Culture-independent analysis of endophytic bacterial communities associated with Brazilian sugarcane

Sugarcane is an economically important culture in Brazil. Endophytic bacteria live inside plants, and can provide many benefits to the plant host. We analyzed the bacterial diversity of sugarcane cultivar RB-72454 by cultivation-independent techniques. Total DNA from sugarcane stems from a commercial plantation located in Paraná State was extracted. Partial 16S rRNA genes were amplified and sequenced for library construction. Of 152 sequences obtained, 52% were similar to 16S rRNA from Pseudomonas sp, and 35.5% to Enterobacter sp. The genera Pantoea, Serratia, Citrobacter, and Klebsiella were also represented. The endophytic communities in these sugarcane samples were dominated by the families Enterobacteriaceae and Pseudomonadaceae (class Gammaproteobacteria).

Naringenin degradation by the endophytic diazotroph Herbaspirillum seropedicae SmR1

Several bacteria are able to degrade flavonoids either to use them as carbon sources or as a detoxification mechanism. Degradation pathways have been proposed for several bacteria, but the genes responsible are not known. We identified in the genome of the endophyte Herbaspirillum seropedicae SmR1 an operon potentially associated with the degradation of aromatic compounds. We show that this operon is involved in naringenin degradation and that its expression is induced by naringenin and chrysin, two closely related flavonoids. Mutation of fdeA, the first gene of the operon, and fdeR, its transcriptional activator, abolished the ability of H. seropedicae to degrade naringenin.

The RecX protein interacts with the RecA protein and modulates its activity in Herbaspirillum seropedicae

DNA repair is crucial to the survival of all organisms. The bacterial RecA protein is a central component in the SOS response and in recombinational and SOS DNA repairs. The RecX protein has been characterized as a negative modulator of RecA activity in many bacteria. The recA and recX genes of Herbaspirillum seropedicae constitute a single operon, and evidence suggests that RecX participates in SOS repair. In the present study, we show that the H. seropedicae RecX protein (RecX Hs) can interact with the H. seropedicaeRecA protein (RecA Hs) and that RecA Hs possesses ATP binding, ATP hydrolyzing and DNA strand exchange activities. RecX Hs inhibited 90% of the RecA Hs DNA strand exchange activity even when present in a 50-fold lower molar concentration than RecA Hs. RecA Hs ATP binding was not affected by the addition of RecX, but the ATPase activity was reduced. When RecX Hs was present before the formation of RecA filaments (RecA-ssDNA), inhibition of ATPase activity was substantially reduced and excess ssDNA also partially suppressed this inhibition. The results suggest that the RecX Hs protein negatively modulates the RecA Hs activities by protein-protein interactions and also by DNA-protein interactions.

The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae

Background

Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner.

Results

A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization.

Conclusions

Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice.

Identification and characterization of PhbF: a DNA binding protein with regulatory role in the PHB metabolism of Herbaspirillum seropedicae SmR1

Background

Herbaspirillum seropedicae SmR1 is a nitrogen fixing endophyte associated with important agricultural crops. It produces polyhydroxybutyrate (PHB) which is stored intracellularly as granules. However, PHB metabolism and regulatory control is not yet well studied in this organism.

Results

In this work we describe the characterization of the PhbF protein from H. seropedicae SmR1 which was purified and characterized after expression in E. coli. The purified PhbF protein was able to bind to eleven putative promoters of genes involved in PHB metabolism in H. seropedicae SmR1. In silico analyses indicated a probable DNA-binding sequence which was shown to be protected in DNA footprinting assays using purified PhbF. Analyses using lacZ fusions showed that PhbF can act as a repressor protein controlling the expression of PHB metabolism-related genes.

Conclusions

Our results indicate that H. seropedicae SmR1 PhbF regulates expression of phb-related genes by acting as a transcriptional repressor. The knowledge of the PHB metabolism of this plant-associated bacterium may contribute to the understanding of the plant-colonizing process and the organism's resistance and survival in planta.

Genome of Herbaspirillum seropedicae strain SmR1, a specialized diazotrophic endophyte of tropical grasses

The molecular mechanisms of plant recognition, colonization, and nutrient exchange between diazotrophic endophytes and plants are scarcely known. Herbaspirillum seropedicae is an endophytic bacterium capable of colonizing intercellular spaces of grasses such as rice and sugar cane. The genome of H. seropedicae strain SmR1 was sequenced and annotated by The Paraná State Genome Programme--GENOPAR. The genome is composed of a circular chromosome of 5,513,887 bp and contains a total of 4,804 genes. The genome sequence revealed that H. seropedicae is a highly versatile microorganism with capacity to metabolize a wide range of carbon and nitrogen sources and with possession of four distinct terminal oxidases. The genome contains a multitude of protein secretion systems, including type I, type II, type III, type V, and type VI secretion systems, and type IV pili, suggesting a high potential to interact with host plants. H. seropedicae is able to synthesize indole acetic acid as reflected by the four IAA biosynthetic pathways present. A gene coding for ACC deaminase, which may be involved in modulating the associated plant ethylene-signaling pathway, is also present. Genes for hemagglutinins/hemolysins/adhesins were found and may play a role in plant cell surface adhesion. These features may endow H. seropedicae with the ability to establish an endophytic life-style in a large number of plant species.

Herbaspirillum seropedicae rfbB and rfbC genes are required for maize colonization

In this study we disrupted two Herbaspirillum seropedicae genes, rfbB and rfbC, responsible for rhamnose biosynthesis and its incoporation into LPS. GC-MS analysis of the H. seropedicae wild-type strain LPS oligosaccharide chain showed that rhamnose, glucose and N-acetyl glucosamine are the predominant monosaccharides, whereas rhamnose and N-acetyl glucosamine were not found in the rfbB and rfbC strains. The electrophoretic pattern of the mutants LPS was drastically altered when compared with the wild type. Knockout of rfbB or rfbC increased the sensitivity towards SDS, polymyxin B sulfate and salicylic acid. The mutants attachment capacity to maize root surface plantlets was 100-fold lower than the wild type. Interestingly, the wild-type capacity to attach to maize roots was reduced to a level similar to that of the mutants when the assay was performed in the presence of isolated wild-type LPS, glucosamine or N-acetyl glucosamine. The mutant strains were also significantly less efficient in endophytic colonization of maize. Expression analysis indicated that the rfbB gene is upregulated by naringenin, apigenin and CaCl(2). Together, the results suggest that intact LPS is required for H. seropedicae attachment to maize root and internal colonization of plant tissues.

The glnAntrBC operon of Herbaspirillum seropedicae is transcribed by two oppositely regulated promoters upstream of glnA

Herbaspirillum seropedicae is an endophytic bacterium that fixes nitrogen under microaerophilic conditions. The putative promoter sequences glnAp1 (sigma70-dependent) and glnAp2 (sigma54), and two NtrC-binding sites were identified upstream from the glnA, ntrB and ntrC genes of this microorganism. To study their transcriptional regulation, we used lacZ fusions to the H. seropedicae glnA gene, and the glnA-ntrB and ntrB-ntrC intergenic regions. Expression of glnA was up-regulated under low ammonium, but no transcription activity was detected from the intergenic regions under any condition tested, suggesting that glnA, ntrB and ntrC are co-transcribed from the promoters upstream of glnA. Ammonium regulation was lost in the ntrC mutant strain. A point mutation was introduced in the conserved -25/-24 dinucleotide (GG-->TT) of the putative sigma54-dependent promoter (glnAp2). Contrary to the wild-type promoter, glnA expression with the mutant glnAp2 promoter was repressed in the wild-type strain under low ammonium levels, but this repression was abolished in an ntrC background. Together our results indicate that the H. seropedicae glnAntrBC operon is regulated from two functional promoters upstream from glnA, which are oppositely regulated by the NtrC protein.

Identification of NH4+-regulated genes of Herbaspirillum seropedicae by random insertional mutagenesis

Random mutagenesis using transposons with promoterless reporter genes has been widely used to examine differential gene expression patterns in bacteria. Using this approach, we have identified 26 genes of the endophytic nitrogen-fixing bacterium Herbaspirillum seropedicae regulated in response to ammonium content in the growth medium. These include nine genes involved in the transport of nitrogen compounds, such as the high-affinity ammonium transporter AmtB, and uptake systems for alternative nitrogen sources; nine genes coding for proteins responsible for restoring intracellular ammonium levels through enzymatic reactions, such as nitrogenase, amidase, and arginase; and a third group includes metabolic switch genes, coding for sensor kinases or transcription regulation factors, whose role in metabolism was previously unknown. Also, four genes identified were of unknown function. This paper describes their involvement in response to ammonium limitation. The results provide a preliminary profile of the metabolic response of Herbaspirillum seropedicae to ammonium stress.

Control of autogenous activation of Herbaspirillum seropedicae nifA promoter by the IHF protein

Analysis of the expression of the Herbaspirillum seropedicae nifA promoter in Escherichia coli and Herbaspirillum seropedicae, showed that nifA expression is primarily dependent on NtrC but also required NifA for maximal expression under nitrogen-fixing conditions. Deletion of the IHF (integration host factor)-binding site produced a promoter with two-fold higher activity than the native promoter in the H. seropedicae wild-type strain but not in a nifA strain, indicating that IHF controls NifA auto-activation. IHF is apparently required to prevent overexpression of the NifA protein via auto-activation under nitrogen-fixing conditions in H. seropedicae.

Inter-domain cross-talk controls the NifA protein activity of Herbaspirillum seropedicae

Herbaspirillum seropedicae is an endophytic diazotroph, which colonizes sugar cane, wheat, rice and maize. The activity of NifA, a transcriptional activator of nif genes in H. seropedicae, is controlled by ammonium ions through a mechanism involving its N-terminal domain. Here we show that this domain interacts specifically in vitro with the N-truncated NifA protein, as revealed by protection against proteolysis, and this interaction caused an inhibitory effect on both the ATPase and DNA-binding activities of the N-truncated NifA protein. We suggest that the N-terminal domain inhibits NifA-dependent transcriptional activation by an inter-domain cross-talk between the catalytic domain of the NifA protein and its regulatory N-terminal domain in response to fixed nitrogen.

Control of nitrogenase reactivation by the GlnZ protein in Azospirillum brasilense

The glnZ mutant of Azospirillum brasilense (strain 7611) showed only partial recovery (20 to 40%) after 80 min of ammonia-induced nitrogenase switch-off, whereas the wild type recovered totally within 10 min. In contrast, the two strains showed identical anoxic-induced switch-on/switch-off, indicating no cross talk between the two reactivation mechanisms.

Uridylylation of the PII protein from Herbaspirillum seropedicae

The PII protein is apparently involved in the control of NifA activity in Herbaspirillum seropedicae. To evaluate the probable role of PII in signal transduction, uridylylation assays were conducted with purified H. seropedicae PII and Escherichia coli GlnD, or a cell-free extract of H. seropedicae as sources of uridylylating activity. The results showed that alpha-ketoglutarate and ATP stimulate uridylylation whereas glutamine inhibits uridylylation. Deuridylylation of PII-UMP was dependent on glutamine and inhibited by ATP and alpha-ketoglutarate. PII uridylylation and (or) deuridylylation in response to these effectors suggests that PII is a nitrogen level signal transducer in H. seropedicae.

Recent developments in the structural organization and regulation of nitrogen fixation genes in Herbaspirillum seropedicae

Herbaspirillum seropedicae is a nitrogen-fixing bacterium found in association with economically important gramineae. Regulation of nitrogen fixation involves the transcriptional activator NifA protein. The regulation of NifA protein and its truncated mutant proteins is described and compared with that of other nitrogen fixation bacteria. Nitrogen fixation control in H. seropedicae, of the beta-subgroup of Proteobacteria, has regulatory features in common with Klebsiella pneumoniae, of the gamma-subgroup, at the level of nifA expression and with rhizobia and Azospirillum brasilense, of the alpha-subgroup, at the level of control of NifA by oxygen.

Potential roles for the glnB and ntrYX genes in Azospirillum brasilense

Three Azospirillum brasilense mutants constitutive for nitrogen fixation (Nif(C)) in the presence of NH4(+) and deficient in nitrate-dependent growth were used as tools to define the roles of the glnB and ntrYX genes in this organism. Mutant HM14 was complemented for nitrate-dependent growth and NH4(+) regulation of nitrogenase by plasmid pL46 which contains the ntrYX genes of A. brasilense. Mutant HM26 was restored for NH4(+) regulation and nitrate-dependent growth by plasmid pJC1, carrying the A. brasilense glnB gene expressed from a constitutive promoter. Mutant HM053, on the other hand, was not complemented for NH4(+) regulation of nitrogenase and nitrate-dependent growth by both plasmids pJCI and pL46. The levels and control of glutamine synthetase activity of all mutants were not affected by both plasmids pL46 (ntrYX) and pJC1 (glnB). These results support the characterization of strains HM14 as an ntrYX mutant and strain HM26 as a glnB mutant and the involvement of ntrYX and glnB in the regulation of the general nitrogen metabolism in A. brasilense.

The transcriptional activator NtrC controls the expression and activity of glutamine synthetase in Herbaspirillum seropedicae

The role of the Ntr system in Herbaspirillum seropedicae was determined via ntrB and ntrC mutants. Three phenotypes were identified in these mutants: Nif(-), deficiency in growth using nitrate, and low glutamine synthetase (GS) activity. All phenotypes were restored by the plasmid pKRT1 containing the intact glnA, ntrB and ntrC genes of H. seropedicae. The promoter region of glnA was subcloned into a beta-galactosidase fusion vector and the results suggested that NtrC positively regulates the glnA promoter in response to low nitrogen. The H. seropedicae ntrC and ntrB mutant strains showed a deficiency of adenylylation/deadenylylation of GS, indicating that NtrC and NtrB are involved in both transcription and activity control of GS in this organism.

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.

Nitrogenase of Azotobacter chroococcum. Kinetics of the reduction of oxidized iron-protein by sodium dithionite

The kinetics of the reduction of oxidized Fe-protein of nitrogenase from Azotobacter chroococcum by sodium dithionite were studied by stopped-flow and rapid-freezing e.p.r. (electron-paramagnetic-resonance) spectroscopy. The appearance of the gav. = 1.94 e.p.r. signal (0.24 electron integrated intensity/mol) was associated with a one-electron reduction by SO2--with k greater than 10(8)M-1-S-1 at 23 degrees C. A value of k = 1.75s-1 was obtained for the rate of dissociation of S2O42- into 2SO2-- at 23 degrees C. Further reductions by SO2-- occurred in three slower phases with rate constants in the range 10(4) -10(6)M-1-S-1. These latter phases have no corresponding e.p.r. signal changes and are probably associated with enzymically inactive protein. The high rate of reduction by SO2-- of the Fe-protein alone (k greater than 10(8)M-1-S-1) relative to the rate of oxidation of the Fe-protein in the catalytically active Fe:Mo-Fe protein complex (k = 2.2 X 1O(2)s-1) and the observation that in the steady state the Fe-protein is substantially oxidized means that at normal assay concentrations another reaction must limit the rate of reduction of Fe-protein during turnover.

The electron transport to nitrogenase in Mycobacterium flavum

1. Two ferredoxin-type iron-sulfur proteins have been isolated from Mycobacterium flavum 301 grown under nitrogen-fixing, iron-sufficient conditions. No flavodoxin was observed. 2. These ferredoxins are apparently soluble: they were present in the supernatant fraction after disrupting by decompression. Only small amounts were present in particulate fractions. 3. The two ferredoxins were separated by chromatography on DEAE-cellulose, Sephadex or electrophoresis. 4. Both ferredoxins mediated the transfer of electrons from illuminated spinach chloroplasts to a nitrogenase preparation to reduce acetylene. Ferredoxin II was specifically about five times more active than ferredoxin I. Ferredoxin II was also active in the photosynthetic NADP+-reduction whereas ferredoxin I was not. 5. Both ferredoxins were reversibly reduced by either sodium dithionite, illuminated spinach chloroplasts or hydrogen plus hydrogenase from Clostridium pasteurianum. 6. Attempts to determine the primary electron donor for nitrogen fixation in Mycobacterium flavum were unsuccessful. Acetylene reduction in Mycobacterium extracts was obtained only with sodium dithionite or illuminated spinach chloroplasts as electron donors. The reduction of the electron carrier (e.g. ferredoxin) rather than the transfer of electrons from the reduced carrier to nitrogenase was rate-limiting.

Nitrogenase from Azotobacter chroococcum. Purification and properties of the component proteins

1. A large-scale purification of the nitrogenase components from Azotobacter chroococcum yielded two non-haem iron proteins, both of which were necessary for nitrogenase activity and each had a specific activity of approximately 2000 +/- 300 nmol of acetylene reduced/mg protein per min in the presence of sautrating amounts of the other. This procedure freed the Mo-Fe protein from a protein contaminant which had an electron paramagnetic resonance signal at g = 1.94. 2. Both proteins were purified to homogeneity as determined by disc gel electrophoresis and ultracentrifugal analysis. Both proteins were oxygen-sensitive but not cold-labile. Ultracentrifugal analysis indicated that both proteins dissociated to a slight degree at concentrations below 2 mg/ml. 3. The larger of the two proteins had a molecular weight of 227 000 and contained 1.9 +/- 0.3 atoms of Mo, 23 +/- 2 atoms of Fe, 20 +/- 2 acid-labile sulphide and 47 tryptophan residues/mol. The protein consists of 4 subunits of mol. wt 60 000 (approx.). The reduced protein showed electron paramagmetic resonance signals at g = 4.29, 3.65 and 2.013 but not in the area of g = 5 to 6. Upon oxidation abosrbance increased throughout the visible region of the ultraviolet visible spectrum, with a maximum difference between oxidised and reduced protein occurring at 430 nm. 4. The smaller protein had a molecular weight of 64 000 and contained 4 g-atoms of Fe and 4 acid-labile sulphide groups/mol but no tryptophan. It had two subunits of mol. wt 30 800. The reduced protein showed electron paramagnetic resonance signhe protein retained almost full activity after oxidation with phenazine methosulphate. The ultraviolet visible spectrum of oxidised protein was clearly different from that of the oxygen-inactivated protein: it had a sharp peak at 269 nm and a broad absorbance between 340 and 470 nm with a maximum difference between oxidised and reduced forms at 430 nm. Oxygen-inactivated protein showed a sharp peak at 277.5 nm and broad peaks from 305 to 360, 400 to 425 and 435 to 475 nm. 5. Amino acid analyses of both proteins showed that most common amino acids were present with a preponderance of acidic residues. Analyses of compositional relatedness showed that the nitrogenase proteins from A. chroococcum were most closely related to those from A. vinelandii and least so to those from Clostridium pasteurianum.

Nitrogenases of Klebsiella pneumoniae and Azotobacter chroococum. Complex formation between the component proteins

1. Sedimentation velocity analyses of mixtures of highly purified component proteins of Azotobacter chroococcum are consistent with the formation of a tight 1 : 1 complex in the absence of Na2 S2 O4. 1 : 1 complex formation between complementary proteins from A. chroococcum and Klebsiella pneumoniae was also observed. The addition of 5 mM Na2 S2 O4 weakened the interaction between the A. chroococcum proteins and also the interaction between complementary proteins of A. chroococcum and K. pneumoniae. 2. Steady-state kinetic data for acetylene reduction at low protein concentrations have been used to calculate association constants at 30 degrees C for the 1 : 1 protein complexes of nitrogenase proteins from A. chroococcum, K. pneumoniae and mixtures of complementary proteins from both organisms. Values centered around 3 - 10(7) M-1 were obtained. 3. The temperature dependence of the association constant for the complex formed by the K. pneumoniae proteins exhibited a sharp break at 17 degrees C with deltaH = 0 and deltaH = 418 kJ - mol-1 above and below 17 degrees C, respectively. 4. The Arrhenius plot for acetylene reduction by the complex formed by the K. pneumoniae proteins was linear over the range 12-40 degrees C with deltaH = 80 kJ - mol-1.