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1.
Reversal of nucleobase methylation by dioxygenases.
Xu, GL, Bochtler, M
Nature chemical biology. 2020;(11):1160-1169
Abstract
The repertoire of nucleobase methylation in DNA and RNA, introduced by chemical agents or enzymes, is large. Most methylation can be reversed either directly by restoration of the original nucleobase or indirectly by replacement of the methylated nucleobase with an unmodified nucleobase. In many direct and indirect demethylation reactions, ALKBH (AlkB homolog) and TET (ten eleven translocation) hydroxylases play a role. Here, we suggest a chemical classification of methylation types. We then discuss pathways for removal, emphasizing oxidation reactions. We highlight the recently expanded repertoire of ALKBH- and TET-catalyzed reactions and describe the discovery of a TET-like protein that resembles the hydroxylases but uses an alternative co-factor and catalyzes glyceryl transfer rather than hydroxylation.
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2.
Mutations in NBAS and SCYL1, genetic causes of recurrent liver failure in children: Three case reports and a literature review.
Chavany, J, Cano, A, Roquelaure, B, Bourgeois, P, Boubnova, J, Gaignard, P, Hoebeke, C, Reynaud, R, Rhomer, B, Slama, A, et al
Archives de pediatrie : organe officiel de la Societe francaise de pediatrie. 2020;(3):155-159
Abstract
Acute liver failure (ALF) in childhood is a life-threatening emergency. ALF is often caused by drug toxicity, autoimmune hepatitis, inherited metabolic diseases, and infections. However, despite thorough investigations, a cause cannot be determined in approximately 50% of cases. Here, we report three cases with recurrent ALF caused by NBAS and SCYL1 pathogenic variants. These patients did not present with any other phenotypic sign usually associated with NBAS and SCYL1 pathogenic variants. Two of them underwent liver transplantation and are healthy without recurrence of ALF. We propose NBAS and SCYL1 genetic analysis in children with unexplained fever-triggered recurrent ALF even without a typical phenotype.
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3.
Characteristic and role of chromosomal type II toxin-antitoxin systems locus in Enterococcus faecalis ATCC29212.
Li, Z, Shi, C, Gao, S, Zhang, X, Lu, D, Liu, G
Journal of microbiology (Seoul, Korea). 2020;(12):1027-1036
Abstract
The Gram-positive bacterium Enterococcus faecalis is currently one of the major pathogens of nosocomial infections. The lifestyle of E. faecalis relies primarily on its remarkable capacity to face and survive in harsh environmental conditions. Toxin-antitoxin (TA) systems have been linked to the growth control of bacteria in response to adverse environments but have rarely been reported in Enterococcus. Three functional type II TA systems were identified among the 10 putative TA systems encoded by E. faecalis ATCC29212. These toxin genes have conserved domains homologous to MazF (DR75_1948) and ImmA/IrrE family metallo-endopeptidases (DR75_1673 and DR75_2160). Overexpression of toxin genes could inhibit the growth of Escherichia coli. However, the toxin DR75_1673 could not inhibit bacterial growth, and the bacteriostatic effect occurred only when it was coexpressed with the antitoxin DR75_1672. DR75_1948-DR75_1949 and DR75_160-DR75_2161 could maintain the stable inheritance of the unstable plasmid pLMO12102 in E. coli. Moreover, the transcription levels of these TAs showed significant differences when cultivated under normal conditions and with different temperatures, antibiotics, anaerobic agents and H2O2. When DR75_2161 was knocked out, the growth of the mutant strain at high temperature and oxidative stress was limited. The experimental characterization of these TAs loci might be helpful to investigate the key roles of type II TA systems in the physiology and environmental stress responses of Enterococcus.
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4.
Management versus miscues in the cytosolic labile iron pool: The varied functions of iron chaperones.
Philpott, CC, Patel, SJ, Protchenko, O
Biochimica et biophysica acta. Molecular cell research. 2020;(11):118830
Abstract
Iron-containing proteins rely on the incorporation of a set of iron cofactors for activity. The cofactors must be synthesized or assembled from raw materials located within the cell. The chemical nature of this pool of raw material - referred to as the labile iron pool - has become clearer with the identification of micro- and macro-molecules that coordinate iron within the cell. These molecules function as a buffer system for the management of intracellular iron and are the focus of this review, with emphasis on the major iron chaperone protein coordinating the labile iron pool: poly C-binding protein 1.
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5.
Differential regulation of a placental SAM68 and sFLT1 gene pathway and the relevance to maternal vitamin D sufficiency.
Awe, O, Sinkway, JM, Chow, RP, Wagener, Q, Schulz, EV, Yu, JY, Nietert, PJ, Wagner, CL, Lee, KH
Pregnancy hypertension. 2020;:196-203
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Abstract
OBJECTIVE The goal of this study was to determine if an axis of placental gene expression associated with early onset and severe preeclampsia (EOSPE) was operative in term pregnancy and correlated with vitamin D sufficiency. METHODS qPCR analysis of NKX2-5, SAM68, sFLT1 and membrane bound VEGFR1/FLT1 mRNA expression was conducted in placentas from 43 subjects enrolled in a vitamin D3 pregnancy supplementation trial. Pair-wise rank order correlations between patient-specific gene expression levels were calculated, and their relationship to maternal 25(OH)D status was assessed by a two-sample Wilcoxon test. Additionally, we probed the mechanistic link between SAM68 and sFLT1 using siRNA depletion in a human trophoblast cell line model. RESULTS Positive and highly significant correlations were found between SAM68 vs. sFLT1 and SAM68 vs. FLT1 expression levels, as were significant and differential correlations between the expression of these genes and perinatal 25(OH)D status. The variability when stratified by race/ethnicity was qualitatively distinct from those previously observed in EOSPE. Mechanistic studies confirmed a functional role for SAM68 protein in the regulation of sFLT1 expression. NKX2-5 expression was not significantly correlated with sFLT1 or SAM68 expression in these samples, suggesting that its expression may be significant at earlier stages of pregnancy or be restricted to pathological settings. CONCLUSIONS These data further support our overarching hypothesis that SAM68 expression is a key determinant of VEGFR1 isoform expression in the placenta, and provide additional insights into how this gene pathway may be differentially deployed or modified in normal and pathological pregnancies.
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6.
Expression of PBRM1 as a prognostic predictor in metastatic renal cell carcinoma patients treated with tyrosine kinase inhibitor.
Cai, W, Wang, Z, Cai, B, Yuan, Y, Kong, W, Zhang, J, Chen, Y, Liu, Q, Huang, Y, Huang, J, et al
International journal of clinical oncology. 2020;(2):338-346
Abstract
OBJECTIVE PBRM1, located on 3p21, functions as a tumor suppressor and somatic mutation of PBRM1 is frequent in clear cell renal cell carcinoma (ccRCC). This study aims to determine the influence of PBRM1 expression on the prognosis of patients with mRCC receiving tyrosine kinase inhibitor (TKI) treatment. METHODS We identified 116 mRCC patients who were administered sunitinib or sorafenib as first-line therapy, between January 2006 and December 2016 at our institution. PBRM1 expression was assessed by immunohistochemistry. The Kaplan-Meier method was used to estimate the progression-free survival (PFS) and overall survival (OS), log-rank test was used to compare the survival outcomes between patients with low and high PBRM1 expression levels, and the Cox proportional hazard regression model was used to estimate the prognostic value. Prognostic accuracy was determined using Harrell concordance index, and nomograms were built to evaluate the prognosis of mRCC. RESULTS Patients with low PBRM1 expression had significantly shorter median PFS (9 vs 26 months, P < 0.001) and OS (21 vs 44 months, P < 0.001) than those with high expression. Multivariate analysis showed that PBRM1 expression was an independent predictor of PFS (HR 1.975, P = 0.013) and OS (HR 2.282, P = 0.007). The model built by the addition of PBRM1 improved the C-index of PFS and OS to 0.72 and 0.82, respectively. CONCLUSIONS The expression of PBRM1 could be a significant prognostic factor for mRCC patients treated with targeted therapy, and it increases the prognostic accuracy of the established prognostic model.
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7.
Chronic stress induces formation of stress granules and pathological TDP-43 aggregates in human ALS fibroblasts and iPSC-motoneurons.
Ratti, A, Gumina, V, Lenzi, P, Bossolasco, P, Fulceri, F, Volpe, C, Bardelli, D, Pregnolato, F, Maraschi, A, Fornai, F, et al
Neurobiology of disease. 2020;:105051
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are fatal neurodegenerative diseases characterized by the presence of neuropathological aggregates of phosphorylated TDP-43 (P-TDP-43) protein. The RNA-binding protein TDP-43 participates also to cell stress response by forming stress granules (SG) in the cytoplasm to temporarily arrest translation. The hypothesis that TDP-43 pathology directly arises from SG has been proposed but is still under debate because only sub-lethal stress conditions have been tested experimentally so far. In this study we reproduced a mild and chronic oxidative stress by sodium arsenite to better mimic the persistent and subtle alterations occurring during the neurodegenerative process in primary fibroblasts and induced pluripotent stem cell-derived motoneurons (iPSC-MN) from ALS patients carrying mutations in TARDBP and C9ORF72 genes. We found that not only the acute sub-lethal stress usually used in literature, but also the chronic oxidative insult was able to induce SG formation in both primary fibroblasts and iPSC-MN. We also observed the recruitment of TDP-43 into SG only upon chronic stress in association to the formation of distinct cytoplasmic P-TDP-43 aggregates and a significant increase of the autophagy marker p62. A quantitative analysis revealed differences in both the number of cells forming SG in mutant ALS and healthy control fibroblasts, suggesting a specific genetic contribution to cell stress response, and in SG size, suggesting a different composition of these cytoplasmic foci in the two stress conditions. Upon removal of arsenite, the recovery from chronic stress was complete for SG and P-TDP-43 aggregates at 72 h with the exception of p62, which was reduced but still persistent, supporting the hypothesis that autophagy impairment may drive pathological TDP-43 aggregates formation. The gene-specific differences observed in fibroblasts in response to oxidative stress were not present in iPSC-MN, which showed a similar formation of SG and P-TDP-43 aggregates regardless their genotype. Our results show that SG and P-TDP-43 aggregates may be recapitulated in patient-derived neuronal and non-neuronal cells exposed to prolonged oxidative stress, which may be therefore exploited to study TDP-43 pathology and to develop individualized therapeutic strategies for ALS/FTD.
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8.
A combined Far-FTIR, FTIR Spectromicroscopy, and DFT Study of the Effect of DNA Binding on the [4Fe4S] Cluster Site in EndoIII.
Hassan, A, Macedo, LJA, Souza, JCP, Lima, FCDA, Crespilho, FN
Scientific reports. 2020;(1):1931
Abstract
Endonuclease III (EndoIII) is a DNA glycosylase that contains the [4Fe4S] cluster, which is essential for the protein to bind to damaged DNA in a process called base excision repair (BER). Here we propose that the change in the covalency of Fe-S bonds of the [4Fe4S] cluster caused by double-stranded (ds)-DNA binding is accompanied by a change in their strength, which is due to alterations of the electronic structure of the cluster. Micro-FTIR spectroscopy in the mid-IR region and FTIR spectroscopy in the far IR (450 and 300 cm-1) were used independently to study the structural changes in EndoIII and the behavior of the [4Fe4S] cluster it contains, in the native form and upon its binding to ds-DNA. Structural changes in the DNA itself were also examined. The characteristics vibrational modes, corresponding to Fe-S (sulfide) and Fe-S (thiolate) bonds were identified in the cluster through far IR spectroscopy as well through quantum chemistry calculations. Based on the experimental results, these vibrational modes shift in their spectral positions caused by negatively charged DNA in the vicinity of the cluster. Modifications of the Fe-S bond lengths upon DNA binding, both of the Fe-S (sulfide) and Fe-S (thiolate) bonds in the [4Fe4S] cluster of EndoIII are responsible for the stabilization of the cluster towards higher oxidation state (3+), and hence its redox communication along the ds-DNA helix.
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9.
PredDBP-Stack: Prediction of DNA-Binding Proteins from HMM Profiles using a Stacked Ensemble Method.
Wang, J, Zheng, H, Yang, Y, Xiao, W, Liu, T
BioMed research international. 2020;:7297631
Abstract
DNA-binding proteins (DBPs) play vital roles in all aspects of genetic activities. However, the identification of DBPs by using wet-lab experimental approaches is often time-consuming and laborious. In this study, we develop a novel computational method, called PredDBP-Stack, to predict DBPs solely based on protein sequences. First, amino acid composition (AAC) and transition probability composition (TPC) extracted from the hidden markov model (HMM) profile are adopted to represent a protein. Next, we establish a stacked ensemble model to identify DBPs, which involves two stages of learning. In the first stage, the four base classifiers are trained with the features of HMM-based compositions. In the second stage, the prediction probabilities of these base classifiers are used as inputs to the meta-classifier to perform the final prediction of DBPs. Based on the PDB1075 benchmark dataset, we conduct a jackknife cross validation with the proposed PredDBP-Stack predictor and obtain a balanced sensitivity and specificity of 92.47% and 92.36%, respectively. This outcome outperforms most of the existing classifiers. Furthermore, our method also achieves superior performance and model robustness on the PDB186 independent dataset. This demonstrates that the PredDBP-Stack is an effective classifier for accurately identifying DBPs based on protein sequence information alone.
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10.
The Trinity of cGAS, TLR9, and ALRs Guardians of the Cellular Galaxy Against Host-Derived Self-DNA.
Kumar, V
Frontiers in immunology. 2020;:624597
Abstract
The immune system has evolved to protect the host from the pathogens and allergens surrounding their environment. The immune system develops in such a way to recognize self and non-self and develops self-tolerance against self-proteins, nucleic acids, and other larger molecules. However, the broken immunological self-tolerance leads to the development of autoimmune or autoinflammatory diseases. Pattern-recognition receptors (PRRs) are expressed by immunological cells on their cell membrane and in the cytosol. Different Toll-like receptors (TLRs), Nod-like receptors (NLRs) and absent in melanoma-2 (AIM-2)-like receptors (ALRs) forming inflammasomes in the cytosol, RIG (retinoic acid-inducible gene)-1-like receptors (RLRs), and C-type lectin receptors (CLRs) are some of the PRRs. The DNA-sensing receptor cyclic GMP-AMP synthase (cGAS) is another PRR present in the cytosol and the nucleus. The present review describes the role of ALRs (AIM2), TLR9, and cGAS in recognizing the host cell DNA as a potent damage/danger-associated molecular pattern (DAMP), which moves out to the cytosol from its housing organelles (nucleus and mitochondria). The introduction opens with the concept that the immune system has evolved to recognize pathogens, the idea of horror autotoxicus, and its failure due to the emergence of autoimmune diseases (ADs), and the discovery of PRRs revolutionizing immunology. The second section describes the cGAS-STING signaling pathway mediated cytosolic self-DNA recognition, its evolution, characteristics of self-DNAs activating it, and its role in different inflammatory conditions. The third section describes the role of TLR9 in recognizing self-DNA in the endolysosomes during infections depending on the self-DNA characteristics and various inflammatory diseases. The fourth section discusses about AIM2 (an ALR), which also binds cytosolic self-DNA (with 80-300 base pairs or bp) that inhibits cGAS-STING-dependent type 1 IFN generation but induces inflammation and pyroptosis during different inflammatory conditions. Hence, this trinity of PRRs has evolved to recognize self-DNA as a potential DAMP and comes into action to guard the cellular galaxy. However, their dysregulation proves dangerous to the host and leads to several inflammatory conditions, including sterile-inflammatory conditions autoinflammatory and ADs.