The cold-inducible icl gene encoding thermolabile isocitrate lyase of a psychrophilic bacterium, Colwellia maris. (1/120)

The gene encoding isocitrate lyase (ICL; EC of a psychrophilic bacterium, Colwellia maris, was cloned and sequenced. The ORF of the gene (icl) was 1584 bp long, and the predicted gene product consisted of 528 aa (molecular mass 58150 Da) and showed low homology with the corresponding enzymes from other organisms. The analyses of amino acid content and primary structure of the C. maris ICL suggested that it possessed many features of a cold-adapted enzyme. Primer extension and Northern blot analyses revealed that two species of the icl mRNAs with differential lengths of 5'-untranslated regions (TS1 and TS2) were present, of which the 5' end (TS1 and TS2 sites) were G and A, located at 130 and 39 bases upstream of the translation start codon, respectively. The levels of TS1 and TS2 mRNAs were increased by both acetate and low temperature. The induction of icl expression by low temperature took place in the C. maris cells grown on succinate as the carbon source but not acetate. Furthermore, a similar manner of inductions was also found in the levels of the translation and the enzyme activity in cell-free extract. These results suggest that the icl gene, encoding thermolabile isocitrate lyase, of C. maris is important for acetate utilization and cold adaptation.  (+info)

Psychromonas marina sp. nov., a novel halophilic, facultatively psychrophilic bacterium isolated from the coast of the Okhotsk Sea. (2/120)

A facultatively psychrophilic bacterium, strain 4-22T, was isolated from a cold current off the Monbetsu coast of the Okhotsk Sea in Hokkaido, Japan. The isolate was a rod-shaped facultative anaerobe that reduced nitrate to nitrite and hydrolysed starch, DNA and alginic acid, but not chitin or gelatin. The isolate grew at 0 degrees C, but not at 26 degrees C; the optimum growth temperature was 14-16 degrees C. NaCl was required for growth. The DNA G+C content was 43.5 mol%. The whole-cell fatty acids consisted of significant amounts of an unsaturated fatty acid, C16:1, and a saturated fatty acid, C16:0. A polyunsaturated fatty acid, docosahexaenoic acid (C22:6), was also detected (1.6%). Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 4-22T was closely related to Psychromonas antarctica (95.7% similarity). DNA-DNA hybridization revealed a relatedness of 31% between strain 4-22T and P. antarctica. Based on physiological and biochemical characteristics and the phylogenetic position as determined by 16S rRNA gene analysis and DNA-DNA relatedness, it is concluded that the isolate represents a novel species, for which the name Psychromonas marina sp. nov. is proposed. The type strain is 4-22T (= JCM 10501T = IAM 14899T = NCIMB 13792T).  (+info)

Psychromonas kaikoae sp. nov., a novel from the deepest piezophilic bacterium cold-seep sediments in the Japan Trench. (3/120)

Two strains of obligately piezophilic bacteria were isolated from sediment collected from the deepest cold-seep environment with chemosynthesis-based animal communities within the Japan Trench, at a depth of 7434 m. The isolated strains, JT7301 and JT7304T, were closely affiliated with members of the genus Psychromonas on the basis of 16S rDNA sequence analysis. Hybridization values for DNA-DNA relatedness between these strains and the Psychromonas antarctica reference strain were significantly lower than that accepted as the phylogenetic definition of a species. The optimal temperature and pressure for growth of the isolates were 10 degrees C and 50 MPa and they produced both eicosapentaenoic acid (C20:5omega3) and docosahexaenoic acid (C22:6) in the membrane layer. Based on the taxonomic differences observed, the isolated strains appear to represent a novel obligately piezophilic Psychromonas species. The name Psychromonas kaikoae sp. nov. (type strain JT7304T = JCM 11054T = ATCC BAA-363T) is proposed. This is the first proposed obligately piezophilic species of the genus Psychromonas.  (+info)

Microbulbifer salipaludis sp. nov., a moderate halophile isolated from a Korean salt marsh. (4/120)

A Gram-negative, non-motile, non-spore-forming, moderately halophilic rod (strain SM-1T) was isolated from salt marsh around the junction of the Youngsan River and the Yellow Sea in Korea and subjected to a polyphasic taxonomic study. This organism grew optimally at 37 degrees C and was able to grow at 10 and 45 degrees C. It grew optimally in the presence of 2-3% (w/v) NaCl. The major fatty acids in strain SM-1T were iso-C15:0 and C16:0. Strain SM-1T and Microbulbifer hydrolyticus DSM 11525T were characterized by having ubiquinone-8 as the predominant respiratory lipoquinone. The DNA G+C content of strain SM-1T was 59 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SM-1T formed a coherent cluster with M. hydrolyticus; this relationship was supported by a bootstrap resampling value of 100%. The level of 16S rDNA identity between strain SM-1T and the type strain of M. hydrolyticus was 98.6%. The mean level of DNA-DNA relatedness between strain SM-1T and the type strain of M. hydrolyticus was 20.6%. Therefore, on the basis of phenotypic properties, phylogeny and genomic data, strain SM-1T should be placed in the genus Microbulbifer as a member of a novel species, for which the name Microbulbifer salipaludis sp. nov. is proposed. The type strain of the novel species is strain SM-1T (=KCCM 41586T =JCM 11542T).  (+info)

Psychromonas profunda sp. nov., a psychropiezophilic bacterium from deep Atlantic sediments. (5/120)

A psychropiezophilic bacterium, strain 2825T (=LMG 21260T =JCM 11437T), isolated from deep Atlantic sediments at a depth of 2770 m and a temperature of 2 degrees C, was found by polyphasic analysis to represent a novel species of the genus Psychromonas, Psychromonas profunda sp. nov. It is a strict psychrophile and a moderate piezophile, whose degree of piezophily is increased markedly when the temperature is raised to 10 degrees C. The piezophily of P. profunda is intermediate between that of the type species, Psychromonas antarctica, which is not piezophilic, and that of Psychromonas kaikoae, which is an obligate piezophile.  (+info)

Psychromonas arctica sp. nov., a novel psychrotolerant, biofilm-forming bacterium isolated from Spitzbergen. (6/120)

Using starch as a carbon source at a cultivation temperature of 4 degrees C, a number of Gram-negative, aerobic strains was isolated from sea-ice and sea-water samples collected at Spitzbergen in the Arctic. Analysis of the genetic diversity of the novel isolates by random amplification of polymorphic DNA (RAPD) and ERIC fingerprinting revealed a homogenic group of biofilm-forming bacteria that contained small extrachromosomal elements. As a representative of the group, strain Pull 5.3T, isolated from a sea-water sample, was used for detailed characterization. The results of phylogenetic analysis indicated that the newly isolated strain is a member of the gamma-subclass of the Proteobacteria and belongs to the genus Psychromonas. On the basis of DNA-DNA hybridization experiments, chemotaxonomic studies and phenotypic characterization, strain Pull 5.3T (=CECT 5674T =DSM 14288T) clearly represents a novel species, for which the name Psychromonas arctica sp. nov. is proposed.  (+info)

Marinobacter litoralis sp. nov., a moderately halophilic bacterium isolated from sea water from the East Sea in Korea. (7/120)

A Gram-negative, motile, non-spore-forming and moderately halophilic rod-shaped strain, SW-45T, was isolated from sea water of the East Sea in Korea. The organism grew optimally at 30-37 degrees C and grew at 4 and 46 degrees C. It grew in the presence of 0.5-18% (v/w) NaCl, with an optimum of 2-7% NaCl. Strain SW-45T was chemotaxonomically characterized by having ubiquinone-9 (Q-9) as the major respiratory lipoquinone and C16 : 0, C18 : 1omega9c and C16 : 1omega9c as the predominant fatty acids. The DNA G + C content was found to be 55 mol%. Phylogenetic analysis based on 16S rDNA sequences showed that strain SW-45T forms a coherent cluster with the clade comprising the two Marinobacter species. 16S rDNA sequence similarities between strain SW-45T and the Marinobacter species was 94.9% to Marinobacter hydrocarbonoclasticus DSM 8798T and 95.3% to Marinobacter aquaeolei DSM 11845T. Levels of DNA-DNA relatedness between strain SW-45T and the type strains of M. hydrocarbonoclasticus and M. aquaeolei were respectively 4.3 and 5.5%. On the basis of phenotypic properties, phylogeny and genomic data, strain SW-45T (=KCCM 41591T =JCM 11547T) should be placed in the genus Marinobacter as a member of a novel species, for which the name Marinobacter litoralis sp. nov. is proposed. As part of this study, the major respiratory lipoquinone of M. hydrocarbonoclasticus and M. aquaeolei was also found to be Q-9.  (+info)

Genomic analysis and initial characterization of the chitinolytic system of Microbulbifer degradans strain 2-40. (8/120)

The marine bacterium Microbulbifer degradans strain 2-40 produces at least 10 enzyme systems for degrading insoluble complex polysaccharides (ICP). The draft sequence of the 2-40 genome allowed a genome-wide analysis of the chitinolytic system of strain 2-40. The chitinolytic system includes three secreted chitin depolymerases (ChiA, ChiB, and ChiC), a secreted chitin-binding protein (CbpA), periplasmic chitooligosaccharide-modifying enzymes, putative sugar transporters, and a cluster of genes encoding cytoplasmic proteins involved in N-acetyl-D-glucosamine (GlcNAc) metabolism. Each chitin depolymerase was detected in culture supernatants of chitin-grown strain 2-40 and was active against chitin and glycol chitin. The chitin depolymerases also had a specific pattern of activity toward the chitin analogs 4-methylumbelliferyl-beta-D-N,N'-diacetylchitobioside (MUF-diNAG) and 4-methylumbelliferyl-beta-D-N,N',N"-triacetylchitotrioside (MUF-triNAG). The depolymerases were modular in nature and contained glycosyl hydrolase family 18 domains, chitin-binding domains, and polycystic kidney disease domains. ChiA and ChiB each possessed polyserine linkers of up to 32 consecutive serine residues. In addition, ChiB and CbpA contained glutamic acid-rich domains. At 1,271 amino acids, ChiB is the largest bacterial chitinase reported to date. A chitodextrinase (CdxA) with activity against chitooligosaccharides (degree of polymerization of 5 to 7) was identified. The activities of two apparent periplasmic (HexA and HexB) N-acetyl-beta-D-glucosaminidases and one cytoplasmic (HexC) N-acetyl-beta-D-glucosaminidase were demonstrated. Genes involved in GlcNAc metabolism, similar to those of the Escherichia coli K-12 NAG utilization operon, were identified. NagA from strain 2-40, a GlcNAc deacetylase, was shown to complement a nagA mutation in E. coli K-12. Except for the GlcNAc utilization cluster, genes for all other components of the chitinolytic system were dispersed throughout the genome. Further examination of this system may provide additional insight into the mechanisms by which marine bacteria degrade chitin and provide a basis for future research on the ICP-degrading systems of strain 2-40.  (+info)