Grimontia sedimenti strain:S25
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ABSTRACT:
PROVIDER: PRJNA607756 | ENA |
REPOSITORIES: ENA
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Project description:A Gram-stain-negative, rod and rod-curved shaped motile bacterium designated strain S25<sup>T</sup> was obtained from benthic sediment collected near the Kubbar Island coral reefs south of Kuwait. Phenotypic analysis revealed that strain S25<sup>T</sup> was slightly halophilic, mesophilic and facultative anaerobic, fermenting d-glucose, d-ribose, d-mannose, d-mannitol, maltose, fructose, gentiobiose, cellobiose, melibiose, trehalose and sucrose. It was positive for oxidase and indole production and negative for arginine dihydrolase and lysine and ornithine decarboxylases. It contained C<sub>16 : 1</sub> <i> ω</i>7<i>c</i>/C<sub>16 : 1</sub> <i> ω</i>6<i>c</i> (summed feature 3), C<sub>18 : 1</sub> ω7<i>c</i> (summed feature 8) and C<sub>16 : 0</sub> as the major fatty acids. Strain S25<sup>T</sup> grew optimally at 30 °C and pH 8 in the presence of 3 % (w/v) NaCl. Phylogenetic analysis based on 16S rRNA sequences revealed that strain S25<sup>T</sup> is related to species of the genus <i>Grimontia</i>, having 99.15 % similarity to '<i>Grimontia indica</i>' AK16<sup>T</sup>, 99.08 % to <i>Grimontia celer</i> 96-237<sup>T</sup> and 98.66 % to <i>Grimontia marina</i> IMCC 5001<sup>T</sup>. The DNA G+C content was 48.8 mol% and the full genome analysis for the strain S25<sup>T</sup> showed that the bacterium has a genome size of 5 158 621 bp and contains 4730 predicted protein-encoding genes. The average nucleotide identity values between the S25<sup>T</sup> genome and the genomes of its nearest matches ranged between 81.39 and 94.16 %. The strain was distinguishable from the phylogenetically related genera through differences in several phenotypic properties. On the basis of the phenotypic, phylogenetic and genetic data, strain S25<sup>T</sup> represents a novel species in the genus <i>Grimontia</i>, for which the name <i>Grimontia sedimenti</i> sp. nov. is proposed. The type strain of <i>Grimontia sedimenti</i> is S25<sup>T</sup> (=DSM 28878<sup>T</sup>=LMG 28315<sup>T</sup>).
| S-EPMC8375428 | BioStudies
Project description:Grimontia indica strain AK16(T) sp. nov. is the type strain of G. indica sp. nov. a new species within the genus Grimontia. This strain, whose genome is described here, was isolated from seawater sample collected from southeast coast of Palk Bay, India. G. indica AK16(T) is a Gram-negative, facultative aerobic rod shaped bacterium. There are only two other strains in the genus Grimontia one of which, Grimontia hollisae CIP 101886(T), is a reported human pathogen isolated from human stool sample while the other, 'Grimontia marina IMCC5001(T)', was isolated from a seawater sample. As compared to the pathogenic strain Grimontia hollisae CIP 101886(T), the strain AK16(T) lacks some genes for pathogenesis like the accessory colonization factors AcfA and AcfD, which are required for the colonization of the bacterium in the host body. While it carries some pathogenesis genes like OmpU, which are related to pathogenesis of Vibrio strains. This suggests that the life cycle of AK16(T) may include some pathogenic interactions with marine animal(s), or it may be an opportunistic pathogen. Study of the Grimontia genus is important because of the severe pathogenic traits exhibited by a member of the genus with only three species reported in total. The study will provide some vital information which may be useful in future clinical studies on the genus.
| S-EPMC3897461 | BioStudies
Project description:Here is the genome sequence of Haloparvum sedimenti DYS4, the type species of the genus Haloparvum, isolated from a salt mine. The DNA G+C content of this genome was 68.27 mol%. The scaffold N50 was 96,635 bp. The completely sequenced and annotated genome is 3,243,052 bp and contains 3,313 genes.
| S-EPMC5721132 | BioStudies
Project description:Streptococcus agalactiae (Lancefield group B; GBS) is one of the major pathogens in fish production, especially in Nile tilapia (Oreochromis niloticus). The genomic characteristics of GBS isolated from fish must be more explored. Thus, we present here the genome of GBS S25, isolated from Nile tilapia from Brazil.
| S-EPMC4974326 | BioStudies
Project description:There is an increasing interest in determining the role of ribosomal proteins (RPs) in the regulation of MDM2-p53 pathway in coordinating cellular response to stress. Herein, we report a novel regulatory role of ribosomal protein S25 (RPS25) in MDM2-mediated p53 degradation and a feedback regulation of S25 by p53. We demonstrated that S25 interacted with MDM2 and inhibited its E3 ligase activity, resulting in the reduction of MDM2-mediated p53 ubiquitination and the stabilization and activation of p53. S25, MDM2 and p53 formed a ternary complex following ribosomal stress. The nucleolar localization and MDM2-binding domains of S25 were critical for its role in MDM2-mediated p53 regulation. Knockdown of S25 by siRNA attenuated the induction and activation of p53 following ribosomal stress. S25 stabilized and cooperated with MDMX to regulate MDM2 E3 ligase activity. Furthermore, S25 was identified to be a transcriptional target of p53; p53 directly bound to S25 promoter and suppressed S25 expression. Our results suggest that there is a S25-MDM2-p53 regulatory feedback loop, which may have an important role in cancer development and progression.
| S-EPMC6714567 | BioStudies
Project description:Impetigo is a contagious skin infection predominantly caused by <i>Staphylococcus aureus</i>. Decontamination of <i>S. aureus</i> from the skin is becoming more difficult because of the emergence of antibiotic-resistant strains. Bacteriophage endolysins are less likely to invoke resistance and can eliminate the target bacteria without disturbance of the normal microflora. In this study, we investigated the therapeutic potential of a recombinant endolysin derived from kayvirus S25-3 against staphylococcal impetigo in an experimental setting. First, the recombinant S25-3 endolysin required an incubation period of over 15 minutes to exhibit efficient bactericidal effects against <i>S. aureus</i>. Second, topical application of the recombinant S25-3 endolysin decreased the number of intraepidermal staphylococci and the size of pustules in an experimental mouse model of impetigo. Third, treatment with the recombinant S25-3 endolysin increased the diversity of the skin microbiota in the same mice. Finally, we revealed the genus-specific bacteriolytic effect of recombinant S25-3 endolysin against staphylococci, particularly <i>S. aureus</i>, among human skin commensal bacteria. Therefore, topical treatment with recombinant S25-3 endolysin can be a promising disease management procedure for staphylococcal impetigo by efficient bacteriolysis of <i>S. aureus</i> while improving the cutaneous bacterial microflora.
| S-EPMC6784202 | BioStudies
Project description:Streptococcus agalactiae strain:S25 Genome sequencing and assembly
| PRJNA323652 | ENA
Project description:Grimontia indica strain:AK16 Genome sequencing and assembly
| PRJNA178257 | ENA
Project description:The near-germline antibody S25-2 exhibits a remarkable cross-reactivity for oligosaccharides containing the bacterial lipopolysaccharide carbohydrate 3-deoxy-D-manno-oct-2-ulosonic acid (Kdo). The recent synthesis of a variety of Kdo analogues permits a detailed structural analysis of the importance of specific interactions in antigen recognition by S25-2. The Kdo disaccharide analogue Kdo-(2?4)-5,6-dehydro-Kdo lacks a 5-OH group on the second Kdo residue and has been cocrystallized with S25-2. The structure reveals that the modification of the Kdo residue at position 5 results in a rearrangement of intramolecular hydrogen bonds in the antigen that allows it to assume a novel conformation in the antibody-combining site. The cross-reactive binding of S25-2 to this synthetic ligand highlights the adaptability of this antibody to non-natural synthetic analogues.
| S-EPMC3539693 | BioStudies
Project description:Raoultella planticola strain:S25 Genome sequencing
| PRJNA566120 | ENA