The three-dimensional structures of two beta-agarases. (1/251)

Agars are important gelifying agents for biochemical use and the food industry. To cleave the beta-1,4-linkages between beta-d-galactose and alpha-l-3,6-anhydro-galactose residues in the red algal galactans known as agars, marine bacteria produce polysaccharide hydrolases called beta-agarases. Beta-agarases A and B from Zobellia galactanivorans Dsij have recently been biochemically characterized. Here we report the first crystal structure of these two beta-agarases. The two proteins were overproduced in Escherichia coli and crystallized, and the crystal structures were determined at 1.48 and 2.3 A for beta-agarases A and B, respectively. The structure of beta-agarase A was solved by the multiple anomalous diffraction method, whereas beta-agarase B was solved with molecular replacement using beta-agarase A as model. Their structures adopt a jelly roll fold with a deep active site channel harboring the catalytic machinery, namely the nucleophilic residues Glu-147 and Glu-184 and the acid/base residues Glu-152 and Glu-189 for beta-agarases A and B, respectively. The structures of the agarases were compared with those of two lichenases and of a kappa-carrageenase, which all belong to family 16 of the glycoside hydrolases in order to pinpoint the residues responsible for their widely differing substrate specificity. The relationship between structure and enzymatic activity of the two beta-agarases from Z. galactanivorans Dsij was studied by analysis of the degradation products starting with different oligosaccharides. The combination of the structural and biochemical results allowed the determination of the number of subsites present in the catalytic cleft of the beta-agarases.  (+info)

Vitellibacter vladivostokensis gen. nov., sp. nov., a new member of the phylum Cytophaga-Flavobacterium-Bacteroides. (2/251)

A novel heterotrophic, yellow-orange-pigmented, non-motile, asporogenic, strictly aerobic, Gram-negative, oxidase and catalase-positive bacterium KMM 3516(T) was isolated from the holothurian Apostichopus japonicus collected from Troitsa Bay in the Gulf of Peter the Great (Sea of Japan) during November 1997. 16S rDNA sequence analysis revealed that strain KMM 3516(T) was a member of the family FLAVOBACTERIACEAE: The DNA G+C content of KMM 3516(T) was 41.3 mol%. Major respiratory quinone was MK-6. Predominant fatty acids were i15 : 0 and alpha15 : 0 (68.8 and 8.4 %, respectively). On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic characteristics, the novel bacterium has been designated Vitellibacter vladivostokensis gen. nov., sp. nov. The type strain is KMM 3516(T) (=NBRC 16718(T)).  (+info)

Arenibacter troitsensis sp. nov., isolated from marine bottom sediment. (3/251)

A novel marine, heterotrophic, aerobic, pigmented, non-motile bacterium was isolated from a bottom sediment sample collected from Troitsa Bay in the Gulf of Peter the Great, Sea of Japan, during June 2000. 16S rDNA sequence analysis revealed that this bacterium was a member of the family FLAVOBACTERIACEAE: On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the bacterium was shown to belong to a novel species of the genus Arenibacter, for which the name Arenibacter troitsensis sp. nov. is proposed. The type strain is KMM 3674(T) (=JCM 11736(T)).  (+info)

Mesonia algae gen. nov., sp. nov., a novel marine bacterium of the family Flavobacteriaceae isolated from the green alga Acrosiphonia sonderi (Kutz) Kornm. (4/251)

The taxonomic position of four heterotrophic, aerobic, Gram-negative, non-motile and moderately halophilic marine bacteria, isolated from the green alga Acrosiphonia sonderi (Kutz) Kornm, was established. 16S rDNA sequence analysis indicated that the strains studied are members of the family Flavobacteriaceae, in which they form a distinct lineage. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic data, the novel bacteria were classified as Mesonia algae gen. nov., sp. nov. The type strain is KMM 3909(T) (=KCTC 12089(T)=CCUG 47092(T)).  (+info)

Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. (5/251)

Two heterotrophic, aerobic, Gram-negative, pigmented and non-motile marine bacteria that were isolated from the green alga Ulva fenestrata were studied by polyphasic taxonomic methods. 16S rDNA sequence analysis indicated that strain KMM 3912T formed a distinct lineage within the family Flavobacteriaceae. On the basis of phenotypic, chemotaxonomic, genotypic and phylogenetic analyses, the novel bacteria were classified as Ulvibacter litoralis gen. nov., sp. nov. The type strain is KMM 3912T (=KCTC 12104T=CCUG 47093T).  (+info)

Gillisia limnaea gen. nov., sp. nov., a new member of the family Flavobacteriaceae isolated from a microbial mat in Lake Fryxell, Antarctica. (6/251)

A taxonomic study was performed on three strains isolated from microbial mats in Lake Fryxell, McMurdo Dry Valleys, Antarctica. Phylogenetic analysis based on 16S rRNA gene sequences indicated that these strains belong to the family Flavobacteriaceae, in which they form a distinct lineage. The isolates are Gram-negative, chemoheterotrophic, aerobic, rod-shaped cells. They are psychrophilic and yellow-pigmented, with DNA G+C contents in the range 37.8-38.9 mol%. Whole-cell fatty acid profiles revealed mainly branched fatty acids and 17 : 0 2-OH. On the basis of genotypic, phenotypic, chemotaxonomic and phylogenetic results, it is proposed that the isolates represent a novel species in a new genus, Gillisia limnaea gen. nov., sp. nov. The type strain is LMG 21470(T) (=DSM 15749(T)).  (+info)

Tenacibaculum skagerrakense sp. nov., a marine bacterium isolated from the pelagic zone in Skagerrak, Denmark. (7/251)

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.  (+info)

Cellulophaga pacifica sp. nov. (8/251)

Three marine, heterotrophic, aerobic, agarolytic, pigmented and gliding bacteria were isolated in June 2000 from a sea water sample that was collected in the Gulf of Peter the Great, Sea of Japan, and analysed in a polyphasic taxonomic study. 16S rDNA sequence analysis indicated that strains KMM 3664(T), KMM 3669 and KMM 3915 were members of the family Flavobacteriaceae. Based on phenotypic, chemotaxonomic, genotypic and phylogenetic data, the isolates were classified in the genus Cellulophaga as members of a novel species, Cellulophaga pacifica sp. nov. The type strain is KMM 3664(T) (=JCM 11735(T)=LMG 21938(T)).  (+info)