Acetylation Modification Research Articles

β-hydroxybutyrate impairs bovine oocyte maturation via pyruvate dehydrogenase (PDH) associated energy metabolism abnormality.

Background: Ketosis is one of the most frequent and costly metabolic disorders in high-producing dairy cows, and negatively associated with the health and reproductive performance of bovine. Ketosis is mainly caused by the accumulation of ketone body β-hydroxybutyric acid and its diagnosis is based on β-hydroxybutyrate (βHB) concentration in blood. Methods: In this study, we investigated the effects of βHB on bovine oocyte maturation in the concentration of subclinical (1.2mM) βHB and clinical (3.6mM). Results: The results showed βHB disrupted bovine oocyte maturation and development capacity. Further analysis showed that βHB induced oxidative stress and mitochondrial dysfunction, as indicated by the increased level of reactive oxygen species (ROS), disrupted mitochondrial structure and distribution, and depolarized membrane potential. Furthermore, oxidative stress triggered early apoptosis, as shown by the enhanced levels of Caspase-3 and Annexin-V. Moreover, 3.6mM βHB induced the disruption of the pyruvate dehydrogenase (PDH) activity, showing with the decrease of the global acetylation modification and the increase of the abnormal spindle rate. Conclusion: Our study showed that βHB in subclinical/clinical concentration had toxic effects on mitochondrial function and PDH activity, which might affect energy metabolism and epigenetic modification of bovine oocytes and embryos.

The Histone Deacetylase HstD Regulates Fungal Growth, Development and Secondary Metabolite Biosynthesis in Aspergillus terreus.

Histone acetylation modification significantly affects secondary metabolism in filamentous fungi. However, how histone acetylation regulates secondary metabolite synthesis in the lovastatin (a lipid-lowering drug) producing Aspergillus terreus remains unknown because protein is involved and has been identified in this species. Here, the fungal-specific histone deacetylase gene, hstD, was characterized through functional genomics in two marine-derived A. terreus strains, Mj106 and RA2905. The results showed that the ablation of HstD resulted in reduced mycelium growth, less conidiation, and decreased lovastatin biosynthesis but significantly increased terrein biosynthesis. However, unlike its homologs in yeast, HstD was not required for fungal responses to DNA damage agents, indicating that HstD likely plays a novel role in the DNA damage repair process in A. terreus. Furthermore, the loss of HstD resulted in a significant upregulation of H3K56 and H3K27 acetylation when compared to the wild type, suggesting that epigenetic functions of HstD, as a deacetylase, target H3K27 and H3K56. Additionally, a set of no-histone targets with potential roles in fungal growth, conidiation, and secondary metabolism were identified for the first time using acetylated proteomic analysis. In conclusion, we provide a comprehensive analysis of HstD for its targets in histone or non-histone and its roles in fungal growth and development, DNA damage response, and secondary metabolism in A. terreus.

Comprehensive analysis of acetylation-related genes for the prognosis and immunotherapy response of gastric cancer.

38 Background: Although clinical researchers have made great progress in the treatment of gastric cancer, the overall survival time of gastric cancer patients remains unfavorable,It has been reported that HDAC1 is a prognostic marker for survival. However, the relationship between acetylation modification and the prognosis and treatment of gastric cancer has not been elaborated so far. Therefore, we carried out a systematic study and hope to provide novel therapeutic targets. Methods: We obtained the RNA sequencing data of GC patients and the corresponding clinical features from GEO database. T-test was performed to analyze the difference in expression of acetylation-related genes in normal and tumor samples from TCGA-STAD dataset.Using median expression as the threshold, univariate cox regression was performed to analyze the prognostic differences in overall survival (OS) for each acetylation-related gene. ssGSEA was utilized to analyze the percentage of infiltration of 28 immune cells in different clusters. Subsequently, we performed functional enrichment analysis of the differential genes using DAVID.used TIDE to analyze the effect of immune checkpoint inhibition. In addition, we compared the differences in TIDE scores across scoring subgroups. Results: By comparing 32 normal samples and 362 tumor samples in the TCGA dataset, we found that most acetylation-related genes are differentially expressed.most of the KAT genes were amplified more frequently than the deletion frequency, especially KAT2A and ESC1, while the deletion frequency of HDAC4 was high.CREBBP and KAT6A genes were mutated with high frequency.The results of acetylation-related gene clustering were divided into two subgroups (KAT-KDAC-cluster 1 and KAT-KDAC-cluster 2), Cluster 1 was mainly enriched in processes such as mismatch repair and homologous recombination during DNA replication, and cluster 2 was mainly enriched in calcium signaling, insulin signaling pathway and actin cytoskeleton regulation.We filtered out 9 genes most associated with GC were screened by random forest, and 2 of them were found to be unrelated to patient prognosis by univariate analysis, resulting in 7 genes, including FERMT2, CALD1, TGFBII, PPP1R14A, PPPIR3C, ADAMTS1, and RBPMS2.and KAT-KDAC scores were calculated.KAT-KDAC score group had lower TIDE scores, predicting better immune efficacy for patients in the low-KAT-KDAC score group. Conclusions: Expression of acetylation-related genes affects the prognosis of gastric cancer.

The role of Mycobacterium tuberculosis acetyltransferase and protein acetylation modifications in tuberculosis.

Tuberculosis (TB) is a widespread infectious disease caused by Mycobacterium tuberculosis (M. tb), which has been a significant burden for a long time. Post-translational modifications (PTMs) are essential for protein function in both eukaryotic and prokaryotic cells. This review focuses on the contribution of protein acetylation to the function of M. tb and its infected macrophages. The acetylation of M. tb proteins plays a critical role in virulence, drug resistance, regulation of metabolism, and host anti-TB immune response. Similarly, the PTMs of host proteins induced by M. tb are crucial for the development, treatment, and prevention of diseases. Host protein acetylation induced by M. tb is significant in regulating host immunity against TB, which substantially affects the disease's development. The review summarizes the functions and mechanisms of M. tb acetyltransferase in virulence and drug resistance. It also discusses the role and mechanism of M. tb in regulating host protein acetylation and immune response regulation. Furthermore, the current scenario of isoniazid usage in M. tb therapy treatment is examined. Overall, this review provides valuable information that can serve as a preliminary basis for studying pathogenic research, developing new drugs, exploring in-depth drug resistance mechanisms, and providing precise treatment for TB.

Genome-Wide Acetylation Modification of H3K27ac in Bovine Rumen Cell Following Butyrate Exposure.

Butyrate contributes epigenetically to the changes in cellular function and tissue development of the rumen in ruminant animals, which might be achieved by its genetic or epigenetic regulation of gene expression. To explore the role of butyrate on bovine rumen epithelial function and development, this study characterized genome-wide H3K27ac modification changes and super-enhancer profiles in rumen epithelial primary cells (REPC) induced with butyrate by ChIP-seq, and analyzed its effects on gene expression and functional pathways by integrating RNA-seq data. The results showed that genome-wide acetylation modification was observed in the REPC with 94,675 and 48,688 peaks in the butyrate treatment and control group, respectively. A total of 9750 and 5020 genes with increased modification (H3K27ac-gain) and decreased modification (H3K27ac-loss) were detected in the treatment group. The super-enhancer associated genes in the butyrate-induction group were involved in the AMPK signaling pathway, MAPK signaling pathway, and ECM-receptor interaction. Finally, the up-regulated genes (PLCG1, CLEC3B, IGSF23, OTOP3, ADTRP) with H3K27ac gain modification by butyrate were involved in cholesterol metabolism, lysosome, cell adhesion molecules, and the PI3K-Akt signaling pathway. Butyrate treatment has the role of genome-wide H3K27ac acetylation on bovine REPC, and affects the changes in gene expression. The effect of butyrate on gene expression correlates with the acetylation of the H3K27ac level. Identifying genome-wide acetylation modifications and expressed genes of butyrate in bovine REPC cells will expand the understanding of the biological role of butyrate and its acetylation.

Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis

Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. We report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing, we identify specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determine that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we show that removal of Glucose transporter 1 and Lactate dehydrogenase A gene activity from developing retinal progenitors arrests eye morphogenesis. Surprisingly, we uncover that lactate-mediated upregulation of key eye-field transcription factors is controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase activity. Our results identify an unexpected bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.

EMDL-ac4C: identifying N4-acetylcytidine based on ensemble two-branch residual connection DenseNet and attention.

Introduction: N4-acetylcytidine (ac4C) is a critical acetylation modification that has an essential function in protein translation and is associated with a number of human diseases. Methods: The process of identifying ac4C sites by biological experiments is too cumbersome and costly. And the performance of several existing computational models needs to be improved. Therefore, we propose a new deep learning tool EMDL-ac4C to predict ac4C sites, which uses a simple one-hot encoding for a unbalanced dataset using a downsampled ensemble deep learning network to extract important features to identify ac4C sites. The base learner of this ensemble model consists of a modified DenseNet and Squeeze-and-Excitation Networks. In addition, we innovatively add a convolutional residual structure in parallel with the dense block to achieve the effect of two-layer feature extraction. Results: The average accuracy (Acc), mathews correlation coefficient (MCC), and area under the curve Area under curve of EMDL-ac4C on ten independent testing sets are 80.84%, 61.77%, and 87.94%, respectively. Discussion: Multiple experimental comparisons indicate that EMDL-ac4C outperforms existing predictors and it greatly improved the predictive performance of the ac4C sites. At the same time, EMDL-ac4C could provide a valuable reference for the next part of the study. The source code and experimental data are available at: https://github.com/13133989982/EMDLac4C.

Modification of Starches and Flours by Acetylation and Its Dual Modifications: A Review of Impact on Physicochemical Properties and Their Applications.

Various modification treatments have been carried out to improve the physicochemical and functional properties of various types of starch and flour. Modification by acetylation has been widely used to improve the quality and stability of starch. This review describes the effects of acetylation modification and its dual modifications on the physicochemical properties of starch/flour and their applications. Acetylation can increase swelling power, swelling volume, water/oil absorption capacity, and retrogradation stability. The dual modification of acetylation with cross-linking or hydrothermal treatment can improve the thermal stability of starch/flour. However, the results of the modifications may vary depending on the type of starch, reagents, and processing methods. Acetylated starch can be used as an encapsulant for nanoparticles, biofilms, adhesives, fat replacers, and other products with better paste stability and clarity. A comparison of various characteristics of acetylated starches and their dual modifications is expected to be a reference for developing and applying acetylated starches/flours in various fields and products.

Preparation and Antioxidant Activity of Acetylated Mung Bean Peel Polysaccharides.

Mung bean peel polysaccharides are one of the main active components in mung bean peel. Acetylated mung bean peel polysaccharides were prepared by extracting and acetylating them, and characterized by infrared and ultraviolet methods to preliminarily understand the structural characteristics and activity of acetylated mung bean peel polysaccharides. Acetylation modification can improve the structure of polysaccharides, thereby causing changes in their properties. The product obtained after acetylation modification exhibited new characteristic absorption peaks at 1732cm-1, and the scavenging ability of hydroxyl radicals was improved. Therefore, acetylation modification of mung bean peel polysaccharides could enhance the activity by improving the structure, which provided an experimental basis for the application of mung bean peel polysaccharides.

Effect of temperature during acetylation and heat moisture treatment on the structural and physicochemical properties and application of wheat starch

Some modification techniques have been developed to improve positive attributes and increase application of native starch. In this study, acetylated wheat starch was synthesized using maleic anhydride (MA) and the effect of acetylation temperature and heat moisture treatment (HMT) on the starch was examined. After acetylation modification, the thermal stability of starch decreased except that its freeze–thaw stability increased. Fourier transform infrared spectroscopy showed two new peaks at 1720 and 1570 cm−1 on acetylated starch because of CO and RCOO−, respectively. X-ray diffraction suggested the modification altered the relative crystallinity but not crystalline type. Moreover, temperature controlled the reactions types of MA, and high temperature could promote the formation of crosslinked starch which revealed by the gelatinization to begin at a higher temperature. Starch that acetylated at 30 °C exhibited the higher final viscosity (3674.5 cP) and swelling capacity (18.6 g/g) than those of native starch (871.7 cP and 13.5 g/g, respectively), and counterpart that acetylated at 65 °C or HMT showed increased resistant starch content (5.1%–7.7%) compared with the native wheat (2.8%). Additionally, the stability of the free sulfhydryl, disulfide bond of frozen dough which contained modified starch was improved. Therefore, acetylated starch could be developed as a potential candidate for foods.

Melatonin improves the quality of rotenone-exposed mouse oocytes through association with histone modifications

Rotenone, an insecticide that inhibits mitochondrial complex I and generates oxidative stress, is responsible for neurological disorders and affects the female reproductive system. However, the underlying mechanism is not fully understood. Melatonin, a potential free-radical scavenger, has been shown to protect the reproductive system from oxidative damage. In this study, we investigated the impact of rotenone on mouse oocyte quality and evaluated the protective effect of melatonin on oocytes exposed to rotenone. Our results showed that rotenone impaired mouse oocyte maturation and early embryo cleavage. However, melatonin prevented these negative effects by ameliorating rotenone-induced mitochondrial dysfunction and dynamic imbalance, intracellular Ca2+ homeostasis damage, ER stress, early apoptosis, meiotic spindle formation disruption, and aneuploidy in oocytes. Additionally, RNA sequencing analysis showed that rotenone exposure changed the expression of multiple genes involved in histone methylation and acetylation modifications that result in mouse meiotic defects. However, melatonin partially rescued these defects. These findings suggest that melatonin has protective effects against rotenone-induced mouse oocyte defects.

Programmable Acetylation Modification of Bacterial Proteins by a Cas12a-Guided Acetyltransferase.

Protein lysine acetylation (PLA) is a crucial post-translational modification in organisms that regulates a variety of metabolic and physiological activities. Many advances have been made in PLA-related research; however, the quick and accurate identification of causal relationships between specific protein acetylation events and phenotypic outcomes at the proteome level remains challenging due to the lack of efficient targeted modification techniques. In this study, based on the characteristics of transcription-translation coupling in bacteria, we designed and constructed an in situ targeted protein acetylation (TPA) system integrating the dCas12a protein, guiding element crRNA, and bacterial acetylase At2. Rapid identification of multiple independent protein acetylation and cell phenotypic analyses in Gram-negative Escherichia coli and Gram-positive Clostridium ljungdahlii demonstrated that TPA is a specific and efficient targeting tool for protein modification studies and engineering.

Metformin Promotes Proliferation of Mouse Female Germline Stem Cells by Histone Acetylation Modification of Traf2.

Female germline stem cells (FGSCs) are adult stem cells that can both self-renew and differentiate into mature oocytes. Although small-molecule compounds are capable of regulating the development of FGSCs, the effects and mechanisms of action of metformin, a commonly used drug for diabetes, on FGSCs are largely unknown. Here, we found that metformin promoted the viability and proliferation of FGSCs through H3K27ac modification. To elucidate the mechanism by which metformin promoted FGSCs proliferation, Chromatin Immunoprecipitation Sequencing of histone 3 lysine 27 acetylation (H3K27ac) in FGSCs was performed with or without metformin-treatment. The results indicate that metformin modulates FGSCs via the mitogen-activated protein kinase (MAPK) signaling pathway, and tumor necrosis factor receptor associated factor 2 (Traf2) was identified as an important target gene for H3K27ac modification during FGSCs proliferation. Subsequent experiments showed metformin promoted FGSCs proliferation by H3K27ac modification of Traf2 to regulate MAPK signaling. Our findings deepen understanding of how H3K27ac modifications regulate FGSCs development and provide a theoretical basis for the prevention and treatment of premature ovarian failure, polycystic ovary syndrome, infertility, and related diseases.

Chemoproteomic mapping of the glycolytic targetome in cancer cells.

Hyperactivated glycolysis is a metabolic hallmark of most cancer cells. Although sporadic information has revealed that glycolytic metabolites possess nonmetabolic functions as signaling molecules, how these metabolites interact with and functionally regulate their binding targets remains largely elusive. Here, we introduce a target-responsive accessibility profiling (TRAP) approach that measures changes in ligand binding-induced accessibility for target identification by globally labeling reactive proteinaceous lysines. With TRAP, we mapped 913 responsive target candidates and 2,487 interactions for 10 major glycolytic metabolites in a model cancer cell line. The wide targetome depicted by TRAP unveils diverse regulatory modalities of glycolytic metabolites, and these modalities involve direct perturbation of enzymes in carbohydrate metabolism, intervention of an orphan transcriptional protein's activity and modulation of targetome-level acetylation. These results further our knowledge of how glycolysis orchestrates signaling pathways in cancer cells to support their survival, and inspire exploitation of the glycolytic targetome for cancer therapy.

Decreased acetylation of HDGF improves oviduct production in Rana dybowskii, Rana amurensis, and Rana huanrenensis

The oviduct of female Rana dybowskii is a functional food and can be used as a component of Traditional Chinese medicine. The differentially expressed genes enriched was screened in cell growth of three Rana species. We quantitatively analyzed 4549 proteins using proteomic techniques, enriching the differentially expressed proteins of Rana for growth and signal transduction. The results showed that log2 expression of hepatoma-derived growth factor (HDGF) was increased. We further verified 5 specific differential genes (EIF4a, EIF4g, HDGF1, HDGF2 and SF1) and found that HDGF expression was increased in Rana dybowskii. Through acetylation modification analysis, we identified 1534 acetylation modification sites in 603 proteins, including HDGF, and found that HDGF acetylation expression was significantly reduced in Rana dybowskii. Our results suggest that HDGF is involved in the development of oviductus ranae, which is regulated by acetylation modification.

Preparation of Acetylated Grapefruit Peel Polysaccharide.

Grapefruit peel polysaccharide has antioxidant, antitumor, hypoglycemic and other biological activities, and chemical modification can further improve the properties of the polysaccharide. Acetylation modification of polysaccharides has the advantages of simple operation, low cost and little pollution, and is widely used at present. Different degrees of acetylation modification have different effects on the properties of polysaccharides, so it is necessary to optimize the preparation technology of acetylated grapefruit peel polysaccharides. In this article, acetylated grapefruit peel polysaccharide was prepared by acetic anhydride method. With the degree of acetyl substitution as the evaluation index, combined with the analysis of sugar content and protein content in the polysaccharide before and after modification, the effects of three feeding ratios of 1:0.6, 1 : 1.2 and 1 : 1.8 (polysaccharide: acetic anhydride, mass/volume) on acetylation modification were explored through single factor experiments. The results showed that the optimum ratio of material to liquid for acetylation modification of grapefruit peel polysaccharide was 1:0.6. Under these conditions, the degree of substitution of acetylated grapefruit peel polysaccharide was 0.323, the sugar content was 59.50 % and the protein content was 1.038 %. The results provide some reference for the study of acetylated grapefruit peel polysaccharide.

Enhancer remodeling drives MLL oncogene-dependent transcriptional dysregulation in leukemia stem cells.

Acute myeloid leukemia (AML) with mixed-lineage leukemia (MLL) gene rearrangement (MLLr) comprises a cellular hierarchy in which a subpopulation of cells serves as functional leukemia stem cells (LSCs). They are maintained by a unique gene expression program and chromatin states, which are thought to reflect the actions of enhancers. Here, we delineate the active enhancer landscape and observe pervasive enhancer malfunction in LSCs. Reconstruction of regulatory networks revealed a master set of hematopoietic transcription factors. We show that EP300 is an essential transcriptional coregulator for maintaining LSC oncogenic potential because it controls essential gene expression through modulation of H3K27 acetylation and assessments of transcription factor dependencies. Moreover, the EP300 inhibitor A-485 affects LSC growth by targeting enhancer activity via histone acetyltransferase domain inhibition. Together, these data implicate a perturbed MLLr-specific enhancer accessibility landscape, suggesting the possibility for disruption of the LSC enhancer regulatory axis as a promising therapeutic strategy in AML.

Adenine nucleotide translocase: Current knowledge in post-translational modifications, regulations and pathological implications for human diseases.

Adenine nucleotide translocases (ANTs) are central to mitochondrial integrity and bioenergetic metabolism. This review aims to integrate the progresses and knowledge on ANTs over the last few years, contributing to a potential implication of ANTs for various diseases. Structures, functions, modifications, regulators and pathological implications of ANTs for human diseases are intensively demonstrated here. ANTs have four isoforms (ANT1-4), responsible for exchanging ATP/ADP, possibly composing of pro-apoptotic mPTP as a major component, and mediating FA-dependent uncoupling of proton efflux. ANT can be modified by methylation, nitrosylation and nitroalkylation, acetylation, glutathionylation, phosphorylation, carbonylation and hydroxynonenal-induced modifications. Compounds, including bongkrekic acid, atractyloside calcium, carbon monoxide, minocycline, 4-(N-(S-penicillaminylacetyl)amino) phenylarsonous acid, cardiolipin, free long-chain fatty acids, agaric acid, long chain acyl-coenzyme A esters, all have an ability to regulate ANT activities. ANT impairment leads to bioenergetic failure and mitochondrial dysfunction, contributing to pathogenesis of diseases, such as diabetes (deficiency), heart disease (deficiency), Parkinson's disease (reduction), Sengers Syndrome (decrease), cancer (isoform shifting), Alzheimer's Disease (coaggregation with Tau), Progressive External Opthalmoplegia (mutation), and Fascioscapulohumeral muscular dystrophy (overexpression). This review improves the understanding of the mechanism of ANT in pathogenesis of human diseases, and opens a window for novel therapeutic strategies targeted on ANT in diseases.

Proteomics and Lysine Acetylation Modification Reveal the Responses of Pakchoi (Brassica rapa L. ssp. chinensis) to Oxybenzone Stress.

The broad-spectrum UV filter oxybenzone is toxic to plants at environmentally relevant concentrations. Lysine acetylation (LysAc) is one of the essential post-translational modifications (PTMs) in plant signaling responses. The goal of this study was to uncover the LysAc regulatory mechanism in response to toxic exposures to oxybenzone as a first step in elucidating xenobiotic acclimatory reactions by using the model Brassica rapa L. ssp. chinensis. A total of 6124 sites on 2497 proteins were acetylated, 63 proteins were differentially abundant, and 162 proteins were differentially acetylated under oxybenzone treatment. Bioinformatics analysis showed that a large number of antioxidant proteins were significantly acetylated under oxybenzone treatment, implying that LysAc alleviated the adverse effects of reactive oxygen species (ROS) by inducing antioxidant systems and stress-related proteins; the significant changes in acetylation modification of enzymes involved in different branches of carbon metabolism in plants under oxybenzone treatment mean that plants can change the direction of carbon flow allocation by regulating the activities of carbon metabolism-related enzymes. Our results profile the protein LysAc under oxybenzone treatment and propose an adaptive mechanism at the post-translational level of vascular plants in response to pollutants, providing a dataset reference for future related research.

Modeling of covalent modifications of histones to estimate the binding affinity.

Covalent histone modifications such as methylation, acetylation, phosphorylation, and other epigenetic modifications of the chromatin play an essential role in regulating eukaryotic cells of which most of these reactions are catalyzed by the enzymes. The binding energy of enzymes is often determined by experimental data via mathematical and statistical models due to specific modifications. Many theoretical models have been introduced to study histone modifications and reprogramming experiments in mammalian cells, in which all efforts in determining the affinity binding are essential part of the work. Here, we introduce a one-dimensional statistical Potts model to accurately determine the enzyme's binding free energy using the experimental data for various types of cells. We study the methylation of lysine 4 and 27 on histone H3 and suppose that each histone has one modification site with one of the seven states: H3K27me3, H3K27me2, H3K27me1, unmodified, H3K4me1, H3K4me2, and H3K4me3. Based on this model, the histone covalent modification is described. Moreover, by using simulation data, the histone's binding free energy and the energy of chromatin states are determined, when they are subject to changes from unmodified to active or repressive states, by finding the probability of the transition.