A proteomic approach for the identification of novel lysine methyltransferase substrates

Dan Levy; Chih Long Liu; Ze Yang; Aaron M Newman; Ash A Alizadeh; Paul J Utz; Or Gozani

doi:10.1186/1756-8935-4-19

A proteomic approach for the identification of novel lysine methyltransferase substrates

Epigenetics Chromatin. 2011 Oct 24:4:19. doi: 10.1186/1756-8935-4-19.

Authors

Dan Levy^#¹, Chih Long Liu^#^{1

2}, Ze Yang¹, Aaron M Newman^{3

4}, Ash A Alizadeh^{3

4}, Paul J Utz², Or Gozani¹

Affiliations

¹ Department of Biology, Stanford University, Stanford, CA 94305, USA.
² Division of Immunology and Rheumatology, Stanford University, Stanford, CA 94305, USA.
³ Divisions of Oncology, Department of Medicine, Stanford University, Stanford, CA 94305, USA.
⁴ Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA.

^# Contributed equally.

Abstract

Background: Signaling via protein lysine methylation has been proposed to play a central role in the regulation of many physiologic and pathologic programs. In contrast to other post-translational modifications such as phosphorylation, proteome-wide approaches to investigate lysine methylation networks do not exist.

Results: In the current study, we used the ProtoArray® platform, containing over 9,500 human proteins, and developed and optimized a system for proteome-wide identification of novel methylation events catalyzed by the protein lysine methyltransferase (PKMT) SETD6. This enzyme had previously been shown to methylate the transcription factor RelA, but it was not known whether SETD6 had other substrates. By using two independent detection approaches, we identified novel candidate substrates for SETD6, and verified that all targets tested in vitro and in cells were genuine substrates.

Conclusions: We describe a novel proteome-wide methodology for the identification of new PKMT substrates. This technological advance may lead to a better understanding of the enzymatic activity and substrate specificity of the large number (more than 50) PKMTs present in the human proteome, most of which are uncharacterized.