Characterization of Rhizobium japonicum hydrogen uptake genes

Intra- and interspecies transfer and expression of Rhizobium japonicum hydrogen uptake genes and autotrophic growth capability

Cosmids containing hydrogen uptake genes have previously been isolated in this laboratory. Four new cosmids that contain additional hup gene(s) have now been identified by conjugal transfer of a Rhizobium japonicum 122DES gene bank into a Tn5-generated Hup(-) mutant and screening for the acquisition of Hup activity. The newly isolated cosmids, pHU50-pHU53, contain part of the previously isolated pHU1 but extend as far as 20 kilobases beyond its border. pHU52 complements five of six Hup(-) mutants and confers activity on several Hup(-) wild-type R. japonicum strains in the free-living state and where tested in nodules. Transconjugants obtained from interspecies transfer of pHU52 to Rhizobium meliloti 102F28, 102F32, and 102F51 and Rhizobium leguminosarum 128C53 showed hydrogen-dependent methyleneblue reduction, performed the oxyhydrogen reaction, and showed hydrogen-dependent autotrophic growth by virtue of the introduced genes. The identity of the presumptive transconjugants was confirmed by antibiotic-resistance profiles and by plant nodulation tests.

Isolation of genes involved in nodulation competitiveness from Rhizobium leguminosarum bv. trifolii T24

Rhizobium leguminosarum bv. trifolii T24 produces a potent anti-rhizobial compound, trifolitoxin, and exclusively nodulates clover roots when in mixed inoculum with trifolitoxin-sensitive strains of R. leguminosarum bv. trifolii [Schwinghamer, E. A. & Belkengren R. P. (1968) Arch. Mikrobiol. 64, 130-145]. In the present study, the isolation of trifolitoxin production and resistance genes is described. A cosmid genomic library of T24 was prepared in pLAFR3. No trifolitoxin expression was observed in the resulting Escherichia coli cosmid clones. One cosmid clone was identified that restored trifolitoxin production and nodulation competitiveness in three nonproducing mutants of T24. The recombinant plasmid from this cosmid clone, pTFX1, also conferred trifolitoxin production and resistance when transferred to symbiotically effective strains of R. leguminosarum bvs. trifolii, phaseoli, and viceae. Cosmid pTFX1 also conferred expression of trifolitoxin production when present in strains of Rhizobium meliloti and Agrobacterium tumefaciens. No trifolitoxin expression was observed in strains of Bradyrhizobium japonicum or Rhizobium sp. (cowpea) with pTFX1. Southern blot analysis with a biotinylated pTFX1 probe did not suggest that these genes were plasmid-borne. Transfer of pTFX1 to T24 or its derivatives resulted in 6- to 10-fold higher level of trifolitoxin production than wild-type T24.

Transposon Tn5-Generated Bradyrhizobium japonicum Mutants Unable To Grow Chemoautotrophically with H(2)

Twelve Tn5-induced mutants of Bradyrhizobium japonicum unable to grow chemoautotrophically with CO(2) and H(2) (Aut) were isolated. Five Aut mutants lacked hydrogen uptake activity (Hup). The other seven Aut mutants possessed wild-type levels of hydrogen uptake activity (Hup), both in free-living culture and symbiotically. Three of the Hup mutants lacked hydrogenase activity both in free-living culture and as nodule bacteroids. The other two mutants were Hup only in free-living culture. The latter two mutants appeared to be hypersensitive to repression by oxygen, since Hup activity could be derepressed under 0.4% O(2). All five Hup mutants expressed both ex planta and symbiotic nitrogenase activities. Two of the seven Aut Hup mutants expressed no free-living nitrogenase activity, but they did express it symbiotically. These two strains, plus one other Aut Hup mutant, had CO(2) fixation activities 20 to 32% of the wild-type level. The cosmid pSH22, which was shown previously to contain hydrogenase-related genes of B. japonicum, was conjugated into each Aut mutant. The Aut Hup mutants that were Hup both in free-living culture and symbiotically were complemented by the cosmid. None of the other mutants was complemented by pSH22. Individual subcloned fragments of pSH22 were used to complement two of the Hup mutants.

Symbiotic Expression of Cosmid-Borne Bradyrhizobium japonicum Hydrogenase Genes

The expression of cosmid-borne Bradyrhizobium japonicum hydrogenase genes in alfalfa, clover, and soybean nodules harboring Rhizobium transconjugants was studied. Cosmid pHU52 conferred hydrogen uptake (Hup) activity in both free-living bacteria and in nodules on the different plant hosts, although in nodules the instability of the cosmid resulted in low levels of Hup activity. In contrast, cosmid pHU1, which does not confer Hup activity on free-living bacteria, gave a Hup phenotype in nodules on alfalfa and soybean. Nodules formed by B. japonicum USDA 123Spc(pHU1) recycled about 90% of nitrogenase-mediated hydrogen evolution. Both subunits of hydrogenase (30- and 60-kilodalton polypeptides) were detected in enzyme-linked immunosorbent assays of bacteroid preparations from nodules harboring B. japonicum strains with pHU1 or pHU52. Neither pHU53 nor pLAFR1 conferred detectable Hup activity in either nodules or free-living bacteria. Based on the physical maps of pHU1 and pHU52, it is suggested that a 5.5-kilobase EcoRI fragment unique to pHU52 contains a gene or part of a gene required for Hup activity in free-living bacteria but not in nodules. This conclusion is supported by the observation that two Tn5 insertions in the chromosome of B. japonicum USDA 122DES obtained by marker exchange with Tn5-mutagenized pHU1 abolished Hup activity in free-living bacteria but not in nodules.

Influence of the Bradyrhizobium japonicum Hydrogenase on the Growth of Glycine and Vigna Species

The effect of the Bradyrhizobium japonicum hydrogenase on nitrogen fixation was evaluated by comparing the growth of Vigna and Glycine species inoculated with a Hup mutant and its Hup revertant. In all experiments, the growth of plants inoculated with the strain without hydrogenase was at least equal to the growth of the strain with hydrogenase. For Glycine usuriensis and Glycine max cv. Hodgson in liquid culture, the growth was higher with the Hup strain. It is possible that reduced rates of nitrogen fixation in the presence of hydrogenase are due to O(2) depletion caused by the hydrogen oxidizing, since the oxygen pressure in the air appears to be a limiting factor of symbiotic nitrogen fixation in the soybean.

Increased Nitrogenase-Dependent H 2 Photoproduction by hup Mutants of Rhodospirillum rubrum

Transposon Tn 5 mutagenesis was used to isolate mutants of Rhodospirillum rubrum which lack uptake hydrogenase (Hup) activity. Three Tn 5 insertions mapped at different positions within the same 13-kb Eco RI fragment (fragment E1). Hybridization experiments revealed homology to the structural hydrogenase genes hupSLM from Rhodobacter capsulatus and hupSL from Bradyrhizobium japonicum in a 3.8-kb Eco RI- Cla I subfragment of fragment E1. It is suggested that this region contains at least some of the structural genes encoding the nickel-dependent uptake hydrogenase of R. rubrum . At a distance of about 4.5 kb from the fragment homologous to hupSLM , a region with homology to a DNA fragment carrying hypDE and hoxXA from B. japonicum was identified. Stable insertion and deletion mutations were generated in vitro and introduced into R. rubrum by homogenotization. In comparison with the wild type, the resulting hup mutants showed increased nitrogenase-dependent H 2 photoproduction. However, a mutation in a structural hup gene did not result in maximum H 2 production rates, indicating that the capacity to recycle H 2 was not completely lost. Highest H 2 production rates were obtained with a mutant carrying an insertion in a nonstructural hup -specific sequence and with a deletion mutant affected in both structural and nonstructural hup genes. Thus, besides the known Hup activity, a second, previously unknown Hup activity seems to be involved in H 2 recycling. A single regulatory or accessory gene might be responsible for both enzymes. In contrast to the nickel-dependent uptake hydrogenase, the second Hup activity seems to be resistant to the metal chelator EDTA.

Rapid and efficient selection of recombinant site-directed mutants of Bradyrhizobium japonicum by colony hybridization

Due to the high incidence of spontaneous antibiotic resistance and slow growth of Bradyrhizobium japonicum strains, screening for site-directed mutants is cumbersome and time-consuming. A rapid method for selection of recombinant site-directed mutants of B. japonicum was developed. A kanamycin (Km) and a spectinomycin (Sp) cassette were each used to replace DNA fragments in the chromosome by homologous recombination. The primary new features of this method involve a simple plate selection for the antibiotic (Km or Sp) resistant mutants, then colony streaking, and lysis for DNA hybridization on a nitrocellulose filter enabling direct identification of the recombinant site-directed mutants. This method has permitted us to quickly and easily identify a large number of positive recombinant mutants from a large number of individual colonies. The procedure eliminates the need to first isolate genomic DNA from each mutant for Southern hybridization. All of the tested site-directed mutants from this method were confirmed to exhibit the expected mutant phenotype.

Molecular analysis of a microaerobically induced operon required for hydrogenase synthesis in Rhizobium leguminosarum biovar viciae

The nucleotide sequence (6138 bp) of a microaerobically inducible region (hupV/VI) from the Rhizobium leguminosarum bv. viciae hydrogenase gene cluster has been determined. Six genes, arranged as a single operon, were identified, and designated hypA, B, F, C, D and E based on the sequence similarities of all of them, except hypF, to genes from the hydrogenase pleiotropic operon (hyp) from Escherichia coli. The gene products from hypBFCDE were identified by in vivo expression analysis in E. coli, and their molecular sizes were consistent with those predicted from the nucleotide sequence. Transposon Tn5 insertions into hypB, hypF, hypD and hypE resulted in R. leguminosarum mutants that lacked any hydrogenase activity in symbiosis with peas, but still were able to synthesize the polypeptide for the hydrogenase large subunit. The gene products HypA, HypB, HypF and HypD contained CX2C motifs characteristic of metal-binding proteins. In addition, HypB bore a long histidine-rich stretch of amino acids near the N-terminus, suggesting a possible role in nickel binding for this protein. The gene product HypF, which was translationally coupled to HypB, presented two cysteine motifs (CX2CX18CX2C) with a capacity to form zinc finger-like structures in the N-terminal third of the protein. A role in nickel metabolism in relation to hydrogenase synthesis is postulated for proteins HypB and HypF.

Identification of a potential transcriptional regulator of hydrogenase activity in free-living Bradyrhizobium japonicum strains

In Bradyrhizobium japonicum, Tn5 insertions in a particular chromosomal DNA fragment result in a Hup- phenotype in free-living conditions without affecting hydrogenase (Hup) activity in the symbiotic state. By determination of the nucleotide sequence of this region, we were able to identify the nature of the inactivated genes. The fragment is located 9 kb downstream of the hydrogenase structural genes and contains one incomplete and three complete open reading frames. They are designated hypD', hypE, hoxX and hoxA respectively, since the deduced amino acid sequences display very strong homology with genes involved in the regulation of hydrogenase activity in Escherichia coli, Rhodobacter capsulatus, Azotobacter vinelandii (hypD' and hypE) and Alcaligenes eutrophus (hoxX and hoxA). This is the first report on transcriptional activators of the hup genes in B. japonicum. Implications of these findings with respect to regulation of hydrogenase synthesis by hydrogen, oxygen and nickel in free-living B. japonicum are discussed.

A genetic region downstream of the hydrogenase structural genes of Bradyrhizobium japonicum that is required for hydrogenase processing

Deletion of a 2.9-kb chromosomal EcoRI fragment of DNA located 2.2 kb downstream from the end of the hydrogenase structural genes resulted in the complete loss of hydrogenase activity. The normal 65- and 35-kDa hydrogenase subunits were absent in the deletion mutants. Instead, two peptides of 66.5 and 41 kDa were identified in the mutants by use of anti-hydrogenase subunit-specific antibody. A hydrogenase structural gene mutant did not synthesize either the normal hydrogenase subunits or the larger peptides. Hydrogenase activity in the deletion mutants was complemented to near wild-type levels by plasmid pCF1, containing a 6.5-kb BglII fragment, and the 65- and 35-kDa hydrogenase subunits were also recovered in the mutants containing pCF1.

Integration ofhup cosmid pHU52 into the chromosomal DNA ofCicer-Rhizobium using Tn5 as an homologous sequence

Cosmid pHU52, which carrieshup genes ofBradyrhizobium japonicum, has been integrated into theCicer-Rhizobium G36-84 genome via Tn5-mediated homologous recombination. Tn5 was inserted into both the cosmid pHU52 and the chromosome ofCicer-Rhizobium to provide a region of DNA homology, without affecting the expression of necessary genes. An incompatible plasmid, pPH1JI, was used to select those few cells that had undergone recombination. The integration of the cosmid was demonstrated by Southern blot analysis. Chromosomal integration of thehup genes maximized stability and minimized the potential for their horizontal transfer to other bacterial species. The integratedhup genes were found to expressex planta as well in nodules. The method described illustrates how a given gene can be stably integrated into the chromosome.

Two open reading frames (ORFs) identified near the hydrogenase structural genes in Azotobacter vinelandii, the first ORF may encode for a polypeptide similar to rubredoxins

Sequencing of 744 base pairs (bp) of a cloned section of DNA from Azotobacter vinelandii reveals two complete, closely-spaced open reading frames (ORF1 and ORF2). Both ORFs are transcribed from the same DNA strand as that of the structural genes for hydrogenase (hoxK and hoxG, Menon, A.L. et al. (1990) Gene 96, 67-74), and are located downstream from the latter genes. The distance between the end of hoxG and the beginning of ORF1 is approx. 3.0 kilobases (kb). Most of the deduced amino acid sequence of ORF1 shares high homology with rubredoxin sequences. Some of the deduced amino acid sequence of ORF2 shares homology with that of a reported partial ORF from Rhodobacter capsulatus, ORF located within a region of DNA required for dihydrogen oxidation in that organism. Implications of these findings with respect to dihydrogen metabolism are discussed.

Identification of a locus within the hydrogenase gene cluster involved in intracellular nickel metabolism in Bradyrhizobium japonicum

A 0.6-kb fragment of DNA involved in intracellular Ni metabolism was isolated and cloned from a cosmid containing 23.2 kb of hydrogenase-related genes of Bradyrhizobium japonicum. This locus is located 8.3 kb upstream of the hydrogenase structural genes. The hydrogenase activity of a mutant with a gene-directed mutation at this locus (strain JHK7) showed dependency on nickel provided during hydrogenase derepression. The hydrogenase activity was only 20% of that in the wild-type strain, JH, at a concentration of 0.5 microM NiCl2. The hydrogenase activity in JH reached its maximum at 3 microM NiCl2, whereas the mutant (JHK7) reached wild-type levels of hydrogenase activity when derepressed in 50 microM NiCl2. Studies with the hup-lacZ transcriptional fusion plasmid pSY7 in JHK7 showed that the mutant JHK7 expressed less promoter activity under low-nickel conditions than did strain JH. The mutant accumulated less nickel during a 45-h hydrogenase derepression period than did the wild type. However, both JHK7 and the JH wild-type strain had the same short-term Ni transport rates, and the KmS for Ni of both strains were about 62 microM. When incubated under non-hydrogenase-derepression conditions, the mutant accumulated Ni at the same rate as strain JH. However, this stored source of nickel was unable to restore hydrogenase expression ability of the mutant to wild-type levels during derepression without nickel. The results indicate that the locus identified in B. japonicum is not involved in nickel-specific transport; indeed, it was not at all homologous to the "nickel transporter" hoxN gene of Alcaligenes eutrophus.(ABSTRACT TRUNCATED AT 250 WORDS)

Cloning, sequencing and characterization of the [NiFe]hydrogenase-encoding structural genes (hoxK and hoxG) from Azotobacter vinelandii

The Azotobacter vinelandii [NiFe]hydrogenase-encoding structural genes were isolated from an A. vinelandii genomic cosmid library. Nucleotide (nt) sequence analysis showed that the two genes, hoxK and hoxG, which encode the small and large subunits of the enzyme, respectively, form part of an operon that contains at least one other gene. The hoxK gene encodes a polypeptide of 358 amino acids (aa) (39,209 Da). The deduced aa sequence encodes a possible 45-aa N-terminus extension, not present in the purified A. vinelandii hydrogenase small subunit, which could be a cellular targeting sequence. The hoxG gene is downstream form, and overlaps hoxK by 4 nt and encodes a 602-aa polypeptide of 66,803 Da. The hoxK and hoxG gene products display homology to aa sequences of hydrogenase small and large subunits, respectively, from other organisms. The hoxG gene lies 16 nt upstream from a third open reading frame which could encode a 27,729-Da (240-aa) hydrophobic polypeptide containing 53% nonpolar and 11% aromatic aa. The significance of this possible third gene is not known at present.

Differential expression of hydrogen uptake (hup) genes in vegetative and symbiotic cells of Rhizobium leguminosarum

The genetic determinants responsible for H2-uptake (hup genes) in Rhizobium leguminosarum are organized in six transcriptional units, designated regions hupI to hupVI, with region hupI coding for the hydrogenase structural genes (Leyva et al. 1990). Regulation of the expression of hup genes from R. leguminosarum was examined by using hup-lacZ fusions and mRNA dot-blot analysis. None of the six hup regions is transcribed in vegetative cells grown under normal aerobic conditions, whereas all six regions are transcribed in pea bacteroids. Additionally, exposure of cell cultures to low oxygen tensions specifically induces the expression of regions hupV and hupVI. By studying the expression of hupV- and hupVI-lacZ fusions in R. meliloti mutants it was determined that the microaerobic induction of these two regions is dependent on the regulatory fixLJ system, and that this control is exerted through fixK. Such expression was also shown to be nifA and ntrA independent. The functions of the hupV and hupVI gene products are unknown. The possibility that they play a regulatory role in hup gene expression is unlikely, since pea bacteroids from R. leguminosarum Hup- mutants carrying Tn5 insertions in regions hupV and hupVI contained normal levels of mRNA transcripts corresponding to the remaining hup regions.

Development and Partial Characterization of Nearly Isogenic Pea Lines (Pisum sativum L.) that Alter Uptake Hydrogenase Activity in Symbiotic Rhizobium

Some Rhizobium bacteria have H(2)-uptake (Hup) systems that oxidize H(2) evolved from nitrogenase in leguminous root nodules. Pea (Pisum sativum L.) cultivars ;JI1205' and ;Alaska' produce high Hup (Hup(++)) and moderate Hup (Hup(+)) phenotypes, respectively, in Rhizobium leguminosarum 128C53. The physiological significance and biochemical basis of this host plant genetic effect are unknown. The purpose of this investigation was to advance basic Hup studies by developing nearly isogenic lines of peas that alter Hup phenotypes in R. leguminosarum strains containing hup genes. Eight pairs of nearly isogenic pea lines that produce Hup(++) and Hup(+) phenotypes in R. leguminosarum 128C53 were identified in 173 F(2)-derived F(6) families produced from crosses between JI1205 and Alaska. Tests with the pea isolines and three strains of hup-containing R. leguminosarum showed that the isolines altered Hup activity significantly (P </= 0.05) in 19 of 24 symbiotic combinations. Analyses of Hup phenotypes in F(6) families, the F(1) population, and two backcrosses suggested involvement of a single genetic locus. Three of the eight pairs of isolines were identified as being suitable for physiological studies, because the two lines in each pair showed similar growth, N assimilation, and flowering traits under nonsymbiotic conditions. Tests of those lines under N(2)-dependent conditions with isogenic Hup(+) and negligible Hup (Hup(-)) mutants of R. leguminosarum 128C53 showed that, in symbioses with Hup(+) rhizobia, two out of three Hup(++) pea lines decreased N(2) fixation relative to Hup(+) peas. In one of those cases, however, the Hup(++) plant line also decreased fixation by Hup(-) rhizobia. When results were averaged across all rhizobia tested, Hup(+) pea isolines had 8.2% higher dry weight (P </= 0.05) and fixed 12.6% more N(2) (P </= 0.05) than Hup(++) isolines. Pea lines described here may help identify host plant factors that influence rhizobial Hup activity and should assist in clarifying how Hup systems influence other physiological processes.

Genetic organization of the hydrogen uptake (hup) cluster from Rhizobium leguminosarum

In symbiosis with peas, Rhizobium leguminosarum UPM791 induces the synthesis of a hydrogen uptake (Hup) system that recycles hydrogen generated in nodules by nitrogenase. A cosmid (pAL618) containing hup genes from this strain on a 20-kilobase-pair (kb) DNA insert has previously been isolated in our laboratory (A. Leyva, J. M. Palacios, T. Mozo, and T.Ruiz-Argüeso, J. Bacteriol. 169:4929-4934, 1987). Here we show that cosmid pAL618 contains all of the genetic information required to confer high levels of hydrogenase activity on the naturally Hup- strains R. leguminosarum UML2 and Rhizobium phaseoli CFN42, and we also describe in detail the organization of hup genes on pAL618. To study hup gene organization, site-directed transposon mutagenesis and complementation analysis were carried out. According to the Hup phenotype associated with the transposon insertions, hup genes were found to span a 15-kilobase-pair region within pAL618 insert DNA. Complementation analysis revealed that Hup- mutants fell into six distinct complementation groups that define six transcriptional units, designated regions hupI to hupVI. Region hupI was subcloned and expressed in Escherichia coli cells under the control of a bacteriophage T7 promoter. A polypeptide of ca. 65 kilodaltons that was cross-reactive with antiserum against the large subunit of Bradyrhizobium japonicum hydrogenase was detected both in E. coli cells carrying the cloned hupI region and in pea bacteroids from strain UPM791, indicating that region hupI codes for structural genes of R. leguminosarum hydrogenase.

Identification of a Locus Upstream from the Hydrogenase Structural Genes That Is Involved in Hydrogenase Expression in Bradyrhizobium japonicum

A locus involved in the expression of the uptake hydrogenase system of Bradyrhizobium japonicum was identified adjacent to genes encoding the hydrogenase subunits. A cloned fragment of DNA was used to complement to autotrophy a Hup − putative regulatory mutant of B. japonicum . The mutant strain lacked hydrogenase activity and synthesized low levels of the large subunit of hydrogenase as determined by Western gels. Tn 5 -induced mutagenesis located the region within the fragment which was necessary for complementation of the mutant phenotype. The locus identified is adjacent to that encoding the small subunit of hydrogenase; its right border is <0.5 kilobase upstream from the hydrogenase transcriptional start site, and its left border is between 1 and 2.5 kilobases from that start site. However, the locus is outside the region previously shown to contain hup -related genes of B. japonicum . Thus, the localization of this gene describes a previously unidentified hup -related gene on a region of DNA not previously shown to contain hup -specific DNA.

Identification and isolation of genes essential for H2 oxidation in Rhodobacter capsulatus

Mutants of Rhodobacter capsulatus unable to grow photoautotrophically with H2 and CO2 were isolated. Those lacking uptake hydrogenase activity as measured by H2-dependent methylene blue reduction were analyzed genetically and used in complementation studies for the isolation of the wild-type genes. Results of further subcloning and transposon Tn5 mutagenesis suggest the involvement of a minimum of five genes. Hybridization to the 2.2-kilobase-pair SstI fragment that lies within the coding region for the large and small subunits of Bradyrhizobium japonicum uptake hydrogenase showed one region of strong homology among the R. capsulatus fragments isolated, which we interpret to mean that one or both structural genes were among the genes isolated.

Cloning and characterization of hydrogen uptake genes from Rhizobium leguminosarum

A gene library of genomic DNA from the hydrogen uptake (Hup)-positive strain 128C53 of Rhizobium leguminosarum was constructed by using the broad-host-range mobilizable cosmid vector pLAFR1. The resulting recombinant cosmids contained insert DNA averaging 21 kilobase pairs (kb) in length. Two clones from the above gene library were identified by colony hybridization with DNA sequences from plasmid pHU1 containing hup genes of Bradyhizobium japonicum. The corresponding recombinant cosmids, pAL618 and pAL704, were isolated, and a region of about 28 kb containing the sequences homologous to B. japonicum hup-specific DNA was physically mapped. Further hybridization analysis with three fragments from pHU1 (5.9-kb HindIII, 2.9-kb EcoRI, and 5.0-kb EcoRI) showed that the overall arrangement of the R. leguminosarum hup-specific region closely parallels that of B. japonicum. The presence of functional hup genes within the isolated cosmid DNA was demonstrated by site-directed Tn5 mutagenesis of the 128C53 genome and analysis of the Hup phenotype of the Tn5 insertion strains in symbiosis with peas. Transposon Tn5 insertions at six different sites spanning 11 kb of pAL618 completely suppressed the hydrogenase activity of the pea bacteroids.

Conserved Plasmid Hydrogen-Uptake ( hup )-Specific Sequences within Hup + Rhizobium leguminosarum Strains

Thirteen Rhizobium leguminosarum strains previously reported as H 2 -uptake hydrogenase positive (Hup + ) or negative (Hup − ) were analyzed for the presence and conservation of DNA sequences homologous to cloned Bradyrhizobium japonicum hup -specific DNA from cosmid pHU1 (M. A. Cantrell, R. A. Haugland, and H. J. Evans, Proc. Natl. Acad. Sci. USA 80:181-185, 1983). The Hup phenotype of these strains was reexamined by determining hydrogenase activity induced in bacteroids from pea nodules. Five strains, including H 2 oxidation-ATP synthesis-coupled and -uncoupled strains, induced significant rates of H 2 -uptake hydrogenase activity and contained DNA sequences homologous to three probe DNA fragments (5.9-kilobase [kb] Hin dIII, 2.9-kb Eco RI, and 5.0-kb Eco RI) from pHU1. The pattern of genomic DNA Hin dIII and Eco RI fragments with significant homology to each of the three probes was identical in all five strains regardless of the H 2 -dependent ATP generation trait. The restriction fragments containing the homology totalled about 22 kb of DNA common to the five strains. In all instances the putative hup sequences were located on a plasmid that also contained nif genes. The molecular sizes of the identified hup-sym plasmids ranged between 184 and 212 megadaltons. No common DNA sequences homologous to B. japonicum hup DNA were found in genomic DNA from any of the eight remaining strains showing no significant hydrogenase activity in pea bacteroids. These results suggest that the identified DNA region contains genes essential for hydrogenase activity in R. leguminosarum and that its organization is highly conserved within Hup + strains in this symbiotic species.

A genetic locus essential for formate-dependent growth of Bradyrhizobium japonicum

A genetic locus essential for the formate-dependent growth of Bradyrhizobium japonicum was isolated by complementation of ethyl methanesulfonate-induced mutants with a cosmid gene library of B. japonicum DNA. Three related cosmids containing 18.7 kilobase pairs of B. japonicum DNA in common were identified as being able to restore formate-dependent growth capability to mutants lacking either ribulosebisphosphate carboxylase or both ribulosebisphosphate carboxylase and phosphoribulokinase activities. To further localize the complementing gene(s), a series of four deletions spanning a total of 16.1 kilobase pairs were introduced into the B. japonicum chromosome. Each resulting deletion mutant lacked formate dehydrogenase activity and lacked ribulosebisphosphate carboxylase activity and immunologically detectable protein. Three of the four also lacked phosphoribulokinase activity. Two other mutants in which the deletion-bearing recombinant plasmid had integrated into the chromosome also lacked ribulosebisphosphate carboxylase activity and protein and phosphoribulokinase activities. The genetic locus defined by these mutants could contain the structural genes for these enzymes or a regulatory gene(s) controlling their expression or both.

Cloning and expression of Bradyrhizobium japonicum uptake hydrogenase structural genes in Escherichia coli

To identify the structural genes for the components of Bradyrhizobium japonicum uptake hydrogenase (Mr 60,000 and 30,000), we have expressed these genes in Escherichia coli and shown that the products cross-react with antibodies to the respective hydrogenase subunits. We constructed subclones of overlapping DNA fragments from an uptake hydrogenase-complementing cosmid, pHU52 [Lambert, G. R., Cantrell, M. A., Hanus, F. J., Russell, S. A., Haddad, K. R. & Evans, H. J. (1985) Proc. Natl. Acad. Sci. USA 82, 3232-3236], in pMZ 545, a plasmid expression vector. DNA fragments inserted into one or more of the four cloning sites downstream from the E. coli lac operon promoter (Plac) on pMZ 545 generate transcriptional, but not translational, fusions. Two subclones that directed the synthesis of Mr 60,000 and 30,000 proteins in E. coli "maxicells" were identified. The DNA inserts from these subclones were then inserted down-stream of the bacteriophage lambda PL promoter on a transcriptional fusion vector. When the PL promoter was activated in vivo by heat inactivation of the temperature sensitive cI repressor of lambda in an appropriate E. coli strain, the respective fragments expressed higher levels of Mr 60,000 and 30,000 proteins that could be detected in immunoblots. These data provide direct evidence for the presence of uptake hydrogenase structural genes on the uptake hydrogenase-complementing cosmid pHU52.

Cloning of DNA fragments carrying hydrogenase genes of Rhodopseudomonas capsulata

A cosmid library of Rhodopseudomonas capsulata DNA was constructed in Escherichia coli HB101 using the broad-host-range cosmid vector pLAFR1. More than ninety per cent of the clones in the bank contained cosmids with DNA inserts averaging 20 kilobase pairs in length. Mutants deficient in uptake hydrogenase (Hup-) were obtained from R. capsulata strain B10 by ethylmethylsulfonate (EMS) mutagenesis. The content of hydrogenase protein in Hup- mutant cells was tested by rocket immunoelectrophoresis. Hup- mutants (Rifr) were complemented with the clone bank by conjugation and, from the transconjugants selected by rifampicin and tetracycline resistance, Hup+ transconjugants were screened for the ability to grow photoautotrophically and to reduce methylene blue in a colony assay. The recombinant plasmid pAC57 restored hydrogenase activity in the Hup- mutants RCC8, RCC10, RCC12 and ST410 whereas pAG202 restored that of IR4. The cloned R. capsulata DNA insert of pAC57 gave 5 restriction fragments by cleavage with EcoRI endonuclease. Fragment 1 (7 kb) restored hydrogenase activity in Hup- mutant strains RCC12 and ST410 and fragment 5 (1.3 kb) in strains RCC8 and RCC10. Since the 2 cosmids pAC57 and pAG202 are different cosmids, as indicated by restriction analyses and absence of cross hybridization, it is concluded that at least two hup genes are required for the expression of hydrogenase activity in R. capsulata.

Genetics of hydrogenase from aerobic lithoautotrophic bacteria

Aerobic facultatively autotrophic hydrogen bacteria are distinguished on the basis of their hydrogen-oxidizing enzyme system (Hox). The major group, represented by Paracoccus denitrificans and Pseudomonas facilis, contains a membrane-bound, electron transport-coupled protein. Species of Nocardia are characterized by the possession of a cytoplasmic NAD-dependent hydrogenase. Both enzymes are present in strains of Alcaligenes. All hydrogenases from lithoautotrophs are H2-consuming nickel-iron-sulfur proteins. Despite these common characteristics, hydrogenases differ in catalytic and molecular properties, in particular in the regulation of enzyme synthesis. Hydrogenase formation is either inducible by H2 (e.g. P. denitrificans strain F1, Alcaligenes hydrogenophilus) or subject to derepression in response to the supply of reductant, temperature, and oxygen (e.g. Alcaligenes eutrophus). The only plasmid-encoded Hox function has been conclusively identified in species of Alcaligenes. Structural and regulatory hox genes reside on megaplasmids, ranging in size between 400 and 500 kilobase pairs (kb). Most of the plasmids are self-transmissible by conjugation. Hox genes of A. eutrophus H16 have been localized by plasmid curing, genetic transfer, molecular cloning and analysis of plasmid deletions and insertions. They seem to be clustered in a DNA sequence of approximately 50 kb, representing several transcriptional units. In addition, a chromosomally encoded regulatory function is required for the expression of plasmid-linked hox genes. Plasmid pHGl of A. eutrophus H16 has been transferred to the non-lithoautotrophic soil bacterium JMP222. Both hydrogenases are expressed in the new host. The current state of hydrogenase genetics in Alcaligenes is discussed in reference to hydrogenase systems of other lithoautotrophic bacteria.

Organization of genes necessary for growth of the hydrogen-methanol autotroph Xanthobacter sp. strain H4-14 on hydrogen and carbon dioxide

Mutants unable to grow on H2 and CO2 were isolated in the hydrogen-methanol autotroph Xanthobacter sp. strain H4-14 and complemented with a clone bank constructed in a broad-host-range cosmid vector. The mutants fell into two classes. Class I mutants (Cfx-) cannot grow on hydrogen or methanol and are deficient in one or more of the key enzymes of the Calvin Cycle. Class II mutants (Hox-) can grow on methanol but not on hydrogen and lack hydrogenase activity. Restriction maps of the complementing clones show that each class is not linked to the other. Subcloning and Tn5 mutagenesis have localized the regions of DNA complementing these mutants. The region complementing a class I mutant which is deficient in ribulosebisphosphate carboxylase activity is approximately 3.2 kilobase pairs in size. Expression of this enzyme activity from cloned DNA gave evidence for the orientation of an operon containing the structural genes for this enzyme. The region complementing most of the class II mutants is 3 to 4.5 kilobase pairs in size.

Isolation of genes (nif/hup cosmids) involved in hydrogenase and nitrogenase activities in Rhizobium japonicum

Recombinant cosmids containing a Rhizobium japonicum gene involved in both hydrogenase (Hup) and nitrogenase (Nif) activities were isolated. An R. japonicum gene bank utilizing broad-host-range cosmid pLAFR1 was conjugated into Hup- Nif- R. japonicum strain SR139. Transconjugants containing the nif/hup cosmid were identified by their resistance to tetracycline (Tcr) and ability to grow chemoautotrophically (Aut+) with hydrogen. All Tcr Aut+ transconjugants possessed high levels of H2 uptake activity, as determined amperometrically. Moreover, all Hup+ transconjugants tested possessed the ability to reduce acetylene (Nif+) in soybean nodules. Cosmid DNAs from 19 Hup+ transconjugants were transferred to Escherichia coli by transformation. When the cosmids were restricted with EcoRI, 15 of the 19 cosmids had a restriction pattern with 13.2-, 4.0-, 3.0-, and 2.5-kilobase DNA fragments. Six E. coli transformants containing the nif/hup cosmids were conjugated with strain SR139. All strain SR139 transconjugants were Hup+ Nif+. Moreover, one nif/hup cosmid was transferred to 15 other R. japonicum Hup- mutants. Hup+ transconjugants of six of the Hup- mutants appeared at a frequency of 1.0, whereas the transconjugants of the other nine mutants remained Hup-. These results indicate that the nif/hup gene cosmids contain a gene involved in both nitrogenase and hydrogenase activities and at least one and perhaps other hup genes which are exclusively involved in H2 uptake activity.