Fine-tuning of lysine side chain modulates the activity of histone lysine methyltransferases

Abbas H K Al Temimi,Romano Buijs,Thomas J Boltje,Jasmin Mecinović,Floris P J T Rutjes,Christian J Van Noortwijk,Paul B White,Jona Merx,Giordano Proietti

doi:10.1038/s41598-020-78331-0

Abstract

Histone lysine methyltransferases (KMTs) play an important role in epigenetic gene regulation and have emerged as promising targets for drug discovery. However, the scope and limitation of KMT catalysis on substrates possessing substituted lysine side chains remain insufficiently explored. Here, we identify new unnatural lysine analogues as substrates for human methyltransferases SETD7, SETD8, G9a and GLP. Two synthetic amino acids that possess a subtle modification on the lysine side chain, namely oxygen at the γ position (KO, oxalysine) and nitrogen at the γ position (KN, azalysine) were incorporated into histone peptides and tested as KMTs substrates. Our results demonstrate that these lysine analogues are mono-, di-, and trimethylated to a different extent by trimethyltransferases G9a and GLP. In contrast to monomethyltransferase SETD7, SETD8 exhibits high specificity for both lysine analogues. These findings are important to understand the substrate scope of KMTs and to develop new chemical probes for biomedical applications.

Highlights

Histone lysine methyltransferases (KMTs) play an important role in epigenetic gene regulation and have emerged as promising targets for drug discovery
The main chain of lysine in histones was found to be crucial for the catalytic activity of K MTs17, while the conformational freedom of the lysine side chain appear to play an important role in efficient KMT c atalysis[23]
The results show that histone lysine methyltransferases possess different activities towards lysine and simple lysine analogues; monomethyltransferase SETD7 is more restrictive towards K O and K N compared to SETD8 and trimethyltransferases GLP and G9a

Summary

Introduction

Histone lysine methyltransferases (KMTs) play an important role in epigenetic gene regulation and have emerged as promising targets for drug discovery. In contrast to monomethyltransferase SETD7, SETD8 exhibits high specificity for both lysine analogues These findings are important to understand the substrate scope of KMTs and to develop new chemical probes for biomedical applications. The unstructured and flexible N-terminal histone tails are subject to a plethora of posttranslational modifications (PTMs), including methylation, acetylation, phosphorylation, ubiquitination, and many o thers[1] These modifications are key regulators of the stability and activity of histones, biomolecular interactions, and the structure and function of human chromatin[2,3,4]. Histone lysine methylation can be removed by lysine demethylases (KDMs), and is recognized by specific N ε-methyllysine binding reader proteins[1] Defects in these epigenetic regulators are linked with various diseases, including, but not limited to, cancer[9]. Enzymatic assays and computational studies pinpointed that the Nε-lysine functionality is exclusively required for the biocatalytic potential of KMTs and that the terminal amino group of lysine in histone peptides cannot be replaced by non-amino n ucleophiles[21]

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Conclusion