Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces

An obligately anaerobic, Gram-stain-positive, non-motile, non-spore-forming and rod-shaped strain AGMB00832^T was isolated from swine faeces. Phylogenetic analysis based on the 16S rRNA gene, together with the housekeeping genes, gyrB and rpoD, revealed that strain AGMB00832^T belonged to the genus Faecalicatena and was most closely related to Faecalicatena orotica KCTC 15331^T. In biochemical analysis, strain AGMB00832^T was shown to be negative for catalase, oxidase and urease. Furthermore, the isolate was positive for β-glucosidase, β-glucuronidase, glutamic acid decarboxylase, proline arylamidase, acid phosphatase and naphthol-AS-BI-phosphohydrolase. The major cellular fatty acids (>?10%) of the isolate were C_14:0, C_16:0 and C_18:1ω11t DMA. Based on the whole genome sequence analysis, the DNA G?+?C content of strain AGMB00832^T was 44.2 mol%, and the genome size and numbers of rRNA and tRNA genes were 5,175,159 bp, 11 and 53, respectively. The average nucleotide identity and digital DNA–DNA hybridization values between strain AGMB00832^T and related strains were ≤?77.4 and 22.5%, respectively. Furthermore, the genome analysis revealed the presence of genes for alkaline shock protein 23 and cation/proton antiporters, which may facilitate growth of strain AGMB00832^T in alkaline culture condition. On the basis of polyphasic taxonomic approach, strain AGMB00832^T represents a novel species within the genus Faecalicatena, for which the name Faecalicatena faecalis sp. nov. is proposed. The type strain is AGMB00832^T (=?KCTC 15946^T?=?NBRC 114613^T).

     

Nakamurella panacisegetis sp. nov. and proposal for reclassification of Humicoccus flavidus Yoon et al., 2007 and Saxeibacter lacteus Lee et al., 2008 as Nakamurella flavida comb. nov. and Nakamurella lactea comb. nov

A novel actinobacterial strain, designated P4-7(T), was isolated from soil of a ginseng field located in Geumsan County, Korea. Cells of the strain were aerobic, Gram-stain-positive, non-motile, short rods. The isolate contained MK-8(H(4)) as the predominant menaquinone, iso-C(16:0), anteiso-C(15:0) and anteiso-C(17:0) as the major fatty acids, diphosphatidylglycerol, phosphatidylethanolamine and phosphatidylinositol as the major polar lipids, glucose, mannose, xylose, ribose and rhamnose as whole-cell sugars, and meso-diaminopimelic acid as the diagnostic diamino acid in the cell-wall peptidoglycan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P4-7(T) belongs to the family Nakamurellaceae and is most closely related to Nakamurella multipartita, Humicoccus flavidus and Saxeibacter lacteus (96.3, 97.0 and 96.4% similarity to the respective type strains). Based on comparative analyses of the 16S rRNA and rpoB gene sequences and chemotaxonomic data, it is proposed that H. flavidus and S. lacteus be transferred to the genus Nakamurella. Combined genotypic and phenotypic data also suggested that strain P4-7(T) be placed in a novel species of the genus Nakamurella, for which the name Nakamurella panacisegetis sp. nov. is proposed; the type strain is P4-7(T) (=KCTC 19426(T)=CECT 7604(T)).     

Shewanella seohaensis sp. nov., isolated from a tidal flat sediment

A Gram-negative, motile and rod-shaped bacterial strain, designated S7-3^T, was isolated from a tidal flat sediment at Saemankum on the western coast of Korea. Phylogenetic analyses based on 16S rRNA gene and gyrB sequences showed that strain S7-3^T belonged to the genus Shewanella, clustering with Shewanella decolorationis S12^T. Strain S7-3^T exhibited 98.8 % 16S rRNA gene sequence similarity and 96.8 % gyrB sequence similarity to S. decolorationis S12^T, respectively. The 16S rRNA gene sequence similarity values between strain S7-3^T and other members of the genus Shewanella were in the range of 93.0–98.0 %. Strain S7-3^T contained simultaneously both menaquinones (MK) and ubiquinones (Q); the predominant menaquinone was MK-7 and the predominant ubiquinones were Q-7 and Q-8. The fatty acid profiles of strain S7-3^T and S. decolorationis JCM 21555^T were similar; major components were C_17:1 ω8c, iso-C_15:0 and iso-C_15:0 2-OH and/or C_16:1 ω7c. The DNA G+C content of strain S7-3^T was 51.8 mol% and its mean DNA–DNA relatedness value with S. decolorationis JCM 21555^T was 43 %. Differential phenotypic properties of strain S7-3^T, together with the phylogenetic and genetic distinctiveness, revealed that this strain is distinguishable from recognized Shewanella species. On the basis of the data presented, strain S7-3^T is considered to represent a novel Shewanella species, for which the name Shewanella seohaensis sp. nov. is proposed. The type strain is S7-3^T (=KCTC 23556^T = CCUG 60900^T).     

Draft Genome Sequence of the Extremely Halophilic Archaeon Halogranum salarium B-1T

Halogranum salarium is an extremely halophilic archaeon isolated from evaporitic salt crystals and belongs to the family Halobacteriaceae. Here, we present the 4.5-Mb draft genome sequence of the type strain (B-1^T) of H. salarium. This is the first report of the draft genome sequence of a haloarchaeon in the genus Halogranum.     

Bis deficiency results in early lethality with metabolic deterioration and involution of spleen and thymus

Bcl-2 interacting cell death suppressor (Bis), also known as Bag3 or CAIR-1, is involved in antistress and antiapoptotic pathways. In addition to Bcl-2, Bis binds to several proteins, suggesting it has diverse functions in normal and pathological conditions. To better define the physiological function of Bis in vivo, we developed bis-deficient mice with a cre-loxP system. Targeted disruption of exon 4 of the bis gene was demonstrated by Southern blotting and PCR, and Western blotting showed that no intact or truncated Bis protein was synthesized in bis(-/-) mice. While heterozygotes were fertile and appeared normal, Bis-deficient mice showed growth retardation and died by 3 wk after birth. The relative weight of the thymus and spleen was reduced and the total numbers of white blood cells, splenocytes, and thymocytes were significantly reduced compared with wild-type littermates. Serum profiles indicated significant hypoglycemia as well as decrease in triglyceride and cholesterol levels. Expression profiles of metabolic genes indicated that gluconeogenesis and beta-oxidation are activated in the liver of bis(-/-) mice. This activation, as well as a decrease in peripheral fat and an induction of fatty liver, appears to be an adaptive response to hypoglycemia. Our study reveals that the absence of Bis has considerable influences on postnatal growth and survival, possibly due to a nutritional impairment.     

Regulation of the murine TR2/HVEM gene expression by IRF

TR2 (TNFR-related 2, HVEM, or TNFRSF-14), a member of the TNFR family, is involved in a number of immune responses. While TR2 is expressed on the surface of T cells during the resting state, little is known regarding how expression of the TR2 gene is regulated. To understand the mechanisms regulating the expression of TR2 in T cells, we analyzed the 5' flanking region of TR2. We identified an important region for the activity of the TR2 promoter using site directed mutagenesis. Using EMSA analysis, we found that IRF-2 was bound to the promoter region of the TR2 gene during the resting state of EL-4 T cells. Transfection of IRF-2 expression plasmid and of dominant negative IRF-2 mutant further confirmed our results. Together, these data demonstrate that IRF-2 is involved in the regulation of TR2 expression in EL-4 T cells.