scholarly journals The interaction of canonical Wnt/β-catenin signaling with protein lysine acetylation

2022 ◽  
Vol 27 (1) ◽  
Author(s):  
Hongjuan You ◽  
Qi Li ◽  
Delong Kong ◽  
Xiangye Liu ◽  
Fanyun Kong ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Protein Function ◽  
Protein Modification ◽  
Epigenetic Modification ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Post Translational Modification ◽  
Histone Protein ◽  
Protein Lysine Acetylation ◽  
Canonical Wnt

AbstractCanonical Wnt/β-catenin signaling is a complex cell-communication mechanism that has a central role in the progression of various cancers. The cellular factors that participate in the regulation of this signaling are still not fully elucidated. Lysine acetylation is a significant protein modification which facilitates reversible regulation of the target protein function dependent on the activity of lysine acetyltransferases (KATs) and the catalytic function of lysine deacetylases (KDACs). Protein lysine acetylation has been classified into histone acetylation and non-histone protein acetylation. Histone acetylation is a kind of epigenetic modification, and it can modulate the transcription of important biological molecules in Wnt/β-catenin signaling. Additionally, as a type of post-translational modification, non-histone acetylation directly alters the function of the core molecules in Wnt/β-catenin signaling. Conversely, this signaling can regulate the expression and function of target molecules based on histone or non-histone protein acetylation. To date, various inhibitors targeting KATs and KDACs have been discovered, and some of these inhibitors exert their anti-tumor activity via blocking Wnt/β-catenin signaling. Here, we discuss the available evidence in understanding the complicated interaction of protein lysine acetylation with Wnt/β-catenin signaling, and lysine acetylation as a new target for cancer therapy via controlling this signaling.

scholarly journals Acetylproteomics analyses reveal critical features of lysine-ε-acetylation in Arabidopsis and a role of 14-3-3 protein acetylation in alkaline response

2022 ◽  
Vol 2 (1) ◽  
Author(s):  
Jianfei Guo ◽  
Xiaoqiang Chai ◽  
Yuchao Mei ◽  
Jiamu Du ◽  
Haining Du ◽  
...  
Keyword(s):  
Metabolic Regulation ◽  
Alkaline Stress ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Post Translational Modification ◽  
Evolutionarily Conserved ◽  
Lysine Residues ◽  
Protein Lysine Acetylation ◽  
Subsequent Activation

AbstractLysine-ε-acetylation (Kac) is a post-translational modification (PTM) that is critical for metabolic regulation and cell signaling in mammals. However, its prevalence and importance in plants remain to be determined. Employing high-resolution tandem mass spectrometry, we analyzed protein lysine acetylation in five representative Arabidopsis organs with 2 ~ 3 biological replicates per organ. A total of 2887 Kac proteins and 5929 Kac sites were identified. This comprehensive catalog allows us to analyze proteome-wide features of lysine acetylation. We found that Kac proteins tend to be more uniformly expressed in different organs, and the acetylation status exhibits little correlation with the gene expression level, indicating that acetylation is unlikely caused by stochastic processes. Kac preferentially targets evolutionarily conserved proteins and lysine residues, but only a small percentage of Kac proteins are orthologous between rat and Arabidopsis. A large portion of Kac proteins overlap with proteins modified by other PTMs including ubiquitination, SUMOylation and phosphorylation. Although acetylation, ubiquitination and SUMOylation all modify lysine residues, our analyses show that they rarely target the same sites. In addition, we found that “reader” proteins for acetylation and phosphorylation, i.e., bromodomain-containing proteins and GRF (General Regulatory Factor)/14-3-3 proteins, are intensively modified by the two PTMs, suggesting that they are main crosstalk nodes between acetylation and phosphorylation signaling. Analyses of GRF6/14-3-3λ reveal that the Kac level of GRF6 is decreased under alkaline stress, suggesting that acetylation represses plant alkaline response. Indeed, K56ac of GRF6 inhibits its binding to and subsequent activation of the plasma membrane H+-ATPase AHA2, leading to hypersensitivity to alkaline stress. These results provide valuable resources for protein acetylation studies in plants and reveal that protein acetylation suppresses phosphorylation output by acetylating GRF/14-3-3 proteins.

Deep learning based prediction of reversible HAT/HDAC-specific lysine acetylation

2019 ◽  
Vol 21 (5) ◽  
pp. 1798-1805 ◽  
Author(s):  
Kai Yu ◽  
Qingfeng Zhang ◽  
Zekun Liu ◽  
Yimeng Du ◽  
Xinjiao Gao ◽  
...  
Keyword(s):  
Deep Learning ◽  
Protein Interactions ◽  
Web Server ◽  
Data Sets ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Protein Protein Interactions ◽  
Cellular Processes ◽  
Protein Lysine Acetylation ◽  
Specific Regulation

Abstract Protein lysine acetylation regulation is an important molecular mechanism for regulating cellular processes and plays critical physiological and pathological roles in cancers and diseases. Although massive acetylation sites have been identified through experimental identification and high-throughput proteomics techniques, their enzyme-specific regulation remains largely unknown. Here, we developed the deep learning-based protein lysine acetylation modification prediction (Deep-PLA) software for histone acetyltransferase (HAT)/histone deacetylase (HDAC)-specific acetylation prediction based on deep learning. Experimentally identified substrates and sites of several HATs and HDACs were curated from the literature to generate enzyme-specific data sets. We integrated various protein sequence features with deep neural network and optimized the hyperparameters with particle swarm optimization, which achieved satisfactory performance. Through comparisons based on cross-validations and testing data sets, the model outperformed previous studies. Meanwhile, we found that protein–protein interactions could enrich enzyme-specific acetylation regulatory relations and visualized this information in the Deep-PLA web server. Furthermore, a cross-cancer analysis of acetylation-associated mutations revealed that acetylation regulation was intensively disrupted by mutations in cancers and heavily implicated in the regulation of cancer signaling. These prediction and analysis results might provide helpful information to reveal the regulatory mechanism of protein acetylation in various biological processes to promote the research on prognosis and treatment of cancers. Therefore, the Deep-PLA predictor and protein acetylation interaction networks could provide helpful information for studying the regulation of protein acetylation. The web server of Deep-PLA could be accessed at http://deeppla.cancerbio.info.

scholarly journals Combined Metabolic and Chemical (CoMetChem) Labeling Using Stable Isotopes – a Strategy to Reveal Site-Specific Histone Acetylation and Deacetylation Rates by LC-MS

2021 ◽  
Author(s):  
Alienke van Pijkeren ◽  
Jörn Dietze ◽  
Alejandro Sánchez Brotons ◽  
Tim Lijster ◽  
Andrei Barcaru ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Protein Modification ◽  
High Resolution Mass Spectrometry ◽  
Reaction Rates ◽  
Lysine Acetylation ◽  
Chemical Labeling ◽  
Comprehensive Description ◽  
Site Specific ◽  
New Approach

Histone acetylation is an important, reversible post-translational protein modification and a hallmark of epigenetic regulation. However, little is known about the dynamics of this process, due to the lack of analytical methods that can capture site-specific acetylation and deacetylation reactions. We present a new approach that combines metabolic and chemical labeling (CoMetChem) using uniformly 13C-labeled glucose and stable isotope labeled acetic anhydride. Thereby, chemically equivalent, fully acetylated histone species are generated enabling accurate relative quantification of site-specific lysine acetylation in tryptic peptides using high-resolution mass spectrometry. We show that CoMetChem enables site-specific quantification of the incorporation or loss of lysine acetylation over time, allowing the determination of reaction rates for acetylation and deacetylation. Thus, the CoMetChem methodology provides a comprehensive description of site-specific acetylation dynamics. <br>

scholarly journals Combined Metabolic and Chemical (CoMetChem) Labeling Using Stable Isotopes – a Strategy to Reveal Site-Specific Histone Acetylation and Deacetylation Rates by LC-MS

2021 ◽  
Author(s):  
Alienke van Pijkeren ◽  
Jörn Dietze ◽  
Alejandro Sánchez Brotons ◽  
Tim Lijster ◽  
Andrei Barcaru ◽  
...  
Keyword(s):  
Histone Acetylation ◽  
Protein Modification ◽  
High Resolution Mass Spectrometry ◽  
Reaction Rates ◽  
Lysine Acetylation ◽  
Chemical Labeling ◽  
Comprehensive Description ◽  
Site Specific ◽  
New Approach

Histone acetylation is an important, reversible post-translational protein modification and a hallmark of epigenetic regulation. However, little is known about the dynamics of this process, due to the lack of analytical methods that can capture site-specific acetylation and deacetylation reactions. We present a new approach that combines metabolic and chemical labeling (CoMetChem) using uniformly 13C-labeled glucose and stable isotope labeled acetic anhydride. Thereby, chemically equivalent, fully acetylated histone species are generated enabling accurate relative quantification of site-specific lysine acetylation in tryptic peptides using high-resolution mass spectrometry. We show that CoMetChem enables site-specific quantification of the incorporation or loss of lysine acetylation over time, allowing the determination of reaction rates for acetylation and deacetylation. Thus, the CoMetChem methodology provides a comprehensive description of site-specific acetylation dynamics. <br>

DIABETES-POST-TRANSLATIONAL PROTEIN MODIFICATION FOR DEVELOPMENT OF NEW DRUGS

INDIAN DRUGS ◽  
2014 ◽  
Vol 51 (09) ◽  
pp. 5-11
Author(s):  
P Menon ◽  
◽  
M S Kumar
Keyword(s):  
Glucose Level ◽  
Protein Modification ◽  
Epigenetic Modification ◽  
The Body ◽  
New Drugs ◽  
Metabolic Memory ◽  
Peroxisome Proliferator ◽  
Post Translational Modification ◽  
High Molecular Weight Adiponectin ◽  
Post Translational Modifications

Diabetes is a disorder associated with improper use of glucose by the body leading to increased level of glucose in the blood stream. Beta cells in the pancreas produce the hormone insulin, which is responsible for the movement of glucose into cells where it is utilized to produce energy. Due to the shortage of insulin in diabetic condition, the level of glucose in the bloodstream increases. The level of glucose within cells fall and thus the cells are not able to produce energy using glucose. It also gives rise to various other complications such as blindness, kidney failure, numbness in toes, delayed wound healing, cardiovascular complications, weight gain, loss of consciousness, disorientation etc. which in itself may be dangerous. The root cause of diabetes may either be lack of insulin being produced by the pancreas or development of resistance towards insulin leading to no effect of insulin on the glucose level. Post-translational modifications of protein control various biological processes. It is also considered as an important process in the pathogenesis of diabetes mellitus.In the current review, we will discuss the recent developments in post translational modification of genes associated with diabetes as well as epigenetic modification and metabolic memory that maybe responsible for the onset of diabetes and its associated complications. Currently research is being conducted on high molecular weight adiponectin, peroxisome proliferator-activated receptors (PPARγ), epigenetic histone modifications and Calpain 10 (CAPN10 gene encoded) protein based upon the post translational modifications they undergo and how these modifications affect glucose level regulation. This review article aims at shedding light upon recent advances in biotechnology that are focussed on studying the nature of protein modifications that result in diabetes and finding ways to prevent these modifications or stimulate a new modification that may result in better control of the disease state if not a cure.

Protein acetyltransferases mediate bacterial adaptation to a diverse environment

2021 ◽  
Author(s):  
Aiswarya Dash ◽  
Rahul Modak
Keyword(s):  
Stress Responses ◽  
Cell Formation ◽  
Metabolic Enzyme ◽  
Lysine Acetylation ◽  
Post Translational Modification ◽  
Cellular Processes ◽  
Ph Tolerance ◽  
Diverse Environment ◽  
Protein Lysine Acetylation ◽  
Acetyl Transfer

Protein lysine acetylation is a conserved post-translational modification that modulates several cellular processes. Protein acetylation and its physiological implications are well understood in eukaryotes; however, its role is emerging in bacteria. Lysine acetylation in bacteria is fine-tuned by the concerted action of lysine acetyltransferases (KATs), protein deacetylases (KDACs), metabolic intermediates- acetyl-coenzyme A (Ac-CoA) and acetyl phosphate (AcP). AcP mediated nonenzymatic acetylation is predominant in bacteria due to its high acetyl transfer potential whereas, enzymatic acetylation by bacterial KATs (bKAT) are considered less abundant. Se Pat , the first bKAT discovered in Salmonella enterica , regulates the activity of the central metabolic enzyme- acetyl-CoA synthetase, through its acetylation. Recent studies have highlighted the role of bKATs in stress responses like pH tolerance, nutrient stress, persister cell formation, antibiotic resistance and pathogenesis. Bacterial genomes encode many putative bKATs of unknown biological function and significance. Detailed characterization of putative and partially characterized bKATs is important to decipher the acetylation mediated regulation in bacteria. Proper synthesis of information about the diverse roles of bKATs is missing to date, which can lead to the discovery of new antimicrobial targets in future. In this review, we provide an overview of the diverse physiological roles of known bKATs, and their mode of regulation in different bacteria. We also highlight existing gaps in the literature and present questions that may help understand the regulatory mechanisms mediated by bKATs in adaptation to a diverse habitat.

scholarly journals Structural analysis of GNAT acetyltransferases and protein acetylation

2014 ◽  
Vol 70 (a1) ◽  
pp. C299-C299
Author(s):  
Misty Kuhn ◽  
Karolina Majorek ◽  
Ekaterina Filippova ◽  
George Minasov ◽  
Alan Wolfe ◽  
...  
Keyword(s):  
Infectious Diseases ◽  
High Throughput ◽  
Structural Genomics ◽  
Bacterial Species ◽  
Lysine Acetylation ◽  
Protein Acetylation ◽  
Human Pathogens ◽  
Active Site Residues ◽  
Post Translational Modification ◽  
Lysine Residues

The Center for Structural Genomics for Infectious Diseases (CSGID) applies structural genomics approaches to biomedically relevant proteins from human pathogens and provides the infectious disease community with a high throughput pipeline for structure determination. Target proteins include drug targets, essential enzymes, virulence factors and vaccine candidates. Bacterial species generally have many acetyl-coenzyme A dependent GCN5-like Acetyl Transferases (GNATs), however, the substrates of most of them are unknown. Proteomic analysis has also revealed extensive post-translational modification of bacterial proteins, especially acetylation of lysine Nε. These observations led the CSGID to develop a high throughput substrate screen and initiate characterization of bacterial GNATs. One of the bacterial GNATs that acetylates lysine residues, is the Pseudomonas aeruginosa protein PA4794, that acetylates both peptides having a C-terminal lysine and the drug, chloramphenicol. Surprisingly, the acetylation of these two substrates by PA4794 is catalyzed by the enzyme using different active site residues and different kinetic mechanisms. Although it was expected that the GNATs would play a major role in protein acetylation, much of the lysine acetylation observed in bacteria is actually due to the metabolite acetylphosphate (1,2). Crystal structures and proteomics experiments revealed what makes some lysine residues particularly sensitive to acetylphosphate dependent lysine acetylation and what is required for subsequent enzymatic deacetylation. CSGID is funded with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Contracts No. HHSN272200700058C and HHSN272201200026C and Midwest Center for Structural Genomics by grant GM094585

Protein acetylation as a means to regulate protein function in tune with metabolic state

2014 ◽  
Vol 42 (4) ◽  
pp. 1037-1042 ◽  
Author(s):  
Lei Shi ◽  
Benjamin P. Tu
Keyword(s):  
Energy Metabolism ◽  
Present Article ◽  
Protein Function ◽  
Protein Acetylation ◽  
Post Translational Modification ◽  
Metabolic State ◽  
Acetyl Coa ◽  
Acetyl Group ◽  
Regulate Protein

Protein acetylation has emerged as a prominent post-translational modification that can occur on a wide variety of proteins. The metabolite acetyl-CoA is a key intermediate in energy metabolism that also serves as the acetyl group donor in protein acetylation modifications. Therefore such acetylation modifications might be coupled to the intracellular availability of acetyl-CoA. In the present article, we summarize recent evidence suggesting that the particular protein acetylation modifications enable the regulation of protein function in tune with acetyl-CoA availability and thus the metabolic state of the cell.

scholarly journals Comprehensive Proteomic Analysis of Lysine Acetylation in Nicotiana benthamiana After Sensing CWMV Infection

2021 ◽  
Vol 12 ◽  
Author(s):  
Bowen Yuan ◽  
Tingting Liu ◽  
Ye Cheng ◽  
Shiqi Gao ◽  
Linzhi Li ◽  
...  
Keyword(s):  
Nicotiana Benthamiana ◽  
Lysine Acetylation ◽  
Biological Processes ◽  
Post Translational Modification ◽  
Cellular Regulation ◽  
Histone 3 ◽  
Protein Lysine Acetylation ◽  
Related Proteins ◽  
Chinese Wheat

Protein lysine acetylation (Kac) is an important post-translational modification mechanism in eukaryotes that is involved in cellular regulation. To investigate the role of Kac in virus-infected plants, we characterized the lysine acetylome of Nicotiana benthamiana plants with or without a Chinese wheat mosaic virus (CWMV) infection. We identified 4,803 acetylated lysine sites on 1,964 proteins. A comparison of the acetylation levels of the CWMV-infected group with those of the uninfected group revealed that 747 sites were upregulated on 422 proteins, including chloroplast localization proteins and histone H3, and 150 sites were downregulated on 102 proteins. Nineteen conserved motifs were extracted and 51 percent of the acetylated proteins located on chloroplast. Nineteen Kac sites were located on histone proteins, including 10 Kac sites on histone 3. Bioinformatics analysis results indicated that lysine acetylation occurs on a large number of proteins involved in biological processes, especially photosynthesis. Furthermore, we found that the acetylation level of chloroplast proteins, histone 3 and some metabolic pathway-related proteins were significantly higher in CWMV-infected plants than in uninfected plants. In summary, our results reveal the regulatory roles of Kac in response to CWMV infection.

scholarly journals Identification of novel protein lysine acetyltransferases inEscherichia coli

2018 ◽  
Author(s):  
David G. Christensen ◽  
Jesse G. Meyer ◽  
Jackson T. Baumgartner ◽  
Alexandria K. D’Souza ◽  
William C. Nelson ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Substrate Specificity ◽  
Lysine Acetylation ◽  
Acetyl Phosphate ◽  
Protein Acetylation ◽  
Active Site Residues ◽  
Post Translational Modification ◽  
Post Translational Modifications ◽  
E Coli ◽  
Enzymatic Mechanism

AbstractPost-translational modifications, such as Nε-lysine acetylation, regulate protein function. Nε-lysine acetylation can occur either non-enzymatically or enzymatically. The non-enzymatic mechanism uses acetyl phosphate (AcP) or acetyl coenzyme A (AcCoA) as acetyl donors to modify an Nε-lysine residue of a protein. The enzymatic mechanism uses Nε-lysine acetyltransferases (KATs) to specifically transfer an acetyl group from AcCoA to Nε-lysine residues on proteins. To date, only one KAT (YfiQ, also known as Pka and PatZ) has been identified inE. coli. Here, we demonstrate the existence of 4 additionalE. coliKATs: RimI, YiaC, YjaB, and PhnO. In a genetic background devoid of all known acetylation mechanisms (most notably AcP and YfiQ) and one deacetylase (CobB), overexpression of these putative KATs elicited unique patterns of protein acetylation. We mutated key active site residues and found that most of them eliminated enzymatic acetylation activity. We used mass spectrometry to identify and quantify the specificity of YfiQ and the four novel KATs. Surprisingly, our analysis revealed a high degree of substrate specificity. The overlap between KAT-dependent and AcP-dependent acetylation was extremely limited, supporting the hypothesis that these two acetylation mechanisms play distinct roles in the post-translational modification of bacterial proteins. We further showed that these novel KATs are conserved across broad swaths of bacterial phylogeny. Finally, we determined that one of the novel KATs (YiaC) and the known KAT (YfiQ) can negatively regulate bacterial migration. Together, these results emphasize distinct and specific non-enzymatic and enzymatic protein acetylation mechanisms present in bacteria.ImportanceNε-lysine acetylation is one of the most abundant and important post-translational modifications across all domains of life. One of the best-studied effects of acetylation occurs in eukaryotes, where acetylation of histone tails activates gene transcription. Although bacteria do not have true histones, Nε-lysine acetylation is prevalent; however, the role of these modifications is mostly unknown. We constructed anE. colistrain that lacked both known acetylation mechanisms to identify four new Nε-lysine acetyltransferases (RimI, YiaC, YjaB, and PhnO). We used mass spectrometry to determine the substrate specificity of these acetyltransferases. Structural analysis of selected substrate proteins revealed site-specific preferences for enzymatic acetylation that had little overlap with the preferences of the previously reported acetyl-phosphate non-enzymatic acetylation mechanism. Finally, YiaC and YfiQ appear to regulate flagellar-based motility, a phenotype critical for pathogenesis of many organisms. These acetyltransferases are highly conserved and reveal deeper and more complex roles for bacterial post-translational modification.

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