A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions

Masaaki Shiina; Keisuke Hamada; Taiko Inoue-Bungo; Mariko Shimamura; Akiko Uchiyama; Shiho Baba; Ko Sato; Masaki Yamamoto; Kazuhiro Ogata

doi:10.1016/j.jmb.2014.07.020

A novel allosteric mechanism on protein-DNA interactions underlying the phosphorylation-dependent regulation of Ets1 target gene expressions

J Mol Biol. 2015 Apr 24;427(8):1655-69. doi: 10.1016/j.jmb.2014.07.020. Epub 2014 Jul 30.

Authors

Masaaki Shiina¹, Keisuke Hamada¹, Taiko Inoue-Bungo², Mariko Shimamura², Akiko Uchiyama², Shiho Baba², Ko Sato², Masaki Yamamoto³, Kazuhiro Ogata⁴

Affiliations

¹ Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan.
² Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan.
³ RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan; SPring-8/JASRI, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan.
⁴ Department of Biochemistry, Yokohama City University Graduate School of Medicine, 3-9 Fukuura, Kanazawa-ku, Yokohama 236-0004, Japan; RIKEN SPring-8 Center, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5148, Japan. Electronic address: ogata@med.yokohama-cu.ac.jp.

PMID: 25083921
DOI: 10.1016/j.jmb.2014.07.020

Abstract

Cooperative assemblies of transcription factors (TFs) on target gene enhancers coordinate cell proliferation, fate specification, and differentiation through precise and complicated transcriptional mechanisms. Chemical modifications, such as phosphorylation, of TFs induced by cell signaling further modulate the dynamic cooperativity of TFs. In this study, we found that various Ets1-containing TF-DNA complexes respond differently to calcium-induced phosphorylation of Ets1, which is known to inhibit Ets1-DNA binding. Crystallographic analysis of a complex comprising Ets1, Runx1, and CBFβ at the TCRα enhancer revealed that Ets1 acquires robust binding stability in the Runx1 and DNA-complexed state, via allosteric mechanisms. This allows phosphorylated Ets1 to be retained at the TCRα enhancer with Runx1, in contrast to other Ets1 target gene enhancers including mb-1 and stromelysin-1. This study provides a structure-based model for cell-signaling-dependent regulation of target genes, mediated via chemical modification of TFs.

Keywords: Ets1; Runx1; TCRα enhancer; allosteric regulation; phosphorylation.

Publication types

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

MeSH terms

Animals
Base Sequence
Cell Line
Core Binding Factor Alpha 2 Subunit / chemistry
Core Binding Factor Alpha 2 Subunit / metabolism*
Core Binding Factor beta Subunit / chemistry
Core Binding Factor beta Subunit / metabolism*
Crystallography, X-Ray
DNA / chemistry
DNA / metabolism*
Humans
Mice
Models, Molecular
Phosphorylation
Protein Binding
Protein Conformation
Proto-Oncogene Protein c-ets-1 / chemistry
Proto-Oncogene Protein c-ets-1 / metabolism*
Transcriptional Activation

Substances

Core Binding Factor Alpha 2 Subunit
Core Binding Factor beta Subunit
ETS1 protein, human
Proto-Oncogene Protein c-ets-1
DNA

Associated data

PDB/3WTS
PDB/3WTT
PDB/3WTU
PDB/3WTX
PDB/3WTY