Protein Arginine Deiminase 4 Antagonizes Methylglyoxal-induced Histone Glycation

Abstract

Protein arginine deiminase 4 (PAD4) facilitates the post-translational citrullination of the core histones H3 and H4. While the precise epigenetic function of this modification has not been resolved, it was shown to associate with general chromatin decompaction and to compete with arginine methylation. Recently, we showed that histones are subjected to methylglyoxal (MGO)-induced glycation on nucleophilic side chains, particularly arginines, under metabolic stress conditions. These non-enzymatic adducts change chromatin architecture and the epigenetic landscape by competing with enzymatic modifications. Here we report that PAD4 antagonizes histone MGOglycation by protecting the reactive sites with oxygen substitution, as well as by converting already-glycated arginine residues into citrulline. Moreover, we show that similar to the deglycase DJ-1, PAD4 is overexpressed and histone citrullination is upregulated in breast cancer tumors, suggesting an additional mechanistic link to PAD4's oncogenic properties.Metabolic syndromes and diabetes increase the risk for certain diseases such as cancer. However, the mechanism behind this correlation is poorly understood. Methylglyoxal (MGO), a reactive dicarbonyl sugar metabolite found in cells under metabolic stress, can non-enzymatically modify arginine and lysine residues in histone proteins, making it a new epigenetic marker linking metabolism and disease. Histone MGO-glycation induces changes in chromatin architecture and the epigenetic landscape, and abrogates gene transcription. In this study, we found that protein arginine deiminase 4 (PAD4) exhibits dual functions to antagonize histone MGO-glycation: removing glycation adducts from arginines and converting the unmodified side chains into citrulline, which protects them from undergoing glycation. This unprecedented biochemical mechanism demonstrates a potential function of PAD4 in cancer cells.

Non-enzymatic Covalent Modifications as a New Chapter in the Histone Code

“…Alternatively, protein arginine deiminase 4 (PAD4) has been shown to convert arginine side chains, including those that have been glycated with MGO, into citrulline. Although it does not regenerate the unmodified substrate, it does stall the glycation cascade to prevent the formation of AGEs as well as protect the arginine from being a glycation substrate again [58].…”

“…Several of these limitations have been overcome through technical and analytical innovations. Firstly, alternate sample preparations, including a high-salt isolation strategy, have been described and recently used to analyze MGO and ribose glycation NECMs on histones while avoiding extreme pH reagents [19,58,77,78]. Secondly, a label-free approach for the quantitative analysis and discovery of lysine and arginine modifications (QuARKMod) for complex biological samples was developed (Figure 4A).…”

Non-enzymatic covalent modifications: a new link between metabolism and epigenetics

“…Histones are primary glycation substrates because of their long half-lives and abundant lysine (Lys) and arginine (Arg) residues (Zheng et al, 2019). While different types of aldoseinduced histone glycation have been observed through both in vitro and in vivo experiments for decades (Talasz et al, 2002), an epigenetic link and working model in disease states has only been recently reported (Zheng et al, 2019).…”

“…Beyond enzyme-mediated epigenetic modifications, chemically reactive metabolites have been shown to directly modify nucleotides and histones via spontaneous non-enzymatic reactions (Zheng et al, 2019). Unlike canonical post-translational modifications (PTMs), non-enzymatic covalent modifications (NECMs) accumulate over time and are much more dependent on the cellular microenvironment (Harmel and Fiedler, 2018).…”

“…Indeed, NECMs have emerged as a new family of chromatin modifications with direct effect on its structure and function. These NECMs have been identified on DNA, RNA and histones and are implicated in disease states; however, their pathophysiological mechanisms, particularly, the presence of any causative relationships, remain elusive (Zheng et al, 2019). In this review, we summarize recent advances in NECM characterization, categorize them based on chemical reactions, and discuss their corresponding functions in disease progression, subsequently providing new perspectives regarding the link between metabolism, diet, and epigenetic regulation.…”