Physical basis of the inducer-dependent cooperativity of the Central glycolytic genes Repressor/DNA complex

The Central glycolytic genes Repressor (CggR) from Bacillus subtilis belongs to the SorC family of transcription factors that control major carbohydrate metabolic pathways. Recent studies have shown that CggR binds as a tetramer to its tandem operator DNA sequences and that the inducer metabolite, fructose 1,6-bisphosphate (FBP), reduces the binding cooperativity of the CggR/DNA complex. Here, we have determined the effect of FBP on the size, shape and stoichiometry of CggR complexes with full-length and half-site operator sequence by small-angle X-ray scattering, size-exclusion chromatography, fluorescence cross-correlation spectroscopy and noncovalent mass spectrometry (MS). Our results show that CggR forms a compact tetrameric assembly upon binding to either the full-length operator or two half-site DNAs and that FBP triggers a tetramer–dimer transition that leaves a single dimer on the half-site or two physically independent dimers on the full-length target. Although the binding of other phospho-sugars was evidenced by MS, only FBP was found to completely disrupt dimer–dimer contacts. We conclude that inducer-dependent dimer–dimer bridging interactions constitute the physical basis for CggR cooperative binding to DNA and the underlying repression mechanism. This work provides experimental evidences for a cooperativity-based regulation model that should apply to other SorC family members

Socioeconomic differences in caesarean section - Are they explained by medical need? An analysis of patient record data of a large Kenyan hospital

Background: Caesarean section (C-section) rates are often low among the poor and very high among the better-off in low- and middle-income countries. We examined to what extent these differences are explained by medical need in an African context. Methods: We analyzed electronic records of 12,209 women who gave birth in a teaching hospital in Kenya in 2014. C-section rates were calculated by socioeconomic position (SEP), using maternal occupation (professional, small business, housewife, student) as indicator. We assessed if women had documented clinical indications according to hospital guidelines and if socioeconomic differences in C-section rates were explained by indication. Results: Indication for C-section according to hospital guidelines was more prevalent among professionals than housewives (16% vs. 9% of all births). The C-section rate was also higher among professionals than housewives (21.1% vs. 15.8% [OR 1.43; 95%CI 1.23-1.65]). This C-section rate difference was largely explained by indication (4.7 of the 5.3 percentage point difference between professionals and housewives concerned indicated C-sections, often with previous C-section as indication). Repeat C-sections were near-universal (99%). 43% of primary C-sections had no documented indication. Over-use was somewhat higher among professionals than housewives (C-section rate among women without indication: 6.6 and 5.5% respectively), which partly explained socioeconomic differences in primary C-section rate. Conclusions: Socioeconomic differences in C-section rates can be largely explained by unnecessary primary C-sections and higher supposed need due to previous C-section. Prevention of unnecessary primary C-sections and promoting safe trial of labor should be priorities in addressing C-section over-use and reducing inequalities. Tweetable abstract: Unnecessary primary C-sections and ubiquitous repeat C-sections drive overall C-section rates and C-section inequalities

The Cyclophilin-Binding Agent Sanglifehrin A Is a Dendritic Cell Chemokine and Migration Inhibitor

Sanglifehrin A (SFA) is a cyclophilin-binding immunosuppressant but the immunobiology of action is poorly understood. We and others have reported that SFA inhibits IL-12 production and antigen uptake in dendritic cells (DC) and exhibits lower activity against lymphocytes. Here we show that SFA suppresses DC chemokine production and migration. Gene expression analysis and subsequent protein level confirmation revealed that SFA suppressed CCL5, CCL17, CCL19, CXCL9 and CXCL10 expression in human monocyte-derived DC (moDC). A systems biology analysis, Onto Express, confirmed that SFA interferes with chemokine-chemokine receptor gene expression with the highest impact. Direct comparison with the related agent cyclosporine A (CsA) and dexamethasone indicated that SFA uniquely suppresses moDC chemokine expression. Competitive experiments with a 100-fold molar excess of CsA and with N-Methyl-Val-4-cyclosporin, representing a nonimmunosuppressive derivative of CsA indicated chemokine suppression through a cyclophilin-A independent pathway. Functional assays confirmed reduced migration of CD4+ Tcells and moDCs to supernatant of SFA-exposed moDCs. Vice versa, SFA-exposed moDC exhibited reduced migration against CCL19. Moreover, SFA suppressed expression of the ectoenzyme CD38 that was reported to regulate DC migration and cytokine production. These results identify SFA as a DC chemokine and migration inhibitor and provide novel insight into the immunobiology of SFA

Methods of probing the interactions between small molecules and disordered proteins

It is generally recognized that a large fraction of the human proteome is made up of proteins that remain disordered in their native states. Despite the fact that such proteins play key biological roles and are involved in many major human diseases, they still represent challenging targets for drug discovery. A major bottleneck for the identification of compounds capable of interacting with these proteins and modulating their disease-promoting behaviour is the development of effective techniques to probe such interactions. The difficulties in carrying out binding measurements have resulted in a poor understanding of the mechanisms underlying these interactions. In order to facilitate further methodological advances, here we review the most commonly used techniques to probe three types of interactions involving small molecules: (1) those that disrupt functional interactions between disordered proteins; (2) those that inhibit the aberrant aggregation of disordered proteins, and (3) those that lead to binding disordered proteins in their monomeric states. In discussing these techniques, we also point out directions for future developments.Gabriella T. Heller is supported by the Gates Cambridge Trust Scholarship. Francesco A. Aprile is supported by a Senior Research Fellowship award from the Alzheimer’s Society, UK (grant number 317, AS-SF-16-003)

Actinoplanes siamensis sp. nov., isolated from soil

A Gram-positive filamentous bacterial strain that developed large campanulate sporangia at the ends of sporangiophores on substrate mycelium was isolated from bamboo forest soil in Thailand. According to the results of a polyphasic taxonomic study, our isolate had typical characteristics of members of the genus Actinoplanes. The 16S rRNA gene sequence analysis also indicated that strain A-T 6646<sup>T</sup> belonged to the genus Actinoplanes, being most closely related to Actinoplanes liguriensis DSM 43865<sup>T</sup> (97.61 %) and Actinoplanes octamycinicus NBRC 14524<sup>T</sup> (97.52 %). The DNA-DNA relatedness values, which differentiate the new strain from the most closely related species, were significantly below 70 %. The cell-wall peptidoglycan contained meso-diaminopimelic acid. The whole-cell sugars contained xylose and arabinose. The predominant menaquinone was MK-9(H<sub>4</sub>). The diagnostic phospholipids were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol. The predominant cellular fatty acids were iso-C<sub>16: 0</sub>, anteiso-C<sub>17: 0</sub>, iso-C<sub>15: 0</sub> and anteiso-C<sub>15: 0</sub>. Following an evaluation of phenotypic, chemotaxonomic and genotypic studies, the isolate is proposed to represent a novel species to be named Actinoplanes siamensis sp. nov. The type strain is A-T 6646<sup>T</sup> (= BCC 46194<sup>T</sup> = NBRC 109076<sup>T</sup>). 2013 IUM