Anaerocolumna sedimenticola sp. nov., isolated from fresh water sediment

Strain CBA3638^T was isolated from the Geum River sediment, Republic of Korea. The cells of strain CBA3638^T were Gram-stain-positive, strictly anaerobic, rod-shaped, and 0.5–1.0 μm wide, and 4.0–4.5 μm long. Optimal growth occurred at 37 °C, pH 7.0, and 1.0% (w/v) NaCl. Based on the 16S rRNA gene sequence, the phylogenetic analysis showed that strain CBA3638^T belongs to the genus Anaerocolumna in the family Lachnospiraceae, and is most closely related to Anaerocolumna cellulosilytica (94.6–95.0%). The DDH value with A. cellulosilytica SN021^T showed 15.0% relatedness. The genome of strain CBA3638^T consisted of one circular chromosome that is 5,500,435 bp long with a 36.7 mol% G?+?C content. The genome contained seven 16S-5S-23S rRNA operons and one antibiotic resistance-related transporter gene (mefA). Quinones were not detected. The predominant cellular fatty acids were C_16:0 and C_14:0 and the polar lipids were diphosphatidylglycerol, phosphatidylcholine, and uncharacterised polar lipids. Based on the polyphasic taxonomic analysis, we propose strain CBA3638^T as a novel species in the genus Anaerocolumna, with the name Anaerocolumna sedimenticola sp. nov. The type strain is CBA3638^T (=?KACC 21652^T?=?DSM 110663^T).

     

Protein tyrosine phosphatase 1B inhibitors isolated from Morus bombycis

Bioassay-guided fractionation of the chloroform-soluble fraction of Morus bombycis, using an in vitro PTP1B inhibitory assay led to the identification of three 2-arylbenzofurans, albafuran A (1), mulberrofuran W (2) and mulberrofuran D (6), along with three chalcone-derived Diels–Alder products, kuwanon J (3), kuwanon R (4), and kuwanon V (5). Compounds 1–6 showed remarkable inhibitory activity against PTP1B with IC₅₀ values ranging from 2.7 to 13.8 μM. Inhibition kinetics were analyzed by Lineweaver–Burk plots, which suggested that compounds 1–6 inhibited PTP1B in a mixed-type manner. The present results indicate that the respective lipophilic and hydroxyl groups of 2-arylbenzofurans and chalcone-derived Diels–Alder products play an important role in inhibition of PTP1B.     

Isolation of the protein tyrosine phosphatase 1B inhibitory metabolite from the marine-derived fungus Cosmospora sp. SF-5060

In the course of bioassay-guided study on the EtOAc extract of a culture broth of the marine-derived fungus Cosmospora sp. SF-5060, aquastatin A (1) was isolated as a protein tyrosine phosphatase 1B (PTP1B) inhibitory component produced by the fungus. The compound was isolated by various chromatographic methods, and the structure was determined mainly by analysis of NMR spectroscopic data. Compound 1 exhibited potent inhibitory activity against PTP1B with IC₅₀ value of 0.19 μM, and the kinetic analyses of PTP1B inhibition by compound 1 suggested that the compound is inhibiting PTP1B activity in a competitive manner. Aquastatin A (1) also showed modest but selective inhibitory activity toward PTP1B over other protein tyrosine phosphatases, such as TCPTP, SHP-2, LAR, and CD45. In addition, the result of hydrolyzing aquastatin A (1) suggested that the dihydroxypentadecyl benzoic acid moiety in the molecule is responsible for the inhibitory activity.     

MEK1 plays contrary stage-specific roles in skeletal myogenic differentiation

The role of extracellular signal-regulated kinase (ERK) signaling in skeletal myogenesis has been reported to be both stimulatory and inhibitory. We propose that this discrepancy may arise from the stage-specific, different roles of mitogen-activated protein kinase kinase 1 (MEK1). We found that the phosphorylated MEK1 level of differentiating C2C12 cells was low on day 1 (early-stage) and reached a maximum on days 2–3 (mid-stage). Cells treated at early stage with the MEK-specific inhibitors, PD184352 and U0126, reduced both the MHC protein level and MCK promoter activity, demonstrating that high MEK1 activity at the mid-stage is required for myogenic differentiation. In contrast, treatment with the ERK-specific inhibitors, FR180204 and ERK inhibitor I, had no effect. However, because the sustained overexpression of constitutively active MEK1 inhibits myogenic differentiation, we further analyzed the stage-specific role of MEK1 using the Tet-Off expression system. The results demonstrated that myogenic differentiation was inhibited if active MEK1 expression was induced earlier than day 1 in differentiation condition, but stimulated if induced after that, demonstrating that activated MEK1 plays differential roles depending on activation time. In addition, the induction of active MEK1 at 12 h enhanced the Id2 protein level, while the induction at 36 h resulted in reduction. Thus, MEK1 plays stage-specific and contrary roles in myogenesis, and MEK1 activated at the mid-stage promotes muscle differentiation independent of ERK.     

Ca-induced stimulation of the membrane binding of Escherichia coli SecA and its association with signal peptides of secretory proteins

Previously, it was found that Ca²⁺ stimulates the intrinsic Escherichia coli SecA ATPase activity [Kim et al., FEBS Lett. 493 (2001) 12-16]. Now, we suggest that Ca²⁺ is required for efficient interaction of SecA with membranes and the signal peptide of ribose-binding protein. When the amount of external Ca²⁺ was enhanced, the amounts of membrane-bound SecA and its lipid/ATPase activity increased. In the presence of entrapped Ca²⁺ in liposomes, the binding was also stimulated in a Ca²⁺ concentration-dependent manner. The effect of Ca²⁺ on the functional regulation of SecA was also evident in the presence of the signal peptides of secretory proteins, which the interaction of SecA with the signal peptide increased with increasing Ca²⁺ concentration in the presence of membranes. However, other divalent cations including Mg²⁺, Mn²⁺, and Zn²⁺ had inhibitory or no effect, suggesting a specific role of Ca²⁺ in SecA interaction with lipid bilayers and signal peptides.     

A Robust Genome‐Wide Scan Statistic of the Wellcome Trust Case–Control Consortium

Summary In genome‐wide association (GWA) studies, test statistics that are efficient and robust across various genetic models are preferable, particularly for studying multiple diseases in the Wellcome Trust Case–Control Consortium ( WTCCC, 2007 , Nature 447 , 661–678). A new test statistic, the minimum of the p‐values of the trend test and Pearson's test, was considered by the WTCCC. It is referred to here as MIN2. Because the minimum of two p‐values is no longer a valid p‐value itself, the WTCCC only used it to rank single nucleotide polymorphisms (SNPs) but did not report the p‐values of the associated SNPs when MIN2 was used for ranking. Given its importance in practice, we derive the asymptotic null distribution of MIN2, study some of its analytical properties related to GWA studies, and compare it with existing methods (the trend test, Pearson's test, MAX3, and the constrained likelihood ratio test [CLRT]) by simulations across a wide range of possible genetic models: the recessive (REC), additive (ADD), multiplicative (MUL), dominant (DOM), and overdominant models. The results show that MAX3 and CLRT have greater efficiency robustness than other tests when the REC, ADD/MUL, and DOM models are possible, whereas Pearson's test and MIN2 have greater efficiency robustness if the possible genetic models also include the overdominant model. We conclude that robust tests (MAX3, MIN2, CLRT, and Pearson's test) are preferable to a single trend test for initial GWA studies. The four robust tests are applied to more than 100 SNPs associated with 11 common diseases identified by the two WTCCC GWA studies.     

ATM blocks tunicamycin-induced endoplasmic reticulum stress

Endoplasmic reticulum stress (ER-stress) is associated with ataxia telangiectasia mutated (ATM) gene. We present here conclusive data showing that ATM blocks ER-stress induced by tunicamycin or ionizing radiation (IR). X-box protein-1 (XBP-1) splicing, GRP78 expression and caspase-12 activation were increased by tunicamycin or IR in Atm-deficient AT5BIVA fibroblasts. Activation of caspase-12 and caspase-3 by tunicamycin was significantly reduced in cells transfected with wild-type Atm (AT5BIVA/wtATM). Atm knockdown by siRNA, however, noticeably elevated ER-stress and chemosensitivity to tunicamycin. In summary, we present substantial data demonstrating that ATM blocks the ER stress signaling associated with cancer cell proliferation.