Transcription initiation in Streptomyces coelicolor A3(2)

Recent studies into the stringent response and the discovery of a number of RNA polymerase binding proteins suggests that the model for bacterial transcription initiation in Actinobacteria may differ from that in Escherichia coli. In E. coli, the alarmone ppGpp, together with DksA, binds to RNA polymerase to elicit the stringent response. However, the ppGpp binding site on RNA polymerase is not conserved in S. coelicolor, although the organism possesses a DksA homologue. Deletion of DksA did not affect the growth and development of S. coelicolor, although its overexpression stimulated antibiotic production. Evidence is presented that suggests that this occurs through binding to the RNA polymerase secondary channel. The biological role of this protein remains unknown. CarD and RbpA are two RNA polymerase­‐binding proteins present in all Actinobacteria, including S. coelicolor and M. tuberculosis. Both proteins are critical for growth and have been identified as transcriptional activators from σHrdB­‐dependent promoters in vitro. Here it was demonstrated that CarD and RbpA activate transcription from rRNA promoters with a poorly conserved ­‐35 element. Surprisingly it was also found that both proteins can inhibit transcription from synthetic promoters with highly conserved ­‐35 elements. Chromatin immunoprecipitation followed by high throughput sequencing (ChIP­‐seq) experiments revealed that CarD and RbpA are found exclusively at promoter regions. RbpA is localised only at promoters recognised by σHrdB, whereas CarD also co‐localises with the alternative sigma factor σR during oxidative stress indicating that it lacks RNA polymerase holoenzyme specificity. The sigma specificity of RbpA was tested by the generation of sigma mutants that were defective in binding. In vivo, in vitro and ChIP­‐seq data presented in this study suggest that CarD and RbpA have an overlapping role in transcription initiation at σHrdB­‐dependent promoters in S. coelicolor

Structural, functional, and genetic analyses of the actinobacterial transcription factor RbpA

Gene expression is highly regulated at the step of transcription initiation, and transcription activators play a critical role in this process. RbpA, an actinobacterial transcription activator that is essential in Mycobacterium tuberculosis (Mtb), binds selectively to group 1 and certain group 2 σ-factors. To delineate the molecular mechanism of RbpA, we show that the Mtb RbpA σ-interacting domain (SID) and basic linker are sufficient for transcription activation. We also present the crystal structure of the Mtb RbpA-SID in complex with domain 2 of the housekeeping σ-factor, σ(A). The structure explains the basis of σ-selectivity by RbpA, showing that RbpA interacts with conserved regions of σ(A) as well as the nonconserved region (NCR), which is present only in housekeeping σ-factors. Thus, the structure is the first, to our knowledge, to show a protein interacting with the NCR of a σ-factor. We confirm the basis of selectivity and the observed interactions using mutagenesis and functional studies. In addition, the structure allows for a model of the RbpA-SID in the context of a transcription initiation complex. Unexpectedly, the structural modeling suggests that RbpA contacts the promoter DNA, and we present in vivo and in vitro studies supporting this finding. Our combined data lead to a better understanding of the mechanism of RbpA function as a transcription activator

Scaling relations in fossil galaxy groups

Using Chandra X-ray observations and optical imaging and spectroscopy of a flux-limited sample of 5 fossil groups, supplemented by additional systems from the literature, we provide the first detailed study of the scaling properties of fossils compared to normal groups and clusters. In general, all the fossils we study show regular and symmetric X-ray emission, indicating an absence of recent major group mergers. We confirm that, for a given optical luminosity of the group, fossils are more X-ray luminous than non-fossil groups. Fossils, however, fall comfortably on the conventional L_X-T_X relation of galaxy groups and clusters, suggesting that their X-ray luminosity and their gas temperature are both boosted, arguably, as a result of their early formation. This is supported by other scaling relations including the L_X-sigma and T_X-sigma relations in which fossils show higher X-ray luminosity and temperature for a given group velocity dispersion. We find that mass concentration in fossils is higher than in non-fossil groups and clusters. In addition, the M_X-T_X relation suggests that fossils are hotter, for a given total gravitational mass, both consistent with an early formation epoch for fossils. We show that the mass-to-light ratio in fossils is rather high but not exceptional, compared to galaxy groups and clusters. The entropy of the gas in low mass fossils appears to be systematically lower than that in normal groups, which may explain why the properties of fossils are more consistent with an extension of cluster properties. We conclude that the cuspy potential raises the luminosity and temperature of the IGM in fossils. However, this works in conjunction with lower gas entropy, which may arise from less effective preheating of the gas.Comment: 12 pages, 10 figures, Accepted for publication in MNRA

Key interactions by conserved polar amino acids located at the transmembrane helical boundaries in Class B GPCRs modulate activation, effector specificity and biased signalling in the glucagon-like peptide-1 receptor

Class B GPCRs can activate multiple signalling effectors with the potential to exhibit biased agonism in response to ligand stimulation. Previously, we highlighted key TM domain polar amino acids that were crucial for the function of the GLP-1 receptor, a key therapeutic target for diabetes and obesity. Using a combination of mutagenesis, pharmacological characterisation, mathematical and computational molecular modelling, this study identifies additional highly conserved polar residues located towards the TM helical boundaries of Class B GPCRs that are important for GLP-1 receptor stability and/or controlling signalling specificity and biased agonism. This includes (i) three positively charged residues (R3.30227, K4.64288, R5.40310) located at the extracellular boundaries of TMs 3, 4 and 5 that are predicted in molecular models to stabilise extracellular loop 2, a crucial domain for ligand affinity and receptor activation; (ii) a predicted hydrogen bond network between residues located in TMs 2 (R2.46176), 6 (R6.37348) and 7 (N7.61406 and E7.63408) at the cytoplasmic face of the receptor that is important for stabilising the inactive receptor and directing signalling specificity, (iii) residues at the bottom of TM 5 (R5.56326) and TM6 (K6.35346 and K6.40351) that are crucial for receptor activation and downstream signalling; (iv) residues predicted to be involved in stabilisation of TM4 (N2.52182 and Y3.52250) that also influence cell signalling. Collectively, this work expands our understanding of peptide-mediated signalling by the GLP-1 receptor

Effects of fluoxetine on functional outcomes after acute stroke (FOCUS): a pragmatic, double-blind, randomised, controlled trial

Background Results of small trials indicate that fluoxetine might improve functional outcomes after stroke. The FOCUS trial aimed to provide a precise estimate of these effects. Methods FOCUS was a pragmatic, multicentre, parallel group, double-blind, randomised, placebo-controlled trial done at 103 hospitals in the UK. Patients were eligible if they were aged 18 years or older, had a clinical stroke diagnosis, were enrolled and randomly assigned between 2 days and 15 days after onset, and had focal neurological deficits. Patients were randomly allocated fluoxetine 20 mg or matching placebo orally once daily for 6 months via a web-based system by use of a minimisation algorithm. The primary outcome was functional status, measured with the modified Rankin Scale (mRS), at 6 months. Patients, carers, health-care staff, and the trial team were masked to treatment allocation. Functional status was assessed at 6 months and 12 months after randomisation. Patients were analysed according to their treatment allocation. This trial is registered with the ISRCTN registry, number ISRCTN83290762. Findings Between Sept 10, 2012, and March 31, 2017, 3127 patients were recruited. 1564 patients were allocated fluoxetine and 1563 allocated placebo. mRS data at 6 months were available for 1553 (99·3%) patients in each treatment group. The distribution across mRS categories at 6 months was similar in the fluoxetine and placebo groups (common odds ratio adjusted for minimisation variables 0·951 [95% CI 0·839–1·079]; p=0·439). Patients allocated fluoxetine were less likely than those allocated placebo to develop new depression by 6 months (210 [13·43%] patients vs 269 [17·21%]; difference 3·78% [95% CI 1·26–6·30]; p=0·0033), but they had more bone fractures (45 [2·88%] vs 23 [1·47%]; difference 1·41% [95% CI 0·38–2·43]; p=0·0070). There were no significant differences in any other event at 6 or 12 months. Interpretation Fluoxetine 20 mg given daily for 6 months after acute stroke does not seem to improve functional outcomes. Although the treatment reduced the occurrence of depression, it increased the frequency of bone fractures. These results do not support the routine use of fluoxetine either for the prevention of post-stroke depression or to promote recovery of function. Funding UK Stroke Association and NIHR Health Technology Assessment Programme

Cystic nephroma and mixed epithelial and stromal tumor of kidney: A detailed clinicopathologic analysis of 34 cases and proposal for renal epithelial and stromal tumor (REST) as a unifying term

cCystic nephroma (CN) and mixed epithelial and stromal tumor (MEST) are rare benign renal neoplasms that have overlapping clinical and morphologic features, including predominance in middle-aged women, variably cystic architecture, eosinophilic cells, and hobnail cells lining the cysts and ovarian-type stroma. The aim of this study was to analyze and compare the histologic features and immunohistochemical profile of these tumors. We studied 34 cases from 5 large academic institutions. Twenty tumors were diagnosed as CNs, 18 in women and 2 in men, their age ranged from 24 to 63 (mean 48; median 50) years. Fourteen tumors were diagnosed as MESTs, all in women, their age ranged from 26 to 84 (mean 52; median 51) years. Histologically, all tumors were weil-circumscribed except for one MEST. The stromal/epithelial ratio was approximately 2.3 in MESTs versus 0.3 in CNs; cellular ovarian-type stroma composed 45% of the stroma in MESTs and 12% of the stroma of CNs. Stromal hyalinization was prominent in both. Five MESTs showed stromal luteinization. In the epithelial component, the relative amount of large cysts, medium to small cysts, and phyllodes-type glands was: 65%/ 25%/10% in CNs versus 25%/40%/35% in MESTs. The epithelial component ranged from flat to cuboidal to hobnail cells in both types of tumors. No significant atypia of either component was seen, although the epithelial cells showed reactive changes. Immunohistochemical stains for estrogen receptors and progesterone receptors showed 62% and 85% positivity in the stromal component of MESTs versus 19% and 40% in CNs. CD10 positivity was seen in 77% of MESTs versus 50% of CNs. calretinin was seen in 69% of MESTs versus 41% of CNs. and inhibin in 42% of MESTs versus 36% of CNs, although the staining was focal. Follow-up in both categories of tumors (mean 3.2 y, median 3 y for CNs and mean 2.5 y, median of 2 y for MESTs) showed no evidence of recurrence, or metastases in keeping with their benign nature. This study highlights the remarkable similarity between CN and MEST in sex predilection, age distribution, and morphologic attributes of both the epithelial and stromal components and immunohistochemical profile albeit with variation in individual categories with higher prevalence of stromal to epithelial ratio, prominent ovarian stroma, smaller cysts with phyllodes glands pattern and stromal luteinization being more common in MESTI- and large cysts, thin septae and low stromal to epithelial ratio in CN. The presence of ovarian-type stroma and mollerian related immunohistochemical markers raises the possibility that these tumors may originate from mullerian remnants misplaced during embryogenesis. On the basis of detailed morphologic analysis of this series of CN and MEST, we propose a unifying term of "renal epithelial and stromal tumor" (REST) to encompass the spectrum of findings observed in these tumors at least until new molecular studies can prove or disprove this challenging hypothesis