Systematic identification of the lysine methylome using methyllysine binding domains
Abstract
Post-translational modifications (PTM) are vital regulators of protein function and homeostasis. The role of dynamic regulations of non-histone lysine methylated proteins (NHKMP) recently began to be recognized in DNA damage repair, apoptosis and transcriptional pathways. My goal was to identify components of the NHKMP network to understand its importance in a healthy versus diseased cellular state. I used membrane peptide arrays to systematically characterize nine naturally occurring lysine methyl binding domains (KMBD). Five KMBDs were chosen based on their overlapping specificities to achieve maximum coverage of lysine methylated peptides. These five KMBDs was used to enrich for methylated lysine peptides from a trypsinized HEK293 cell lysate and followed by mass spectrometry identification. We identified 229 NHKMP and 301 novel sites from HEK293. The amount of NHKMPs and sites that I have identified in total was unprecedented: this allows us to gain valuable insights into components of the lysine methylome network.