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PubMed1994

Microbial endoglycosidases for analyses of oligosaccharide chains in glycoproteins.

Microbial endoglycosidases are useful for elucidating the structure and function of the oligosaccharide chains of glycoconjugates. Most of the microbial endo-beta-N-acetylglucosaminidases including Endo-H can preferentially act on high-mannose type chains of asparagine-linked oligosaccharides of various glycoproteins. Among them, Flavobacterium sp. enzyme is produced in large amounts by the inducing cultivation. Using this enzyme, the role of oligosaccharide chains in various microbial glycoenzymes such as Rhizopus glucoamylase, and yeast invertase was examined. The findings suggested that the oligosaccharide chains of them are essential participants in the stabilization of the enzyme and in the protection from proteolytic inactivation. Novel endo-beta-N-acetylglucosaminidases were also found in the culture broths of microorganisms. Unlike most microbial endo-beta-N-acetylglucosaminidases, Endo-M of Mucor hiemalis could act on a complex type oligosaccharide chains, which is similar to Endo-F2 in multiple form of Endo-F from Flavobacterium meningosepticum. The complete amino acid sequences of Endo-F1, -F2, -F3, -H, and Flavobacterium sp. enzyme were determined. All of them had two highly conserved regions common to a number of chitinases. Endo-alpha-N-acetylgalactosaminidase which hydrolyzes the O-glycosidic linkages in glycoproteins was found in the culture broth of only a few microorganisms. The production of Alcaligenes sp. enzyme was highly induced by the addition of porcine gastric mucin in the culture medium. There is some evidence that endo-alpha-N-acetylgalactosaminidases may recognize not only the glycon but also the aglycon amino acids.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

PubMed1993

Phylogenetic diversity of the genus Cytophaga revealed by 16S rRNA sequencing and menaquinone analysis.

To clarify the intra- and intergeneric relationships of the genus Cytophaga, 16S rRNA sequences and respiratory isoprenoid quinones were determined for the type strains of the 21 validly published species and one isolate in the genus Cytophaga. The sequence analysis revealed extreme heterogeneity of this genus, which diverged into nine distinct lines of descent. Each lineage of Cytophaga was characterized by possessing either menaquinone-6 (MK-6) or MK-7. The MK-6-possessing species were located in the two lineages that were remote from MK-7 species. One of the MK-6 lineages was composed only of terrestrial species and the other only of marine species. Flavobacterium aquatile, the type species of the genus Flavobacterium, was located in the MK-6 terrestrial lineage. The terrestrial Cytophaga species with MK-6 should be transferred to the genus Flavobacterium. The marine facultative anaerobes with MK-7 were located in the bacteroides branch, and possessed signature sequences with features intermediate between the bacteroides and the flavobacteria subdivisions. Cytophaga hutchinsonii, the type species of the genus Cytophaga, had a close relationship only with Cytophaga aurantiaca. The genus Cytophaga should be restricted to these two cellulose-degrading species. The genus Cytophaga is so heterogeneous that it should be divided into several genera and higher taxa in accordance with the phylogenetic relationships.

Base Sequence↗

PubMed1980

In vitro activity of cefoperazone against nonfermenters and Aeromonas hydrophila.

The in vitro activity of cefoperazone against 380 strains (33 species and unnamed groups) of nonferenters and 20 strains of Aeromonas hydrophila was studied by a microdilution method of determining minimal inhibitory concentrations. For comparison, the activities of ampicillin, ticarcillin, and cefamandole were simultaneously studied. Cefoperazone was the most active drug against Pseudomonas sp., Achromobacter xylosoxidans, Flavobacterium meningosepticum. Flavobacterium sp. (group IIb), Group IVc biotype 2, Group Ve, and Aeromonas hydrophila. Against other organisms it was equivalent in activity to or less active than comparative antibiotics. The only organisms which were usually resistant to 128 microgram of cefoperazone per ml were strains of Flavobacterium odoratum and Group IIk biotype 1.

Aeromonas↗

PubMed1981

Kinetic explanation for accumulation of nitrite, nitric oxide, and nitrous oxide during bacterial denitrification.

The kinetics of denitrification and the causes of nitrite and nitrous oxide accumulation were examined in resting cell suspensions of three denitrifiers. An Alcaligenes species and a Pseudomonas fluorescens isolate characteristically accumulated nitrite when reducing nitrate; a Flavobacterium isolate did not. Nitrate did not inhibit nitrite reduction in cultures grown with tungstate to prevent formation of an active nitrate reductase; rather, accumulation of nitrite seemed to depend on the relative rates of nitrate and nitrite reduction. Each isolate rapidly reduced nitrous oxide even when nitrate or nitrite had been included in the incubation mixture. Nitrate also did not inhibit nitrous oxide reduction in Alcaligenes odorans, an organism incapable of nitrate reduction. Thus, added nitrate or nitrite does not always cause nitrous oxide accumulation, as has often been reported for denitrifying soils. All strains produced small amounts of nitric oxide during denitrification in a pattern suggesting that nitric oxide was also under kinetic control similar to that of nitrite and nitrous oxide. Apparent K(m) values for nitrate and nitrite reduction were 15 muM or less for each isolate. The K(m) value for nitrous oxide reduction by Flavobacterium sp. was 0.5 muM. Numerical solutions to a mathematical model of denitrification based on Michaelis-Menten kinetics showed that differences in reduction rates of the nitrogenous compounds were sufficient to account for the observed patterns of nitrite, nitric oxide, and nitrous oxide accumulation. Addition of oxygen inhibited gas production from NO(3) by Alcaligenes sp. and P. fluorescens, but it did not reduce gas production by Flavobacterium sp. However, all three isolates produced higher ratios of nitrous oxide to dinitrogen as the oxygen tension increased. Inclusion of oxygen in the model as a nonspecific inhibitor of each step in denitrification resulted in decreased gas production but increased ratios of nitrous oxide to dinitrogen, as observed experimentally. The simplicity of this kinetic model of denitrification and its ability to unify disparate observations should make the model a useful guide in research on the physiology of denitrifier response to environmental effectors.

Journal Article↗

PubMed1991

Purification and characterization of a secreted recombinant phosphotriesterase (parathion hydrolase) from Streptomyces lividans.

A heterologous phosphotriesterase (parathion hydrolase), previously cloned from a Flavobacterium species into Streptomyces lividans, was secreted at high levels and purified to homogeneity. N-terminal analysis revealed that it had been processed in the same manner as the native membrane-bound Flavobacterium hydrolase. The enzyme consisted of a single polypeptide with an apparent molecular weight of 35,000 as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Substrate specificity studies showed Kms of 68 microM for parathion, 46 microM for O-ethyl O-p-nitrophenyl phenylphosphonothioate, 599 microM for methyl parathion, and 357 microM for p-nitrophenyl ethyl(phenyl)phosphinate. Temperature and pH optima were 45 degrees C and 9.0, respectively. The purified enzyme was inhibited by 1 mM dithiothreitol and 1 mM CuSO4. After chelation and inactivation by o-phenanthroline, however, activity could be partially restored by 1 mM CuCl or 1 mM CuSO4. The results showed that the purified recombinant parathion hydrolase has the same characteristics as the native Flavobacterium hydrolase. This system provides a source of milligram quantities of parathion hydrolase for future structural and mechanism studies and has the potential to be used in toxic waste treatment strategies.

Amino Acid Sequence↗

PubMed2000

Bacterial community structure and physiological state within an industrial phenol bioremediation system.

The structure of bacterial populations in specific compartments of an operational industrial phenol remediation system was assessed to examine bacterial community diversity, distribution, and physiological state with respect to the remediation of phenolic polluted wastewater. Rapid community fingerprinting by PCR-based denaturing gradient gel electrophoresis (DGGE) of 16S rDNA indicated highly structured bacterial communities residing in all nine compartments of the treatment plant and not exclusively within the Vitox biological reactor. Whole-cell targeting by fluorescent in situ hybridization with specific oligonucleotides (directed to the alpha, beta and gamma subclasses of the class Proteobacteria [alpha-, beta-, and gamma-Proteobacteria, respectively], the Cytophaga-Flavobacterium group, and the Pseudomonas group) tended to mirror gross changes in bacterial community composition when compared with DGGE community fingerprinting. At the whole-cell level, the treatment compartments were numerically dominated by cells assigned to the Cytophaga-Flavobacterium group and to the gamma-Proteobacteria. The alpha subclass Proteobacteria were of low relative abundance throughout the treatment system whilst the beta subclass of the Proteobacteria exhibited local dominance in several of the processing compartments. Quantitative image analyses of cellular fluorescence was used as an indicator of physiological state within the populations probed with rDNA. For cells hybridized with EUB338, the mean fluorescence per cell decreased with increasing phenolic concentration, indicating the strong influence of the primary pollutant upon cellular rRNA content. The gamma subclass of the Proteobacteria had a ribosome content which correlated positively with total phenolics and thiocyanate. While members of the Cytophaga-Flavobacterium group were numerically dominant in the processing system, their abundance and ribosome content data for individual populations did not correlate with any of the measured chemical parameters. The potential importance of the gamma-Proteobacteria and the Cytophaga-Flavobacteria during this bioremediation process was highlighted.

Aged↗

PubMed1992

Evaluation of the 4-hour RapID NF Plus method for identification of 345 gram-negative nonfermentative rods.

The ability of the RapID NF Plus system (Innovative Diagnostic Systems, Inc., Atlanta, Ga.) to identify 345 nonfermentative gram-negative rods was evaluated. Kits were inoculated with no. 1 McFarland suspensions, and reactions were interpreted after a 4-h incubation at 35 degrees C. Overall, the method correctly identified 311 strains (90.1%) without additional tests and 21 strains (6.1%) with additional tests, and 13 strains (3.8%) were misidentified. Five of 13 misidentified strains were Alcaligenes faecalis-Alcaligenes odorans misidentified as Alcaligenes xylosoxidans; however, all strains were xylose negative but nitrate positive and could have been A. faecalis group I-Alcaligenes piechaudii. The system does not differentiate between Pseudomonas fluorescens and Pseudomonas putida, and all Acinetobacter species are identified as Acetinobacter calcoaceticus. Additionally, no subspecies differentiation is made between A. xylosoxidans subsp. xylosoxidans and A. xylosoxidans subsp. denitrificans. All strains of the former Flavobacterium group IIb are identified as Flavobacterium indologenes-Flavobacterium gleum, and no species identification of the genus Methylobacterium is attempted. The system is easy to set up and interpret and provides an accurate commercial nonautomated method for same-day identification of gram-negative nonfermenters.

Bacteriological Techniques↗

PubMed1997

Prolyl endopeptidase inhibitors derived from actinomycetes.

Four prolyl endopeptidase inhibitors isolated from actinomycetes, named propeptin, SNA-8073-B, staurosporine, and enduracidin were classified into 3 groups on the basis of their inhibition potency against prolyl endopeptidase from a bacterium (Flavobacterium) and a mammal (human placenta). Staurosporine inhibited the enzyme from Flavobacterium more strongly than that from human placenta. Enduracidin inhibited the enzyme from human placenta more strongly than that from Flavobacterium. Propeptin and SNA-8073-B, both new compounds, inhibited the enzymes from both origins to the same extent.

Actinomycetaceae↗

PubMed1994

[Susceptibilities of glucose non-fermentative gram-negative bacilli to antibiotics].

Glucose non-fermentative Gram-negative bacilli are important nosocomial pathogens. This study concerned with susceptibilities to antibacterial agents of strains of Glucose non-fermentative Gram-negative bacilli that were isolated from cultures of clinical materials at 123 hospital laboratories throughout Japan from September to December of 1991. The tests for susceptibilities were performed according to the disk dilution method recommended by NCCLS. The following bacteria were tested: Pseudomonas aeruginosa, Pseudomonas cepacia, Acinetobacter calcoaceticus, Alcaligenes spp., Alcaligenes xylosoxidans, Flavobacterium spp. and Xanthomonas maltophilia. The antibacterial agents tested were as follows: piperacillin (PIPC), ceftazidime (CAZ), aztreonam (AZT), imipenem (IPM), minocycline (MINO), gentamicin, amikacin (AMK) and ofloxacin (OFLX). 1. Eighty percent of the strains of P. aeruginosa and P. cepacia were sensitive to CAZ. More than ninety percent of the strains of A. calcoaceticus were sensitive to IPM, MINO, OFLX. To PIPC and IPM, about eighty percent of the strains of Alcaligenes spp. and A. xylosoxidans were sensitive. The strains of Flavobacterium spp. and X. maltophilia showed high sensitivities to MINO. 2. Annual changes in antimicrobial susceptibility patterns over 4 years (1988-1991) show that there has been a gradual increase in sensitive strains of P. aeruginosa to PIPC, CAZ and AMK. Sensitive strains of P. cepacia to AZT, IPM and MINO, and A. calcoaceticus to CAZ and MINO also have gradually increased. No yearly changes were observed in high sensitivity to MINO of the strains of Flavobacterium spp. and X. maltophilia.

Anti-Bacterial Agents↗

PubMed1977

Properties and biodegradation of a bioemulsifier from Corynebacterium hydrocarboclastus.

An extracellular polymer was produced by continuous fermentation of Corynebacterium hydrocarboclastus on kerosene in a 24 liter reactor. This polymer was composed of protein, lipid, and carbohydrates. The polymer possessed surface active properties, and had two critical micelle concentrations. Its effectiveness was quite comparable to the effectiveness of synthetic surface active agents such as Tween 80 and Span 20; however, its efficiency was much lower. The polymer also had emulsifying properties. Maximum emulsification was obtained at pH 6. The emulsifying properties were unaffected by high salt concentration [up to 5% (w/v) in Na+], and tolerated a water hardness up to 5,000 ppm. A 2 hr treatment of the polymer at temperatures higher than 65 degrees C resulted in a loss of its emulsifying properties. Two microorganisms, named SLYS and Y, isolated from soil, were able to grow on the polymer as sole carbon and energy source, thus proving its biodegradability. SLYS was tentatively identified as Flavobacterium breve and Y as Flavobacterium devorans.

Bacterial Proteins↗

PubMed1993

The first demonstration of a procaryotic glycosylasparaginase.

Glycosylasparaginase was purified to near homogeneity from intracellular lysates of Flavobacterium meningosepticum. The enzyme is a heterodimer with an estimated molecular weight of 38 kDa and consists of one alpha-subunit (18 kDa) and one beta-subunit (16 kDa). The beta-subunit of the Flavobacterium enzyme has a direct evolutionary relationship to the beta-subunit of mammalian glycosylasparaginases as evidenced by: (1) strong cross-reactivity with antibodies made to the denatured rat beta-subunit, (2) a high degree of homology with the amino-terminus of the corresponding eukaryotic enzymes, and (3) irreversible inactivation with 5-diazo-4-oxo-L-norvaline, a reagent known to react with the catalytic amino-terminal threonine residue on the beta-subunit of a mammalian glycosylasparaginase.

Amidohydrolases↗

PubMed1992

The effect of signal sequences on the efficiency of secretion of a heterologous phosphotriesterase by Streptomyces lividans.

A heterologous phosphotriesterase (parathion hydrolase) containing the native Flavobacterium species signal sequence was previously shown to be secreted by Streptomyces lividans. Western blot analysis of the recombinant phosphotriesterase produced by S. lividans demonstrated only the mature form extracellularly but both processed and unprocessed forms in cell-associated samples. To investigate the efficiency of secretion in Streptomyces, a construction was made that substituted a native Streptomyces beta-galactosidase signal sequence for the Flavobacterium signal sequence. This resulted in a higher proportion of hydrolase in the extracellular fluid and a lower proportion of parathion hydrolase remaining cell-associated. These results suggest that use of a native Streptomyces signal sequence may result in more efficient secretion of heterologous proteins.

Amino Acid Sequence↗

PubMed1990

Pressure transducers: an overlooked source of sepsis in the intensive care unit.

Between January 1988 and May 1989 twenty cases of bacteremia due to Flavobacterium sp. occurred in 17 patients admitted to a surgical intensive care unit. Epidemiologic studies disclosed that the source of the Flavobacterium bacteremias was contaminated reusable pressure transducers. Despite the use of disposable domes spread of the bacteria from the contaminated transducer heads to the fluids given to the patients occurred. An indirect contamination by hands at the time the equipment was initially assembled must have been the mode of transmission. Reinstitution of routine disinfection of the transducer heads controlled the outbreak. Disposable domes failed to prevent septicemia from contaminated pressure transducers.

Cross Infection↗

PubMed2001

Isolation and characterization of a Chryseobacterium strain from the gut of the American cockroach, Periplaneta americana.

A 16S rDNA sequence cloned directly from whole-gut microbiota of the American cockroach, Periplaneta americana, indicated the presence of a member of the Bacteroides/Flavobacterium group most closely related to the genus Flavobacterium. In an attempt to confirm this finding, we isolated a yellow-pigmented bacterium (strain FR2) from the hindgut of this insect. Strain FR2 was phylogentically and phenotypically most similar to species of Flavobacterium and related bacteria, namely Chryseobacterium indologenes. Fifty-four other yellow-pigmented bacteria isolated during a 1-year study shared the salient phenotypic characteristics of Chryseobacterium spp., and thus were considered the same phenotype. This phenotype's abundance was related to the fiber content of the insect diet, being consistently detected only in cockroaches fed a high-fiber diet (30% crude fiber by weight). The highest population density was in the hindgut, ranging from 2 x 10(6) to 1.2 x 10(7) colony forming units ml(-1) during a 1-year period. The nature of the symbiosis between the FR2 phenotype and P. americana is discussed.

Animals↗

PubMed1988

The mechanism of experimental adipocere formation: hydration and dehydrogenation in microbial synthesis of hydroxy and oxo fatty acids.

The enzyme preparations from Flavobacterium meningosepticum solubilized by sonication catalyzed not only hydration of oleic acid to produce 10-hydroxystearic acid but dehydrogenation of this product. The mechanism of the hydration and dehydrogenation was proved by gas chromatography-mass spectrometry of 10-hydroxy and 10-oxostearic acids produced in the presence of D2O or H2(18)O. The activity of these enzymes was increased by preincubating Flavobacterium meningosepticum with oleic acid.

Chromatography, Thin Layer↗

PubMed1999

The response of the microbial community of marine sediments to organic carbon input under anaerobic conditions.

Cyanobacterial biomass was added to anaerobic sediment to simulate the natural input of complex organic substrate that occurs in nature after algae blooms. Sediments were incubated at 0 degree C, 8 degrees C and 24 degrees C for 13 days. Community dynamics were measured by fluorescence in situ hybridisation (FISH), denaturing gradient gel electrophoresis (DGGE), and sequencing of 16S rDNA PCR products. Metabolic changes were followed by the analysis of total carbon mineralisation, sulfate reduction, and ammonium production rates. The addition of organic material resulted in significant changes in the composition of the microbial community at all temperatures tested. Sulfate reduction was the main mineralisation process detected. However, not sulfate-reducers but rather members of the Cytophaga-Flavobacterium phylogenetic cluster showed the highest increase in the bacterial cells as detected by FISH. We conclude that these organisms play an important role in the anaerobic decomposition of complex organic material perhaps because they are the main catalysts of macromolecule hydrolysis and fermentation. The molecular methods also indicated a stimulation of ribosome synthesis. The detection of a large number of rRNA-rich cells belonging to the Cytophaga-Flavobacterium phylogenetic cluster further supports the importance of their role in the degradation of complex organic material in anaerobic marine sediments. Their detection in high numbers in the field may indicate recent deposition events.

Anaerobiosis↗

PubMed1983

Evidence showing that a proline-specific endopeptidase has an absolute requirement for a trans peptide bond immediately preceding the active bond.

The proline-specific endopeptidase (EC 3.4.21.26) from Flavobacterium meningosepticum is specific for the cleavage of peptide bonds on the C-terminal side of prolyl residues. Such bonds will normally exist in the all-trans configuration. However, the preceding peptide bond in the sequence (i.e., on the N-terminal side of the prolyl residue) will exist as a mixture of cis and trans forms in solution. In this study, the activity of the proline-specific endopeptidase toward the substrates N-Cbz-Gly-Pro-MCA (where MCA = 4-methylcoumarinyl-7-amine) and N-Cbz-Gly-Pro-Leu-Gly has been examined. At a high ratio of enzyme activity/substrate concentration, the hydrolysis pattern for each substrate shows two well-separated kinetic phases. It is concluded that the fast kinetic phase, whose velocity depends on enzyme concentration, results from the direct hydrolysis of the active substrate bond (i.e., either the Pro-MCA or Pro-Leu bond, respectively) in molecules where the preceding Gly-Pro bond is trans. The slow phase, whose velocity is independent of enzyme concentration, is rate-limited by the cis-to-trans isomerization of those substrate molecules which initially have the preceding Gly-Pro bond in the cis configuration. That is, substrate molecules having the cis form of the Gly-Pro bond which precedes the active bond cannot be hydrolyzed directly but must first isomerize to the trans form before cleavage can occur. The amplitude, relaxation time, and activation energy for the slow phase are consistent with this interpretation. Thus, the proline-specific endopeptidase from Flavobacterium has an absolute requirement for a trans peptide bond at the position immediately preceding the active bond.

Amino Acid Sequence↗

PubMed2003

Mixed culture optimization for marigold flower ensilage via experimental design and response surface methodology.

Endogenous microorganisms isolated from the marigold flower (Tagetes erecta) were studied to understand the events taking place during its ensilage. Studies of the cellulase enzymatic activity and the ensilage process were undertaken. In both studies, the use of approximate second-order models and multiple lineal regression, within the context of an experimental mixture design using the response surface methodology as optimization strategy, determined that the microorganisms Flavobacterium IIb, Acinetobacter anitratus, and Rhizopus nigricans are the most significant in marigold flower ensilage and exhibit high cellulase activity. A mixed culture comprised of 9.8% Flavobacterium IIb, 41% A. anitratus, and 49.2% R. nigricans used during ensilage resulted in an increased yield of total xanthophylls extracted of 24.94 g/kg of dry weight compared with 12.92 for the uninoculated control ensilage.

Acinetobacter↗