Short-term regulation of the nitrogenase activity in Rhodopseudomonas sphaeroides

Expression and association of group IV nitrogenase NifD and NifH homologs in the non-nitrogen-fixing archaeon Methanocaldococcus jannaschii

Using genomic analysis, researchers previously identified genes coding for proteins homologous to the structural proteins of nitrogenase (J. Raymond, J. L. Siefert, C. R. Staples, and R. E. Blankenship, Mol. Biol. Evol. 21:541-554, 2004). The expression and association of NifD and NifH nitrogenase homologs (named NflD and NflH for "Nif-like" D and H, respectively) have been detected in a non-nitrogen-fixing hyperthermophilic methanogen, Methanocaldococcus jannaschii. These homologs are expressed constitutively and do not appear to be directly involved with nitrogen metabolism or detoxification of compounds such as cyanide or azide. The NflH and NflD proteins were found to interact with each other, as determined by bacterial two-hybrid studies. Upon immunoisolation, NflD and NflH copurified, along with three other proteins whose functions are as yet uncharacterized. The apparent presence of genes coding for NflH and NflD in all known methanogens, their constitutive expression, and their high sequence similarity to the NifH and NifD proteins or the BchL and BchN/BchB proteins suggest that NflH and NflD participate in an indispensable and fundamental function(s) in methanogens.

Effect of nitrogen compounds on nitrogenase activity inHerbaspirillum seropedicaeSMR1

The effect of nitrogen compounds on growth and nitrogenase activity of Herbaspirillum seropedicae SMR1 was determined. L-Glutamate or L-glutamine as sole nitrogen sources supported growth, and nitrogenase activity was observed only after exhaustion of L-glutamate or L-glutamine from the culture medium. L-Serine, L-alanine, or ammonium chloride supported growth but not acetylene reduction activity. No growth was observed with L-histidine, L-lysine, L-arginine, or with the amines methylammonium chloride, tetramethylammonium chloride, or ethylenediamine chloride. All the compounds promoted the switch off of nitrogenase activity except L-histidine, L-lysine, or L-arginine, which were not taken up. The results showed that H. seropedicae cannot utilize exogenously added L-histidine, L-arginine, L-lysine, methylammonium chloride, tetramethylammonium chloride, or ethylediamine as the sole N source for growth. The inability of the positively charged amino acids to promote nitrogenase switch off might be a result of the lack of transport systems and the eventual further metabolism of these compounds.Key words: Herbaspirillum seropedicae, nitrogenase inactivation, amino compounds uptake.

Presence of a second mechanism for the posttranslational regulation of nitrogenase activity in Azospirillum brasilense in response to ammonium

Although ADP-ribosylation of dinitrogenase reductase plays a significant role in the regulation of nitrogenase activity in Azospirillum brasilense, it is not the only mechanism of that regulation. The replacement of an arginine residue at position 101 in the dinitrogenase reductase eliminated this ADP-ribosylation and revealed another regulatory system. While the constructed mutants had a low nitrogenase activity, NH4+ still partially inhibited their nitrogenase activity, independent of the dinitrogenase reductase ADP-ribosyltransferase/dinitrogenase reductase activating glycohydrolase (DRAT/DRAG) system. These mutated dinitrogenase reductases also were expressed in a Rhodospirillum rubrum strain that lacked its endogenous dinitrogenase reductase, and they supported high nitrogenase activity. These strains neither lost nitrogenase activity nor modified dinitrogenase reductase in response to darkness and NH4+, suggesting that the ADP-ribosylation of dinitrogenase reductase is probably the only mechanism for posttranslational regulation of nitrogenase activity in R. rubrum under these conditions.

Changes in the NAD(P)H concentration caused by addition of nitrogenase 'switch-off' effectors in Rhodospirillum rubrum G-9, as measured by fluorescence

The effect of nitrogenase 'switch-off' effectors on the concentration of NAD(P)H in Rhodospirillum rubrum G-9 was investigated by fluorescence. A rapid decrease in fluorescence was observed when cells, either N2-grown or nitrogen-starved, were subjected to the effectors, but not when sodium chloride or Tris buffer was added. No effects on the fluorescence were observed in non-nitrogen fixing cultures except when NAD+ was added. The results strongly indicate that the redox state of the pyridine nucleotide pool affects the control of the regulation of nitrogenase activity in R. rubrum.

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.

Purification and properties of a nif-specific flavodoxin from the photosynthetic bacterium Rhodobacter capsulatus

A flavodoxin was isolated from iron-sufficient, nitrogen-limited cultures of the photosynthetic bacterium Rhodobacter capsulatus. Its molecular properties, molecular weight, UV-visible absorption spectrum, and amino acid composition suggest that it is similar to the nif-specific flavodoxin, NifF, of Klebsiella pneumoniae. The results of immunoblotting showed that R. capsulatus flavodoxin is nif specific, since it is absent from ammonia-replete cultures and is not synthesized by the mutant strain J61, which lacks a nif-specific regulator (NifR1). Growth of cultures under iron-deficient conditions causes a small amount of flavodoxin to be synthesized under ammonia-replete conditions and increases its synthesis under N2-fixing conditions, suggesting that its synthesis is under a dual system of control with respect to iron and fixed nitrogen availability. Here we show that flavodoxin, when supplemented with catalytic amounts of methyl viologen, is capable of efficiently reducing nitrogenase in an illuminated chloroplast system. Thus, this nif-specific flavodoxin is a potential in vivo electron carrier to nitrogenase; however, its role in the nitrogen fixation process remains to be established.

Posttranslational regulation of nitrogenase in Rhodobacter capsulatus: existence of two independent regulatory effects of ammonium

In the photosynthetic bacterium Rhodobacter capsulatus, nitrogenase activity is regulated by ADP-ribosylation of component II in response to the addition of ammonium to cultures or to the removal of light. The ammonium stimulus results in a fast and almost complete inhibition of the in vivo acetylene reduction activity, termed switch-off, which is reversed after the ammonium is exhausted. In the present study of the response of cells to ammonium, ADP-ribosylation of component II occurred but could not account for the extent and timing of the inhibition of activity. The presence of an additional response was confirmed with strains expressing mutant component II proteins; although these proteins are not a substrate for ADP-ribosylation, the strains continued to exhibit a switch-off response to ammonium. This second regulatory response of nitrogenase to ammonium was found to be synchronous with ADP-ribosylation and was responsible for the bulk of the observed effects on nitrogenase activity. In comparison, ADP-ribosylation in R. capsulatus was found to be relatively slow and incomplete but responded independently to both known stimuli, darkness and ammonium. Based on the in vitro nitrogenase activity of both the wild type and strains whose component II proteins cannot be ADP-ribosylated, it seems likely that the second response blocks either the ATP or the electron supply to nitrogenase.

Biochemical genetics revisited: the use of mutants to study carbon and nitrogen metabolism in the photosynthetic bacteria

The biochemical genetics approach is defined as the use of mutants, in comparative studies with the wild-type, to obtain information about biochemical and physiological processes in complex metabolic systems. This approach has been used extensively, for example in studies on the bioenergetics of the photosynthetic bacteria, but has been applied less frequently to studies of intermediary carbon and nitrogen metabolism in phototrophic organisms. Several important processes in photosynthetic bacteria--the regulation of nitrogenase synthesis and activity, the control of intracellular redox balance during photoheterotrophic growth, and chemotaxis--have been shown to involve metabolism. However, current understanding of carbon and nitrogen metabolism in these organisms is insufficient to allow a complete understanding of these phenomena. The purpose of the present review is to give an overview of carbon and nitrogen metabolism in the photosynthetic bacteria, with particular emphasis on work carried out with mutants, and to indicate areas in which the biochemical genetics approach could be applied successfully. In particular, it will be argued that, in the case of Rhodobacter capsulatus and Rb. sphaeroides, two species which are fast-growing, possess a versatile metabolism, and have been extensively studied genetically, it should be possible to obtain a complete, integrated description of carbon and nitrogen metabolism, and to undertake a qualitative and quantitative analysis of the flow of carbon and reducing equivalents during photoheterotrophic growth. This would require a systematic biochemical genetic study employing techniques such as HPLC, NMR, and mass spectrometry, which are briefly discussed. The review is concerned mainly with Rb. capsulatus and Rb. sphaeroides, since most studies with mutants have been carried out with these organisms. However, where possible, a comparison is made with other species of purple non-sulphur bacteria and with purple and green sulphur bacteria, and recent literature relevant to these organisms has been cited.

Ammonium inhibition of nitrogenase activity in Herbaspirillum seropedicae

The effect of oxygen, ammonium ion, and amino acids on nitrogenase activity in the root-associated N2-fixing bacterium Herbaspirillum seropedicae was investigated in comparison with Azospirillum spp. and Rhodospirillum rubrum. H. seropedicae is microaerophilic, and its optimal dissolved oxygen level is from 0.04 to 0.2 kPa for dinitrogen fixation but higher when it is supplied with fixed nitrogen. No nitrogenase activity was detected when the dissolved O2 level corresponded to 4.0 kPa. Ammonium, a product of the nitrogenase reaction, reversibly inhibited nitrogenase activity when added to derepressed cell cultures. However, the inhibition of nitrogenase activity was only partial even with concentrations of ammonium chloride as high as 20 mM. Amides such as glutamine and asparagine partially inhibited nitrogenase activity, but glutamate did not. Nitrogenase in crude extracts prepared from ammonium-inhibited cells showed activity as high as in extracts from N2-fixing cells. The pattern of the dinitrogenase and the dinitrogenase reductase revealed by the immunoblotting technique did not change upon ammonium chloride treatment of cells in vivo. No homologous sequences were detected with the draT-draG probe from Azospirillum lipoferum. There is no clear evidence that ADP-ribosylation of the dinitrogenase reductase is involved in the ammonium inhibition of H. seropedicae. The uncoupler carbonyl cyanide m-chlorophenylhydrazone decreased the intracellular ATP concentration and inhibited the nitrogenase activity of whole cells. The ATP pool was not significantly disturbed when cultures were treated with ammonium in vivo. Possible mechanisms for inhibition by ammonium of whole-cell nitrogenase activity in H. seropedicae are discussed.

Identification and Characterization of a Bacteroid-Specific Dehydrogenase Complex in Rhizobium leguminosarum PRE

In membranes of Rhizobium leguminosarum bacteroids isolated from nitrogen-fixing pea root nodules, two different protein complexes with NADH dehydrogenase activity were detected. One of these complexes, with a molecular mass of 110 kilodaltons, was also found in membranes of free-living rhizobia, but the other, with a molecular mass of 550 kilodaltons, appeared to be present only in bacteroids. The bacteroid-specific complex, referred to as DH1, probably consists of at least four different subunits. Using antibodies raised against the separate polypeptides, we found that a 35,000-molecular-weight polypeptide (35K polypeptide) in the DH1 complex is bacteroid specific, while the other proposed subunits were also detectable in cytoplasmic membranes of free-living bacteria. Dehydrogenase complex DH1 is also present in bacteroids of a R. leguminosarum nifA mutant, indicating that the synthesis of the dehydrogenase is not dependent on the gene product of this nif -regulatory gene. A possible involvement of the bacteroid-specific DH1 complex in electron transport to nitrogenase is discussed.

Ammonia switch-off of nitrogenase from Rhodobacter sphaeroides and Methylosinus trichosporium: no evidence for Fe protein modification

In vivo switch-off of nitrogenase activity by NH4+ is a reversible process in Rhodobacter sphaeroides and Methylosinus trichosporium OB3b. The same pattern of switch-off in Rhodospirillum rubrum is explained by ADP-ribosylation of one of the Fe protein subunits, however, no evidence of covalent modification could be found in the subunits from either R. sphaeroides or M. trichosporium. Fe protein subunits from these organisms showed no variant behaviour on SDS-PAGE, nor were they 32P-labeled following switch-off. These observations suggest either that the attachment of the modifying group to the Fe protein in these organisms is quite labile and does not survive in vitro manipulation, or that the mechanism of switch-off is different than that seen in Rhodospirillum.

Molecular aspects of nitrogen fixation by photosynthetic prokaryotes

The photosynthetic prokaryotes possess diverse metabolic capabilities, both in carrying out different types of photosynthesis and in their other growth modes. The nature of the coupling of these energy-generating processes with the basic metabolic demands of the cell, such as nitrogen fixation, has stimulated research for many years. In addition, nitrogen fixation by photosynthetic prokaryotes exhibits several unique features; the oxygen-evolving cyanobacteria have developed various strategies for protection of the oxygen-labile nitrogenase proteins, and some photosynthetic bacteria have been found to regulate their nitrogenase (N2ase) activity in a rapid response to fixed nitrogen, thus saving substantial amounts of energy. Recent advances in the biochemistry, physiology, and genetics of nitrogen fixation by cyanobacteria and photosynthetic bacteria are reviewed, with special emphasis on the unique features found in these organisms. Several major topics in cyanobacterial nitrogen fixation are reviewed. The isolation and characterization of N2ase and the isolation and sequence of N2ase structural genes have shown a great deal of similarity with other organisms. The possible pathways of electron flow to N2ase, the mechanisms of oxygen protection, and the control of nif expression and heterocyst differentiation will be discussed. Several recent advances in the physiology and biochemistry of nitrogen fixation by the photosynthetic bacteria are reviewed. Photosynthetic bacteria have been found to fix nitrogen microaerobically in darkness. The regulation of nif expression and possible pathways of electron flow to N2ase are discussed. The isolation of N2ase proteins, particularly the covalent modification of the Fe protein, the nature of the modifying group, properties of the activating enzyme, and regulating factors of the inactivation/activation process are reviewed.

Membrane electrogenesis and sodium transport in filamentous nitrogen-fixing cyanobacteria

Transport of Na+ and its relationship with membrane potential (delta psi m) was examined in Anabaena L-31 (a fresh water cyanobacterium) and Anabaena torulosa (a brackish water cyanobacterium) which require Na+ for diazotrophic growth. The data on the effect of N,N'-dicyclohexylcarbodiimide indicated that delta psi m was generated by electrogenic proton extrusion predominantly mediated by ATPase(s). In addition, operation of a plasmalemmabound, non-ATP-requiring, H+-pumping terminal oxidase was suggested by the sensitivity of delta psi m to anaerobiosis, cyanide and azide, all of which inhibit aerobic respiration. The response of delta psi m to external pH and external Na+ or K+ concentrations indicated that a diffusion potential of Na+ or K+ may not contribute significantly to delta psi m. Kinetic studies showed that Na+ influx was unlikely to be a result of Na+/NA+ exchange but was a carrier-mediated secondary active transport insensitive to low concentrations (less than 10 mM) of external K+. There was a close correspondence between changes in delta psi m and Na+ influx; all the treatments which caused depolarisation (such as low temperature, dark, cyanide, azide, anaerobiosis, ATPase inhibitors) lowered Na+ influx whereas treatments which caused hyperpolarisation (such as 2,4-dinitrophenol, nigericin) enhanced Na+ influx. Remarkably low intracellular Na+ concentrations were maintained by these cyanobacteria by means of active efflux of the cation. The basic mechanism of Na+ transport in the fresh water and the brackish water cyanobacterium was similar but the latter demonstrated less influx, more efficient efflux, more affinity of carriers for Na+ and less accumulation of Na+, all attributes favouring salt tolerance.

Adenine nucleotide levels in Rhodospirillum rubrum during switch-off of whole-cell nitrogenase activity

Adenine nucleotide pools were measured in Rhodospirillum rubrum cultures that contained nitrogenase. The average energy charge [([ATP] + 1/2[ADP])/([ATP] + [ADP] + [AMP])] was found to be 0.66 and 0.62 in glutamate-grown and N-limited cultures respectively. Treatment of glutamate-grown cells with darkness, ammonia, glutamine, carbonyl cyanide m-chlorophenylhydrazone, or phenazine methosulphate resulted in perturbations in the adenine nucleotide pools, and led to loss of whole-cell nitrogenase activity and modification in vivo of the Fe protein. Treatment of N-limited cells resulted in similar changes in adenine nucleotide pools but not enzyme modification. No correlations were found between changes in adenine nucleotide pools or ratios of these pools and switch-off of nitrogenase activity by Fe protein modification in vivo. Phenazine methosulphate inhibited whole-cell activity at low concentrations. The effect on nitrogenase activity was apparently independent of Fe protein modification.

H+/ATP stoichiometry of cowpea Rhizobium sp. strain 32H1 cells grown under nitrogen-fixing and nitrogen-nonfixing conditions

The obligate aerobe Cowpea Rhizobium sp. strain 32H1 in axenic culture is able to fix N2 when grown under 0.2% O2 but not when grown under 21% O2. It was, therefore, of interest to investigate ATP synthesis in these cells grown under the two conditions. When respiring in buffers having pHs ranging from 6 to 8.5, cells grown under either O2 tension maintained an intracellular pH more alkaline than the exterior. The transmembrane chemical gradient of H+ (delta pH) was essentially the same under both conditions of growth, decreasing from ca. 90 mV at medium pH 6 to ca. 30 mV at pH 8.5. However, the transmembrane electrical gradient (delta psi) was significantly higher in cells grown under 21% O2 (150 to 166 mV) than in cells grown under 0.2% O2, the latter being 16 mV at pH 6 and increasing to 88 mV at pH 8.5. Therefore, the proton motive force of 21% O2-grown cells ranged from 237 mV at external pH 6 to 185 mV at pH 8.5, compared with a proton motive force of 114 to 121 mV in the 0.2% O2-grown cells. The cells grown in 0.2% O2 had the same proton motive force whether tested at 21 or at 0.2% O2. The phosphorylation potential, calculated from the intracellular ATP, ADP, and Pi concentrations, was 424 mV in the 21% O2-grown cells and 436 mV in the 0.2% O2-grown cells. Thus, the 21% O2-grown cells translocated 1.8 to 2.3 H+/ATP synthesized by the H+-ATPase, whereas the H+/ATP ratio for 0.2% O2-grown cells was 3.7 to 3.8.

Effect of ammonia, darkness, and phenazine methosulfate on whole-cell nitrogenase activity and Fe protein modification in Rhodospirillum rubrum

A procedure for the immunoprecipitation of Fe protein from cell extracts was developed and used to monitor the modification of Fe protein in vivo. The subunit pattern of the isolated Fe protein after sodium dodecyl sulfate-polyacrylamide gel electrophoresis was assayed by Coomassie brilliant blue protein staining and autoradiographic 32P detection of the modifying group. Whole-cell nitrogenase activity was also monitored during Fe protein modification. The addition of ammonia, darkness, oxygen, carbonyl cyanide m-chlorophenylhydrazone, and phenazine methosulfate each resulted in a loss of whole-cell nitrogenase activity and the in vivo modification of Fe protein. For ammonia and darkness, the rate of loss of nitrogenase activity was similar to that for Fe protein modification. The reillumination of a culture incubated in the dark brought about a rapid recovery of nitrogenase activity and the demodification of Fe protein. Cyclic dark-light treatments resulted in matching cycles of nitrogenase activity and Fe protein modification. Carbonyl cyanide m-chlorophenylhydrazone and phenazine methosulfate treatments caused an immediate loss of nitrogenase activity, whereas Fe protein modification occurred at a slower rate. Oxygen treatment resulted in a rapid loss of activity but only an incomplete modification of the Fe protein.

Inhibition of nitrogenase activity by ammonium chloride in Azotobacter vinelandii

In Azotobacter vinelandii cells, the short-term inhibition of nitrogenase activity by NH4Cl was found to depend on several factors. The first factor is the dissolved oxygen concentration during the assay of nitrogenase. When cells are incubated with low concentrations of oxygen, nitrogenase activity is low and ammonia inhibits strongly. With more oxygen, nitrogenase activity increases. Cells incubated with an optimum amount of oxygen have maximum nitrogenase activity, and the extent of inhibition by ammonia is small. With higher amounts of oxygen, the nitrogenase activity of the cells is decreased and strongly inhibited by ammonia. The second factor found to be important for the inhibition of nitrogenase activity by NH4Cl was the pH of the medium. At a low pH, NH4+ inhibits more strongly than at a higher pH. The third factor that influenced the extent of ammonia inhibition was the respiration rate of the cells. When cells are grown with excess oxygen, the respiration rate of the cells is high and inhibition of nitrogenase activity by ammonia is small. Cells grown under oxygen-limited conditions have a low respiration rate and NH4Cl inhibition of nitrogenase activity is strong. Our results explain the contradictory reports described in the literature for the NH4Cl inhibition of nitrogenase in A. vinelandii.