Protein deacetylation by SIRT1: An emerging key post-translational modification in metabolic regulation

ABSTRACTDrosophila melanogaster has been a working horse of genetics and cell biology for more than a century. However, proteomic-based methods have been limited due to technical obstacles, especially the lack of reliable labelling methods. Here, we advanced a chemically defined food source into stable-isotope labelling of amino acids in flies (SILAF). It allows for the rapid generation of a large number of flies with full incorporation of lysine-6. SILAF followed by fractionation and enrichment gave proteomic insights at a depth of 5,966 proteins and 7,496 phosphorylation sites, which substantiated metabolic regulation on enzymatic level. Furthermore, the label can be traced and predicts protein turnover rates during different developmental stages. The ease and versatility of the method actuates the fruit fly as an appealing model in proteomic and post-translational modification studies and it enlarges potential metabolic applications based on heavy amino acid diets.

Download Full-text

Ghrelin octanoylation by ghrelin O-acyltransferase: Unique protein biochemistry underlying metabolic signaling

Biochemical Society Transactions ◽

10.1042/bst20180436 ◽

2019 ◽

Vol 47 (1) ◽

pp. 169-178 ◽

Cited By ~ 9

Author(s):

James L. Hougland

Keyword(s):

Metabolic Regulation ◽

Peptide Hormone ◽

Acyl Donor ◽

Post Translational Modification ◽

Small Peptide ◽

Protein Biochemistry ◽

Physiological Processes ◽

Unique Protein ◽

The Status ◽

Membrane Bound

Abstract Ghrelin is a small peptide hormone that requires a unique post-translational modification, serine octanoylation, to bind and activate the GHS-R1a receptor. Ghrelin signaling is implicated in a variety of neurological and physiological processes, but is most well known for its roles in controlling hunger and metabolic regulation. Ghrelin octanoylation is catalyzed by ghrelin O-acyltransferase (GOAT), a member of the membrane-bound O-acyltransferase (MBOAT) enzyme family. From the status of ghrelin as the only substrate for GOAT in the human genome to the source and requirement for the octanoyl acyl donor, the ghrelin–GOAT system is defined by multiple unique aspects within both protein biochemistry and endocrinology. In this review, we examine recent advances in our understanding of the interactions and mechanisms leading to ghrelin modification by GOAT, discuss the potential sources for the octanoyl acyl donor required for ghrelin's activation, and summarize the current landscape of molecules targeting ghrelin octanoylation through GOAT inhibition.

Download Full-text

Establishment of an Efficient Immortalization Strategy Using HMEJ-Based bTERT Insertion for Bovine Cells

International Journal of Molecular Sciences ◽

10.3390/ijms222212540 ◽

2021 ◽

Vol 22 (22) ◽

pp. 12540

Author(s):

Zihan Zhang ◽

Zhuo Han ◽

Ying Guo ◽

Xin Liu ◽

Yuanpeng Gao ◽

...

Keyword(s):

Cell Lines ◽

Metabolic Regulation ◽

Ectopic Expression ◽

Fibroblast Cell ◽

Future Application ◽

Bovine Bone ◽

Primary Cells ◽

Post Translational Modification ◽

Human Telomerase Reverse Transcriptase ◽

Wide Range

Immortalized cell lines have been used in a wide range of applications in research on immune disorders and cellular metabolic regulation due to the stability and uniformity of their cellular characteristics. At present, the investigation into molecular functions and signaling pathways within bovine cells remains largely limited by the lack of immortalized model cells. Current methods for immortalizing bovine cells are mainly restricted to the ectopic expression of human telomerase reverse transcriptase (hTERT) through transient transfection or virus-mediated delivery, which have defects in efficiency and reliability. In this study, we identified bovine TERT (bTERT) as a novel potent biofactor for immortalizing bovine cells with great advantages over hTERT, and established an efficient and easily manipulated strategy for the immortalization of bovine primary cells. Through the homology-mediated end-joining-based insertion of bTERT at the ROSA26 locus, we successfully generated immortalized bovine fetal fibroblast cell lines with stable characteristics. The observed limitation of this strategy in immortalizing bovine bone marrow-derived macrophages was attributed to the post-translational modification of bTERT, causing inhibited nuclear localization and depressed activity of bTERT in this terminally differentiated cell. In summary, we constructed an innovative method to achieve the high-quality immortalization of bovine primary cells, thereby expanding the prospects for the future application of immortalized bovine model cell lines.

Download Full-text

Abstract 121: Metabolic Regulation of Ischemia/Reperfusion: Role of the Unfolded Protein Response

Circulation Research ◽

10.1161/res.119.suppl_1.121 ◽

2016 ◽

Vol 119 (suppl_1) ◽

Author(s):

Zhao Wang

Keyword(s):

Unfolded Protein Response ◽

Protein Modification ◽

Metabolic Regulation ◽

Ischemia Reperfusion ◽

Loss Of Function ◽

Post Translational Modification ◽

Cardiac Damage ◽

Unfolded Protein ◽

The Unfolded Protein Response ◽

Protein Response

Myocardial infarction is a leading cause of death worldwide. The most effective approach to mitigate cardiac damage is timely and efficient restoration of occlusion in coronary artery. This process, ischemia/reperfusion (I/R), triggers additional damage (I/R damage), which may substantially contribute to the final cardiac infarction. Despite extensive efforts and paramount clinical interests, effective therapeutics remains vacant. A better understanding of the pathology of I/R damage is therefore urgently required. Most processes in I/R are potent inducers of the unfolded protein response (UPR), a cellular adaptive process to accommodate protein-folding stress. We have shown that the most conserved branch of the UPR, the Xbp1s pathway, is strongly induced by I/R. Using both gain- and loss-of-function approaches, we revealed that Xbp1s is necessary and sufficient to protect heart against I/R injury. We went further to discover that Xbp1s is a direct upstream transcriptional factor for multiple, key enzymes of the hexosamine biosynthetic pathway (HBP). The final production of HBP, UDP-GlcNAc, is the obligate substrate for O-GlcNAc protein modification, a prominent post-translational modification. Acute induction of O-GlcNAc modification confers strong protection against various stresses. Upregulation of Xbp1s therefore induces the HBP, UDP-GlcNAc production, consequent O-GlcNAc protein modification, and more importantly, cardioprotection against I/R damage. We found that modulation of the necroptosis pathway participates in Xbp1s-mediated cardioprotection. Elucidation of the pathology of I/R injury will greatly advance our understanding of underlying mechanisms and help identify potential therapeutic targets to tackle the devastating coronary heart disease.

Download Full-text

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

Stress Biology ◽

10.1007/s44154-021-00024-z ◽

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.

Download Full-text

Ancient Regulatory Role of Lysine Acetylation in Central Metabolism

mBio ◽

10.1128/mbio.01894-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 36

Author(s):

Ernesto S. Nakayasu ◽

Meagan C. Burnet ◽

Hanna E. Walukiewicz ◽

Christopher S. Wilkins ◽

Anil K. Shukla ◽

...

Keyword(s):

Protein Function ◽

Active Sites ◽

Metabolic Regulation ◽

Lysine Acetylation ◽

Post Translational Modification ◽

Protein Activity ◽

Direct Role ◽

Data Set ◽

Evolutionarily Conserved ◽

Lysine Residues

ABSTRACT Lysine acetylation is a common protein post-translational modification in bacteria and eukaryotes. Unlike phosphorylation, whose functional role in signaling has been established, it is unclear what regulatory mechanism acetylation plays and whether it is conserved across evolution. By performing a proteomic analysis of 48 phylogenetically distant bacteria, we discovered conserved acetylation sites on catalytically essential lysine residues that are invariant throughout evolution. Lysine acetylation removes the residue’s charge and changes the shape of the pocket required for substrate or cofactor binding. Two-thirds of glycolytic and tricarboxylic acid (TCA) cycle enzymes are acetylated at these critical sites. Our data suggest that acetylation may play a direct role in metabolic regulation by switching off enzyme activity. We propose that protein acetylation is an ancient and widespread mechanism of protein activity regulation. IMPORTANCE Post-translational modifications can regulate the activity and localization of proteins inside the cell. Similar to phosphorylation, lysine acetylation is present in both eukaryotes and prokaryotes and modifies hundreds to thousands of proteins in cells. However, how lysine acetylation regulates protein function and whether such a mechanism is evolutionarily conserved is still poorly understood. Here, we investigated evolutionary and functional aspects of lysine acetylation by searching for acetylated lysines in a comprehensive proteomic data set from 48 phylogenetically distant bacteria. We found that lysine acetylation occurs in evolutionarily conserved lysine residues in catalytic sites of enzymes involved in central carbon metabolism. Moreover, this modification inhibits enzymatic activity. Our observations suggest that lysine acetylation is an evolutionarily conserved mechanism of controlling central metabolic activity by directly blocking enzyme active sites.

Download Full-text

Global Profiling of 2-hydroxyisobutyrylome in Common Wheat

10.1101/2020.03.05.978155 ◽

2020 ◽

Author(s):

Ning Zhang ◽

Lingran Zhang ◽

Linjie Li ◽

Junyou Geng ◽

Lei Zhao ◽

...

Keyword(s):

Western Blot ◽

Common Wheat ◽

Protein Interactions ◽

Mammalian Cells ◽

Metabolic Regulation ◽

Trichostatin A ◽

Affinity Purification ◽

Phosphoglycerate Kinase ◽

Post Translational Modification

AbstractAs a novel post-translational modification (PTM), lysine 2-hydroxyisobutyrylation (Khib) has been found to play a role in active gene transcription in mammalian cells and yeast, but the function of Khib proteins in plants remains unknown. In this study, we used western blot to demonstrate that Khib is an evolutionarily-conserved PTM in wheat and its donators, with the highest Khib abundance occurring in hexaploidy wheat. Additionally, global profiling using affinity purification and mass spectroscopy of 2-hydroxyisobutyrylome revealed that there were 3348 lysine modification sites from 1074 proteins in common wheat (Triticum aestivum L.). Moreover, bioinformatic data indicated that Khib proteins participate in a wide variety of biological and metabolic pathways. Immunoprecipitation and western blot confirmed that Khib proteins had an in vivo origin. A comparison of Khib and other major PTMs revealed that Khib proteins were simultaneously modified by multiple PTMs. Using mutagenesis experiments and Co-IP, we demonstrated that Khib on K206 is a key regulatory modification of phosphoglycerate kinase enzymatic activity and found that de-Khib on K206 affects protein interactions. Furthermore, Khib production of low-molecular-weight proteins was a response to the deacetylase inhibitors nicotinamide and trichostatin A. This study provides evidence that enhances our current understanding of Khib in wheat plants, including the cooperation between this PTM and metabolic regulation.

Download Full-text

An O-GlcNAcylomic Approach Reveals ACLY as a Potential Target in Sepsis in the Young Rat

International Journal of Molecular Sciences ◽

10.3390/ijms22179236 ◽

2021 ◽

Vol 22 (17) ◽

pp. 9236

Author(s):

Manon Denis ◽

Thomas Dupas ◽

Antoine Persello ◽

Justine Dontaine ◽

Laurent Bultot ◽

...

Keyword(s):

Arterial Pressure ◽

Metabolic Regulation ◽

Therapeutic Potential ◽

Young Population ◽

Post Translational Modification ◽

Atp Citrate Lyase ◽

E Coli ◽

Citrate Lyase ◽

Old Rats ◽

Young Rat

Sepsis in the young population, which is particularly at risk, is rarely studied. O-GlcNAcylation is a post-translational modification involved in cell survival, stress response and metabolic regulation. O-GlcNAc stimulation is beneficial in adult septic rats. This modification is physiologically higher in the young rat, potentially limiting the therapeutic potential of O-GlcNAc stimulation in young septic rats. The aim is to evaluate whether O-GlcNAc stimulation can improve sepsis outcome in young rats. Endotoxemic challenge was induced in 28-day-old rats by lipopolysaccharide injection (E. Coli O111:B4, 20 mg·kg−1) and compared to control rats (NaCl 0.9%). One hour after lipopolysaccharide injection, rats were randomly assigned to no therapy, fluidotherapy (NaCl 0.9%, 10 mL·kg−1) ± NButGT (10 mg·kg−1) to increase O-GlcNAcylation levels. Physiological parameters and plasmatic markers were evaluated 2h later. Finally, untargeted mass spectrometry was performed to map cardiac O-GlcNAcylated proteins. Lipopolysaccharide injection induced shock with a decrease in mean arterial pressure and alteration of biological parameters (p < 0.05). NButGT, contrary to fluidotherapy, was associated with an improvement of arterial pressure (p < 0.05). ATP citrate lyase was identified among the O-GlcNAcylated proteins. In conclusion, O-GlcNAc stimulation improves outcomes in young septic rats. Interestingly, identified O-GlcNAcylated proteins are mainly involved in cellular metabolism.

Download Full-text

Metabolic engineering of CHO cells to prepare glycoproteins

Emerging Topics in Life Sciences ◽

10.1042/etls20180056 ◽

2018 ◽

Vol 2 (3) ◽

pp. 433-442 ◽

Cited By ~ 1

Author(s):

Qiong Wang ◽

Michael J. Betenbaugh

Keyword(s):

Metabolic Engineering ◽

Cho Cells ◽

Genetic Manipulation ◽

Chinese Hamster ◽

Post Translational Modification ◽

Effector Functions ◽

Recombinant Glycoproteins ◽

Production Platform ◽

Chemical Inhibitors ◽

Amino Acid Mutations

As a complex and common post-translational modification, N-linked glycosylation affects a recombinant glycoprotein's biological activity and efficacy. For example, the α1,6-fucosylation significantly affects antibody-dependent cellular cytotoxicity and α2,6-sialylation is critical for antibody anti-inflammatory activity. Terminal sialylation is important for a glycoprotein's circulatory half-life. Chinese hamster ovary (CHO) cells are currently the predominant recombinant protein production platform, and, in this review, the characteristics of CHO glycosylation are summarized. Moreover, recent and current metabolic engineering strategies for tailoring glycoprotein fucosylation and sialylation in CHO cells, intensely investigated in the past decades, are described. One approach for reducing α1,6-fucosylation is through inhibiting fucosyltransferase (FUT8) expression by knockdown and knockout methods. Another approach to modulate fucosylation is through inhibition of multiple genes in the fucosylation biosynthesis pathway or through chemical inhibitors. To modulate antibody sialylation of the fragment crystallizable region, expressions of sialyltransferase and galactotransferase individually or together with amino acid mutations can affect antibody glycoforms and further influence antibody effector functions. The inhibition of sialidase expression and chemical supplementations are also effective and complementary approaches to improve the sialylation levels on recombinant glycoproteins. The engineering of CHO cells or protein sequence to control glycoforms to produce more homogenous glycans is an emerging topic. For modulating the glycosylation metabolic pathways, the interplay of multiple glyco-gene knockouts and knockins and the combination of multiple approaches, including genetic manipulation, protein engineering and chemical supplementation, are detailed in order to achieve specific glycan profiles on recombinant glycoproteins for superior biological function and effectiveness.

Download Full-text

Dicarbonyl derived post-translational modifications: chemistry bridging biology and aging-related disease

Essays in Biochemistry ◽

10.1042/ebc20190057 ◽

2020 ◽

Vol 64 (1) ◽

pp. 97-110

Author(s):

Christian Sibbersen ◽

Mogens Johannsen

Keyword(s):

Mass Spectrometry ◽

Future Research ◽

Amino Acid Residues ◽

Post Translational Modification ◽

Dicarbonyl Compounds ◽

Protein Targets ◽

Post Translational Modifications ◽

Reactive Protein ◽

Glycation End Products ◽

Direct Mass Spectrometry

Abstract In living systems, nucleophilic amino acid residues are prone to non-enzymatic post-translational modification by electrophiles. α-Dicarbonyl compounds are a special type of electrophiles that can react irreversibly with lysine, arginine, and cysteine residues via complex mechanisms to form post-translational modifications known as advanced glycation end-products (AGEs). Glyoxal, methylglyoxal, and 3-deoxyglucosone are the major endogenous dicarbonyls, with methylglyoxal being the most well-studied. There are several routes that lead to the formation of dicarbonyl compounds, most originating from glucose and glucose metabolism, such as the non-enzymatic decomposition of glycolytic intermediates and fructosyl amines. Although dicarbonyls are removed continuously mainly via the glyoxalase system, several conditions lead to an increase in dicarbonyl concentration and thereby AGE formation. AGEs have been implicated in diabetes and aging-related diseases, and for this reason the elucidation of their structure as well as protein targets is of great interest. Though the dicarbonyls and reactive protein side chains are of relatively simple nature, the structures of the adducts as well as their mechanism of formation are not that trivial. Furthermore, detection of sites of modification can be demanding and current best practices rely on either direct mass spectrometry or various methods of enrichment based on antibodies or click chemistry followed by mass spectrometry. Future research into the structure of these adducts and protein targets of dicarbonyl compounds may improve the understanding of how the mechanisms of diabetes and aging-related physiological damage occur.

Download Full-text