lower than concentrations in other plant organs.Comparison of nonnodulated roots, nodulated roots (after removal of nodules), and nodules indicated that nodules may compete successfully with roots for carbohydrates, especially the disaccharides sucrose, alpha,alpha-trehalose, and maltose. Based on the isolation of protoplasts and bacteroids, it was tentatively concluded that the highest concentrations of cyclitols in soybean nodules are located in the infected region and that, inside infected cells, the highest concentrations of d-pinitol and myo-inositol are outside of bacteroids.Evidence for the identification of d-chiro-inositol and maltose in soybean nodules is presented.

Journal Article↗

PubMed1979

Association between Azotobacter and other soil bacteria and its effect on nitrogen fixation.

The association between A. vinelandii and either Agrobacterium sp. or Micrococcus sp., which are usually found as contaminants in Azotobacter cultures, was investigated. In comparison with pure cultures, association increased the microbiol counts in addition to increasing nitrogen fixation rates and efficiency. In liquid cultures higher Azotobacter densities were observed in the top 5 cm of the column concomitant with lowering the economic coefficient of utilization of carbonaceous compounds, which resulted in low efficiency of nitrogen fixation. In deep layers, lower amounts of nitrogen gain were obtained, but higher efficiencies of N2-fixation were recorded. In sand cultures, the biggest amounts of fixed nitrogen were in the 5--15 cm layer of the soil column and in deeper layers economic utilization of sugars occurred, but nitrogen gain sharply decreased.

Azotobacter↗

PubMed2002

Quantifying nitrogen-fixation in feather moss carpets of boreal forests.

Biological nitrogen (N) fixation is the primary source of N within natural ecosystems, yet the origin of boreal forest N has remained elusive. The boreal forests of Eurasia and North America lack any significant, widespread symbiotic N-fixing plants. With the exception of scattered stands of alder in early primary successional forests, N-fixation in boreal forests is considered to be extremely limited. Nitrogen-fixation in northern European boreal forests has been estimated at only 0.5 kg N ha(-1) yr(-1); however, organic N is accumulated in these ecosystems at a rate of 3 kg N ha(-1) yr(-1) (ref. 8). Our limited understanding of the origin of boreal N is unacceptable given the extent of the boreal forest region, but predictable given our imperfect knowledge of N-fixation. Herein we report on a N-fixing symbiosis between a cyanobacterium (Nostoc sp.) and the ubiquitous feather moss, Pleurozium schreberi (Bird) Mitt. that alone fixes between 1.5 and 2.0 kg N ha(-1) yr(-1) in mid- to late-successional forests of northern Scandinavia and Finland. Previous efforts have probably underestimated N-fixation potential in boreal forests.

Acetylene↗

PubMed1993

Cloning and nucleotide sequencing of Rhizobium meliloti aminotransferase genes: an aspartate aminotransferase required for symbiotic nitrogen fixation is atypical.

In Rhizobium meliloti, an aspartate aminotransferase (AspAT) encoded within a 7.3-kb HindIII fragment was previously shown to be required for symbiotic nitrogen fixation and aspartate catabolism (V. K. Rastogi and R.J. Watson, J. Bacteriol. 173:2879-2887, 1991). A gene coding for an aromatic aminotransferase located within an 11-kb HindIII fragment was found to complement the AspAT deficiency when overexpressed. The genes encoding these two aminotransferases, designated aatA and tatA, respectively, have been localized by subcloning and transposon Tn5 mutagenesis. Sequencing of the tatA gene revealed that it encodes a protein homologous to an Escherichia coli aromatic aminotransferase and most of the known AspAT enzymes. However, sequencing of the aatA gene region revealed two overlapping open reading frames, neither of which encoded an enzyme with homology to the typical AspATs. Polymerase chain reaction was used to selectively generate one of the candidate sequences for subcloning. The cloned fragment complemented the original nitrogen fixation and aspartate catabolism defects and was shown to encode an AspAT with the expected properties. Sequence analysis showed that the aatA protein has homology to AspATs from two thermophilic bacteria and the eukaryotic tyrosine aminotransferases. These aminotransferases form a distinct class in which only 13 amino acids are conserved in comparison with the well-known AspAT family. DNA homologous to the aatA gene was found to be present in Agrobacterium tumefaciens and other rhizobia but not in Klebsiella pneumoniae or E. coli.

Amino Acid Sequence↗