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PubMed1997

The heterocyst-specific fdxH gene product of the cyanobacterium Anabaena sp. PCC 7120 is important but not essential for nitrogen fixation.

To clarify the role of the heterocyst-specific [2Fe-2S] ferredoxin in cyanobacterial nitrogen fixation, mutational analysis of the Anabaena 7120 fdxH gene region was carried out. First, the DNA sequence of the wild-type 3509-bp EcoRI fragment downstream of the fdxH gene was determined. Genes homologous to ORF3 from the fdxH gene regions of A. variabilis and Plectonema boryanum, the mop genes of Clostridium pasteurianum encoding molybdo-pterin binding proteins, and ORF3 from the A. variabilis hydrogenase gene cluster were identified within the sequenced region. For mutational analysis the Anabaena 7120 mutant strains LAK4, BMB92, and KSH10 were constructed. In LAK4 the fdxH coding region is disrupted by an interposon, whereas BMB92 is deleted for a 2799-bp NheI fragment encompassing fdxH, ORF3, mop, ORF4, and ORF5. Mutant strain KSH10 is a derivative of BMB92, complemented for fdxH but not for the other genes located further downstream. Analysis of the Nif phenotype of these mutant strains showed that FdxH is necessary for maximum nitrogenase activity and optimal growth under nitrogen-fixing conditions, but not absolutely essential for diazotrophic growth. The role of alternative electron donors for nitrogenase, which might substitute for FdxH, is discussed. Iron concentrations (1 microM Fe) sufficient to induce synthesis of the vegetative cell flavodoxin did not stimulate diazotrophic growth of the fdxH mutant strains, suggesting that FdxH was not replaced by a NifJ-flavodoxin system. Comparison of LAK4 and BMB92 indicated that one of the genes located downstream of fdxH might also play a (minor) role in nitrogen fixation.

Anabaena↗

PubMed1978

Nitrogen fixation by Rhizobium in pure cultures.

Strains of Rhizobium trifolii and Rhizobium meliloti were tested for their asymbiotic nitrogen fixation ability. From among ten tested strains two R. trifolii and one R. meliloti expressed nitrogenase activity within the range of 1.3--9.3 nM C2H4/h/mg protein. Asymbiotic nitrogen fixation was affected by the composition of the medium.

Nitrogen Fixation↗

PubMed2001

Effect of butachlor on growth and nitrogen fixation by Anabaena sphaerica.

Present study was carried out to examine the effect of Butachlor on growth and nitrogen fixation by Anabaena sphaerica. The increased concentration of the pesticide did not have any adverse effect on the alga. Rather it accelerated the algal contribution in terms of biomass and nitrogen fixation.

Acetanilides↗

PubMed1984

Osmoregulation in Klebsiella pneumoniae: enhancement of anaerobic growth and nitrogen fixation under stress by proline betaine, gamma-butyrobetaine, and other related compounds.

Exogenous proline betaine ( stachydrine or N- dimethylproline ) or gamma-butyrobetaine (gamma-trimethylaminobutyrate), at a concentration as low as 1 mM, were found to stimulate the growth rate of Klebsiella pneumoniae, wild type M5A1 , in media of inhibitory osmotic strength (0.8 M NaC1). Simultaneously, nitrogen fixation by whole cells, a process particularly sensitive to osmotic stress, was strongly enhanced by these compounds. However, in the absence of sodium chloride, both the growth and nitrogen fixation were not affected by the addition of the methylammonium derivatives in the medium. The sensitivity of the nitrogen fixation to osmotic stress was used as a bioassay to evaluate the potentiality of osmoprotective compound in relation to the number of methyl groups on the nitrogen atom of glycine, proline, and gamma-aminobutyrate. Experiments with sarcosine ( monomethylglycine ), dimethylglycine, and glycine betaine ( trimethylglycine ), or experiments with mono- and di- methylproline or gamma-mono-, gamma-di, gamma-tri- methylaminobutyrate , indicated that the greatest stress tolerance was always obtained with the more N-methylated compounds.

Anaerobiosis↗

PubMed1978

Membrane energization in relation with nitrogen fixation in Azotobacter vinelandii and Rhizobium leguminosarum bacteroids.

Nitrogen fixation in A. vinelandii and R. leguminosarum bacteroides shows identical characteristics with respect to the dependence on membrane energization, the sensitivity to uncouplers, the ATP/ADP-ratio, and the dependences on flavodoxinhydroquinone as electrondonor. Although we have been successful in preparing inside-out vesicles which can be energized, attempts to couple these membranes to N2-ase were still unsuccessful. One of the major problems could be the failure to energize these vesicles directly by ATP. Although subject to polymerisation after addition of MgCl2, it could be shown that the actual mol.wt. of the O2-stable N2-ase complex is about 300,000 in agreement with a 1:1:1 stoichiometry of the three constituent proteins, namely, component I, component II and the 2Fe-2S protein.

Adenosine Diphosphate↗

PubMed1993

Activity of purified NIFA, a transcriptional activator of nitrogen fixation genes.

The NIFA protein activates transcription of nitrogen fixation (nif) operons by the sigma 54-holoenzyme form of RNA polymerase. We purified active NIFA from Klebsiella pneumoniae in the form of a maltose-binding protein (MBP)-NIFA fusion; proteolytic release of MBP yielded inactive and insoluble NIFA. MBP-NIFA activated transcription from the nifHDK promoter in a purified transcription system. Like the related transcriptional activator NTRC, MBP-NIFA catalyzed the ATP-dependent isomerization of closed complexes between sigma 54-holoenzyme and a promoter to open complexes. MBP-NIFA had a broader nucleotide specificity than NTRC, being able to utilize pyrimidine in addition to purine nucleoside triphosphates. Both MBP-NIFA and a purified C-terminal fragment of NIFA bound to the upstream activation sequence for the nifHDK promoter, as assessed by DNAse I footprinting. When assays were performed at 37 degrees C instead of the usual 30 degrees C, transcriptional activation, open complex formation, and DNA binding by MBP-NIFA were all abolished, consistent with the known heat lability of NIFA. However, the purified C-terminal fragment of NIFA still bound the upstream activation sequence at 37 degrees C, indicating that the function of the helix-turn-helix DNA-binding motif is not inherently heat-labile.

ATP-Binding Cassette Transporters↗

PubMed2006

Role of the central region of NifL in conformational switches that regulate nitrogen fixation.

The NifL regulatory protein is an anti-activator that tightly regulates transcription of genes required for nitrogen fixation in Azotobacter vinelandii by controlling the activity of its partner protein NifA through the formation of a protein-protein complex. NifL modulates the activity of NifA in response to the redox, carbon and nitrogen status to ensure that nitrogen fixation occurs only under physiological conditions that are appropriate for nitrogenase activity. The domain architecture of NifL is similar to that of some histidine protein kinases, with two N-terminal PAS (PER, ARNT, SIM) domains, one of which contains an FAD cofactor that senses the redox status, and a C-terminal domain containing conserved residues that constitutes the nucleotide-binding domain of the GHKL (gyrase, Hsp90, histidine kinase, MutL) superfamily of ATPases. We have evidence that the central region of NifL, which is located between the PAS domains and the C-terminal GHKL nucleotide-binding domain, plays a crucial role in the propagation of signals perceived in response to the redox and fixed nitrogen status and that this region participates in conformational changes that switch NifL between active and inactive states. We have identified a critical arginine residue in the central region of NifL that participates in the conformational switch that activates NifL. Mutations in the central region of NifL that disable the redox-sensing function of NifL but leave the protein competent to respond to the nitrogen signal conveyed by the signal transduction protein GlnK have also been isolated. Our results suggest that the topological relationship between the central region and the GHKL domain may alter as a consequence of conformational changes induced in response to signal perception.

Bacterial Proteins↗

PubMedDate not supplied

Oxygen regulation of expression of nitrogen fixation genes in Rhizobium meliloti.

The sensor kinase FixL and the response regulator FixJ induce the expression of the nitrogen fixation genes of Rhizobium meliloti in response to microaerobiosis, which is a characteristic feature of the plant root nodule interior where the bacteria fix nitrogen. The kinase activity of a purified, soluble derivative of the membrane-bound hemoprotein FixL, designated FixL*, is stimulated under low oxygen conditions, thus increasing FixJ-phosphate levels. FixJ-phosphate is a potent transcriptional activator of the nifA and fixK genes, the products of which, in turn, induce the expression of most if not all of the remaining nitrogen fixation genes. FixL* and FixL*-phosphate also dephosphorylate FixJ-phosphate, and this activity is depressed by low oxygen concentrations. In the current model, gene expression is reciprocally coordinated by the kinase and phosphatase activities of FixL according to changes in oxygen tension.

Bacterial Proteins↗

PubMed1995

The cycHJKL genes of Rhizobium meliloti involved in cytochrome c biogenesis are required for "respiratory" nitrate reduction ex planta and for nitrogen fixation during symbiosis.

We report the genetic and biochemical analysis of Rhizobium meliloti mutants defective in symbiotic nitrogen fixation (Fix-) and "respiratory" nitrate reduction (Rnr-). The mutations were mapped close to the ade-1 and cys-46 chromosomal markers and the mutated locus proved to be identical to the previously described fix-14 locus. By directed Tn5 mutagenesis, a 4.5 kb segment of the chromosome was delimited in which all mutations resulted in Rnr- and Fix- phenotypes. Nucleotide sequence analysis of this region revealed the presence of four open reading frames coding for integral membrane and membrane-anchored proteins. Biochemical analysis of the mutants showed that the four proteins were necessary for the biogenesis of all cellular c-type cytochromes. In agreement with the nomenclature proposed for rhizobial genes involved in the formation of c-type cytochromes, the four genes were designated cycH, cycJ, cycK, and cycL, respectively. The predicted protein product of cycH exhibited a high degree of similarity to the Bradyrhizobium japonicum counterpart, while CycK and CycL shared more than 50% amino acid sequence identity with the Rhodobacter capsulatus Cc11 and Cc12 proteins, respectively. cycJ encodes a novel membrane anchored protein of 150 amino acids. We suggest that this gene cluster codes for (parts of) a multisubunit cytochrome c haem lyase. Moreover, our results indicate that in R. meliloti c-type cytochromes are required for respiratory nitrate reduction ex planta, as well as for symbiotic nitrogen fixation in root nodules.

Amino Acid Sequence↗

PubMed1986

Restriction Endonuclease and nif Homology Patterns of Bradyrhizobium japonicum USDA 110 Derivatives With and Without Nitrogen Fixation Competence.

DNAs from Bradyrhizobium japonicum USDA 110 derivatives that differ in nitrogen-fixing ability produced similar electrophoretic patterns with five different restriction enzymes. Our data support the hypothesis of common ancestry for these derivatives. Derivatives I-110 and L1-110 differed as much as 100-fold in acetylene reduction activity when they were tested with several soybean cultivars in both greenhouse and field experiments. While possessing nodulating ability, derivative L1-110 is deficient in symbiotic nitrogen-fixing ability, whereas derivative I-110 is symbiotically competent. Hybridization of nifDK and nifH probes from B. japonicum to Southern blots of restricted DNAs from strain USDA 110 derivatives produced similar patterns. This finding indicates similar structural gene organization for both derivative I-110 and derivative L1-110 and implies that the difference in symbiotic nitrogen fixation is probably not due to structural gene rearrangements. However, our hybridization data do not rule out the possibility of differences in expression of structural nif genes or alterations in the structure or expression of other genes required for symbiotic nitrogen fixation.

Journal Article↗

PubMed1982

Constitutive expression of nitrogen fixation (nif) genes of Klebsiella pneumoniae due to a DNA duplication.

A spontaneous mutant of Klebsiella pneumoniae exhibiting nitrogen fixing activity in the presence of ammonia was isolated from a nifL ::Mu mutant. The main features of the nif constitutive mutation, designated nif-8388, were as follows: (i) neither ammonia nor bases repressed, but amino acids partially repressed, nitrogen fixation; (ii) the mutation caused an escape from the regulatory effect of glnA and glnG mutations of K. pneumoniae but not that of a glnF mutation; (iii) it enabled the activation of the nifH -lac fusion in the presence of oxygen with or without ammonia and a nifL -lac fusion in the presence of ammonia without oxygen; (iv) the mutation allowed nitrogen fixation at 37 degrees C when plasmid-borne. Restriction analysis and Southern hybridization using Mu DNA and the 8.1-kb nifQBALF EcoRI fragment as probes demonstrated that the nif-8388 mutation was a tandem duplication of 10 kb in the nifL region in which no Mu DNA was present. This duplication led to an operon fusion between nifLA and his since Nifc expression was shown to be increased with a specific inducer of the his operon. These results provide further evidence that the nifA product is a nif-specific activator, and that the nifL product is involved in oxygen repression and temperature control. In addition, they suggest that there is an autoactivation of nifLA transcription by the nifA product and that glnF could act in nif regulation by a mechanism other than the glnG-mediated control of nifLA transcription.

Ammonia↗

PubMed1993

Identification of a new class of nitrogen fixation genes in Rhodobacter capsulatus: a putative membrane complex involved in electron transport to nitrogenase.

DNA sequence analysis of a 12236 bp fragment, which is located upstream of nifE in Rhodobacter capsulatus nif region A, revealed the presence of ten open reading frames. With the exception of fdxC and fdxN, which encode a plant-type and a bacterial-type ferredoxin, the deduced products of these coding regions exhibited no significant homology to known proteins. Analysis of defined insertion and deletion mutants demonstrated that six of these genes were required for nitrogen fixation. Therefore, we propose to call these genes rnfA, rnfB, rnfC, rnfD, rnfE and rnfF (for Rhodobacter nitrogen fixation). Secondary structure predictions suggested that the rnf genes encode four potential membrane proteins and two putative iron-sulphur proteins, which contain cysteine motifs (C-X2-C-X2-C-X3-C-P) typical for [4Fe--4S] proteins. Comparison of the in vivo and in vitro nitrogenase activities of fdxN and rnf mutants suggested that the products encoded by these genes are involved in electron transport to nitrogenase. In addition, these mutants were shown to contain significantly reduced amounts of nitrogenase. The hypothesis that this new class of nitrogen fixation genes encodes components of an electron transfer system to nitrogenase was corroborated by analysing the effect of metronidazole. Both the fdxN and rnf mutants had higher growth yields in the presence of metronidazole than the wild type, suggesting that these mutants contained lower amounts of reduced ferredoxins.

Amino Acid Sequence↗

PubMed2003

Yeast two-hybrid studies on interaction of proteins involved in regulation of nitrogen fixation in the phototrophic bacterium Rhodobacter capsulatus.

Rhodobacter capsulatus contains two PII-like proteins, GlnB and GlnK, which play central roles in controlling the synthesis and activity of nitrogenase in response to ammonium availability. Here we used the yeast two-hybrid system to probe interactions between these PII-like proteins and proteins known to be involved in regulating nitrogen fixation. Analysis of defined protein pairs demonstrated the following interactions: GlnB-NtrB, GlnB-NifA1, GlnB-NifA2, GlnB-DraT, GlnK-NifA1, GlnK-NifA2, and GlnK-DraT. These results corroborate earlier genetic data and in addition show that PII-dependent ammonium regulation of nitrogen fixation in R. capsulatus does not require additional proteins, like NifL in Klebsiella pneumoniae. In addition, we found interactions for the protein pairs GlnB-GlnB, GlnB-GlnK, NifA1-NifA1, NifA2-NifA2, and NifA1-NifA2, suggesting that fine tuning of the nitrogen fixation process in R. capsulatus may involve the formation of GlnB-GlnK heterotrimers as well as NifA1-NifA2 heterodimers. In order to identify new proteins that interact with GlnB and GlnK, we constructed an R. capsulatus genomic library for use in yeast two-hybrid studies. Screening of this library identified the ATP-dependent helicase PcrA as a new putative protein that interacts with GlnB and the Ras-like protein Era as a new protein that interacts with GlnK.

Bacteria↗

PubMed2003

Nitrogen comes down to earth: report from the 5th European Nitrogen Fixation Conference.

For four days and four nights, with almost 50 presentations and more than 175 posters, the 5th European Nitrogen Fixation Conference continued a tradition of excellence, bringing scientists from diverse fields such as microbiology, biochemistry, computational genomics, and plant physiology together to address the complex problems associated with biological nitrogen fixation (BNF). The conference was hosted by the John Innes Center and the University of East Anglia in Norwich, England and took place from September 6 through 10, 2002. A diverse range of topics was presented, from the evolution of rhizobial genomes to the plant genes involved in bacterial and fungal symbiosis, to the structure of nitrogenase, and to the means by which nitrogen is shuttled between the symbiotic bacteria and the plant. Additionally, sessions involving broader issues, such as nitrogen fertilizer use and work being done in developing countries, brought home the importance of the research being carried out in BNF around the world.

Nitrogen↗

PubMed1987

Regulation of Soybean Nitrogen Fixation in Response to Rhizosphere Oxygen: II. Quantification of Nodule Gas Permeability.

Nodule nitrogen fixation rates are regulated by a mechanism which is responsive to the rhizosphere oxygen concentration. In some legumes, this oxygen-sensitive mechanism appears to involve changes in the gas permeability of a diffusion barrier in the nodule cortex. In soybean evidence for such a mechanism has not been found. The purpose of this research was to make quantitative measurements of soybean nodule gas permeability to test the hypothesis that soybean nodule gas permeability is under physiological control and responsive to the rhizosphere oxygen concentration. Intact hydroponically grown soybean plants were exposed to altered rhizosphere oxygen concentrations, and the nodule gas permeability, acetylene reduction and nodule respiration rates were repeatedly assayed. After a change in the external oxygen concentration, nitrogenase activity and nodule respiration rates displayed a short-term transient response after which the values returned to rates similar to those observed under ambient oxygen conditions. In contrast to steady-state nitrogenase activity and nodule respiration, nodule gas permeability was dramatically affected by the change in oxygen concentration. Decreasing the external oxygen concentration to 0.1 cubic millimeter per cubic millimeter resulted in a mean increase in nodule gas permeability of 63%. Increasing the rhizosphere oxygen concentration resulted in decreased nodule gas permeability. These data are consistent with the hypothesis that soybean nodules are capable of regulating nitrogen fixation and nodule respiration rates in response to changes in the rhizosphere oxygen concentration and indicate that the regulatory mechanism involves physiological control of the nodule gas permeability.

Journal Article↗

PubMed2003

Nitrogen fixation in the activated sludge treatment of thermomechanical pulping wastewater: effect of dissolved oxygen.

N-ViroTech, a novel technology which selects for nitrogen-fixing bacteria as the bacteria primarily responsible for carbon removal, has been developed to treat nutrient limited wastewaters to a high quality without the addition of nitrogen, and only minimal addition of phosphorus. Selection of the operating dissolved oxygen level to maximise nitrogen fixation forms a key component of the technology. Pilot scale activated sludge treatment of a thermomechanical pulping wastewater was carried out in nitrogen-fixing mode over a 15 month period. The effect of dissolved oxygen was studied at three levels: 14% (Phase 1), 5% (Phase 2) and 30% (Phase 3). The plant was operated at an organic loading of 0.7-1.1 kg BOD5/m3/d, a solids retention time of approximately 10 d, a hydraulic retention time of 1.4 d and a F:M ratio of 0.17-0.23 mg BOD5/mg VSS/d. Treatment performance was very stable over the three dissolved oxygen operating levels. The plant achieved 94-96% BOD removal, 82-87% total COD removal, 79-87% soluble COD removal, and >99% total extractives removal. The lowest organic carbon removals were observed during operation at 30% DO but were more likely to be due to phosphorus limitation than operation at high dissolved oxygen, as there was a significant decrease in phosphorus entering the plant during Phase 3. Discharge of dissolved nitrogen, ammonium and oxidised nitrogen were consistently low (1.1-1.6 mg/L DKN, 0.1-0.2 mg/L NH4+-N and 0.0 mg/L oxidised nitrogen). Discharge of dissolved phosphorus was 2.8 mg/L, 0.1 mg/L and 0.6 mg/L DRP in Phases 1, 2 and 3 respectively. It was postulated that a population of polyphosphate accumulating bacteria developed during Phase 1. Operation at low dissolved oxygen during Phase 2 appeared to promote biological phosphorus uptake which may have been affected by raising the dissolved oxygen to 30% in Phase 3. Total nitrogen and phosphorus discharge was dependent on efficient secondary clarification, and improved over the course of the study as suspended solids discharge improved. Nitrogen fixation was demonstrated throughout the study using an acetylene reduction assay. Based on nitrogen balances around the plant, there was a 55, 354 and 98% increase in nitrogen during Phases 1, 2 and 3 respectively. There was a significant decrease in phosphorus between Phases 1 and 2, and Phase 3 of the study, as well as a significant increase in nitrogen between Phases 2 and 3 which masked the effect of changing the dissolved oxygen. Operation at low dissolved oxygen appeared to confer a competitive advantage to the nitrogen-fixing bacteria.

Bioreactors↗

PubMed1995

Chloroplast gene sequence data suggest a single origin of the predisposition for symbiotic nitrogen fixation in angiosperms.

Of the approximately 380 families of angiosperms, representatives of only 10 are known to form symbiotic associations with nitrogen-fixing bacteria in root nodules. The morphologically based classification schemes proposed by taxonomists suggest that many of these 10 families of plants are only distantly related, engendering the hypothesis that the capacity to fix nitrogen evolved independently several, if not many, times. This has in turn influenced attitudes toward the likelihood of transferring genes responsible for symbiotic nitrogen fixation to crop species lacking this ability. Phylogenetic analysis of DNA sequences for the chloroplast gene rbcL indicates, however, that representatives of all 10 families with nitrogen-fixing symbioses occur together, with several families lacking this association, in a single clade. This study therefore indicates that only one lineage of closely related taxa achieved the underlying genetic architecture necessary for symbiotic nitrogen fixation in root nodules.

Base Sequence↗

PubMed1979

Nitrogen fixation associated with 'Park' Kentucky bluegrass (Poa pratensis L.).

Associative nitrogen fixation in Kentucky bluegrass (Poa pratensis L.) turfs inoculated with five nitrogen-fixing bacterial isolates was evaluated using the acetylene reduction assay and nitrogen accumulation as indicators of fixation. 'Park' and 'Nugget' Kentucky bluegrass turfs were grown in controlled environment chambers and inoculated with Klebsiella pneumoniae (W-2, W-6, and W-14), Erwinia herbicola (W-8), and Enterobacter cloacae (W-11). 'Park' inoculated with K. pneumoniae (W-6) had significant acetylene reduction activity using undisturbed turfs. Other treatments including turfs treated with heat-killed cells had no significant difference in acetylene reduction. In a second study, "Park' and 'South Dakota Certified' turfs were grown in a greenhouse and inoculated with K. pneumoniae (W-6) and E. herbicola (W-8). 'Park' inoculated with K. pneumoniae (W-6) had increased acetylene reduction activity rates and also a greater nitrogen accumulation in aerial tissues when compared to controls. Acetylene reduction activity was correlated (r = 0.92) to nitrogen accumulation. Other treatments did not effectively increase acetylene reduction activity or nitrogen accumulation.

Acetylene↗