Use of lactose to induce expression of soluble NifA protein domains of Herbaspirillum seropedicae in Escherichia coli

Overexpression and purification are procedures used to allow functional and structural characterization of proteins. Many overexpressed proteins are partially or completely insoluble, and can not be easily purified. The NifA protein is an enhancer-binding protein involved in activating the expression of nif and some fix genes. The NifA protein from many organisms is usually insoluble when over-expressed, and therefore difficult to work with in vitro. In this work we have overexpressed the central + C-terminal and the central domains of the Herbaspirrilum seropedicae NifA protein in an Escherichia coli background. Expression was induced with either IPTG or lactose. The data showed that induction with lactose promoted a significantly higher percentage of these proteins in the soluble fraction than with IPTG. This probably reflects a slower kinetics of induction by lactose.

Genome structure of the genus Azospirillum

Azospirillum species are plant-associated diazotrophs of the alpha subclass of Proteobacteria. The genomes of five of the six Azospirillum species were analyzed by pulsed-field gel electrophoresis. All strains possessed several megareplicons, some probably linear, and 16S ribosomal DNA hybridization indicated multiple chromosomes in genomes ranging in size from 4.8 to 9.7 Mbp. The nifHDK operon was identified in the largest replicon.

Expression of the nifA gene of Herbaspirillum seropedicae: role of the NtrC and NifA binding sites and of the -24/-12 promoter element

The nifA promoter of Herbaspirillum seropedicae contains potential NtrC, NifA and IHF binding sites together with a -12/-24 sigma(N)-dependent promoter. This region has now been investigated by deletion mutagenesis for the effect of NtrC and NifA on the expression of a nifA::lacZ fusion. A 5' end to the RNA was identified at position 641, 12 bp downstream from the -12/-24 promoter. Footprinting experiments showed that the G residues at positions -26 and -9 are hypermethylated, and that the region from -10 to +10 is partially melted under nitrogen-fixing conditions, confirming that this is the active nifA promoter. In H. seropedicae nifA expression from the sigma(N)-dependent promoter is repressed by fixed nitrogen but not by oxygen and is probably activated by the NtrC protein. NifA protein is apparently not essential for nifA expression but it can still bind the NifA upstream activating sequence.

Two roles for integration host factor at an enhancer-dependent nifA promoter

Control of transcription in prokaryotes often involves direct contact of regulatory proteins with RNA polymerase. For the sigma54 RNA polymerase, regulatory proteins bound to distally located enhancers engage the polymerase via DNA looping. The sigma54-dependent nifA promoter of Herbaspirillum seropedicae (Hs) is activated under nitrogen-limiting growth conditions. Potential enhancers for the nitrogen control activators NTRC and NIFA and binding sites for integration host factor (IHF) and sigma54-holoenzyme were identified. DNA footprinting experiments showed that these sites functioned for protein binding. Their involvement in the promoter regulation was explored. In vitro, activation of the Hs nifA promoter by NTRC is stimulated by the DNA bending protein IHF. In marked contrast, activation by NIFA is greatly reduced by IHF, thus diminishing potentially destabilizing autoactivation of the nifA promoter by NIFA. Additionally, high levels of NIFA appear to limit NTRC-dependent activation. This inhibition is IHF dependent. Therefore, IHF acts positively and negatively at the nifA promoter to restrict transcription activation to NTRC and one signal transduction pathway.

Sequencing and functional analysis of the nifENXorf1orf2 gene cluster of Herbaspirillum seropedicae

A 5.1-kb DNA fragment from the nifHDK region of H. seropedicae was isolated and sequenced. Sequence analysis showed the presence of nifENXorf1orf2 but nifTY were not present. No nif or consensus promoter was identified. Furthermore, orf1 expression occurred only under nitrogen-fixing conditions and no promoter activity was detected between nifK and nifE, suggesting that these genes are expressed from the upstream nifH promoter and are parts of a unique nif operon. Mutagenesis studies indicate that nifN was essential for nitrogenase activity whereas nifXorf1orf2 were not. High homology between the C-terminal region of the NifX and NifB proteins from H. seropedicae was observed. Since the NifX and NifY proteins are important for FeMo cofactor (FeMoco) synthesis, we propose that alternative proteins with similar activities exist in H. seropedicae.

In-trans regulation of the N-truncated-NIFA protein of Herbaspirillum seropedicae by the N-terminal domain

The NifA protein is responsible for transcription activation of nif genes in the endophytic diazotroph Herbaspirillum seropedicae. When expressed in Escherichia coli this NifA protein is unable to activate the transcription of a Klebsiella pneumoniae nifH::lacZ fusion. However, a form of NifA lacking the N-terminal domain did activate transcription and its activity was not inhibited by ammonium. In this work we show that when expressed separately, the N-terminal domain of H. seropedicae NifA protein can restore ammonium control of the N-truncated NifA activity in E. coli. This effect is dependent on the relative concentrations of the N-terminal domain and the N-truncated protein and suggests that the N-terminal domain behaves in this respect in a manner similar to that of NifL of the gamma proteobacteria.

Regulation of Azospirillum brasilense nifA gene expression by ammonium and oxygen

The structure and activity of the nifA promoter of Azospirillum brasilense was studied using deletion analysis. An essential region for nifA promoter activity was identified between nucleotides -67 and -47 from the identified transcription start site. A sequence resembling a sigma(70) recognition site occurs in this region and may constitute the nifA gene promoter. The regulation of the nifA gene was studied in plasmid and chromosomal nifA::lacZ fusions. Full expression was obtained under low oxygen levels and in the absence of ammonium ions. Repression of nifA expression involves a synergistic effect between oxygen and ammonium.

Expression and functional analysis of an N-truncated NifA protein of Herbaspirillum seropedicae

In Herbaspirillum seropedicae, an endophytic diazotroph, nif gene expression is under the control of the transcriptional activator NifA. We have over-expressed and purified a protein containing the central and C-terminal domains of the H. seropedicae NifA protein, N-truncated NifA, fused to a His-Tag sequence. This fusion protein was found to be partially soluble and was purified by affinity chromatography. Band shift and footprinting assays showed that the N-truncated NifA protein was able to bind specifically to the H. seropedicae nifB promoter region. In vivo analysis showed that this protein activated the nifH promoter of Klebsiella pneumoniae in Escherichia coli only in the absence of oxygen and this activation was not negatively controlled by ammonium ions.

Control of Herbaspirillum seropedicae NifA activity by ammonium ions and oxygen

The activity of a truncated form of Herbaspirillum seropedicae NifA in different genetic backgrounds showed that its regulatory domain is involved in nitrogen control but not in O2 sensitivity or Fe dependence. The model for nitrogen control involving PII could thus apply to the proteobacteria at large. NifA may have a role in controlling ADP-ribosylation of nitrogenase in Azospirillum brasilense.

Cloning and sequencing of the nitrogenase structural genes nifHDK of Herbaspirillum seropedicae

The nitrogenase structural genes (nifHDK) of the endophytic diazotroph Herbaspirillum seropedicae were isolated from a genomic bank by plate hybridization. Sequence analysis of the DNA showed a consensus promoter region upstream for the nifH gene containing a -24/-12 type promoter together with NifA- and integration host factor (IHF)- binding sites. The derived protein sequences of NifH, NifD and NifK contained conserved cysteine residues for binding iron-sulfur clusters and the iron-molybdenum cofactor. These protein sequences showed the strongest similarities to the nifHDK gene products of the symbiotic diazotroph Bradyrhizobium japonicum (93.5%, 91.3% and 83.3%, respectively), the plant-associated diazotroph Azospirillum brasilense (90.0%, 83.7% and 75.1%, respectively) and to Thiobacillus ferrooxidans (91.0%, 83.4% and 81.1%, respectively) of the same phylogenetic group of the protobacteria.

The ntrBC genes of Azospirillum brasilense are part of a nifR3-like-ntrB-ntrC operon and are negatively regulated

A cosmid able to complement the Nif- and nitrate-dependent growth phenotypes of the Azospirillum brasilense mutant FP9 was isolated from a genomic library of the wild-type strain FP2. A 6-kb DNA region was sequenced and showed two open reading frames (ORFs) identified as the ntrB and ntrC genes. An ORF1 located upstream from the ntrB gene and coding for a 36-kDa polypeptide showed similarity to the nifR3 gene of Rhodobacter capsulatus and the ORF1 of Rhizobium leguminosarum, both located upstream from the ntrB gene in a complex operon. Two other unidentified ORFs (ORF5 and partial ORF4) coding for hydrophobic polypeptides were also observed. delta ORF1-ntrBC, ORF1, ntrB, and ntrC mutants obtained by recombination of suicide plasmids containing an insertion of a promoterless lacZ kanamycin cassette showed decreased nitrogenase activities and were unable to grow on nitrate as the sole N source. These phenotypes were restored by complementation with plasmids containing the ntrC gene. Analysis of lacZ transcriptional fusions suggested that the ORF1-ntrBC operon in Azospirillum brasilense is expressed from a promoter located upstream from the ORF1 and that it is negatively regulated by the ntrC gene product.

Sequences, organization and analysis of the hupZMNOQRTV genes from the Azotobacter chroococcum hydrogenase gene cluster

Hydrogen-uptake (Hup) activity in Azotobacter chroococcum depends upon a cluster of genes spread over 13,687 bp of the chromosome. Six accessory genes of the cluster, hupABYCDE, begin 4.8 kb downstream of the structural genes, hupSL, and are required for the formation of a functional [NiFe] hydrogenase. The sequencing of the intervening 4.8 kb of hup-specific DNA has now been completed. This revealed eight additional closely linked ORFs, which we designated hupZ, hupM, hupN, hupO, hupQ, hupR, hupT and hupV. These genes potentially encode polypeptides with predicted masses of 27.7, 22.3, 11.4, 16.2, 31.3, 8.1, 16.2 and 36.7 kDa, respectively. All eight genes are transcribed from the same strand as hupSL and hupABYCDE. A chroococcum, therefore, has a total of 16 contiguous genes affecting hydrogenase activity beginning with hupS and ending with hupE. The amino acid sequence deduced from hupZ has the characteristics of a b-type cytochrome. Insertion mutagenesis of hupZ resulted in a mutant incapable of supporting O2-dependent H2 oxidation. The deduced amino acid sequence of hupR shares high homology with bacterial rubredoxins. HupZ and HupR may both be involved in transferring electrons from hydrogenase to the electron transport chain. A mutation in hupV knocked out hydrogenase activity entirely; this gene may be involved in processing the large subunit of hydrogenase. It is now clear that the genes controlling [NiFe] hydrogenase activity in many bacteria including Azotobacter chroococcum, Alcaligenes eutrophus, Rhizobium leguminosarum, Rhodobacter capsulatus and Escherichia coli are highly conserved, organized in much the same manner, and likely derived from a common ancestor.

Sequence and structural organization of a nif A-like gene and part of a nifB-like gene of Herbaspirillum seropedicae strain Z78

The deduced amino acid sequence derived from the sequence of a fragment of DNA from the free-living diazotroph Herbaspirillum seropedicae was aligned to the homologous protein sequences encoded by the nifA genes from Azorhizobium caulinodans, Rhizobium leguminosarum, Rhizobium meliloti and Klebsiella pneumoniae. High similarity was found in the central domain and in the C-terminal region. The H. seropedicae putative NifA sequence was also found to contain an interdomain linker similar to that conserved among rhizobial NifA proteins, but not K. pneumoniae or Azotobacter vinelandii. Analysis of the regulatory sequences found 5' from nifA indicated that the expression of this gene in H. seropedicae is likely to be controlled by NifA, NtrC and RpoN, as judged by the presence of specific NifA- and NtrC-binding sites and characteristic -24/-12 promoters. Possible additional regulatory features included an 'anaerobox' and a site for integration host factor. The N-terminus of another open reading frame was found 3' from nifA and tentatively identified as nifB by amino acid sequence comparison. The putative nifB promoter sequence suggests that expression of H. seropedicae nifB may be activated by NifA and dependent on RpoN.

Cloning and mutagenesis of genes encoding the cytochrome bd terminal oxidase complex in Azotobacter vinelandii: mutants deficient in the cytochrome d complex are unable to fix nitrogen in air

The genome of Azotobacter vinelandii contains DNA sequences homologous to the structural genes for the Escherichia coli cytochrome bd terminal oxidase complex. Two recombinant clones bearing cydA- and cydB-like sequence were isolated from an A. vinelandii gene library and subcloned into the plasmid vector pACYC184. Physical mapping demonstrated that the cydA- and cydB-like regions in A. vinelandii are contiguous. The cydAB and flanking DNA was mutagenized by the insertion of Tn5-B20. Mutations in the cydB-hybridizing region resulted in the loss of spectral features associated with cytochromes b595 and d. A new locus, cydB, encoding cytochromes b595 and d in A. vinelandii is proposed. A second region adjacent to cydB was also involved in expression of the cytochrome bd complex in A. vinelandii, since mutations in this region resulted in an increase in the levels of both cytochrome b595 and cytochrome d. The regions involved in expression of the cytochrome bd complex and cydB are transcribed in the same direction. Mutants deficient in cytochromes b595 and d were unable to grow on N-deficient medium when incubated in air but could fix nitrogen when the environmental O2 concentration was reduced to 1.5% (vol/vol). It is proposed that the branch of the respiratory chain terminated by the cytochrome bd complex supports the high respiration rates required for the respiratory protection of nitrogenase.

The identification, characterization, sequencing and mutagenesis of the genes (hupSL) encoding the small and large subunits of the H2-uptake hydrogenase of Azotobacter chroococcum

The structural genes (hupSL) of the membrane-bound NiFe-containing H2-uptake hydrogenase (Hup) of Azotobacter chroococcum were identified by oligonucleotide screening and sequenced. The small subunit gene (hupS) encodes a signal sequence of 34 amino acids followed by a 310-amino-acid, 34156D protein containing 12 cysteine residues. The large subunit gene (hupL) overlaps hupS by one base and codes for a predicted 601-amino-acid, 66433D protein. There are two regions of strong homology with other Ni hydrogenases: a Cys-Thr-Cys-Cys-Ser motif near the N-terminus of HupS and an Asp-Pro-Cys-Leu-Ala-Cys motif near the carboxy-terminus of HupL. Strong overall homology exists between Azotobacter, Bradyrhizobium japonicum and Rhodobacter capsulatus Hup proteins but less exists between the Azotobacter proteins and hydrogenases from Desulfovibrio strains. Mutagenesis of either hupS or hupL genes of A. chroococcum yielded Hup- phenotypes but some of these mutants retained a partial H2-evolving activity. Hybridization experiments at different stages of gene segregation confirmed the multicopy nature of the Azotobacter genome.

Azotobacter chroococcum 7Fe ferredoxin. Two pH-dependent forms of the reduced 3Fe clusters and its conversion to a 4Fe cluster

Ferredoxin from Azotobacter chroococcum has been studied by low-temperature magnetic-circular-dichroism and electron-paramagnetic-resonance spectroscopy. When aerobically isolated ferredoxin contains a [3Fe-4S] and [4Fe-4S] cluster. Anaerobic treatment with dithionite in the presence of ethanediol reduces the [3Fe-4S] cluster to give two spectroscopically distinct forms RI and RII which are reversibly interconvertible with a pKa approximately 7.5. The higher-pH form, RII, has a high affinity for ferrous ion and converts readily to a [4Fe-4S]1+ cluster, scavenging iron from the medium. The presence of the iron chelator EDTA inhibits this conversion.

Effect of chelating agents on hydrogenase in Azotobacter chroococcum. Evidence that nickel is required for hydrogenase synthesis

The chelating agents EDTA, o-phenanthroline, nitrilotriacetic acid (NTA), ethylenediamine-bis(o-hydroxyphenylacetic acid) (EDDA) or dimethylglyoxime prevented the expression of hydrogenase activity in batch cultures of nitrogen-fixing Azotobacter chroococcum, but did not inhibit preformed enzyme. The inhibition was reversed either by adding a mixture of trace elements (Cu2+, Mn2+, Zn2+, Co2+) or Ni2+ or, to a lesser degree, Co2+ alone. Ni2+ or Ni2+ + Fe2+ also enhanced the rate of hydrogenase derepression in A. chroococcum in the absence of any added chelator, if the medium was first extracted with 8-hydroxyquinoline. A. chroococcum accumulated 63Ni2+ by an energy-independent mechanism. Both, Ni2+ uptake and hydrogenase synthesis were equally inhibited by either NTA, EDTA, EDDA or dimethylglyoxime. The evidence suggests a role for Ni2+ in hydrogenase synthesis.

Catalysis of exchange of terminal phosphate groups of ATP and ADP by purified nitrogenase proteins

A crude Azotobacter nitrogenase complex contained a highly active adenylate kinase which caused rapid equilibration of AMP, ADP, and ATP. Purified molybdenum-iron protein preparations also contained measurable adenylate kinase activity which could be removed by adsorption and elution from hydroxylapatite. Independent of adenylate kinase, the highly purified molybdenum-iron protein from both Klebsiella pneumoniae and Azotobacter chroococcum catalyzed the exchange of [32P]orthophosphate with the terminal phosphate of ATP or ADP. The exchange labeling of ATP was stimulated by ferricyanide ion due to the inhibition of ATP hydrolysis linked to substrate reductions which cannot occur in the absence of reductant. This exchange reaction is responsible for reported ATP synthesis by crude nitrogenase preparations. Binding of ATP labeled with 32P in the terminal phosphate group was measured directly with concentrated solutions of the molybdenum-iron nitrogenase protein from K. pneumoniae by the column gel filtration method. The protein was saturated with ATP at a calculated ratio of 4.0 +/- 0.3 mol ATP/mol protein; half-saturation of 220 microM protein occurred at 600 +/- 100 microM. The interactions between adenine nucleotides and the molybdenum-iron protein suggest the involvement of the nucleotides in a role distinct from the established reactions with the iron protein of the nitrogenase complex. A dual role for ATP in the reduction of dinitrogen by isolated nitrogenase proteins would be consistent with the existence of binding sites for ATP on both the iron and molybdenum-iron proteins.

The hydrogen cycle in nitrogen-fixing Azotobacter chroococcum

H2 will support nitrogenase activity (C2H2 reduction) in Azotobacter chroococcum with or without added carbon substrate. Results show that H2 is metabolised to transfer electrons to nitrogenase and to the respiratory chain to produce ATP. H2-supported nitrogenase activity is most significant at low carbon substrate concentrations, but also occurs at saturating concentration. Continuous cultures of N2-fixing A. chroococcum evolved H2 from nitrogenase under O2-N2- and C-limited conditions. This H2 represented a significant proportion of nitrogenase activity. Hydrogenase activity was consistently high under C-limited conditions, but low or undetectable under O2- and N2-limitations. Pre-treatment with 40 per cent C2H2 inhibited hydrogenase activity in C-limited cultures, and H2 evolution increased under air and under Ar:O2 (4:1) mixtures. We deduce that hydrogenase : I, recycles H2 produced by nitrogenase to provide electrons and energy for N2 reduction: II, supports respiratory protection for nitrogenase under C-limited conditions, and III, does not act to prevent any inhibition of N2 reduction by H2 produced by nitrogenase. A scheme for the H2 cycle in N2-fixing A. chroococcum is proposed.

The hydrogenase-nitrogenase relationship in the blue-green algaAnabaena cylindrica

Nitrogen-fixingAnabaena cylindrica cells are found to evolve hydrogen in high quantities in the presence of CO plus C2H2. Studies with the inhibitors dichlorophenyldimethylurea (DCMU), disalicylidenepropanediamine (DSPD), dibromothymoquinone (DBMIB), undecylbenzimidazole (UDB) and chloro-carbonyl-cyanide-phenylhydrazone (CCCP) and also withAnabaena grown on nitrate- and ammonia-nitrogen show that the H2-formation is due to the ATP-dependent H3O(+)-reduction catalysed by nitrogenase. In control experiments CO plus C2H2 inhibited the activities of a cell-free hydrogenase fromClostridium pasteurianum. It is concluded that Anabaena has a hydrogenase whose natural function is to recycle the H2 lost by the action of nitrogenase.