PXD002405

PXD002405 is an original dataset announced via ProteomeXchange.

Title	Quantitative profiling of the enzymatic activity of the protein lysine mono-methyltransferase SMYD2 using SILAC-based proteomics
Description	The significance of non-histone lysine methylation in cell biology and human disease is an emerging area of research exploration, and small molecule inhibitors that selectively and potently target “writers” and “erasers” of methyl-lysine, such as the protein lysine mono-methyltransferase SMYD2, are active areas of drug discovery. It is therefore essential to clarify the substrates of these enzymes in cellular contexts in order to advance and to correctly understand the cellular mechanism(s) of action of these targets. Here, using stable isotopic labelling of amino acids in cell culture (SILAC) coupled with immunoaffinity enrichment of mono-methyl-lysine (Kme1) peptides and mass spectrometry, we report the most comprehensive and large-scale proteomic study of protein mono-methylation, comprising a total of 1032 Kme1 sites identified in esophageal squamous cell carcinoma (ESCC) cells and 1861 Kme1 sites in ESCC cells overexpressing SMYD2. Among these sites was a subset of 35 robust Kme1 sites that were potently down-regulated by both shRNA-mediated knockdown of SMYD2 and LLY-507, a small molecule inhibitor of SMYD2. In addition, we report specific protein sequence motifs that were enriched in Kme1 sites and that were also directly regulated by endogenous SMYD2 activity, indicating that the diversity of SMYD2 substrate specificity of SMYD2 exceeds previous expectations. Furthermore, we reveal that BTF3 and PDAP1 are novel and direct substrates of SMYD2, as well as AHNAK and AHNAK2, two large and highly-repetitive proteins directly and extensively mono-methylated by SMYD2 at several lysine residues. Collectively, our findings provide novel quantitative and insights into the cellular activity and substrate recognition of SMYD2 as well as the global landscape and regulation of protein mono-methylation in cells.
HostingRepository	PRIDE
AnnounceDate	2016-01-11
AnnouncementXML	Submission_2016-01-18_08:59:37.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	XIng-Jun Cao
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	6x(13)C: 4x(15)N labeled L-arginine; acetylated residue; iodoacetamide derivatized residue; monomethylated residue; 6x(13)C: 2x(15)N labeled L-lysine
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-22 02:21:58	ID requested
1	2016-01-11 10:00:55	announced
⏵ 2	2016-01-18 08:59:38	announced	Updated publication reference for PubMed record(s): 26750096.

Olsen JB, Cao XJ, Han B, Chen LH, Horvath A, Richardson TI, Campbell RM, Garcia BA, Nguyen H, Quantitative Profiling of the Activity of Protein Lysine Methyltransferase SMYD2 Using SILAC-Based Proteomics. Mol Cell Proteomics, 15(3):892-905(2016) [pubmed]

curator keyword: Biological

submitter keyword: SILAC, lysine methyltransferase, SMYD2, methylation, immunoaffinity enrichment

Benjamin A. Garcia
contact affiliation	Epigenetics Program, Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
contact email	bgarci@mail.med.upenn.edu
lab head
XIng-Jun Cao
contact affiliation	University of Pennsylvania
contact email	xicao@mail.med.upenn.edu
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002405
     1. Label: PRIDE project
     2. Name: Quantitative profiling of the enzymatic activity of the protein lysine mono-methyltransferase SMYD2 using SILAC-based proteomics