A new family of transcriptional regulators of tungstoenzymes and molybdate/tungstate transport

Bacterial genes for molybdenum-containing and tungsten-containing enzymes are often differentially regulated depending on the metal availability in the environment. Here, we describe a new family of transcription factors with an unusual DNA-binding domain related to excisionases of bacteriophages. These transcription factors are associated with genes for various molybdate and tungstate-specific transporting systems as well as molybdo/tungsto-enzymes in a wide range of bacterial genomes. We used a combination of computational and experimental techniques to study a member of the TF family, named TaoR (for tungsten-containing aldehyde oxidoreductase regulator). In Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, TaoR activates expression of aldehyde oxidoreductase aor and represses tungsten-specific ABC-type transporter tupABC genes under tungsten-replete conditions. TaoR binding sites at aor promoter were identified by electrophoretic mobility shift assay and DNase I footprinting. We also reconstructed TaoR regulons in 45 Deltaproteobacteria by comparative genomics approach and predicted target genes for TaoR family members in other Proteobacteria and Firmicutes.

Genetic transfer in Desulfovibrio desulfuricans

An apparently defective bacteriophage capable of mediating transduction has been identified in culture filtrates of Desulfovibrio desulfuricans (American Type Culture Collection 27774). Phage-mediated intraspecies transfer of antibiotic resistance markers occurs with a frequency of 10(-5) to 10(-6) per recipient cell. The vector contains linear fragments of double-stranded DNA of about 13.5 kilobase pairs, which appear to be random pieces of bacterial DNA. As yet, neither induction nor plaque formation has been observed. To our knowledge, a system of genetic exchange has not been described before for a member of the sulfate-reducing bacteria.

Using population mixtures to optimize the utility of genomic databases: linkage disequilibrium and association study design in India

When performing association studies in populations that have not been the focus of large-scale investigations of haplotype variation, it is often helpful to rely on genomic databases in other populations for study design and analysis - such as in the selection of tag SNPs and in the imputation of missing genotypes. One way of improving the use of these databases is to rely on a mixture of database samples that is similar to the population of interest, rather than using the single most similar database sample. We demonstrate the effectiveness of the mixture approach in the application of African, European, and East Asian HapMap samples for tag SNP selection in populations from India, a genetically intermediate region underrepresented in genomic studies of haplotype variation.

Temporal transcriptomic analysis as Desulfovibrio vulgaris Hildenborough transitions into stationary phase during electron donor depletion

Desulfovibrio vulgaris was cultivated in a defined medium, and biomass was sampled for approximately 70 h to characterize the shifts in gene expression as cells transitioned from the exponential to the stationary phase during electron donor depletion. In addition to temporal transcriptomics, total protein, carbohydrate, lactate, acetate, and sulfate levels were measured. The microarray data were examined for statistically significant expression changes, hierarchical cluster analysis, and promoter element prediction and were validated by quantitative PCR. As the cells transitioned from the exponential phase to the stationary phase, a majority of the down-expressed genes were involved in translation and transcription, and this trend continued at the remaining times. There were general increases in relative expression for intracellular trafficking and secretion, ion transport, and coenzyme metabolism as the cells entered the stationary phase. As expected, the DNA replication machinery was down-expressed, and the expression of genes involved in DNA repair increased during the stationary phase. Genes involved in amino acid acquisition, carbohydrate metabolism, energy production, and cell envelope biogenesis did not exhibit uniform transcriptional responses. Interestingly, most phage-related genes were up-expressed at the onset of the stationary phase. This result suggested that nutrient depletion may affect community dynamics and DNA transfer mechanisms of sulfate-reducing bacteria via the phage cycle. The putative feoAB system (in addition to other presumptive iron metabolism genes) was significantly up-expressed, and this suggested the possible importance of Fe2+ acquisition under metal-reducing conditions. The expression of a large subset of carbohydrate-related genes was altered, and the total cellular carbohydrate levels declined during the growth phase transition. Interestingly, the D. vulgaris genome does not contain a putative rpoS gene, a common attribute of the delta-Proteobacteria genomes sequenced to date, and the transcription profiles of other putative rpo genes were not significantly altered. Our results indicated that in addition to expected changes (e.g., energy conversion, protein turnover, translation, transcription, and DNA replication and repair), genes related to phage, stress response, carbohydrate flux, the outer envelope, and iron homeostasis played important roles as D. vulgaris cells experienced electron donor depletion.

Desulfovibrio desulfuricans G20 Tetraheme Cytochrome Structure at 1.5Å and Cytochrome Interaction with Metal Complexes

The structure of the type I tetraheme cytochrome c(3) from Desulfovibrio desulfuricans G20 was determined to 1.5 Angstrom by X-ray crystallography. In addition to the oxidized form, the structure of the molybdate-bound form of the protein was determined from oxidized crystals soaked in sodium molybdate. Only small structural shifts were obtained with metal binding, consistent with the remarkable structural stability of this protein. In vitro experiments with pure cytochrome showed that molybdate could oxidize the reduced cytochrome, although not as rapidly as U(VI) present as uranyl acetate. Alterations in the overall conformation and thermostability of the metal-oxidized protein were investigated by circular dichroism studies. Again, only small changes in protein structure were documented. The location of the molybdate ion near heme IV in the crystal structure suggested heme IV as the site of electron exit from the reduced cytochrome and implicated Lys14 and Lys56 in binding. Analysis of structurally conserved water molecules in type I cytochrome c(3) crystal structures identified interactions predicted to be important for protein stability and possibly for intramolecular electron transfer among heme molecules.

Global analysis of heat shock response in Desulfovibrio vulgaris Hildenborough

Desulfovibrio vulgaris Hildenborough belongs to a class of sulfate-reducing bacteria (SRB) and is found ubiquitously in nature. Given the importance of SRB-mediated reduction for bioremediation of metal ion contaminants, ongoing research on D. vulgaris has been in the direction of elucidating regulatory mechanisms for this organism under a variety of stress conditions. This work presents a global view of this organism's response to elevated growth temperature using whole-cell transcriptomics and proteomics tools. Transcriptional response (1.7-fold change or greater; Z >/= 1.5) ranged from 1,135 genes at 15 min to 1,463 genes at 120 min for a temperature up-shift of 13 degrees C from a growth temperature of 37 degrees C for this organism and suggested both direct and indirect modes of heat sensing. Clusters of orthologous group categories that were significantly affected included posttranslational modifications; protein turnover and chaperones (up-regulated); energy production and conversion (down-regulated), nucleotide transport, metabolism (down-regulated), and translation; ribosomal structure; and biogenesis (down-regulated). Analysis of the genome sequence revealed the presence of features of both negative and positive regulation which included the CIRCE element and promoter sequences corresponding to the alternate sigma factors sigma(32) and sigma(54). While mechanisms of heat shock control for some genes appeared to coincide with those established for Escherichia coli and Bacillus subtilis, the presence of unique control schemes for several other genes was also evident. Analysis of protein expression levels using differential in-gel electrophoresis suggested good agreement with transcriptional profiles of several heat shock proteins, including DnaK (DVU0811), HtpG (DVU2643), HtrA (DVU1468), and AhpC (DVU2247). The proteomics study also suggested the possibility of posttranslational modifications in the chaperones DnaK, AhpC, GroES (DVU1977), and GroEL (DVU1976) and also several periplasmic ABC transporters.

Insights from linked single nucleotide polymorphisms: what we can learn from linkage disequilibrium

New methods for analyzing sequence polymorphism data have uncovered some striking patterns of linkage disequilibrium in both humans and fruitflies. These methods have revealed examples where the observed amount of linkage disequilibrium is either much more or much less than expected, and have led to advances in our understanding of the forces that affect naturally occurring genetic variation. With the recent explosion of sequence polymorphism data, the prospects for further progress from these methods are quite promising.

Gene conversion and different population histories may explain the contrast between polymorphism and linkage disequilibrium levels

To characterize linkage disequilibrium (LD) levels in human populations, we have analyzed 10 independent noncoding segments in three population samples from the major ethnic groups--that is, Africans, Asians, and Europeans. Descriptive statistics show that LD decays much faster in the African samples than in the non-African ones. With the assumption of an equilibrium model, we estimated the population crossing-over parameter (4N(e)r(bp), where N(e) is the effective population size and r(bp) is the crossing-over rate per generation between adjacent base pairs) in the presence of gene conversion. In the African sample, LD and polymorphism levels lead to similar estimates of effective population size, as expected under an equilibrium model. Conversely, in both non-African samples, LD levels suggest a smaller effective population size than that implied by polymorphism levels. This observation is paralleled by significant departures from an equilibrium model in the spectrum of allele frequencies of the non-African samples. Besides ruling out the possibility that non-African populations are at equilibrium, these results suggest different demographic history (temporal and spatial) of these groups. Interestingly, the African sample fits the expectations of an equilibrium model based on polymorphism and divergence levels and on frequency spectrum. For this sample, the estimated ratio of gene conversion to crossing-over rates is 7.3 for a mean tract length of 500 bp, suggesting that gene conversion may be more frequent than previously thought. These findings imply that disease-association studies will require a much denser map of polymorphic sites in African than in non-African populations.

Why is there so little intragenic linkage disequilibrium in humans ?

The efficient design of association mapping studies relies on a knowledge of the rate of decay of linkage disequilibrium with distance. This rate depends on the population recombination rate, C. An estimate of C for humans is usually obtained from a comparison of physical and genetic maps, assuming an effective population size of approximately 104. We demonstrate that under both a constant population size model and a model of long-term exponential growth, there is evidence for more recombination in polymorphism data than is expected from this estimate. An important contribution of gene conversion to meiotic recombination helps to explain our observation, but does not appear to be sufficient. The occurrence of multiple hits at CpG sites and the presence of population structure are not explanations.

Recombination and the frequency spectrum in Drosophila melanogaster and Drosophila simulans

Most "tests of neutrality" assess whether particular data sets depart from the predictions of a standard neutral model with no recombination. For Drosophila, where nuclear polymorphism data routinely show evidence of genetic exchange, the assumption of no recombination is often unrealistic. In addition, while conservative, this assumption is made at the cost of a great loss in power. Perhaps as a result, tests of the frequency spectrum based on zero recombination suggest an adequate fit of Drosophila polymorphism data to the predictions of the standard neutral model. Here, we analyze the frequency spectrum of a large number of loci in Drosophila melanogaster and D. simulans using two summary statistics. We use an estimate of the population recombination rate based on a laboratory estimate of the rate of crossing over per physical length and an estimate of the species' effective population size. In contrast to previous studies, we find that roughly half of the loci depart from the predictions of the standard neutral model. The extent of the departure depends on the exact recombination rate, but the global pattern that emerges is robust. Interestingly, these departures from neutral expectations are not unidirectional. The large variance in outcomes may be due to a complex demographic history and inconsistent sampling, or to the pervasive action of natural selection.

When did the human population size start increasing?

We analyze the frequency spectra of all available human nuclear sequence data sets by using a model of constant population size followed by exponential growth. Parameters of growth (more extreme than or) comparable to what has been suggested from mtDNA data can be rejected for 6 out of the 10 largest data sets. When the data are separated into African and non-African samples, a constant size no-growth model can be rejected for 4 out of 8 non-African samples. Long-term growth (i.e., starting 50-100 kya) can be rejected for 2 out of 8 African samples and 5 out of 8 non-African ones. Under more complex demographic models, including a bottleneck or population subdivision, more of the data are compatible with long-term growth. One problem with the data used here is that a subset of loci may reflect the action of natural selection as well as of demography. It remains possible that the correct demographic model is one of constant population size followed by long-term growth but that at several loci the demographic signature has been obscured by balancing or diversifying selection. However, it is not clear that the data at these loci are consistent with a simple model of balancing selection; more complicated selective alternatives cannot be tested unless they are made explicit. An alternative explanation is that population size growth is more recent (e.g., upper Paleolithic) and that some of the loci have experienced recent directional selection. Given the available data, the latter hypothesis seems more likely.

Detecting ancient admixture in humans using sequence polymorphism data

A debate of long-standing interest in human evolution centers around whether archaic human populations (such as the Neanderthals) have contributed to the modern gene pool. A model of ancient population structure with recent mixing is introduced, and it is determined how much information (i.e., sequence data from how many unlinked nuclear loci) would be necessary to distinguish between different demographic scenarios. It is found that approximately 50-100 loci are necessary if plausible parameter estimates are used. There are not enough data available at the present to support either the "single origin" or the "multiregional" model of modern human evolution. However, this information should be available in a few years.

Cytochrome c(3) mutants of Desulfovibrio desulfuricans

To explore the physiological role of tetraheme cytochrome c(3) in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20, the gene encoding the preapoprotein was cloned, sequenced, and mutated by plasmid insertion. The physical analysis of the DNA from the strain carrying the integrated plasmid showed that the insertion was successful. The growth rate of the mutant on lactate with sulfate was comparable to that of the wild type; however, mutant cultures did not achieve the same cell densities. Pyruvate, the oxidation product of lactate, served as a poor electron source for the mutant. Unexpectedly, the mutant was able to grow on hydrogen-sulfate medium. These data support a role for tetraheme cytochrome c(3) in the electron transport pathway from pyruvate to sulfate or sulfite in D. desulfuricans G20.

A comparison of estimators of the population recombination rate

Three new estimators of the population recombination rate C = 4Nr are introduced. These estimators summarize the data using the number of distinct haplotypes and the estimated minimum number of recombination events, then calculate the value of C that maximizes the likelihood of obtaining the summarized data. They are compared with a number of previously proposed estimators of the recombination rate. One of the newly proposed estimators is generally better than the others for the parameter values considered here, while the three programs that calculate maximum-likelihood estimates give conflicting results.

Unusual haplotype structure at the proximal breakpoint of In(2L)t in a natural population of Drosophila melanogaster

The existence of temporally stable frequency clines for In(2L)t in natural populations of Drosophila melanogaster suggests a role for selection in the maintenance of this polymorphism. We have collected nucleotide polymorphism data from the proximal breakpoint junction regions of In(2L)t to infer its evolutionary history. The finding of a novel LINE-like element near the In(2L)t breakpoint junction in sampled inverted chromosomes supports a transposable element-mediated origin for this inversion. An analysis of nucleotide variation in a Costa Rican population sample of standard and inverted chromosomes indicates a unique and relatively recent origin for In(2L)t. Additional In(2L)t alleles from three geographically diverse populations reveal no detectable geographic differentiation. Low levels of In(2L)t nucleotide polymorphism suggest a recent increase in the inversion's frequency in tropical populations. An unusual feature of our sample of standard alleles is a marked heterogeneity in levels of linkage disequilibrium among polymorphic sites across the breakpoint region. We introduce a test of neutral equilibrium haplotype structure that corrects both for multiple tests and for an arbitrarily chosen window size. It reveals that an approximately 1.4-kb region immediately spanning the breakpoint has fewer haplotypes than expected under the neutral model, given the expected level of recombination in this genomic region. Certain features of our data suggest that the unusual pattern in standard chromosomes is the product of selection rather than demography.

Genealogies and weak purifying selection

The assumption that selection alters the genealogical tree of a sample of alleles from a population relative to the neutral expectation underlies several "tests of neutrality." Two recent papers have studied the effect of purifying selection; their suggestive but incomplete results indicate that, in the single site case, the shape of a gene genealogy for a locus may differ only from the neutral expectation. We verify this finding for weak selection using the "ancestral selection graph." We consider a wider range of models, including both a four-allele single-site model and an infinite-sites model. Our results confirm the previous claim for the symmetric-mutation single site model. We emphasize, however, that a neutral-seeming genealogy is consistent with detectable effects of selection on the distribution of allele frequences within the sample. With selection operating, the information about a sample cannot be reduced to the genealogy. As a result, a distinction needs to be made between the selected sites themselves, for which the genealogy offers insufficient information, and linked neutral variation. This distinction seems to have been overlooked in previous papers, yet it has significant implications for the interpretation of data on DNA sequence variation. In particular, it predicts that under purifying selection, the frequency spectrum of neutral mutations will not reflect the skew toward rare polymorphisms at replacement sites even if there is no recombination between them. We caution, however, that the effect of weak selection on the genealogy is specific to the model; a (more realistic) model of multiple linked sites could lead to a more distorted genealogy than is observed for a single site.

New shuttle vectors for the introduction of cloned DNA in Desulfovibrio

The pBG1 replicon from the cryptic plasmid of Desulfovibrio desulfuricans G100A was inserted into pTZ18U derivatives to generate a new family of shuttle vectors. These plasmids are stable both in Escherichia coli and in Desulfovibrio, they present a large number of unique restriction sites, and colonies of recombinant clones can be identified by blue/white screening in E. coli. The pBMC, pBMK, and pBMS series carry the cat, npt, or strAB genes as selectable markers, respectively. The pBMC6, pBMK6, and pBMS6 plasmids can be introduced both in D. desulfuricans and in Desulfovibrio fructosovorans by electrotransformation, and the pBMC7, pBMK7, and pBMS7 plasmids contain additional mobilization functions which makes them suitable for conjugation.

A single mutation in the heme 4 environment of Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000) greatly affects the molecule reactivity

The gene encoding Desulfovibrio desulfuricans Norway cytochrome c3 (Mr 26,000), a dimeric octaheme cytochrome belonging to the polyheme cytochrome c3 superfamily, has been cloned and successfully expressed in another sulfate reducing bacteria, D. desulfuricans G201. The gene, named cycD, is monocistronic and encodes a cytochrome precursor of 135 amino acids with an extension at the NH2 terminus of 24 amino acids. This extension acts as a signal sequence which allows export across the cytoplasmic membrane into the periplasmic space. Tyrosine 73, which is in a close contact with the histidine sixth axial ligand to the heme 4 iron atom, has been replaced by a glutamate residue using site-directed mutagenesis. The cytochrome mutant when expressed in D. desulfuricans G201, is correctly folded and matured. A global increase of the oxidoreduction potentials of about 50 mV is measured for the Y73E cytochrome. The mutation also has a strong influence on the interaction of the cytochrome with its redox partner, the hydrogenase. This suggests, like the tetraheme cytochrome c3 (Mr 13, 000), heme 4 is the interactive heme in the cytochrome-hydrogenase complex and that alteration of the heme 4 environment can greatly affect the electron transfer reaction with its redox partner.

Transposon mutagenesis in Desulfovibrio desulfuricans: development of a random mutagenesis tool from Tn7

The transposons Tn5, Tn7, Tn9, and Tn10 or their derivatives have been examined for transposition in the sulfate-reducing bacterium Desulfovibrio desulfuricans G20. Tn7 inserted with a frequency of 10(-4) to 10(-3) into a unique attachment site that shows strong homology with those sites identified in other gram-negative bacteria. Inactivation of the tnsD gene in Tn7, encoding the function directing insertion into the unique site, yielded a derivative that transposed essentially randomly with a frequency of ca. 10(-6) per donor. Derivatives of Tn5, but not wild-type Tn5, were also found to undergo random transposition at a similar frequency. No evidence was obtained for transposition of Tn9 or Tn10.

Regulation of the glnBA operon of Rhodobacter capsulatus

In a recent report identifying the promoters of the Rhodobacter capsulatus glnBA operon, it was suggested that an internal promoter upstream of the glnA gene probably resulted in different levels of glnBA and glnA transcripts (D. Foster-Hartnett and R. G. Kranz, J. Bacteriol. 176:5171-5176, 1994). Therefore, to investigate the regulation, we constructed and examined the expression of a number of translational fusions in R. capsulatus glnBA. The results support a role for posttranscriptional regulation.

DcrA, a c-type heme-containing methyl-accepting protein from Desulfovibrio vulgaris Hildenborough, senses the oxygen concentration or redox potential of the environment

The amino acid sequence of DcrA from Desulfovibrio vulgaris Hildenborough, a strictly anaerobic, sulfate-reducing bacterium, indicated homology with the methyl-accepting chemotaxis proteins from enteric bacteria (A. Dolla, R. Fu, M. J. Brumlik, and G. Voordouw, J. Bacteriol. 174:1726-1733, 1992). The homology is restricted to the cytoplasmic C-terminal signaling domain. The periplasmic N-terminal sensor domain was found to contain a unique sequence, CHHCH, corresponding to a consensus c-type heme binding site. A pretreated, DcrA-specific polyclonal antiserum, generated against DcrA protein overproduced in Escherichia coli, was used for immunoprecipitation of 35S-labeled DcrA from D. vulgaris and Desulfovibrio desulfuricans G200(pJRFR2), a transconjugant that overexpresses functional DcrA. Labeling of the latter with the heme precursor 5-amino-[4-14C]levulinic acid, followed by immunoprecipitation, sodium dodecyl sulfate-polyacrylamide gel electrophoresis, and fluorography, confirmed the presence of c-type heme, while labeling with L-[methyl-3H]methionine in the absence of protein synthesis confirmed that DcrA is a methyl-accepting protein. The base liability of the incorporated radioactivity indicated methyl ester formation like that occurring in the methyl-accepting chemotaxis proteins of enteric bacteria. L-[methyl-3H]methionine labeling of D. desulfuricans G200(pJRFR2) under different conditions indicated that methyl labeling of DcrA decreased upon addition of oxygen and increased upon subsequent addition of the reducing agent dithionite. These results indicate that DcrA may serve as a sensor of oxygen concentration and/or redox potential.

Characterization of a small plasmid from Desulfovibrio desulfuricans and its use for shuttle vector construction

A 2.3-kb plasmid present in about 20 copies per genome was identified in extracts of Desulfovibrio desulfuricans G100A and designated pBG1. It appears to be unable to replicate in Escherichia coli. Although composite plasmids of pBG1 inserted into pTZ18U are stable in E. coli, few if any pBG1-specific transcripts are detectable. The plasmid sequence reveals several features typical of the origin of replication of non-ColE1 enterobacterial plasmids as well as several potential open reading frames. This small replicon has been shown to support the replication of recombinant plasmids in D. desulfuricans G100A and Desulfovibrio fructosovorans. A conjugable shuttle vector has been constructed.

Analysis of the periplasmic [NiFe] hydrogenase transcription unit from Desulfovibrio fructosovorans

Two genes, hynA and hynB, encode the two subunits of the periplasmic [NiFe] hydrogenase in Desulfovibrio fructosovorans. Sequencing downstream from hynB revealed a third open reading frame (hynC) that has the potential for encoding a polypeptide showing 21% identity with the HyaD, HoxM, and HupD proteins, belonging to putative operons encoding Escherichia coli hydrogenase 1, Alcaligenes eutrophus H16 membrane-bound hydrogenase, and Rhizobium leguminosarum uptake hydrogenase, respectively. Northern (RNA) blotting with a structural gene probe revealed the existence of a major transcript of 2.9 kb, which is the appropriate length to contain the two hydrogenase subunits only. In addition, two minor 4.4- and 5.8-kb transcripts that could contain hynABC and additional genes were found. The 5' end of the most abundant [NiFe] hydrogenase mRNA was found 170 bp upstream from the translational start site of hynA. The sequences at -10 and -35 relative to the transcriptional starting site showed 55% homology with the consensus sequences of the Escherichia coli sigma 70-type promoter. The cloning of that particular region as a promoter to control transcription of the lacZ gene in E. coli DH5 alpha or the hynA, hynB, and hynC genes in D. fructosovorans MR400 led to strong expression in both systems.

Site-directed mutagenesis of tetraheme cytochrome c3. Modification of oxidoreduction potentials after heme axial ligand replacement

The nature of the axial ligands of a heme group is an important factor in maintaining the oxidation-reduction potential of a c-type cytochrome. Cytochrome c3 from Desulfovibrio vulgaris Hildenborough contains four bis-histidinyl coordinated hemes with low oxidation-reduction potentials. Site-directed mutagenesis was used to generate a mutant in which histidine 70, the sixth axial ligand of heme 4, has been replaced by a methionine. The mutant protein was expressed in Desulfovibrio desulfuricans G200 at a level similar to the wild type cytochrome. A model for the three-dimensional structure of D. vulgaris Hildenborough cytochrome c3 was generated on the basis of the crystal structure of D. vulgaris Miyazaki cytochrome c3 in order to investigate the effects of the H70M mutation. The model, together with NMR data, suggested that methionine 70 has effectively replaced histidine 70 as the sixth axial ligand of heme 4 without significant alteration of the structure. A large increase of at least 200 mV of one of the four oxidation-reduction potentials was observed by electrochemistry and is interpreted in terms of structure/potential relationships.

Plasmid transfer by conjugation in Desulfovibrio desulfuricans

Conjugational transfer of several IncQ plasmids from Escherichia coli to the strictly anaerobic, sulfate-reducing bacterium Desulfovibrio desulfuricans strain G100A was demonstrated. Plasmid DNA from exconjugants was visualized on agarose gels and was used to transform E. coli to the appropriate antibiotic resistances. Neither transfer of IncW and IncP plasmids to strain G100A, nor transfer of any plasmid to D. desulfuricans strain ATCC 27774 was observed. Conjugation of suicide plasmids containing either Tn5 or Tn9 into D. desulfuricans did not result in detectable transposition. Optimal conditions for conjugational transfer and antibiotic resistance levels of strain G100A were examined.

Physiological functions of hydroperoxidases in Rhodobacter capsulatus

Rhodobacter capsulatus J1 has two hydroperoxidases: a catalase-peroxidase and a peroxidase. A mutant strain, AH18, that had no catalase-peroxidase was isolated. The growth rate under aerobic and photosynthetic conditions, respiration, superoxide dismutase and peroxidase activities, and pigment content of the mutant were similar to those of the wild type. AH18 was more susceptible to killing and to inhibition of nitrogenase by H2O2 but not by molecular oxygen. The incidences of spontaneous mutations were similar in both strains. Viable counts in aerobic but not anaerobic cultures of AH18 started to decline as soon as the cultures reached the stationary phase, and the rate of cell death was much higher in AH18 than in the wild type. It is inferred that the peroxidase provides protection against H2O2 in log-phase cells and that the catalase-peroxidase provides protection under the oxidative conditions that prevail in aging cultures. This protective function might be related to the dual activity of the latter as a catalase and a peroxidase or to its capacity to oxidize NADH, NADPH, and cytochrome c.

Clustering of genes necessary for hydrogen oxidation in Rhodobacter capsulatus

Three cosmids previously shown to contain information necessary for the expression of uptake of hydrogenase in Rhodobacter capsulatus were found to be present in a cluster on the chromosome. Earlier genetic experiments suggested the presence of at least six genes essential for hydrogenase activity that are now shown to be in a region of approximately 18 kb that includes the structural genes for the enzyme. A potential response regulator gene was sequenced as a part of the hup gene region.

Cloning, sequencing, and expression of the gene encoding the high-molecular-weight cytochrome c from Desulfovibrio vulgaris Hildenborough

By using a synthetic deoxyoligonucleotide probe designed to recognize the structural gene for cytochrome cc3 from Desulfovibrio vulgaris Hildenborough, a 3.7-kb XhoI genomic DNA fragment containing the cc3 gene was isolated. The gene encodes a precursor polypeptide of 58.9 kDa, with an NH2-terminal signal sequence of 31 residues. The mature polypeptide (55.7 kDa) has 16 heme binding sites of the form C-X-X-C-H. Covalent binding of heme to these 16 sites gives a holoprotein of 65.5 kDa with properties similar to those of the high-molecular-weight cytochrome c (Hmc) isolated from the same strain by Higuchi et al. (Y. Higuchi, K. Inaka, N. Yasuoka, and T. Yagi, Biochim. Biophys. Acta 911:341-348, 1987). Since the data indicate that cytochrome cc3 and Hmc are the same protein, the gene has been named hmc. The Hmc polypeptide contains 31 histidinyl residues, 16 of which are integral to heme binding sites. Thus, only 15 of the 16 hemes can have bis-histidinyl coordination. A comparison of the arrangement of heme binding sites and coordinated histidines in the amino acid sequences of cytochrome c3 and Hmc from D. vulgaris Hildenborough suggests that the latter contains three cytochrome c3-like domains. Cloning of the D. vulgaris Hildenborough hmc gene into the broad-host-range vector pJRD215 and subsequent conjugational transfer of the recombinant plasmid into D. desulfuricans G200 led to expression of a periplasmic Hmc gene product with covalently bound hemes.

Functional expression of Desulfovibrio vulgaris Hildenborough cytochrome c3 in Desulfovibrio desulfuricans G200 after conjugational gene transfer from Escherichia coli

Plasmid pJRDC800-1, containing the cyc gene encoding cytochrome c3 from Desulfovibrio vulgaris subsp. vulgaris Hildenborough, was transferred by conjugation from Escherichia coli DH5 alpha to Desulfovibrio desulfuricans G200. The G200 strain produced an acidic cytochrome c3 (pI = 5.8), which could be readily separated from the Hildenborough cytochrome c3 (pI = 10.5). The latter was indistinguishable from cytochrome c3 produced by D. vulgaris subsp. vulgaris Hildenborough with respect to a number of chemical and physical criteria.

Purification and properties of acetyl-CoA synthetase from Bradyrhizobium japonicum bacteroids

Acetyl-CoA synthetase was purified 800-fold from Bradyrhizobium japonicum bacteroids. A specific activity of 16 mumol/min per mg of protein was achieved, with a 30-40% yield. The purification scheme consisted of only three consecutive chromatography steps. The enzyme has a native Mr of 150,000, estimated by gel-permeation chromatography, and a subunit Mr of 72,000, determined by SDS/polyacrylamide-gel electrophoresis. The optimum pH and temperature are 8.5 and 50 degrees C respectively. The Km values for acetate, CoA and ATP were 146, 202 and 275 microM respectively. The reaction was specific for acetate, as propionate and oleate were used very poorly. Likewise, the enzyme used only ATP, ADP or dATP; AMP, GTP, XTP and UTP could not replace ATP. Acetyl-CoA synthetase showed a broad specificity for metals; MnCl2 could replace MgCl2. In addition, CaCl2 and CoCl2 were approx. 50% as effective as MgCl2, but FeCl3, NiCl2 or ZnCl2 could not effectively substitute for MgCl2. The enzyme may be regulated by NADP+ and pyruvate; no effect was seen of amino acids, glucose catabolites, reduced nicotinamide nucleotides or acetyl-CoA. Inhibition was seen with AMP, PPi, FMN and pyridoxal phosphate, with Ki values of 720, 222, 397 and 1050 microM respectively.

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.

Acetate-Activating Enzymes of Bradyrhizobium japonicum Bacteroids

Acetyl coenzyme A (acetyl-CoA) synthetase and acetate kinase were localized within the soluble portion of Bradyrhizobium japonicum bacteroids, and no appreciable activity was found elsewhere in the nodule. The presence of each acetate-activating enzyme was confirmed by separation of the two enzyme activities on a hydroxylapatite column, by substrate dependence of each enzyme in both the forward and reverse directions, by substrate specificity, by inhibition patterns, and also by identification of the reaction products by C 18 reverse-phase high-pressure liquid chromatography. Phosphotransacetylase activity, found in the soluble portion of the bacteroid, was dependent on the presence of potassium and was inhibited by added sodium. The greatest acetyl-CoA hydrolase activity was found in the root nodule cytosol, although appreciable activity also was found within the bacteroids. The combined specific activities of acetyl-CoA synthetase and acetate kinase-phosphotransacetylase were approximate to that of the pyruvate dehydrogenase complex, thus providing B. japonicum with sufficient capacity to generate acetyl-CoA.

Properties of a hydrogen-inhibited mutant of Desulfovibrio desulfuricans ATCC 27774

A mutant of Desulfovibrio desulfuricans ATCC 27774 has been obtained which is incapable of sulfate respiration with molecular hydrogen but which grows normally on lactate plus sulfate under argon. Growth characteristics of the mutant suggest that the defect is involved in electron transfer to sulfate or nitrate but not thiosulfate.

Isolation of a recombination-deficient mutant of Rhodopseudomonas capsulata

To facilitate genetic analysis in the purple photosynthetic bacterium Rhodopseudomonas capsulata, a recombination-deficient derivative was sought. A UV irradiation-sensitive mutant (FG106F) was isolated after mutagenesis, and two procedures were used to determine the recombinational capacity of the mutant. First, recombinants were not detected after transduction of this derivative by the phage-like vector gene transfer agent. Second, an R-prime plasmid containing appropriately marked genes for photosynthesis was introduced by conjugation, and again no recombinants were observed. Additional phenotypes displayed by the mutant that are characteristic of a defect in recombination were an increased sensitivity to DNA-damaging antibiotics and a tendency to filament.

Spontaneous Nif- mutants of Rhodopseudomonas capsulata

Revertible, spontaneous Nif- mutants of Rhodopseudomonas capsulata have been shown to accumulate in cultures growing photosynthetically with an amino acid as the nitrogen source such that H2 is maximally produced. The majority of such strains carry mutations which are clustered in a short region of the chromosome, probably representing one or two genes. Because this cluster includes temperature-sensitive mutations, it is also likely that it identifies the structural gene of a polypeptide. The phenotypic characterization of these spontaneous mutants showed (i) an inability to grow with N2 as the nitrogen source, no measurable nitrogenase activity, a reduction or absence of the three polypeptides of the MoFe and Fe proteins of the nitrogenase complex, a faster growth rate on glutamate as the nitrogen source under saturating light, and frequently a small increase in glutamine synthetase activity relative to that of the wild type when grown with glutamate as the nitrogen source. Alterations in other ammonium-assimilatory enzyme activities were not observed. Taken together, these properties suggest that the mutations have affected a regulatory protein necessary for nitrogen fixation.

Mapping of Rhodopseudomonas capsulata nif genes

The endogenous gene transfer system of Rhodopseudomonas capsulata was used to analyze mutations which block the ability to use molecular nitrogen as the sole nitrogen source (nif). With this fine-structure mapping tool, linkage of nif mutations could be reliably established if separated by 2,700 base pairs or less. Eleven independent mutations were analyzed, and five linkage groups were found. The overall chromosomal arrangement of these groups awaits conjugational or physical analysis. A candidate for the inactive subunit of R. capsulata Fe protein was located in gels at a position of about 38,000 molecular weight, 5,000 more than that of the presumed active subunit.

Photoproduction of H 2 from Cellulose by an Anaerobic Bacterial Coculture

Cellulomonas sp. strain ATCC 21399 is a facultatively anaerobic, cellulose-degrading microorganism that does not evolve hydrogen but produces organic acids during cellulose fermentation. Rhodopseudomonas capsulata cannot utilize cellulose, but grows photoheterotrophically under anaerobic conditions on organic acids or sugars. This report describes an anaerobic coculture of the Cellulomonas strain with wild-type R. capsulata or a mutant strain lacking uptake hydrogenase, which photoevolves molecular hydrogen by the nitrogenase system of R. capsulata with cellulose as the sole carbon source. In coculture, the hydrogenase-negative mutant produced 4.6 to 6.2 mol of H 2 per mol of glucose equivalent, compared with 1.2 to 4.3 mol for the wild type.

Expression of the activating enzyme and Fe protein of nitrogenase from Rhodospirillum rubrum

Activating enzyme (AE) is responsible for the in vitro activation of inactive Fe protein of nitrogenase from Rhodospirillum rubrum cells cultured anaerobically with glutamate as the N source. The expression of Fe protein and AE was examined in R. rubrum cultured photosynthetically or aerobically on media containing malate as the carbon source. One of the following N sources was used in each culture: glutamate, glutamine, limiting ammonia, high ammonia, glutamate plus histidine, and high ammonia plus histidine. Chromatophores from every culture exhibited AE activity; activity was highest in glutamate-grown cells. Fe protein was observed by rocket immunoelectrophoresis in cultures with nitrogenase activity. Several Nif-, Gln-, and His- mutants of R. rubrum were assayed for AE activity, nitrogenase activity, and Fe protein. Every mutant expressed AE activity, and Fe protein was observed in those cultures with nitrogenase activity. AE from every preparation was O2 labile, and each O2-denatured AE preparation inhibited activation by active AE.

Dark Anaerobic Dinitrogen Fixation by a Photosynthetic Microorganism

Photosynthetic purple bacteria can grow with dinitrogen gas as the sole nitrogen source under anaerobic conditions with light as the energy source. The bacterium Rhodopseudomonas capsulata can fix nitrogen in darkness with alternative energy conversion systems, namely, anaerobic sugar fermentation and aerobic respiration at low oxygen tension. Although growth on dinitrogen is optimal under photosynthetic conditions, the results show that reduction of dinitrogen is not obligatorily coupled to activity of the photosynthetic apparatus.

Derepression of nitrogenase activity in glutamine auxotrophs of Rhodopseudomonas capsulata

In contrast to wild-type cells, glutamine auxotrophs of the photosynthetic bacterium Rhodopseudomonas capsulata synthesize nitrogenase, produce H2 (catalyzed by nitrogenase), and continue to reduce dinitrogen to ammonia in the presence of exogenous NH4+. The glutamine synthetase activity of such mutants is less than 2% of that observed in the wild type. It appears that glutamine synthetase plays a significant role in regulation of nitrogenase synthesis in R. capsulata.

A pleiotropic mutant of Rhodopseudomonas capsulata defective in nitrogen metabolism

Wild type strains of Rhodopseudomonas capsulata typically can use N2, NH+4, or various nitrogenous organic compounds as N sources for photosynthetic growth. One class of mutants selected for inability to grow on N2 (Nif-) also shows simultaneous loss of capacity to obtain N from numerous organic substrates. When supplied at relatively high concentrations, ammonia can be used as the sole N source for growth of such strains. Enzymatic analysis of one mutant (W11) indicates that the pleiotropic effect on N nutrition is neither due to detectable alteration in the activities of nitrogenase or the initial enzymes responsible for bulk assimilation of ammonia (glutamine synthetase and glutamate synthase) nor to absence of systems required for catabolism of organic N sources. The phenotype of W11 (Nit-; defective in N metabolism) appears to result from loss of ability to grow using low concentrations of ammonia (supplied externally or generated in vivo).

Escherichia coli mutants deficient in guanine-xanthine phosphoribosyltransferase

We studied the purine phosphoribosyltransferases (PRTases) of Escherichia coli and were able to isolate a mutant that is defective in its ability to convert guanine and xanthine to their respective ribonucleotides. The affected gene (gpt) lies between metD and proA and is 78.6% co-transducible with proA. Both this point mutant and a strain with a pro-lac deletion contain less than 2% of wild-type xanthine PRTase activity, yet still contain about 30% of wild-type guanine PRTase activity. Thus, the gpt gene is only one of at least two genes responsible for guanine PRTase activity in E. coli.

Gene transfer agents, bacteriophages, and bacteriocins of Rhodopseudomonas capsulata

Thirty-three wild type strains of Rhodopseudomonas capsulata were examined for ability to engage in genetic recombination through mediation by "gene transfer agent" (GTA) particles. The genetic exchange assays were based on capacity of strains to produce or receive GTA required for restoration of photosynthetic growth competence to a non-photosynthetic "white" mutant or for acquisition of resistance to rifampicin. A majority of the strains could either produce or receive GTA, and it was demonstrated that the agent is species specific. Possible relations between GTA and bacteriophages or bacteriocins were investigated. Sixteen types of virulent phages active on Rps. capsulata were isolated and their host ranges determined. Tests for transduction by the phages gave uniformly negative results. The viruses showed strict species specificity, but there was no apparent correlation between capacity of the Rps. capsulata strains to donate or receive GTA and susceptibility to the phages. A comparable survey disclosed that most of the bacterial strains were sensitive to or capable of producing bacteriocins; the latter also appear to be unrelated to GTA activity. The collection of bacterial strains was also screened for detection of lysogenic properties. None of the isolates is a "true" lysogen, but phages were detected in cultures of two strains, which may be "phage carriers" or pseudolysogens.

Characterization of Rhodopseudomonas capsulata

Thirty-three strains of Rhodopseudomonas capsulata have been studied in order to develop a more comprehensive characterization of the species. On the basis of morphological, nutritional, physiological and other properties, the characteristics of an "ideal biotype" have been defined, which can be used to distinguish Rps. capsulata from similar purple bacteria. In this connection, two properties of Rps. capsulata are of particular note: a) sensitivity to penicillin G is 10(3)-10(5) times greater than that shown by closely related species, and b) all strains examined are susceptible to lysis by one or more strains of host species-specific virulent bacteriophages. It appears that members of the species Rps. capsulata form a stringent taxonomic grouping.