Studies on the structure, mechanism and protein engineering of Bacillus subtilis pimeloyl-CoA synthetase (PCAS)

Biotin is an essential vitamin in plants and mammals functioning as the carbon dioxide carrier within central lipid metabolism. Biotin is composed of a fused bicylic ring system and a five carbon, carboxylic acid chain. Biotin biosynthesis in bacteria is catalysed by a series of enzymes that use fatty acid, amino acid and sulfur-containing substrates. In Bacillus subtilis, pimeloyl-CoA synthetase (PCAS, EC 6.2.1.14, UNIPROT code: P53559, 29.6 kDa) is the first enzyme in the biotin biosynthetic pathway and acts as a highly specific substrate selection gate ensuring the integrity of the carbon chain in biotin synthesis. PCAS catalyses the synthesis of the key acyl-thioester, pimeloyl-CoA in two steps; the first involves activation of pimelic acid (C7 dicarboxylic acid) using ATP to give an acyl-adenylate, enzyme-bound intermediate and pyrophosphate (PPi), and in the second step, this pimeloyl-adenylate reacts with coenzyme A (CoASH) to form the pimeloyl-CoA thioester. This thesis describes the results of biochemical, structural and mechanistic studies of B. subtilis PCAS. Recombinant PCAS was prepared by expressing the B. subtilis BioW gene in E. coli in various hexa-histidine affinity-tagged forms and the enzyme purified in high purity and yield. Enzyme activity and kinetic constants were measured using reverse-phase HPLC and enzyme coupled spectroscopic assays. These revealed the enzyme to have a strict carboxylic acid specificity. In collaboration with colleagues at the University of St. Andrews various commercial and in-house screens were used to obtain diffraction-quality crystals suitable for X-ray crystallography. This also included the generation of seleno-methionine (SeMet) labelled PCAS, as well as heavy-metal derivatives. Structures of B. subtilis PCAS in complex with the substrate pimelic acid and the pimeloyl-adenylate intermediate and product PPi were determined at 2.04 Å and 2.34 Å resolution respectively. The B. subtilis PCAS displays a novel 3D fold and defines a new class (Class IV) in the ANL superfamily of adenylate forming enzymes. The enzyme is a homodimer composed of two domains, a short N-terminus and a large C-terminal domain and the ligand-bound structures revealed the residues potentially involved in substrate specificity and enzyme catalysis. The enzyme uses an internal ruler composed of a number of conserved arginine residues (Arg213, Arg227 and Arg170) to select the correct dicarboxylic acid substrate. The X-ray structures guided the production of a number of site directed mutants to identify residues involved in the catalytic mechanism and stabilising the acyl-adenylate intermediate. This also allowed rational engineering of the PCAS active site to generate mutants with altered substrate specificity. Mutant PCAS Y211F was shown to synthesise both heptanoyl (C7) and octanoyl (C8) mono carboxylic acid-CoA and C8 dicarboxylic-CoA thioester products, highlighting the synthetic potential of PCAS. The PCAS pimeloyl-CoA product is the substrate for the next enzyme in the biotin pathway, a pyridoxal 5‟phosphate (PLP)-dependent 8-amino 7-oxononanoate synthase (AONS). AONS catalyses the condensation of pimeloyl-CoA with L-alanine to give AON which is converted to biotin by the action of three other enzymes. We used genome mining to identify a putative ~66 kDa, bi-functional PCAS/AONS enzyme with an N-terminal PCAS domain fused to C-terminal AONS domain in the organism Corynebacterium amycolatum. A recombinant C. amycolatum PCAS/AONS fusion protein was expressed and purified from E. coli and initial studies suggest that it forms a functional, fused, dimeric enzyme

Multi-scale distribution of coal fractures based on CT digital core deep learning

In order to realize high-precision and high-efficiency identification of multi-scale distribution characteristics of coal fractures, carry out the study of multi-scale distribution characteristics identification methods based on CT digital core deep learning. Industrial CT scanning system is used to collect a large number of coal original CT digital core information array, the CT digital core information array is converted into a two-dimensional gray-scale image and then it is divided into square images of different scales and the image brightness is enhanced to different levels as training samples, Finally, the construction and optimization of model parameters of AlexNet, ResNet-18, GoogLeNet and Inception-V3 models for the identification of CT-containing fractures are realized by Matlab platform. Study the recognition accuracy and verification accuracy of different model training under different number of training samples; Study the accuracy, calculation efficiency and training time of different models for images with different scales and brightness under the same training sample, obtain the optimal model for calculating the fractal dimension of two-dimensional CT images with fractures, then, the fractal distribution characteristics of each fracture image are calculated according to the statistical method of box-counting dimension, compared with the traditional binarization method and human eye recognition method, The applicability of the multi-scale distribution characteristics identification method of coal fractures based on CT digital core deep learning is verified. The result shows: ① ResNet-18 model is the optimal model for calculating the fractal dimension of two-dimensional CT images with cracks when the image sample is brightness 4 and the scale is 3.5 mm to 21 mm, the model has high accuracy and short training time in calculating the fractal dimension of two-dimensional CT fracture images. ② Compared with the traditional binarization method, the multi-scale recognition method of coal fracture based on CT digital core deep learning has the advantages of fast speed, high accuracy and is not easily affected by impurities in coal

Chronic Alcohol Causes Alteration of Lipidome Profiling in Brain

Much efforts have been tried to clarify the molecular mechanism of alcohol-induced brain damage from the perspective of genome and protein; however, the effect of chronic alcohol exposure on global lipid profiling of brain is unclear. In the present study, by using Q-TOF/MS-based lipidomics approach, we investigated the comprehensive lipidome profiling of brain from the rats orally administrated with alcohol daily, continuously for one year. Through systematically analysis of all lipids in prefrontal cortex (PFC) and striatum region, we found that long-term alcohol exposure profoundly modified brain lipidome profiling. Notably, three kinds of lipid classes, glycerophospholipid (GP), glycerolipid (GL) and fatty acyls (FA), were significantly increased in these two brain regions. Interestingly, most of the modified lipids were involved in synthetic pathways of endoplasmic reticulum (ER), which may result in ER stress-related metabolic disruption. Moreover, alcohol-modified lipid species displayed long length of carbon chain with high degree of unsaturation. Taken together, our results firstly present that chronic alcohol exposure markedly modifies brain lipidomic profiling, which may activate ER stress and eventually result in neurotoxicity. These findings provide a new insight into the mechanism of alcohol-related brain damage.Peer reviewe

Sex differences in the utilization and outcomes of endovascular treatment after acute ischemic stroke: A systematic review and meta-analysis

BackgroundStudies of sex differences in the use and outcomes of endovascular treatment (EVT) for acute ischemic stroke report inconsistent resultsMethodsWe systematically searched PubMed and Embase databases for studies examining sex-specific utilization of EVT for acute ischemic stroke published before 31 December 2021. Estimates were compared by study type: randomized clinical trials (RCTs) and non-RCTs (hospital-based, registry-based or administrative data). Random effects odds ratios (ORs) were generated to quantify sex differences in EVT use. To estimate sex differences in functional outcome on the modified Rankin scale after EVT, the female:male ratio of ORs and 95% confidence intervals (CIs) were obtained from ordinal or binary analysis.Results6,396 studies were identified through database searching, of which 594 qualified for a full review. A total of 51 studies (36 non-RCT and 15 RCTs) reporting on sex-specific utilization of EVT were included, and of those 10 estimated the sex differences of EVT on functional outcomes. EVT use was similar in women and men both in non-RCTs (OR: 1.03, 95% CI: 0.96–1.11) and RCTs (1.02, 95% CI: 0.89–1.16), with consistent results across years of publication and regions of study, except that in Europe EVT treatment was higher in women than men (1.15, 95% CI: 1.13–1.16). No sex differences were found in the functional outcome by either ordinal and binary analyses (ORs 0.95, 95% CI: 0.68–1.32] and 0.90, 95% CI: 0.65–1.25, respectively).ConclusionsNo sex differences in EVT utilization or on functional outcomes were evident after acute ischemic stroke from large-vessel occlusion. Further research may be required to examine sex differences in long-term outcomes, social domains, and quality of life.Systematic Review Registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=226100, identifier: CRD42021226100

Who is the main caregiver of the mother during the doing-the-month : is there an association with postpartum depression?

Background: To examine the relationship between the main caregiver during the “doing-the-month” (a traditional Chinese practice which a mother is confined at home for 1 month after giving birth) and the risk of postpartum depression (PPD) in postnatal women. Methods: Participants were postnatal women stayed in hospital and women who attended the hospital for postpartum examination, at 14–60 days after delivery from November 1, 2013 to December 30, 2013. Postpartum depression status was assessed using the Edinburgh Postnatal Depression Scale. Univariate and multivariable logistic regressions were used to identify the associations between the main caregiver during “doing-the-month” and the risk of PPD in postnatal women. Results: One thousand three hundred twenty-five postnatal women with a mean (SD) age of 28 (4.58) years were included in the analyses. The median score (IQR) of PPD was 6.0 (2, 10) and the prevalence of PPD was 27%. Of these postnatal women, 44.5% were cared by their mother-in-law in the first month after delivery, 36.3% cared by own mother, 11.1% by “yuesao” or “maternity matron” and 8.1% by other relatives. No association was found between the main caregivers and the risk of PPD after multiple adjustments. Conclusions: Although no association between the main caregivers and the risk of PPD during doing-the-month was identified, considering the increasing prevalence of PPD in Chinese women, and the contradictions between traditional culture and latest scientific evidence for some of the doing-the-month practices, public health interventions aim to increase the awareness of PPD among caregivers and family members are warranted

Mitigation mechanism of zinc oxide nanoparticles on cadmium toxicity in tomato

Cadmium (Cd) pollution seriously reduces the yield and quality of vegetables. Reducing Cd accumulation in vegetables is of great significance for improving food safety and sustainable agricultural development. Here, using tomato as the material, we analyzed the effect of foliar spraying with zinc oxide nanoparticles (ZnO NPs) on Cd accumulation and tolerance in tomato seedlings. Foliar spraying with ZnO NPs improved Cd tolerance by increasing photosynthesis efficiency and antioxidative capacity, while it reduced Cd accumulation by 40.2% in roots and 34.5% in leaves but increased Zn content by 33.9% in roots and 78.6% in leaves. Foliar spraying with ZnO NPs also increased the contents of copper (Cu) and manganese (Mn) in the leaves of Cd-treated tomato seedlings. Subsequent metabonomic analysis showed that ZnO NPs exposure alleviated the fluctuation of metabolic profiling in response to Cd toxicity, and it had a more prominent effect in leaves than in roots. Correlation analysis revealed that several differentially accumulated metabolites were positively or negatively correlated with the growth parameters and physiol-biochemical indexes. We also found that flavonoids and alkaloid metabolites may play an important role in ZnO NP-alleviated Cd toxicity in tomato seedlings. Taken together, the results of this study indicated that foliar spraying with ZnO NPs effectively reduced Cd accumulation in tomato seedlings; moreover, it also reduced oxidative damage, improved the absorption of trace elements, and reduced the metabolic fluctuation caused by Cd toxicity, thus alleviating Cd-induced growth inhibition in tomato seedlings. This study will enable us to better understand how ZnO NPs regulate plant growth and development and provide new insights into the use of ZnO NPs for improving growth and reducing Cd accumulation in vegetables