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PubMed2004

Characterization and expression of genes from the RubisCO gene cluster of the chemoautotrophic symbiont of Solemya velum: cbbLSQO.

Chemoautotrophic endosymbionts residing in Solemya velum gills provide this shallow water clam with most of its nutritional requirements. The cbb gene cluster of the S. velum symbiont, including cbbL and cbbS, which encode the large and small subunits of the carbon-fixing enzyme ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), was cloned and expressed in Escherichia coli. The recombinant RubisCO had a high specific activity, approximately 3 micromol min(-1) mg protein (-1), and a KCO2 of 40.3 microM. Based on sequence identity and phylogenetic analyses, these genes encode a form IA RubisCO, both subunits of which are closely related to those of the symbiont of the deep-sea hydrothermal vent gastropod Alviniconcha hessleri and the photosynthetic bacterium Allochromatium vinosum. In the cbb gene cluster of the S. velum symbiont, the cbbLS genes were followed by cbbQ and cbbO, which are found in some but not all cbb gene clusters and whose products are implicated in enhancing RubisCO activity post-translationally. cbbQ shares sequence similarity with nirQ and norQ, found in denitrification clusters of Pseudomonas stutzeri and Paracoccus denitrificans. The 3' region of cbbO from the S. velum symbiont, like that of the three other known cbbO genes, shares similarity to the 3' region of norD in the denitrification cluster. This is the first study to explore the cbb gene structure for a chemoautotrophic endosymbiont, which is critical both as an initial step in evaluating cbb operon structure in chemoautotrophic endosymbionts and in understanding the patterns and forces governing RubisCO evolution and physiology.

Animals↗
PubMed2005

Dissimilation of C3-sulfonates.

Cysteate and sulfolactate are widespread natural products in the environment, while propanesulfonate, 3-aminopropanesulfonate and propane-1,3-disulfonate are xenobiotics. While some understanding of the bacterial assimilation of cysteate sulfur has been achieved, details of the dissimilation of cysteate and sulfolactate by microbes together with information on the degradation of the xenobiotics have only recently become available. This minireview centres on bacterial catabolism of the carbon moiety in these C(3)-sulfonates and on the fate of the sulfonate group. Three mechanisms of desulfonation have been established. Firstly, cysteate is converted via sulfopyruvate to sulfolactate, which is desulfonated to pyruvate and sulfite; the latter is oxidized to sulfate by a sulfite dehydrogenase and excreted as sulfate in Paracoccus pantotrophus NKNCYSA. Secondly, sulfolactate can be converted to cysteate, which is cleaved in a pyridoxal 5'-phosphate-coupled reaction to pyruvate, sulfite and ammonium ions; in Silicibacter pomeroyi DSS-3, the sulfite is excreted largely as sulfite. Both desulfonation reactions seem to be widespread. The third desulfonation mechanism is oxygenolysis of, e.g. propanesulfonate(s), about which less is known.

Alkanesulfonic Acids↗
PubMedDate not supplied

Characteristics of the aerobic respiratory chains of the microaerophiles Campylobacter jejuni and Helicobacter pylori.

The respiratory chain enzymes of microaerophilic bacteria should play a major role in their adaptation to growth at low oxygen tensions. The genes encoding the putative NADH:quinone reductases (NDH-1), the ubiquinol:cytochrome c oxidoreductases (bc1 complex) and the terminal oxidases of the microaerophiles Campylobacter jejuni and Helicobacter pylori were analysed to identify structural elements that may be required for their unique energy metabolism. The gene clusters encoding NDH-1 in both C. jejuni and H. pylori lacked nuoE and nuoF, and in their place were genes encoding two unknown proteins. The NuoG subunit in these microaerophilic bacteria appeared to have an additional Fe-S cluster that is not present in NDH-1 from other organisms; but C. jejuni and H. pylori differed from each other in a cysteine-rich segment in this subunit, which is present in some but not all NDH-1. Both organisms lacked genes orthologous to those encoding NDH-2. The subunits of the bc1 complex of both bacteria were similar, and the Rieske Fe-S and cytochrome b subunits had significant similarity to those of Paracoccus denitrificans and Rhodobacter capsulatus, well-studied bacterial bc1 complexes. The composition of the terminal oxidases of C. jejuni and H. pylori was different; both bacteria had cytochrome cbb3 oxidases, but C. jejuni also contained a bd-type quinol oxidase. The primary structures of the major subunits of the cbb3-type (terminal) oxidase of C. jejuni and H. pylori indicated that they form a separate group within the cbb3 protein family. The implications of the results for the function of the enzymes and their adaptation to microaerophilic growth are discussed.

Aerobiosis↗
PubMed2001

Identification and characterization of a periplasmic nitrate reductase in Azospirillum brasilense Sp245.

The Azospirillum brasilense Sp245 napABC genes, encoding nitrate reductase activity, were isolated and sequenced. The derived protein sequences are very similar throughout the whole Nap segment to the NapABC protein sequences of Escherichia coli, Pseudomonas sp. G-179, Ralstonia eutropha, Rhodobacter sphaeroides, and Paracoccus denitrificans. Based on whole-cell nitrate reductase assays with the artificial electron donors benzyl viologen and methyl viologen, and assays with periplasmic cell-free extracts, it was concluded that the napABC-encoded enzyme activity in Azospirillum brasilense Sp245 corresponds to a periplasmic dissimilatory nitrate reductase, which was expressed under anoxic conditions and oxic conditions. A kanamycin-resistant Azospirillum brasilense Sp245 napA insertion mutant was constructed. The mutant still expressed assimilatory nitrate reductase activity, but was devoid of its periplasmic dissimilatory nitrate reductase activity.

Aerobiosis↗
PubMed2003

Bacterial diversity in a marine methanol-fed denitrification reactor at the montreal biodome, Canada.

The bacterial biota of a methanol-fed denitrification reactor used to treat seawater at the Montreal Biodome were investigated using culture-dependent and molecular biology methods. The microbiota extracted from the reactor carriers were cultivated on three media. Three isolate types were recovered and their 16S ribosomal DNA (rDNA) genes were determined. The analysis showed that the isolate types were related to alpha-Proteobacteria. They are members of the Hyphomicrobium and Paracoccus genera and the Phyllobacteriaceae family. Uncultured bacteria were identified through a 16S rDNA library generated from total DNA extracted from the microbiota. Clones were screened for different restriction profiles and for different DGGE (denaturing gradient gel electrophoresis) migration profiles. More than 70% of clones have the same restriction profile, and the sequence of representative clones showed a relation with the Methylophaga members of the Piscirickettsia family (gamma-Proteobacteria). Sequences from other profiles were related to bacterial species involved in denitrification. The number of species in the denitrification reactor was estimated at 15. Bacterial colonization on newly added carriers in the denitrification reactor was monitored by PCR-DGGE. The DGGE migration profiles evolved during the first 5 weeks and then remained essentially unchanged. PCR-DGGE was also used to monitor the microbial profiles in various aquarium locations. As expected, bacterial populations differed from one location to another, except for the sand and trickling filters which presented similar DGGE migration profiles.

Alphaproteobacteria↗
PubMed2006

Identification of acetate- or methanol-assimilating bacteria under nitrate-reducing conditions by stable-isotope probing.

Stable-isotope probing (SIP) was used to identify acetate- or methanol-assimilating bacteria under nitrate-reducing conditions in activated sludge. A sludge sample obtained from wastewater treatment systems was incubated in a denitrifying batch reactor fed with synthetic wastewater containing [(13)C]acetate or [(13)C]methanol as the main carbon source and nitrate as the electron acceptor. We analyzed how growth of bacterial populations was stimulated by acetate or methanol as the external carbon source in nitrogen-removal systems. Most of the acetate- or methanol-assimilating bacteria identified by SIP have been known as denitrifiers in wastewater treatment systems. When acetate was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-labeled DNA were closely related to the 16S rRNA genes of Comamonadaceae (e.g., Comamonas and Acidovorax) and Rhodocyclaceae (e.g., Thauera and Dechloromonas) of the Betaproteobacteria, and Rhodobacteraceae (e.g., Paracoccus and Rhodobacter) of the Alphaproteobacteria. When methanol was used as the carbon source, 16S rRNA gene sequences retrieved from (13)C-DNA were affiliated with Methylophilaceae (e.g., Methylophilus, Methylobacillus, and Aminomonas) and Hyphomicrobiaceae. Rarefaction curves for clones retrieved from (13)C-DNA showed that the diversity levels for methanol-assimilating bacteria were considerably lower than those for acetate-assimilating bacteria. Furthermore, we characterized nitrite reductase genes (nirS and nirK) as functional marker genes for denitrifier communities in acetate- or methanol-assimilating populations and detected the nirS or nirK sequence related to that of some known pure cultures, such as Alcaligenes, Hyphomicrobium, and Thauera. However, most of the nirS or nirK sequences retrieved from (13)C-DNA were clustered in some unidentified groups. On the basis of 16S rRNA gene clone libraries retrieved from (13)C-DNA, these unidentified nir sequences might be identified by examining the nir gene in candidates for true denitrifiers (e.g., the families Comamonadaceae, Hyphomicrobiaceae, Methylophilaceae, and Rhodobacteraceae).

Acetates↗
PubMed2007

Culturable and VBNC Vibrio cholerae: interactions with chironomid egg masses and their bacterial population.

Vibrio cholerae, the etiologic agent of cholera, is autochthonous to various aquatic environments. Recently, it was found that chironomid (nonbiting midges) egg masses serve as a reservoir for the cholera bacterium and that flying chironomid adults are possible windborne carriers of V. cholerae non-O1 non-O139. Chironomids are the most widely distributed insect in freshwater. Females deposit egg masses at the water's edge, and each egg mass contains eggs embedded in a gelatinous matrix. Hemagglutinin/protease, an extracellular enzyme of V. cholerae, was found to degrade chironomid egg masses and to prevent them from hatching. In a yearly survey, chironomid populations and the V. cholerae in their egg masses followed phenological succession and interaction of host-pathogen population dynamics. In this report, it is shown via FISH technique that most of the V. cholerae inhabiting the egg mass are in the viable but nonculturable (VBNC) state. The diversity of culturable bacteria from chironomid egg masses collected from two freshwater habitats was determined. In addition to V. cholerae, representatives of the following genera were isolated: Acinetobacter, Aeromonas, Klebsiella, Shewanella, Pseudomonas, Paracoccus, Exiguobacterium, and unidentified bacteria. Three important human pathogens, Aeromonas veronii, A. caviae, and A. hydrophila, were isolated from chironomid egg masses, indicating that chironomid egg masses may be a natural reservoir for pathogenic Aeromonas species in addition to V. cholerae. All isolates of V. cholerae were capable of degrading chironomid egg masses. This may help explain their host-pathogen relationship with chironomids. In contrast, almost none of the other bacteria that were isolated from the egg masses possessed this ability. Studying the interaction between chironomid egg masses, the bacteria inhabiting them, and V. cholerae could contribute to our understanding of the nature of the V. cholerae-egg mass interactions.

Animals↗
PubMed2000

Aerobic Denitrifiers Isolated from Diverse Natural and Managed Ecosystems.

Twenty-eight bacterial strains were isolated from an ecosystem adapted to fluctuating oxic-anoxic conditions. This ecosystem comprised a mixture of different natural and wastewater treatment environments. Among the 28 strains isolated, 10 exhibited aerobic denitrifying activity, i.e., co-respiration of oxygen and nitrate and simultaneous production of nitrite by 4 of them and of nitrogen gas by the remaining 6. Comparisons between the 16S rDNA sequences of the 10 strains showed that 3 of them were identical to M. aerodenitrificans, whereas RAPD profiles showed that the 3 strains were identical to each other but that they were different from M. aerodenitrificans. This implies that alternating aerobic-anoxic conditions allowed the isolation of a new strain of this aerobic denitrifier. Moreover, other denitrifying bacteria belonging to the genera Paracoccus, Thiobacillus, Enterobacter, Comamonas, and Sphingomonas were isolated in this way. These data imply that a wide variety of bacteria are able to carry out this type of metabolism. M. aerodenitrificans was also detected in methanogenic, denitrifying, nitrifying, phosphate removal, and activated sludge ecosystems by two-step PCR amplification. After 4 months of acclimation to oxic-anoxic phases, the strain was also detected in a canal and in a pond. This suggests that there is no specific natural ecological niche for aerobic denitrifiers but, as soon as selective pressure such as alternating aeration conditions is applied, this metabolism is amplified.

Journal Article↗
PubMed2002

Inhibition of bacterial alpha-glucosidases by castanospermine in pure cultures and activated sludge.

Castanospermine (CAST) is a known and potent inhibitor of various alpha-glucosidases in eukaryotes. In this work, we elucidated whether CAST could also be used for determining bacterial alpha-glucosidase activity, when measured with 4-methylumbelliferyl-alpha- D-glucoside as a substrate, both in a complex bacterial community, in activated sludge and in pure cultures of bacterial isolates. We found that 140 microM CAST inhibited alpha-glucosidase activity by 30% in a pure culture of Pseudomonas stutzeri. The alpha-glucosidase activity in Chryseobacterium gleum was inhibited by 90% at a concentration of 150 microM CAST, whereas the alpha-glucosidase in Paracoccus denitrificans was resistant to the inhibitor. CAST (140 microM) reduced alpha-glucosidase activity in activated sludge by 40%, the respiration rate being reduced by only 12%. No significant inhibition of the respiration rate was observed in Ps. stutzeri or Pa. denitrificans, whereas the respiration rate in C. gleum grown in a medium containing starch was inhibited by 50% with 140 microM CAST. No effect of CAST was observed in C. gleum grown in a complex medium. This indicated that CAST, at the concentration used, did not cause a general negative effect on bacterial activity. The results suggest that the CAST assay may potentially be useful in determining whether alpha-glucosidase activity, starch, poly- and disaccharides contribute appreciably to the overall activity of a bacterial community. However, the assay should not be used for quantitative measurements of such activity.

Bacteria↗
PubMed2002

Ca2+ and the bacterial peroxidases: the cytochrome c peroxidase from Pseudomonas stutzeri.

The production of cytochrome c peroxidase (CCP) from Pseudomonas ( Ps.) stutzeri (ATCC 11607) was optimized by adjusting the composition of the growth medium and aeration of the culture. The protein was isolated and characterized biochemically and spectroscopically in the oxidized and mixed valence forms. The activity of Ps. stutzeri CCP was studied using two different ferrocytochromes as electron donors: Ps. stutzeri cytochrome c(551) (the physiological electron donor) and horse heart cytochrome c. These electron donors interact differently with Ps. stutzeri CCP, exhibiting different ionic strength dependence. The CCP from Paracoccus ( Pa.) denitrificans was proposed to have two different Ca(2+) binding sites: one usually occupied (site I) and the other either empty or partially occupied in the oxidized enzyme (site II). The Ps. stutzeri enzyme was purified in a form with tightly bound Ca(2+). The affinity for Ca(2+) in the mixed valence enzyme is so high that Ca(2+) returns to it from the EGTA which was added to empty the site in the oxidized enzyme. Molecular mass determination by ultracentrifugation and behavior on gel filtration chromatography have revealed that this CCP is isolated as an active dimer, in contrast to the Pa. denitrificans CCP which requires added Ca(2+) for formation of the dimer and also for activation of the enzyme. This is consistent with the proposal that Ca(2+) in the bacterial peroxidases influences the monomer/dimer equilibrium and the transition to the active form of the enzyme. Additional Ca(2+)does affect both the kinetics of oxidation of horse heart cytochrome c (but not cytochrome c(551)) and higher aggregation states of the enzyme. This suggests the presence of a superficial Ca(2+)binding site of low affinity.

Animals↗
PubMed1981

Occurrence of proteins immunoreactive with anti-coupling factor B in phosphorylating membrane preparations.

Coupling factor B has been isolated from beef heart mitochondria, apparently in multiple forms which differ in molecular weight and specific activity. Since it has no known intrinsic catalytic activity, detection and quantitation have been based upon the factor B-dependent stimulation of ATP-linked activities in factor B-deficient sub-mitochondrial particles. This communication reports the development of a reliable and more universally applicable enzyme-linked immunosorbent assay (ELISA) for detection and quantitation of factor B in soluble or membranous preparations. The assay requires nanoliter volumes of rabbit antiserum raised against purified factor B and will detect nanogram amounts of the coupling factor. Analysis of beef heart submitochondrial particles using a competitive binding ELISA indicated a factor B content of 0.27 nmol/mg protein, making factor B stoichiometric with F1 (0.3--0.6 nmol/mg). Furthermore, application of the factor B ELISA has indicated the presence of material cross-reacting with the beef heart factor B-antiserum in phosphorylating membranes from chloroplasts, Escherichia coli, Paracoccus denitrificans and the thermophilic bacterium, PS3. Negative results were obtained with mitochondria and microsomes from rat liver, purple membranes from Halobium halobacterium and sarcoplasmic reticulum from rabbit skeletal muscle.

Animals↗
PubMed1994

Bacterial genes and proteins involved in the biogenesis of c-type cytochromes and terminal oxidases.

A total of nine genes potentially concerned with the biosynthesis of c-type cytochromes have been identified recently in the bacteria Bradyrhizobium japonicum and Rhodobacter capsulatus, and homologous counterparts appear to be present also in Escherichia coli. Most of the respective gene products are membrane-bound, while others are located in the periplasmic space. As inferred from sequence analyses, several of these proteins may play roles in membrane transport or redox processes, both functions being consistent with the required steps in cytochrome c formation (membrane translocation of heme; covalent linkage of protoheme IX to cysteine thiols). Further genes of B. japonicum, E. coli, Bacillus subtilis and Paracoccus denitrificans have been studied whose products are necessary for the formation of intact heme/copper oxidases. Some of them are probably required in protein folding and assembly whereas others appear to be enzymes catalyzing steps in the biosynthesis of the heme cofactors.

Aerobiosis↗
PubMed1996

Primary structure of a ferredoxin-like iron-sulfur subunit of complex I from Neurospora crassa.

We have isolated cDNA clones encoding an iron-sulfur polypeptide subunit of the mitochondrial complex I of Neurospora crassa. The fungal cDNA library was screened by hybridisation with an heterologous probe from Paracoccus denitrificans. The DNA sequence of relevant isolates was determined and revealed an open reading frame encoding a precursor protein of 219 amino acid residues. The gene product is a ferredoxin-like protein that contains two cysteine-rich motives that may each bind a tetranuclear iron-sulfur cluster. The primary structure of the protein is highly homologous to the 23 kDa iron-sulfur subunit of complex I from bovine and P. denitrificans. Interestingly, an alanine residue within the second cluster-binding motif, which is conserved in complex I but replaced by tyrosine in similar chloroplast genes, is substituted for serine in N. crassa.

Amino Acid Sequence↗
PubMed1987

Homology between bacterial DNA and bovine mitochondrial DNA encoding cytochrome c oxidase subunit III.

A segment of mitochondrial DNA encoding the bovine cytochrome c oxidase subunit III gene was isolated and inserted into an Escherichia coli plasmid vector. A 556 base pair fragment of the insert DNA representing about 70% of the 3'-end of the subunit III gene was used to search for homology with bacterial DNA from strains that contain heme aa3-type cytochrome c oxidases. Bacillus subtilis, Thermus thermophilus, and PS3 DNAs all showed strong hybridization to the probe, whereas Paracoccus denitrificans and Rhodopseudomonas sphaeroides DNAs showed only weak hybridization to the probe, even under low stringency conditions.

Animals↗
PubMed1990

Periplasmic and membrane-bound respiratory nitrate reductases in Thiosphaera pantotropha. The periplasmic enzyme catalyzes the first step in aerobic denitrification.

The unusual ability of Thiosphaera pantotropha to catalyze respiratory nitrate reduction under aerobic conditions is shown to correlate with the activity of a periplasmic nitrate reductase that is expressed under both aerobic and anaerobic growth conditions. The organism also synthesizes, but only under anaerobic conditions, a membrane-bound nitrate reductase which resembles the corresponding enzyme in Paracoccus denitrificans in respect of both catalytic properties and inhibition of activity in intact cells in the presence of oxygen.

Aerobiosis↗
PubMed1994

The cupredoxin fold is found in the soluble CuA and CyoA domains of two terminal oxidases.

The CD spectra of the CuA domain from subunit II of Paracoccus cytochrome c oxidase and the CyoA domain of subunit II from E. coli quinol oxidase have been recorded in the wavelength region 260-185 nm. A computer program based on a set of CD spectra of proteins with known structures, and employing the statistical method of variable selection, has been used to estimate the distribution of five forms of secondary structure. The analysis was improved by including the CD spectra of azurin and plastocyanin in the basis set. For the CuA domain, an estimate from the primary structure was also made. The results show that the soluble domains have the cupredoxin fold, with very little helical structure and a predominance of beta-strands. The CyoA domain is very similar to azurin, but the beta-structure in the CuA protein resembles that in plastocyanin.

Azurin↗
PubMed1994

Studies on the proton-translocating NADH:ubiquinone oxidoreductases of mitochondria and Escherichia coli using the inhibitor 1,10-phenanthroline.

Mitochondrial NADH:ubiquinone oxidoreductase (complex I) is uncompetitively inhibited by 1,10-phenanthroline (OP). EPR spectroscopy of submitochondrial particles indicates that OP, similarly to rotenone, inhibits electron transfer between the Fe-S clusters of complex I and the ubiquinone pool. The proton-translocating NADH dehydrogenase (NDH1) of E. coli is more sensitive to OP than is NDH1 of Paracoccus. EPR spectroscopy of membranous E. coli NDH1 shows that two slow- and one fast-relaxing Fe-S clusters become detectable upon reduction by NADH in the presence of OP. However, none of them resembles the mitochondrial cluster 2.

Animals↗
PubMed1990

Microbial metabolism of tholin.

In this paper, we show that a wide variety of common soil bacteria are able to obtain their carbon and energy needs from tholin (a class of complex organic heteropolymers thought to be widely distributed through the solar system; in this case tholin was produced by passage of electrical discharge through a mixture of methane, ammonia, and water vapor). We have isolated aerobic, anaerobic, and facultatively anaerobic bacteria which are able to use tholin as a sole carbon source. Organisms which metabolize tholin represent a variety of bacterial genera including Clostridium, Pseudomonas, Bacillus, Acinetobacter, Paracoccus, Alcaligenes, Micrococcus, Corynebacterium, Aerobacter, Arthrobacter, Flavobacterium, and Actinomyces. Aerobic tholin-using bacteria were first isolated from soils containing unusual or sparse carbon sources. Some of these organisms were found to be facultatively anaerobic. Strictly anaerobic tholin-using bacteria were isolated from both carbon-rich and carbon-poor anaerobic lake muds. In addition, both aerobic and anaerobic tholin-using bacteria were isolated from common soil collected outside the laboratory building. Some, but not all, of the strains that were able to obtain carbon from tholin were also able to obtain their nitrogen requirements from tholin. Bacteria isolated from common soils were tested for their ability to obtain carbon from the water-soluble fraction, the ethanol-soluble fraction, and the water/ethanol-insoluble fraction of the tholin. Of the 3.5 x 10(7) bacteria isolated per gram of common soils, 1.7, 0.5, and 0.2%, respectively, were able to obtain their carbon requirements from the water-soluble fraction, the ethanol-soluble fraction and the water/ethanol-insoluble fraction of the tholin. The palatability of tholins to modern microbes may have implications for the early evolution of microbial life on Earth. Tholins may have formed the base of the food chain for an early heterotrophic biosphere before the evolution of autotrophy on the early Earth. Where tholins are present on other planets, they could possibly be metabolized by contaminant microorganisms transported to these bodies via spacecraft. Thus, the presence of tholins should be taken into account when evaluating the planetary quarantine requirements for probes to other planets.

Amino Acids↗