Solution NMR Structure of the DNA-binding Domain from Scml2 (Sex Comb on Midleg-like 2)

Irina Bezsonova

doi:10.1074/jbc.m113.524009

Abstract

Scml2 is a member of the Polycomb group of proteins involved in epigenetic gene silencing. Human Scml2 is a part of a multisubunit protein complex, PRC1 (Polycomb repressive complex 1), which is responsible for maintenance of gene repression, prevention of chromatin remodeling, preservation of the "stemness" of the cell, and cell differentiation. Although the majority of PRC1 subunits have been recently characterized, the structure of Scml2 and its role in PRC1-mediated gene silencing remain unknown. In this work a conserved protein domain within human Scml2 has been identified, and its structure was determined by solution NMR spectroscopy. This module was named Scm-like embedded domain, or SLED. Evolutionarily, the SLED domain emerges in the first multicellular organisms, consistent with the role of Scml2 in cell differentiation. Furthermore, it is exclusively found within the Scm-like family of proteins, often accompanied by malignant brain tumor domain (MBT) and sterile α motif (SAM) domains. The domain adopts a novel α/β fold with no structural analogues found in the Protein Data Bank (PDB). The ability of the SLED to bind double-stranded DNA was also examined, and the isolated domain was shown to interact with DNA in a sequence-specific manner. Because PRC1 complexes localize to the promoters of a specific subset of developmental genes in vivo, the SLED domain of Scml2 may provide an important link connecting the PRC1 complexes to their target genes.

Highlights

Scml2 is a subunit of the Polycomb repressive complex 1 (PRC1) responsible for epigenetic regulation of gene expression
Human Scml2 is a part of a multisubunit protein complex, PRC1 (Polycomb repressive complex 1), which is responsible for maintenance of gene repression, prevention of chromatin remodeling, preservation of the “stemness” of the cell, and cell differentiation
The results presented in this work suggest that, in addition to its ability to bind methylated histones, Scml2 can directly recognize double-stranded DNA via its SLED domain

Summary

Background

Scml is a subunit of the Polycomb repressive complex 1 (PRC1) responsible for epigenetic regulation of gene expression. In this work a conserved protein domain within human Scml has been identified, and its structure was determined by solution NMR spectroscopy This module was named Scm-like embedded domain, or SLED. PcG proteins form a few distinct multisubunit nuclear complexes, among which Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) are the best studied [2] Both PRC1 and PRC2 covalently modify histones and work together to accomplish their goal: silencing of a group of developmental genes [3]. The MBT domains are ϳ100-amino acid modules that are often found in multiple copies arranged in MBT repeats They are known to bind methylated lysine residues [10], which suggests that Scm-like proteins may be able to recognize methylated histones. The direct interaction of Scml with DNA involving this newly discovered domain may provide an important step in PRC1 recognition of its target genes

EXPERIMENTAL PROCEDURES

A Scml2 Scmh1-a Scmh1-b Scmh1-c Scmh1-d Scmh1-e Scmh1-f Scml4 Sfmbt1 Sfmbt2

RESULTS

DISCUSSION

CONCLUSION