Bioinformatic Analysis and Post-Translational Modification Crosstalk Prediction of Lysine Acetylation

Post-translational modification of proteins by lysine acetylation plays important regulatory roles in living cells. The budding yeast Saccharomyces cerevisiae is a widely used unicellular eukaryotic model organism in biomedical research. S. cerevisiae contains several evolutionary conserved lysine acetyltransferases and deacetylases. However, only a few dozen acetylation sites in S. cerevisiae are known, presenting a major obstacle for further understanding the regulatory roles of acetylation in this organism. Here we use high resolution mass spectrometry to identify about 4000 lysine acetylation sites in S. cerevisiae. Acetylated proteins are implicated in the regulation of diverse cytoplasmic and nuclear processes including chromatin organization, mitochondrial metabolism, and protein synthesis. Bioinformatic analysis of yeast acetylation sites shows that acetylated lysines are significantly more conserved compared with nonacetylated lysines. A large fraction of the conserved acetylation sites are present on proteins involved in cellular metabolism, protein synthesis, and protein folding. Furthermore, quantification of the Rpd3-regulated acetylation sites identified several previously known, as well as new putative substrates of this deacetylase. Rpd3 deficiency increased acetylation of the SAGA (Spt-Ada-Gcn5-Acetyltransferase) complex subunit Sgf73 on K33. This acetylation site is located within a critical regulatory domain in Sgf73 that interacts with Ubp8 and is involved in the activation of the Ubp8-containing histone H2B deubiquitylase complex. Our data provides the first global survey of acetylation in budding yeast, and suggests a wide-ranging regulatory scope of this modification. The provided dataset may serve as an important resource for the functional analysis of lysine acetylation in eukaryotes.

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Comment on ‘YcgC represents a new protein deacetylase family in prokaryotes’

eLife ◽

10.7554/elife.37798 ◽

2018 ◽

Vol 7 ◽

Cited By ~ 4

Author(s):

Magdalena Kremer ◽

Nora Kuhlmann ◽

Marius Lechner ◽

Linda Baldus ◽

Michael Lammers

Keyword(s):

Lysine Acetylation ◽

Post Translational Modification ◽

Donor Molecule ◽

Acetyl Coa ◽

Lysine Deacetylases ◽

Protein Deacetylase ◽

New Protein

Lysine acetylation is a post-translational modification that is conserved from bacteria to humans. It is catalysed by the activities of lysine acetyltransferases, which use acetyl-CoA as the acetyl-donor molecule, and lysine deacetylases, which remove the acetyl moiety. Recently, it was reported that YcgC represents a new prokaryotic deacetylase family with no apparent homologies to existing deacetylases (Tu et al., 2015). Here we report the results of experiments which demonstrate that YcgC is not a deacetylase.

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Identification of Lysine Acetylation Sites on MERS-CoV Replicase pp1ab

Molecular & Cellular Proteomics ◽

10.1074/mcp.ra119.001897 ◽

2020 ◽

Vol 19 (8) ◽

pp. 1303-1309 ◽

Cited By ~ 2

Author(s):

Lin Zhu ◽

Sin-Yee Fung ◽

Guangshan Xie ◽

Lok-Yin Roy Wong ◽

Dong-Yan Jin ◽

...

Keyword(s):

Viral Proteins ◽

Bioinformatic Analysis ◽

Hek293 Cells ◽

Lysine Acetylation ◽

Protein Acetylation ◽

Conservation Level ◽

Life Threatening ◽

Infected Cells ◽

Orbitrap Analysis ◽

First Time

MERS is a life-threatening disease and MERS-CoV has the potential to cause the next pandemic. Protein acetylation is known to play a crucial role in host response to viral infection. Acetylation of viral proteins encoded by other RNA viruses have been reported to affect viral replication. It is therefore of interest to see whether MERS-CoV proteins are also acetylated. Viral proteins obtained from infected cells were trypsin-digested into peptides. Acetylated peptides were enriched by immunoprecipitation and subject to nano-LC-Orbitrap analysis. Bioinformatic analysis was performed to assess the conservation level of identified acetylation sites and to predict the upstream regulatory factors. A total of 12 acetylation sites were identified from 7 peptides, which all belong to the replicase polyprotein pp1ab. All identified acetylation sites were found to be highly conserved across MERS-CoV sequences in NCBI database. Upstream factors, including deacetylases of the SIRT1 and HDAC families as well as acetyltransferases of the TIP60 family, were predicted to be responsible for regulating the acetylation events identified. Western blotting confirms that acetylation events indeed occur on pp1ab protein by expressing NSP4 in HEK293 cells. Acetylation events on MERS-CoV viral protein pp1ab were identified for the first time, which indicate that MERS-CoV might use the host acetylation machinery to regulate its enzyme activity and to achieve optimal replication. Upstream factors were predicted, which might facilitate further analysis of the regulatory mechanism of MERS-CoV replication.

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Lysine Propionylation is a Widespread Post-Translational Modification Involved in Regulation of Photosynthesis and Metabolism in Cyanobacteria

International Journal of Molecular Sciences ◽

10.3390/ijms20194792 ◽

2019 ◽

Vol 20 (19) ◽

pp. 4792 ◽

Cited By ~ 1

Author(s):

Mingkun Yang ◽

Hui Huang ◽

Feng Ge

Keyword(s):

Large Fraction ◽

Bioinformatic Analysis ◽

High Light ◽

Site Directed Mutagenesis ◽

Oxygenic Photosynthesis ◽

Post Translational Modification ◽

Functional Studies ◽

Photosynthetic Organisms ◽

Model Combining ◽

And Function

Lysine propionylation is a reversible and widely distributed post-translational modification that is known to play a regulatory role in both eukaryotes and prokaryotes. However, the extent and function of lysine propionylation in photosynthetic organisms remains unclear. Cyanobacteria are the most ancient group of Gram-negative bacteria capable of oxygenic photosynthesis, and are of great importance to global carbon and nitrogen cycles. Here, we carried out a systematic study of lysine propionylaiton in cyanobacteria where we used Synechocystis sp. PCC 6803 (Synechocystis) as a model. Combining high-affinity anti-propionyllysine pan antibodies with high-accuracy mass spectrometry (MS) analysis, we identified 111 unique lysine propionylation sites on 69 proteins in Synechocystis. Further bioinformatic analysis showed that a large fraction of the propionylated proteins were involved in photosynthesis and metabolism. The functional significance of lysine propionylation on the enzymatic activity of fructose-1,6-bisphosphatase (FbpI) was studied by site-directed mutagenesis and biochemical studies. Further functional studies revealed that the propionylation level of subunit II of photosystem I (PsaD) was obviously increased after high light (HL) treatment, suggesting that propionylation may be involved in high light adaption in Synechocystis. Thus, our findings provide novel insights into the range of functions regulated by propionylation and reveal that reversible propionylation is a functional modification with the potential to regulate photosynthesis and carbon metabolism in Synechocystis, as well as in other photosynthetic organisms.

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Profiling of lysine-acetylated proteins in human urine

10.1101/128207 ◽

2017 ◽

Author(s):

Weiwei Qin ◽

Zhenhuan Du ◽

He Huang ◽

Youhe Gao

Keyword(s):

Human Urine ◽

High Resolution Mass Spectrometry ◽

The Body ◽

Lysine Acetylation ◽

Biological Processes ◽

Post Translational Modification ◽

Post Translational Modifications ◽

Normal Human ◽

Measurable Change

AbstractBiomarker is the measurable change associated with a physiological or pathophysiological process, its nature is change. Contrast to the blood which is under homeostatic controls, urine reflects changes in the body earlier and more sensitive therefore is a better biomarker source. Lysine acetylation is an abundant and highly regulated post-translational modification. It plays a pivotal role in modulating diverse biological processes and is associated with various important diseases. Enrichment or visualization of proteins with specific post-translational modifications provides a method for sampling the urinary proteome and reducing sample complexity. In this study, we used anti-acetyllysine antibody-based immunoaffinity enrichment combined with high-resolution mass spectrometry to profile lysine-acetylated proteins in normal human urine. A total of 629 acetylation sites on 315 proteins were identified, including some very low-abundance proteins. This is the first proteome-wide characterization of lysine acetylation proteins in normal human urine. Our dataset provides a useful resource for the further discovery of the lysine acetylated proteins as biomarker in urine.

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Global Lysine Acetylome Analysis of LPS-Stimulated HepG2 Cells Identified Hyperacetylation of PKM2 as a Metabolic Regulator in Sepsis

International Journal of Molecular Sciences ◽

10.3390/ijms22168529 ◽

2021 ◽

Vol 22 (16) ◽

pp. 8529

Author(s):

Ann-Yae Na ◽

Sanjita Paudel ◽

Soyoung Choi ◽

Jun Hyung Lee ◽

Min-Sik Kim ◽

...

Keyword(s):

Liver Dysfunction ◽

Lactate Level ◽

Hepg2 Cells ◽

Lactate Concentration ◽

Lysine Acetylation ◽

Post Translational Modification ◽

Glycolysis Pathway ◽

The Relationship ◽

Causative Link ◽

Lps Treatment

Sepsis-induced liver dysfunction (SILD) is a common event and is strongly associated with mortality. Establishing a causative link between protein post-translational modification and diseases is challenging. We studied the relationship among lysine acetylation (Kac), sirtuin (SIRTs), and the factors involved in SILD, which was induced in LPS-stimulated HepG2 cells. Protein hyperacetylation was observed according to SIRTs reduction after LPS treatment for 24 h. We identified 1449 Kac sites based on comparative acetylome analysis and quantified 1086 Kac sites on 410 proteins for acetylation. Interestingly, the upregulated Kac proteins are enriched in glycolysis/gluconeogenesis pathways in the Kyoto Encyclopedia of Genes and Genomes (KEGG) category. Among the proteins in the glycolysis pathway, hyperacetylation, a key regulator of lactate level in sepsis, was observed at three pyruvate kinase M2 (PKM2) sites. Hyperacetylation of PKM2 induced an increase in its activity, consequently increasing the lactate concentration. In conclusion, this study is the first to conduct global profiling of Kac, suggesting that the Kac mechanism of PKM2 in glycolysis is associated with sepsis. Moreover, it helps to further understand the systematic information regarding hyperacetylation during the sepsis process.

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Seminal plasma AnnexinA2 protein is a relevant biomarker for stallions which require removal of seminal plasma for sperm survival upon refrigeration†

Biology of Reproduction ◽

10.1093/biolre/ioaa153 ◽

2020 ◽

Vol 103 (6) ◽

pp. 1275-1288

Author(s):

Gemma Gaitskell-Phillips ◽

Francisco E Martín-Cano ◽

José M Ortiz-Rodríguez ◽

Antonio Silva-Rodríguez ◽

Heriberto Rodríguez-Martínez ◽

...

Keyword(s):

Seminal Plasma ◽

High Performance ◽

Semen Quality ◽

Enrichment Analysis ◽

Bioinformatic Analysis ◽

Protein Glycosylation ◽

Pathway Enrichment Analysis ◽

Post Translational Modification ◽

Specific Proteins ◽

Discriminant Variable

Abstract Some stallions yield ejaculates that do not tolerate conservation by refrigeration prior to artificial insemination (AI), showing improvement after removal of most of the seminal plasma (SP) by centrifugation. In this study, the SP-proteome of 10 different stallions was defined through high-performance liquid chromatography with tandem mass spectrometry and bioinformatic analysis in relation to the ability of the ejaculates to maintain semen quality when cooled and stored at 5°C. Stallions were classified into three groups, depending on this ability: those maintaining good quality after direct extension in a commercial extender (good), stallions requiring removal of seminal plasma (RSP) to maintain seminal quality (good-RSP), and stallions, unable to maintain good semen quality even after RSP (poor). Pathway enrichment analysis of the proteins identified in whole equine SP using human orthologs was performed using g: profiler showing enriched Reactome and the Kyoto Encyclopedia of Genes and Genomes pathways related to hexose metabolism, vesicle mediated transport, post translational modification of proteins and immune response. Specific proteins overrepresented in stallions tolerating conservation by refrigeration included a peroxiredoxin-6 like protein, and transcobalamin-2, a primary vitamin B12-binding, and transport protein. Also, the protein involved in protein glycosylation, ST3 beta-galactoside alpha-2,3-sialyltransferase 1 was present in good stallions. These proteins were nearly absent in poor stallions. Particularly, annexinA2 appeared as to be the most powerful discriminant variable for identification of stallions needing RSP prior to refrigeration, with a P = 0.002 and a q value = 0.005. Overall this is the first detailed study of the equine SP-proteome, showing the potential value of specific proteins as discriminant bio-markers for clinical classification of stallions for AI.

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Global analysis of lysine acetylation reveals its role in multiple biological processes in Glycine max

10.21203/rs.3.rs-119455/v1 ◽

2020 ◽

Author(s):

Geng Li ◽

Bin Zheng ◽

Wei Zhao ◽

Ting-Hu Ren ◽

Xing-Hui Zhang ◽

...

Keyword(s):

Carbon Fixation ◽

Global Analysis ◽

Tca Cycle ◽

Metabolic Process ◽

Lysine Acetylation ◽

Post Translational Modification ◽

Ribose Phosphate ◽

Core Histones ◽

Proteomic Investigation ◽

Soybean Leaves

Abstract Protein lysine acetylation (Kac) is an important post-translational modification present in both animal and plant cells. Here, we reported the results from a proteomic investigation of Kac in soybean leaves. We totally identified 3148 acetylation sites in 1538 proteins from three biological replicates, among 59 lysine acetylation sites in core histones, represents the largest acetylome dataset in plants to date. Gene Ontology (GO) functional analysis illustrated that most of the acetylated proteins involved in metabolic processes (include carboxylic acid metabolic process, oxoacid metabolic process, nucleoside metabolic process, nucleoside phosphate metabolic process, and ribose phosphate metabolic process). KEGG pathway enrichment showed Kac plays an important role in Photosynthesis, Carbon fixation in photosynthetic organisms and Citrate cycle (TCA cycle). Meanwhile we also find a total of 17 conserved Kac motifs. All together, our study not only provides the first global and most extensive lysine acetylation analysis in soybean leaves, but also suggest that lysine acetylation is play an important and unique role in plants.

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Protein acetyltransferases mediate bacterial adaptation to a diverse environment

Journal of Bacteriology ◽

10.1128/jb.00231-21 ◽

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.

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Global analysis of lysine acetylation in soybean leaves

Scientific Reports ◽

10.1038/s41598-021-97338-9 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Geng Li ◽

Bin Zheng ◽

Wei Zhao ◽

Tinghu Ren ◽

Xinghui Zhang ◽

...

Keyword(s):

Protein Biosynthesis ◽

Global Analysis ◽

Subcellular Location ◽

Structure Characterization ◽

Lysine Acetylation ◽

Post Translational Modification ◽

Motif Analysis ◽

Bioinformatics Analyses ◽

Oil Crop ◽

Soybean Leaves

AbstractProtein lysine acetylation (Kac) is an important post-translational modification in both animal and plant cells. Global Kac identification has been performed at the proteomic level in various species. However, the study of Kac in oil and resource plant species is relatively limited. Soybean is a globally important oil crop and resouce plant. In the present study, lysine acetylome analysis was performed in soybean leaves with proteomics techniques. Various bioinformatics analyses were performed to illustrate the structure and function of these Kac sites and proteins. Totally, 3148 acetylation sites in 1538 proteins were detected. Motif analysis of these Kac modified peptides extracted 17 conserved motifs. These Kac modified protein showed a wide subcellular location and functional distribution. Chloroplast is the primary subcellular location and cellular component where Kac proteins were localized. Function and pathways analyses indicated a plenty of biological processes and metabolism pathways potentially be influenced by Kac modification. Ribosome activity and protein biosynthesis, carbohydrate and energy metabolism, photosynthesis and fatty acid metabolism may be regulated by Kac modification in soybean leaves. Our study suggests Kac plays an important role in soybean physiology and biology, which is an available resource and reference of Kac function and structure characterization in oil crop and resource plant, as well as in plant kingdom.

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