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PubMed1994

Structural studies on the oligosaccharides isolated from bovine kidney heparan sulphate and characterization of bacterial heparitinases used as substrates.

We prepared a series of oligosaccharides from commercial bovine kidney heparan sulphate after limited digestion with heparitinase I from Flavobacterium heparinum, and determined the structures of eight tetrasaccharides and a hexasaccharide by enzymatic analysis, fast atom bombardment mass spectrometry and 500 MHz 1H NMR spectroscopy. The tetrasaccharides share the common core structure delta 4,5HexA alpha 1-4GlcN alpha 1-4HexA1-4GlcN (where delta 4,5HexA is 4-deoxy-alpha-L-threo-hex-4-enopyranosyluronic acid and HexA is hexuronic acid), with zero, one or two sulphate groups. Seven of them contain non-sulphated glucuronic or iduronic acid, and the other, 2-O-sulphated iduronic acid at the internal position. Although they contain ordinary structures which should be widely distributed in the relatively low-sulphated region of heparan sulphate, five of the tetrasaccharides were isolated for the first time as discrete structures. The structure of the hexasaccharide was determined as delta 4,5HexA alpha 1-4GlcNAc alpha 1-4GlcA beta 1-3Gal beta 1-3Gal beta-1-4 Xyl and is derived from the carbohydrate-protein linkage region of the heparan sulphate chains. The hexasaccharide seems to have been released by the alkaline treatment used to prepare the heparan sulphate. The Gal residues were non-sulphated as are those in the porcine intestinal heparin chains, but in contrast to the sulphated Gal structures previously demonstrated in the carbohydrate-protein linkage region of chondroitin sulphate chains. These oligosaccharides were used to investigate the substrate specificity of heparitinases I and II from F. heparinum. The results revealed that heparitinase I cleaves hexosaminidic bonds linked to non-sulphated glucuronic or iduronic acid residues. The glucosaminidic linkage of the hexasaccharide was sensitive to heparitinase I, but resistant to heparitinase II, demonstrating the differential specificity of these enzymes towards the carbohydrate-protein linkage region.

Animals↗

PubMed1998

Characterization of heparinase from an oral bacterium Prevotella heparinolytica.

Heparinase was purified to homogeneity from the cell extract of an oral bacterium, Prevotella heparinolytica, by a combination of anion exchange chromatography, gel filtration chromatography, and hydroxyapatite chromatography. Properties of the purified P. heparinolytica heparinase (P. heparinase) were investigated. The enzyme exhibited a maximum activity in 50 mM Tris-HCl buffer, pH 7.5-8.0, containing 75 mM sodium acetate, 0.1 M NaCl, and 1 mM CaCl2. Optimum conditions for the maximum activity of P. heparinase were similar to those of the heparinase from Flavobacterium heparinum (F. heparinase). The two enzymes also yielded similar digestion profiles of various glycosaminoglycans and heparin tetrasaccharides, suggesting that they have a similar substrate specificity. Kinetic study of the P. heparinase reaction using porcine intestinal heparin as substrate gave a Km value of 3.8 x 10(-5) M and a Vmax value of 11.4 micromol/min x mg protein. The Michaelis constant of P. heparinase was slightly larger than but not significantly different from that of F. heparinase. The amino acid composition of P. heparinase was also similar to that of F. heparinase, but its N-terminal sequence of 20 amino acid residues was different and hitherto unreported. These results together indicate that these heparinases are different proteins with closely similar enzymatic properties. Since F. heparinum produces not only heparinase but also heparitinase II, which has a broad substrate specificity, F. heparinase may be contaminated with this enzyme. In contrast, P. heparinolytica does not produce heparitinase II, and P. heparinase should prove a useful tool for degrading heparin without the risk of contamination with heparitinase II.

Amino Acid Sequence↗

PubMed1991

Microbial endo-beta-N-acetylglucosaminidases acting on complex-type sugar chains of glycoproteins.

The activity and substrate specificity of endo-beta-N-acetylglucosaminidase [glycopeptide-D-mannosyl-N4-(N-acetyl-D-glucosaminyl)2-asparagine 1,4-N-acetyl-beta-glucosamino-hydrolase, EC 3.2.1.96] obtained from Mucor hiemalis (Endo-M) was compared with that of the enzyme obtained from Flavobacterium meningosepticum (Endo-F), which is the only enzyme available that acts on the complex oligosaccharides of asparagine-linked sugar chains in glycoproteins. They showed almost the same activities toward DNS-ovalbumin glycopeptide containing high-mannose and hybrid asparagine-linked oligosaccharides. However, Endo-M showed high activity towards DNS-asialotransferrin and DNS-transferrin glycopeptides, which contain complex biantennary oligosaccharides. Endo-M could weakly act even on DNS-asialofetuin glycopeptide containing complex triantennary oligosaccharides, while Endo-F could not. SDS-denatured asialotransferrin was deglycosylated by both enzymes in the presence of non-ionic detergent (NP-40) and EDTA, and the deglycosylated protein migrated to a lower molecular weight position than asialotransferrin on SDS-PAGE. However, even in the absence of detergent, Endo-M deglycosylated native asialotransferrin and transferrin. Deglycosylation of asialotransferrin was confirmed by means of Con A-Sepharose 4B column chromatography and SDS-PAGE.

Asialoglycoproteins↗

PubMed1976

Action of chondroitinases. II. Numerical calculation of the degree of multiple attack.

Further investigation was carried out on the action patterns of two chondroitinase-AC [EC 4.2.2.5.] preparations obtained from Arthrobacter aurescens and Flavobacterium heparinum. To infer the action patterns of the chondroitinases, we proposed a new method for the calculation of the degree of multiple attack, based on the concept established by Robyt and French ((1967) Arch. Biochem. Biophys. 122, 8-16). It was shown that the degree of multiple attack (DM) is represented by the ratio of the initial velocity of number-average degree of scission to that of viscosity-average degree of scission. By this method, DM for A-Chase was estimated to be 3.03 and for F-chase, 1.31.

Arthrobacter↗

PubMed1978

Interaction of mucopolysaccharides with glycosaminoglycans on glycosaminoglycan-bound AH-Sepharose 4B.

Chondroitinase C, chondroitinase AC, heparinase, and heparitinase separated from an extract of Flavobacterium heparinum were subjected to affinity chromatography with glycosaminoglycan-bound AH-Sepharose 4B, previously coated non-covalently with glycosaminoglycan, as the matrix. The results suggested the importance of coating the matrix with glycosaminoglycan in the binding of the enzyme protein to the matrix.

Chondroitinases and Chondroitin Lyases↗

PubMed1980

L-Lysine: 2-oxoglutarate 6-aminotransferase. Subunit structure composed of non-identical polypeptides and pyridoxal 5'-phosphate-binding subunit.

L-Lysine:2-oxoglutarate 6-aminotransferase from Flavobacterium lutescence (= Achromobacter liquidum) has been shown to be composed of one each of four non-identical subunits, A, B1, B2, and C. The subunits were isolated by gel filtration, and DEAE-cellulose chromatography in the presence of 8 M urea. Their molecular weights were determined by ultracentrifugation, gel electrophoresis and gel filtration: subunit A 24,000; B1 28,000; B2 28,000; C 45,000. These subunits were all different in amino acid composition. Of the two molecules of bound pyridoxal 5'-phosphate, the one which absorbs at 415 nm is bound to subunit B2 and participates in the catalytic action of the enzyme.

Amino Acids↗

PubMed1981

Degradative removal of heparan sulfate from the surface of an ascites hepatoma, AH 66, by heparitinase.

Heparitinase [EC 4.2.2.8, heparitin sulfate lyase] was prepared from an extract of cultured cells of Flavobacterium heparinum. Purification of the enzyme was achieved by repeating the hydroxyapatite column chromatography. The enzyme was used to degrade heparan sulfate occurring on the surfaces of ascites hepatoma cells, AH 66. From the supernatant of the enzyme-treated cells, breakdown products from heparan sulfate could be detected by paper chromatography. The heparitinase was found to be more effective than trypsin in removing heparan sulfate from the cells. Furthermore, on analyzing glycosaminoglycans and glycopeptides from the enzyme-treated cells and control cells, it was concluded that heparan sulfate was exclusively present on the cell surface and accessible to the heparitinase whereas other cell surface complex carbohydrates remained intact.

Animals↗

PubMed1986

Chemical modification by diethylpyrocarbonate of an essential histidine residue in 3-ketovalidoxylamine A C-N lyase.

3-Ketovalidoxylamine A C-N lyase of Flavobacterium saccharophilum is a monomeric protein with a molecular weight of 36,000. Amino acid analysis revealed that the enzyme contains 5 histidine residues and no cysteine residue. The enzyme was inactivated by diethylpyrocarbonate (DEP) following pseudo-first order kinetics. Upon treatment of the inactivated enzyme with hydroxylamine, the enzyme activity was completely restored. The difference absorption spectrum of the modified versus native enzyme exhibited a prominent peak around 240 nm, but there was no absorbance change above 270 nm. The pH-dependence of inactivation suggested the involvement of an amino acid residue having a pKa of 6.8. These results indicate that the inactivation is due to the modification of histidine residues. Substrates of the lyase, p-nitrophenyl-3-ketovalidamine, p-nitrophenyl-alpha-D-3-ketoglucoside, and methyl-alpha-D-3-ketoglucoside, protected the enzyme against the inactivation, suggesting that the modification occurred at or near the active site. Although several histidine residues were modified by DEP, a plot of log (reciprocal of the half-time of inactivation) versus log (concentration of DEP) suggested that one histidine residue has an essential role in catalysis.

Amino Acids↗

PubMed1994

A prolyl endoproteinase that acts specifically on the extrinsic 18-kDa protein of photosystem II: purification and further characterization.

An endoproteinase, which specifically cleaves the Pro12-Leu13 bond of the extrinsic 18-kDa protein of PSII, was purified from PSII membranes of spinach. The presence of 0.05% (w/v) Tween 20 and 1 M NaCl was essential for maintenance of proteolytic activity during the purification. The molecular mass of the enzyme was estimated to be 95 kDa by gel-filtration chromatography. Active fractions contained a polypeptide of 165 kDa that was converted into diffusely stained polypeptides of 54 kDa upon reduction with dithiothreitol. The Km of the 18-kDa protein in the proteolytic reaction was 0.3 microM. Inhibition of the proteolysis by compounds that contain prolyl bonds revealed that both a prolyl bond and a positive charge are necessary for interaction with the proteinase, but some other structural factor(s) must also be involved in the high-affinity interaction between the proteinase and the 18-kDa protein. Reconstitution of NaCl-treated PSII membranes with the 23-kDa protein and/or the 18-kDa protein revealed that the 18-kDa protein was not cleaved by the proteinase when the substrate protein was functionally associated with the membranes. A comparison of the properties of the proteinase with those of a proline-specific endopeptidase from Flavobacterium suggests that these enzymes are quite different in terms of substrate specificity.

Amino Acid Sequence↗

PubMed1998

A case of spontaneous peritonitis caused by Weeksella virosa.

A case of spontaneous peritonitis caused by Weeksella virosa is reported. This Flavobacterium has never been reported as a cause of spontaneous bacterial peritonitis. The patient responded to antimicrobial therapy. Clinical and therapeutic implications are discussed.

Flavobacterium↗

PubMed1999

Description of Cellulophaga baltica gen. nov., sp. nov. and Cellulophaga fucicola gen. nov., sp. nov. and reclassification of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov.

Phenotypic data indicate that gliding, yellow/orange-pigmented, agar-digesting bacterial strains were members of the Cytophaga-Flavobacterium-Bacteroides (CFB) group. The strains were isolated from the surface of the marine benthic macroalga Fucus serratus L. and the surrounding seawater at three localities in Danish waters. The bacteria were Gram-negative, flexirubin-negative, aerobic, catalase-positive and oxidase-negative and were psychrophilic and halophilic. All strains utilized D-fructose, L-fucose and alpha-ketobutyric acid and degraded alginic acid, carrageenan, starch and autoclaved yeast cells. Amplification with primers specific for repetitive extragenic palindromic elements by PCR divided the strains of this study into two groups. Both groups showed unique PCR amplification patterns compared to reference strains of the CFB group. Phylogenetic analysis of 16S rDNA sequences showed association of these organisms and [Cytophaga] lytica at the genus level. Hybridization of total chromosomal DNA revealed that the new strains and [Cytophaga] lytica ATCC 23178T were clearly distinct from each other and other previously described species of the CFB group. A new genus is described, Cellulophaga gen. nov. comprising two new species, Cellulophaga baltica gen. nov., sp. nov. (NN015840T = LMG 18535T) and Cellulophaga fucicola gen. nov., sp. nov. (NN015860T = LMG 18536T), as well as the emendation of [Cytophaga] lytica to Cellulophaga lytica gen. nov., comb. nov.

Bacteria↗

PubMed1999

Phylogenetic analysis of genus Marinilabilia and related bacteria based on the amino acid sequences of gyrB and emended description of Marinilabilia salmonicolor with Marinilabilia agarovorans as its subjective synonym.

The detailed phylogenetic relationships for genus Marinilabilia and related taxa were analysed by using DNA gyrase B subunit gene (gyrB) sequences. Anaerobic bacteria in the Cytophaga-Flavobacterium-Bacteroides phylum, namely genera Marinilabilia, Bacteroides, Rikenella, Prevotella and Porphyromonas and Cytophaga fermentans, were clustered in the same branch and the facultative anaerobes Marinilabilia and Cytophaga fermentans formed a subcluster in the branch of the anaerobic bacteria. Phylogenetic analysis using 16S rDNA sequences gave a similar result but with a lower bootstrap value for each cluster. The gyrB sequences of Marinilabilia salmonicolor and Marinilabilia agarovorans were the same, and the relatedness of their chromosomal DNA, as determined by DNA-DNA hybridization, was greater than 70%. These genetic aspects led to the conclusion that M. salmonicolor IFO 15948T and M. agarovorans IFO 14957T belong to a single species. Since M. salmonicolor was described first, as Cytophaga salmonicolor, M. salmonicolor is a senior subjective synonym of M. agarovorans. Therefore, the name M. salmonicolor should be retained and strain IFO 14957T should be reclassified as M. salmonicolor. However, the agar-degrading ability of strain IFO 14957T is a prominent biochemical characteristic. It is therefore proposed that strain IFO 14957T should be renamed M. salmonicolor biovar agarovorans.

Amino Acid Sequence↗

PubMed1982

The similarities between Pseudomonas paucimobilis and allied bacteria derived from analysis of deoxyribonucleic acids and electrophoretic protein patterns.

The chromosomal DNA was isolated and purified from 17 strains of Pseudomonas paucimobilis, and from the type or reference strains of Flavobacterium capsulatum, F. devorans, F. multivorum, 'Chromobacterium lividum', Xanthomonas campestris and seven species of Pseudomonas. The DNA base compositions (mol% G + C) of P. paucimobilis strains were between 62.2 and 68.6%, and typical strains had a mean value of 65.3 +/- 0.4 mol%, determined from thermal denaturation temperature. DNA-DNA molecular hybridization with 3H-labelled probe DNA from NCTC 11030 P. paucimobilis (the type strain) indicated that the species comprised a core of 13 closely related strains (74 to 96%), which included F. devorans NCIB 8195 (= ATCC 10829). Four P. paucimobilis strains displayed lower levels of hybridization (less than or equal to 38%). The hybridization results showed that P. paucimobilis was not closely related to allied yellow-pigmented bacteria or to other reference pseudomonads. The electrophoretic protein patterns of representative strains were analysed by computer-assisted techniques and similarity coefficients were calculated. A high degree of congruence was obtained with the DNA hybridization data, and the protein analyses indicated that the four atypical P. paucimobilis strains were heterogeneous and not a single group within the species. The generic affinities of P. paucimobilis, F. capsulatum, 'P. azotocolligans' and P. echinoides are uncertain, but available chemotaxonomic data indicate these species could provide the basis for a new genus.

Bacterial Proteins↗

PubMed1993

Characterization of the 6-aminohexanoate-dimer hydrolase from Pseudomonas sp. NK87.

The DNA base sequence of the Pseudomonas sp. NK87 gene (P-nylB) for 6-aminohexanoate-dimer hydrolase (P-EII), a xenobiotic-compound-degrading enzyme, was determined. It has an open reading frame of 1188 bp, initiated by ATG and terminated by TAG, and coding for 396 amino acids. The base sequence of the open reading frame has 53% sequence similarity to that of the gene for the same enzyme of Flavobacterium sp. KI72 (F-nylB) and 35% sequence similarity with respect to the deduced amino acid sequence. The P-EII enzyme was purified from an Escherichia coli clone in which the P-EII gene was highly expressed. The P-EII enzyme was inhibited by a serine protease inhibitor, diisopropyl fluorophosphate, as was the F-EII enzyme. Double reciprocal plots obtained from various concentrations of 6-aminohexanoate-dimer indicated that the kcat value of the P-EII enzyme (9.2 s-1) was approximately half that of the F-EII enzyme (19 s-1), and the P-EII enzyme had higher affinity toward this substrate (Km for P-EII, 0.6 mM; Km for F-EII, 15 mM). The P-EII enzyme had a temperature optimum of 48 degrees C, and a pH optimum of 7.5. It is speculated that since the P-nylB and F-nylB genes are more diverged from each other than the corresponding nylA genes, the latter may have evolved more recently.

Amidohydrolases↗

PubMed1995

A plasmid encoding enzymes for nylon oligomer degradation: nucleotide sequence and analysis of pOAD2.

The entire nucleotide sequence of nylon oligomer degradative plasmid pOAD2 from Flavobacterium sp. KI723T1 was determined. pOAD2 comprises 45519 bp, with a 66.6 mol% G+C content. The precise loci of the four nylon oligomer degradation genes, namely nylA (6-aminohexanoate-cyclic-dimer hydrolase gene), nylB (6-aminohexanoate-dimer hydrolase), nylB' (a gene having 88% homology to nylB) and nylC (endo-type 6-aminohexanoate oligomer hydrolase), and five IS6100 elements were identified on this plasmid. Comparison of the sequence of pOAD2 with those in the GenBank and EMBL databases revealed that the deduced amino acid sequences from eight regions of pOAD2 had significant similarity with the sequences of gene products such as oppA-F (oligopeptide permeases), ftsX (filamentation temperature sensitive), penDE (isopenicillin N-acyltransferase) and rep (plasmid incompatibility). A functional map of pOAD2 is presented.

Amidohydrolases↗

PubMed1996

Application of a suite of 16S rRNA-specific oligonucleotide probes designed to investigate bacteria of the phylum cytophaga-flavobacter-bacteroides in the natural environment.

We designed a panel of four 16S rRNA-targeted oligonucleotide probes specific for bacteria of the phylum cytophaga-flavobacter-bacteroides (CFB). Probes CF319a and CF319b are targeted to members of the flavobacteria-cytophaga group and the genus Porphyromonas, whereas probe BAC303 has a target region characteristic for the genera Prevotella and Bacteroides within the bacteroides group. The probe FFE8b was developed for species-specific hybridizations with Flavobacterium ferrugineum. All probes were designed by computer-assisted sequence analysis and compared to all currently accessible 16S and 23S rRNA sequences. The oligonucleotides were further evaluated by whole-cell and non-radioactive dot-blot hybridization against reference strains of the CFB phylum and other major lineages of Bacteria. The newly developed probes were used together with other higher-order probes to analyse the structure and community composition in complex environments. In activated sludge samples, members of the flavobacteria-cytophaga group were revealed by in situ hybridization as important constituents of sludge flocs and characteristic colonizers of filamentous bacteria. By application of fluorescent probe BAC303, members of the genera Bacteroides and Prevotella could be visualized without prior cultivation as an important part of the human faecal microflora.

Bacteroides↗

PubMed2004

Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark.

A number of bacteria were isolated from sea water in Skagerrak, Denmark, at 30 m depth. Two of the isolates, strains D28 and D30(T), belonged to the Flavobacteriaceae within the Cytophaga-Flavobacterium-Bacteroides group. Sequencing of 16S rRNA genes of the two strains indicated strongly that they belonged to the genus Tenacibaculum and that they showed greatest similarity to the species Tenacibaculum amylolyticum and Tenacibaculum mesophilum. DNA-DNA hybridization values, DNA base composition and phenotypic characteristics separated the Skagerrak strains from the other species within TENACIBACULUM: Thus, it is concluded that the strains belong to a novel species within the genus Tenacibaculum, for which the name Tenacibaculum skagerrakense sp. nov. is proposed, with strain D30(T) (=ATCC BAA-458(T)=DSM 14836(T)) as the type strain.

Base Composition↗

PubMed2004

Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment.

Three marine strains of the Cytophaga-Flavobacterium-Bacteroides group, designated JC2050T, JC2051T and JC2052T, were obtained from a single sediment sample of getbol, the Korean tidal flat. Comparative 16S rDNA sequence studies revealed that the test strains were not closely related to any validly published genera and that these strains were only distantly related to the genus Cyclobacterium (88.7-91.2%). Phylogenetic analyses demonstrated that the three getbol isolates formed a distinct monophyletic clade within the family Cytophagaceae. Physiological, biochemical and chemotaxonomic data also indicated that these three getbol isolates differed significantly from members of other genera and were sufficiently different from each other to be recognized as separate species. On the basis of polyphasic evidence, a new genus, Hongiella gen. nov., is proposed, with three novel species, Hongiella mannitolivorans sp. nov. (type strain JC2050T=IMSNU 14012T=DSM 15301T), Hongiella halophila sp. nov. (type strain JC2051T=IMSNU 14013T=DSM 15292T) and Hongiella ornithinivorans sp. nov. (type strain JC2052T=IMSNU 14014T=DSM 15282T). Hongiella mannitolivorans is the type species of the genus.

Bacteroides↗