Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A

Anand Chopra; William G Willmore; Kyle K Biggar

doi:10.3390/biom12050641

Insights into a Cancer-Target Demethylase: Substrate Prediction through Systematic Specificity Analysis for KDM3A

Biomolecules. 2022 Apr 27;12(5):641. doi: 10.3390/biom12050641.

Authors

Anand Chopra^{1

2}, William G Willmore^{1

2}, Kyle K Biggar^{1

2}

Affiliations

¹ Institute of Biochemistry, Carleton University, Ottawa, ON K1S 5B6, Canada.
² Department of Biology, Carleton University, Ottawa, ON K1S 5B6, Canada.

Abstract

Jumonji C (JmjC) lysine demethylases (KDMs) catalyze the removal of methyl (-CH₃) groups from modified lysyl residues. Several JmjC KDMs promote cancerous properties and these findings have primarily been in relation to histone demethylation. However, the biological roles of these enzymes are increasingly being shown to also be attributed to non-histone demethylation. Notably, KDM3A has become relevant to tumour progression due to recent findings of this enzyme's role in promoting cancerous phenotypes, such as enhanced glucose consumption and upregulated mechanisms of chemoresistance. To aid in uncovering the mechanism(s) by which KDM3A imparts its oncogenic function(s), this study aimed to unravel KDM3A substrate specificity to predict high-confidence substrates. Firstly, substrate specificity was assessed by monitoring activity towards a peptide permutation library of histone H3 di-methylated at lysine-9 (i.e., H3K9me2). From this, the KDM3A recognition motif was established and used to define a set of high-confidence predictions of demethylation sites from within the KDM3A interactome. Notably, this led to the identification of three in vitro substrates (MLL1, p300, and KDM6B), which are relevant to the field of cancer progression. This preliminary data may be exploited in further tissue culture experiments to decipher the avenues by which KDM3A imparts cancerous phenotypes.

Keywords: KDM3A; lysine demethylase; motif; non-histone; substrate prediction; substrate specificity.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Demethylation
Histones / metabolism
Humans
Jumonji Domain-Containing Histone Demethylases
Lysine*
Neoplasms*
Protein Processing, Post-Translational

Substances

Histones
Jumonji Domain-Containing Histone Demethylases
KDM3A protein, human
KDM6B protein, human
Lysine

Grants and funding

This research was supported by Discovery Grants from the Natural Science and Engineering Council (NSERC) of Canada to K.K.B (grant no. RGPIN-2016-06151) and W.G.W (grant no. RGPIN-2017-06414). A.C. held a Canada Graduate Scholarship—Doctoral (CGS-D), from the NSERC of Canada.