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PubMed1990

Formation of a potent respiratory inhibitor at nitrite reduction by nitrite reductase isolated from the bacterium Paracoccus denitrificans.

A new method of dissimilatory nitrite reductase (cytochrome cd1) isolation from the periplasmic fraction of anaerobically grown cells of the bacterium Paracoccus denitrificans was developed, using ionex and gel permeation chromatography with FPLC system (Pharmacia, Sweden). In experiments with isolated enzyme it was shown that through a nitrite reduction, catalysed by this enzyme, a substance (presumably nitric oxide) was formed which at submicromolar concentrations inhibited terminal cytochrome oxidase of the respiratory chain of the same bacterium. These results help to explain formerly observed sensitivity of bacterial oxidase activity to NO2- and the mechanism of switching the electron flow from O2 to nitrogen terminal acceptors.

Chromatography, High Pressure Liquid↗
PubMed2006

The cytosolic, cell surface and extracellular proteomes of the biotechnologically important soil bacterium Corynebacterium efficiens YS-314 in comparison to those of Corynebacterium glutamicum ATCC 13032.

Reference maps of the cytosolic, cell surface and extracellular proteome fractions of the amino acid-producing soil bacterium Corynebacterium efficiens YS-314 were established. The analysis window covers a pI range from 3 to 7 along with a molecular mass range from 10 to 130 kDa. After second-dimensional separation on SDS-PAGE and Coomassie staining, computational analysis detected 635 protein spots in the cytosolic proteome fraction, whereas 76 and 102 spots were detected in the cell surface and extracellular proteomes, respectively. By means of MALDI-TOF-MS and tryptic peptide mass fingerprinting, 164 cytosolic proteins, 49 proteins of the cell surface and 89 extracellular protein spots were identified, representing in total 177 different proteins. Additionally, reference maps of the three cellular proteome fractions of the close phylogenetic relative Corynebacterium glutamicum ATCC 13032 were generated and used for comparative proteomics. Classification according to the Clusters of Orthologous Groups of proteins scheme and abundance analysis of the identified proteins revealed species-specific differences. The high abundance of molecular chaperones and amino acid biosynthesis enzymes in C. efficiens points to environmental adaptations of this recently discovered amino acid-producing bacterium.

Amino Acid Sequence↗
PubMed1997

Xylanase XynA from the hyperthermophilic bacterium Thermotoga maritima: structure and stability of the recombinant enzyme and its isolated cellulose-binding domain.

The hyperthermophilic bacterium Thermotoga maritima is capable of gaining metabolic energy utilizing xylan. XynA, one of the corresponding hydrolases required for its degradation, is a 120-kDa endo-1,4-D-xylanase exhibiting high intrinsic stability and a temperature optimum approximately 90 degrees C. Sequence alignments with other xylanases suggest the enzyme to consist of five domains. The C-terminal part of XynA was previously shown to be responsible for cellulose binding (Winterhalter C, Heinrich P, Candussio A, Wich G, Liebl W. 1995. Identification of a novel cellulose-binding domain within the multi-domain 120 kDa Xylanase XynA of the hyperthermophilic bacterium Thermotoga maritima. Mol Microbiol 15:431-444). In order to characterize the domain organization and the stability of XynA and its C-terminal cellulose-binding domain (CBD), the two separate proteins were expressed in Escherichia coli. CBD, because of its instability in its ligand-free form, was expressed as a glutathione S-transferase fusion protein with a specific thrombin cleavage site as linker. XynA and CBD were compared regarding their hydrodynamic and spectral properties. As taken from analytical ultracentrifugation and gel permeation chromatography, both are monomers with 116 and 22 kDa molecular masses, respectively. In the presence of glucose as a ligand, CBD shows high intrinsic stability. Denaturation/renaturation experiments with isolated CBD yield > 80% renaturation, indicating that the domain folds independently. Making use of fluorescence emission and far-UV circular dichroism in order to characterize protein stability, guanidine-induced unfolding of XynA leads to biphasic transitions, with half-concentrations c1/2 (GdmCl) approximately 4 M and > 5 M, in accordance with the extreme thermal stability. At acid pH, XynA exhibits increased stability, indicated by a shift of the second guanidine-transition from 5 to 7 M GdmCl. This can be tentatively attributed to the cellulose-binding domain. Differences in the transition profiles monitored by fluorescence emission and dichroic absorption indicate multi-state behavior of XynA. In the case of CBD, a temperature-induced increase in negative ellipticity at 217 nm is caused by alterations in the environment of aromatic residues that contribute to the far-UV CD in the native state.

Amino Acid Sequence↗
PubMed1995

Characterization of tannin acylhydrolase activity in the ruminal bacterium Selenomonas ruminantium.

A strain of the anaerobe Selenomonas ruminantium subsp. ruminantium that is capable of growing on tannic acid or condensed tannin as a sole energy source has been isolated from ruminal contents of feral goats browsing tannin-rich Acacia sp. Growth on tannic acid was accompanied by release of gallic acid into the culture medium but the bacterium was incapable of using gallic acid as a sole energy source. Tannin acylhydrolase (EC 3.1.1.20) activity was measured in crude cell-free extracts of the bacterium. The enzyme has a pH optimum of 7, a temperature optimum of 30-40 degrees C and a molecular size of 59 kDa. In crude extracts, the maximal rate of gallic acid methyl ester hydrolysis was 6.3 micromol min(-1) mg(-1) of protein and the K(m) for gallic acid methyl ester was 1.6 mM. Enzyme activity was displayed in situ in polyacrylamide and isoelectric focusing gels and was demonstrated to increase 17-fold and 36-fold respectively when cells were grown in the presence of gallic acid methyl ester or tannic acid.

Journal Article↗
PubMed1998

Isolation and characterisation of a novel sulphate-reducing bacterium of the Desulfovibrio genus.

A novel sulphate-reducing bacterium (Ind 1) was isolated from a biofilm removed from a severely corroded carbon steel structure in a marine environment. Light microscopy observations revealed that cells were Gram-negative, rod shaped and very motile. Partial 16S rRNA gene sequencing and analysis of the fatty acid profile demonstrated a strong similarity between the new species and members from the Desulfovibrio genus. This was confirmed by the results obtained following purification and characterisation of the key proteins involved in the sulphate-reduction pathway. Several metal-containing proteins, such as two periplasmic proteins: hydrogenase and cytochrome c3, and two cytoplasmic proteins: ferredoxin and sulphite reductase, were isolated and purified. The latter proved to be of the desulfoviridin type which is typical of the Desulfovibrio genus. The study of the remaining proteins revealed a high degree of similarity with the homologous proteins isolated from Desulfovibrio gigas. However, the position of the strain within the phylogenetic tree clearly indicates that the bacterium is closely related to Desulfovibrio gabonensis, and these three strains form a separate cluster in the delta subdivision of the Proteobacteria. On the basis of the results obtained, it is suggested that Ind 1 belongs to a new species of the genus Desulfovibrio, and the name Desulfovibrio indonensis is proposed.

Journal Article↗
PubMed1995

Relative cytokine-stimulating activities of surface components of the oral periodontopathogenic bacterium Actinobacillus actinomycetemcomitans.

The purpose of this study was to determine whether bacterial surface components other than lipopolysaccharide (LPS) could stimulate pro-inflammatory cytokine synthesis by mesenchymal and myelomonocytic cells in vitro. LPS, lipid A-associated proteins (LAP) and saline-extractable surface-associated material (SAM) were isolated from the periodontopathogenic bacterium Actinobacillus actinomycetemcomitans and added to cultures of human gingival fibroblasts (HGFs), human PBMCs and the human myelomonocytic MonoMac-6 cell line. Pro-inflammatory cytokine release into culture supernatants was determined by two-site ELISAs. Contrary to expectation, the highly purified LPS extracted from this bacterium was significantly less potent than the other surface extracts in stimulating release of IL-1 beta, IL-6 and TNF-alpha by all three cell types. The SAM was the most potent cytokine-stimulating agent showing equivalent activity to highly purified E. coli LPS in stimulating IL-6 release by PBMCs. LAP also had cytokine-stimulating activity although it was generally significantly less potent than the SAM. Thus in the case of this organism, which is involved in the pathology of chronic inflammatory diseases the LPS does not appear to be the major cytokine-stimulating component.

Aggregatibacter actinomycetemcomitans↗
PubMed1997

The toxicity of substituted phenolic compounds to a detoxifying and an acetic acid bacterium.

In the detoxifying bacterium Acinetobacter calcoaceticus 69-V and in the acetic acid bacterium Acetobacter methanolicus MB 58, glucose and xylose are oxidized, respectively, via PQQ-dependent membrane-bound dehydrogenases, which are linked to the respiratory chain in a manner enabling energy conservation via electron transport phosphorylation (ETP) in the cytoplasmic membrane. Neither the glucose and gluconic acid nor the xylose and xylonic acid are metabolized. Therefore, measurements of sugar oxidation-driven ATP syntheses ought not to be disturbed by ATP drainage caused by anabolic processes. Studying the effect of substituted phenolic compounds on these energization processes reveals that their toxicity increases with an increasing degree of chlorination and that A. calcoaceticus 69-V is more stable than A. methanolicus MB 58 against chlorinated phenols. On the other hand, A. methanolicus MB 58 is more stable against 2,4-dinitrophenol (2,4-DNP) and 2,4-dichlorophenoxyacetic acid (2,4-D), especially in the acidic pH range, in which the sensitivity of ATP synthesis to the uncouplers is higher than that of respiration. The toxicity caused by protonophoric activities ought to be barely detectable by respiratory and dehydrogenase tests. The luminescence system of Photobacterium phosphoreum tested in the luminescent bacteria test was much more sensitive. This test system should be used as a screening tool and the effects measured must be confirmed by toxicity tests evaluating the stability of bacteria themselves involved in processes of detoxification as well as the production of toxic metabolites, monitored with respect to their velocity and efficiency.

Acinetobacter↗
PubMed2001

Modular structure, local flexibility and cold-activity of a novel chitobiase from a psychrophilic Antarctic bacterium.

The gene archb encoding for the cell-bound chitobiase from the Antarctic Gram-positive bacterium Arthrobacter sp. TAD20 was cloned and expressed in Escherichia coli in a soluble form. The mature chitobiase ArChb possesses four functionally independent domains: a catalytic domain stabilized by Ca(2+), a galactose-binding domain and an immunoglobulin-like domain followed by a cell-wall anchorage signal, typical of cell-surface proteins from Gram-positive bacteria. Binding of saccharides was analyzed by differential scanning calorimetry, allowing to distinguish unequivocally the catalytic domain from the galactose-binding domain and to study binding specificities. The results suggest that ArChb could play a role in bacterium attachment to natural hosts. Kinetic parameters of ArChb demonstrate perfect adaptation to catalysis at low temperatures, as shown by a low activation energy associated with unusually low K(m) and high k(cat) values. Thermodependence of these parameters indicates that discrete amino acid substitutions in the catalytic center have optimized the thermodynamic properties of weak interactions involved in substrate binding at low temperatures. Microcalorimetry also reveals that heat-lability, a general trait of psychrophilic enzymes, only affects the active site domain of ArChb.

Acetylglucosaminidase↗
PubMed1996

Characterization of a novel Spirillum-like bacterium that degrades ferrioxamine-type siderophores.

A novel Gram-negative Spirillum-like bacterium (ASP-1) was isolated from lake water by enrichment culture on desferrioxamine B as sole source of carbon and energy. ASP-1 was able to degrade the siderophores desferrioxamine B and E. The property of siderophore degradation was inducible in the presence of desferrioxamine B. The ferric complexes, however, were not measurably degraded but served as an iron source. Degradation of desferrioxamines in culture was followed by measuring the residual ferrioxamines colorimetrically at 430 nm after addition of iron. Degradation in cell-free assays was followed quantitatively by HPLC on a reversed-phase column measuring the time-dependent disappearance of the desferrioxamines B and E. Cell-free assays also revealed that degradation of the cyclic desferrioxamine E was rapid and complete, whereas degradation of the linear desferrioxamine B yielded two intermediate iron-binding metabolites of shorter chain length. Preparative isolation by HPLC and mass spectrometric analysis of the metabolites revealed masses at 361 and 419 a.m.u., respectively, suggesting a splitting at the two amide bonds. ASP-1 is a nitrogen fixing Spirillum bacterium which could also use ammonium and glucose or several organic acids as a carbon source but grew poorly with amino acids. Physiological comparisons with Aquaspirillum and Azospirillum failed to assign ASP-1 to any of the presently known Spirillum species. Based on 16S rDNA sequence analysis the strain could be placed within the radiation of the Azospirillum/Rhodocista group. The closest relative was Azospirillum irakense, showing 98.8% similarity.

Biodegradation, Environmental↗
PubMed1993

Some properties and occurrence of cytochrome c-552 in the aerobic photosynthetic bacterium Roseobacter denitrificans.

Characteristics and occurrence of cytochrome c-552 from an aerobic photosynthetic bacterium, Roseobacter denitrificans, were described. Relative molecular mass of the cytrochrome was 13.5 kDa on sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and 15,000 by gel filtration. This cytochrome was a acidic protein having a pI of 5.6 and Em was +215 mV at pH 7.0. Absorption peaks were at 278, 408 and 524 nm in the oxidized form and 416, 523 and 552 nm in the reduced form. Amino acid composition and N-terminal amino acid sequence of cytochrome c-552 determined for 24 residues had low similarities to those of cytochrome c-551 of this bacterium, which is homologous to cytochrome c2, although the physico-chemical properties of these two cytochromes were similar to each other. Cytochrome c-552 was maximally synthesized in the light under aerobic conditions but not in the dark. The synthesis also occurred in the presence of alternative acceptors such as trimethylamine N-oxide (TMAO) and nitrate under anaerobic conditions. Our results suggest that cytochrome c-552 is involved in TMAO respiration and denitrification in R. denitrificans, although the effect of light remains to be solved.

Amino Acid Sequence↗
PubMed1992

Characterization of a carbofuran-degrading bacterium and investigation of the role of plasmids in catabolism of the insecticide carbofuran.

A bacterium capable of using the carbamate insecticide carbofuran as a sole source of carbon and energy, was isolated from soil. The ability to catabolise carbofuran phenol, produced by cleavage of the carbamate ester linkage of the insecticide, was lost at very high frequency when the bacterium was grown in the absence of carbofuran. Plasmid analyses together with curing and mating experiments indicated that the presence of a large plasmid (pIH3, greater than 199 kb) was required for the degradation of carbofuran phenol.

Biodegradation, Environmental↗
PubMed1993

Isolation and characterization of a new spore-forming sulfate-reducing bacterium growing by complete oxidation of catechol.

A new mesophilic sulfate-reducing bacterium, strain Groll, was isolated from a benzoate enrichment culture inoculated with black mud from a freshwater ditch. The isolate was a spore-forming, rod-shaped, motile, gram-positive bacterium. This isolate was able of complete oxidation of several aromatic compounds including phenol, catechol, benzoate, p- and m-cresol, benzyl alcohol and vanillate. With hydrogen and carbon dioxide, formate or O-methylated aromatic compounds, autotrophic growth during sulfate reduction or homoacetogenesis was demonstrated. Lactate was not used as a substrate. SO4(2-), SO3(2-), and S2O3(2-) were utilized as electron acceptors. Although strain Groll originated from a freshwater habitat, salt concentrations of up to 30 g.l-1 were tolerated. The optimum temperature for growth was 35-37 degrees C. The G + C content of DNA was 42.1 mol%. This isolate is described as a new species of the genus Desulfotomaculum.

Bacillaceae↗
PubMed1993

Amino acid utilization by the ruminal bacterium Synergistes jonesii strain 78-1.

The ruminal bacterium Synergistes jonesii strain 78-1, which is able to degrade the pyridinediol toxin in the plant Leucaena leucocephala, was studied for its ability to utilise amino acids. The organism used arginine, histidine and glycine from a complex mixture of amino acids, and both arginine and histidine supported growth in a semi-defined medium. The products of (U-14C)-arginine metabolism were CO2 acetate, butyrate, citrulline and ornithine. The labelling pattern of end products from (U-14C)-histidine metabolism differed in that carbon also flowed into formate and propionate. Arginine was catabolised by the arginine deiminase pathway which was characterised by the presence of arginine deiminase, ornithine transcarbamylase and carbamate kinase. This is the first report of a rumen bacterium that uses arginine and histidine as major energy yielding substrates.

Amino Acids↗
PubMed1995

Induced mutagenesis by bleomycin in the purple sulfur bacterium Thiocapsa roseopersicina.

Cell death and mutagenesis in bleomycin-treated cells of Thiocapsa roseopersicina (a purple sulfur bacterium) was studied by cultivation in a semisolid medium (agar-shake technique). This technique has also proven useful in assessing the frequency of antibiotic mutations by detecting and counting individual colonies of Thiocapsa roseopersicina. The frequencies of spontaneous mutants resistant to ampicillin, rifampicin, cloramphenicol, tetracycline, kanamycin, streptomycin, and neomycin were also studied: they ranged between 2 x 10(-9) and 9 x 10(-8). Bleomycin (4 micrograms/ml) sharply increased the frequency of ampicillin-resistant mutants, from 10(-8) (spontaneous) to 4 x 10(-4) (induced), in 17 h. An inducible, error-prone mechanism of DNA synthesis seems to be responsible for this enhancement of the mutagenic effect. this is the first report on the sensitivity to several antibiotics, and capacity of lethality and mutagenesis by bleomycin has been studied in a purple sulfur bacterium.

Ampicillin Resistance↗
PubMed1994

Clostridium grantii sp. nov., a new obligately anaerobic, alginolytic bacterium isolated from mullet gut.

A gram-positive, motile, rod-shaped, strictly anaerobic, sporulating bacterium was isolated from an enrichment initiated with mullet gut contents. The organism grew optimally at 30 degrees C and pH 6.5, and at a salinity of 1/10(3). Out of a variety of polysaccharides tested as growth substrates, only alginate supported growth in either semidefined or complex culture medium. The organism also grew on a variety of mono- and disaccharides. Moles product per 100 mol of alginate monomer degraded were: acetate, 186; ethanol, 19; formate, 54; and CO2, 0.19. Moles product per 100 mol of hexose in cellobiose or glucose degraded were: acetate, 135; ethanol, 61; formate, 63; and CO2, 61. Hydrogen was not detectable during the incubations (detection limit, < 10(-5) atm) and propionate, butyrate, lactate, or succinate were not produced as fermentation end products (< 2 mol per 100 mol of monomer). The G+C content of DNA from the bacterium was 30.2 +/- 0.3 mol%, and the cell walls contained the peptidoglycan component meso-diaminopimelic acid. A phylogenetic analysis of the 16S rDNA sequence indicated that the organism grouped closely with members of the RNA-DNA homology group 1 of the genus Clostridium. However, it differed from other species of the genus with regard to morphology, growth temperature optimum, substrate range, and fermentation pattern and is therefore designated as a new species of Clostridium; the type strain is A-1 (DSM 8605).

Alginates↗
PubMed1996

Sodium-dependent succinate decarboxylation by a new anaerobic bacterium belonging to the genus Peptostreptococcus.

An anaerobic bacterium was isolated from a polluted sediment, with succinate and yeast extract as carbon and energy sources. The new strain was Gram-positive, the cells were coccal shaped, the mol% G+G content of the genomic DNA was 29, and the peptidoglycan was of the L-ornithine-D-glutamic acid type. Comparative sequence analysis of the 16S rRNA gene showed the new strain to belong to the genus Peptostreptococcus. Succinate, fumarate, pyruvate, 3-hydroxybutyrate and lysine supported growth. Succinate was degraded to propionate and presumably CO2, with a stoichiometric cell yield. Key enzymes of the methylmalonyl-CoA decarboxylase pathway were present. The methylmalonyl-CoA decarboxylase activity was avidin-sensitive and sodium dependent, and about 5 mM Na+ was required for maximal activity. Whole cells, however, required at least 50 mM sodium for maximal succinate decarboxylation activity and to support the maximum growth rate. Sodium-dependent energy conservation coupled to succinate decarboxylation is shown for the first time to occur in a bacterium belonging to the group of Gram-positive bacteria containing the peptostreptococci and their relatives.

Bacteria, Anaerobic↗
PubMed1989

Rhodospirillum centenum, sp. nov., a thermotolerant cyst-forming anoxygenic photosynthetic bacterium.

A novel non-sulfur purple photosynthetic bacterium, designated Rhodospirillum centenum, was isolated from an enrichment culture designed to favor growth of anoxygenic photosynthetic N2-fixing bacteria. R. centenum grows optimally at 40-42 degrees C and has the capacity to produce cytoplasmic 'R bodies', refractile structures not observed hitherto in photosynthetic prokaryotes. The bacterium is also unusual among photosynthetic bacteria in that it forms desiccation-resistant cysts when grown aerobically in darkness with butyrate as the sole carbon source.

Cytoplasm↗
PubMed1976

Desulfuromonas acetoxidans gen. nov. and sp. nov., a new anaerobic, sulfur-reducing, acetate-oxidizing bacterium.

Anaerobic sea or fresh water media with acetate and elemental sulfur yielded enrichments of a new type of strictly anaerobic, rod-shaped, laterally flagellated, Gram-negative bacterium. Three pure culture-strains from different sulfide-containing sea water sources were characterized in detail and are described as a new genus and species Desulfuromonas acetoxidans. The new bacterium is unable to ferment organic substances; it obtains energy for growth by anaerobic sulfur respiration. Acetate, ethanol or propanol can serve as carbon and energy source for growth; their oxidation to CO2 is stoichiometrically linked to the reduction of elemental sulfur to sulfide. Organic disulfide compounds, malate or fumarate are the only other electron acceptors used. Butanol and pyruvate are used in the presence of malate only; no other organic compounds are utilized. Biotin is required as a growth factor. The following dry weight yields per mole of substrate are obtained: in the presence of sulfur: 4.21 g on acetate, 9.77 g on ethanol; in the presence of malate: 16.5 g on acetate, 34.2 g on ethanol and 46.2 g on pyruvate. Accumulations of cells are pink; cell suspensions exhibit absorption spectra resembling those of c-type cytochromes (abs. max. at 419, 523 and 553 nm). Malate-ethanol grown cells contain a b-type cytochrome in addition. In the presence of acetate, ethanol or propanol, Desulfuromonas strains form robust growing syntrophic mixed cultures with phototrophic green sulfur bacteria.

Acetates↗