Uncovering Robust Delactoylase and Depyruvoylase Activities of HDAC Isoforms

Abstract

Zinc-dependent histone deacetylases (HDACs) and sirtuins (SIRT) represent two different classes of enzymes which are responsible for deacylation of modified lysine side chains. The repertoire of acyl residues on lysine side chains identified in vivo is rapidly growing, and very recently lysine lactoylation was described to be involved in metabolic reprogramming. Additionally, lysine pyruvoylation represents a marker for aging and liver cirrhosis. Here, we report a systematic analysis of acyl-specificity of human zinc-dependent HDAC and sirtuin isoforms. We identified HDAC3 as a robust delactoylase with several-thousand-fold higher activity as compared to SIRT2, which was claimed to be the major in vivo delactoylase. Additionally, we systematically searched for enzymes, capable of removing pyruvoyl residues from lysine side chains. Using model peptides, we uncovered high depyruvoylase activity for HDAC6 and HDAC8. Interestingly, such substrates have extremely low K M values for both HDAC isoforms, pointing to possible in vivo functions.

Effects of Dimerization on the Deacylase Activities of Human SIRT2

“…By catalyzing the removal of protein acyl modifications, SIRT2 regulates diverse processes including cancer growth, neurodegeneration, metabolism, and inflammation. − The acyl substrates of SIRT2 are chemically diverse and range from small modifications such as acetyl-lysine to much larger, fatty modifications such as myristoyl-lysine . Numerous studies have characterized the substrate-specific enzymology of SIRT2. − Small molecules are being developed to selectively modulate SIRT2’s deacylase activities to understand how different acylations affect disease states and to explore SIRT2’s potential as a therapeutic target. ,− Additionally, novel acyl modifications on lysines continue to be identified as SIRT2 substrates, ,− which increases the challenge of modulating select SIRT2 activities and increases our need for tools that can probe specific SIRT2 functions.…”

Lactylation, an emerging hallmark of metabolic reprogramming: Current progress and open challenges

“…According to a separate study of Zessin et al,HDAC2,HDAC3,HDAC8,SIRT2 and SIRT3 were also potential delactylases in vitro. Similarly, they also confirmed the robust delactoylase, HDAC3, which harbored several-thousand-fold higher activity, compared to the major invivo delactoylase SIRT2 (Zessin et al, 2022). Collectively, many histone deacetylases have the functions of delactylase (Figure 1), but their functional preference and switching mechanism remains a mystery.…”

“…Borrowing from the discovery of lactylases, several studies evaluated zinc-and nicotinamide adenine dinucleotide (NAD)dependent HDACs for their abilities of cleaving ε-N-L-lactyllysine marks (Jennings et al, 2021;Moreno-Yruela et al, 2022;Zessin et al, 2022;Zu et al, 2022). Jennings et al presented the first report of the lactoyllys eraser, sirtuin 2 (SIRT2), which displayed strong capability of removing the L-lactoyllys from synthetic peptides related to pyruvate kinase M2 (PKM2) (Jennings et al, 2021).…”

“…According to the updated results, p300 and HDAC1/3 were confirmed to be highly efficient enzymes mediating the process of histone lactylation and delactylation (Zhang et al, 2019;Cui et al, 2021;Jennings et al, 2021;Moreno-Yruela et al, 2022;Xiong et al, 2022;Yang K. et al, 2022;Zessin et al, 2022;Zu et al, 2022). However, there is no evidence suggesting that which step p300 and HDAC1/3 directly involved in the process from L-lactate, L-lactyl-CoA to lactyllysine, meaning that the putative enzymes in this enzymatic mechanism remain unclear.…”

“…Further, Hmgb1, the so-called alarmins proteins in stressed or activated inflammatory cells, can also be co-modified by L-Lactyl-CoA and acetyl-CoA in polymicrobial sepsis (Yang K. et al, 2022). More interestingly, several studies reported that histone Kla can also partly share the catalytic 'erasers' of protein acetylation, especially for HDAC1/3 (Jennings et al, 2021;Moreno-Yruela et al, 2022;Zessin et al, 2022;Zu et al, 2022).…”