Architecture and subunit arrangement of the complete Saccharomyces cerevisiae COMPASS complex

Yanxing Wang,Min Huang,Catherine C L Wong,Yao Cong,Xiaoyu Hong,Zhanyu Ding,Yu Bao,Xiangyang Liu

doi:10.1038/s41598-018-35609-8

Abstract

Methylation of histone H3 lysine 4 (H3K4) is catalyzed by the multi-component COMPASS or COMPASS-like complex, which is highly conserved from yeast to human, and plays essential roles in gene expression and transcription, cell cycle progression, and DNA repair. Here we present a cryo-EM map of the complete S. cerevisiae COMPASS complex. Through tag or Fab labeling strategy combined with cryo-EM 3D reconstruction and cross-linking and mass spectrometry (XL-MS) analysis, we uncovered new information on the subunit arrangement: Cps50, Cps35, and Cps30 were determined to group together to form the face region in the head of the complex, and Cps40 and the N-terminal portion of Set1 reside on the top of the head. Our map reveals the location of the active center and a canyon in the back of the head. Together, our study provides the first snapshot of the complete architecture of yeast COMPASS and a picture of its subunit interaction network, which could facilitate our understanding of the COMPASS machinery and its functionality.

Highlights

The yeast COMPASS complex consists of seven distinct subunits, including Set[1], Cps60/Bre[2], Cps50/Swd[1], Cps40/Spp[1], Cps35/Swd[2], Cps30/Swd[3], and Cps25/Sdc[14]
By combining subunit-specific eGFP24,25, DID26, or PA–NZ-127–29 labeling strategy with cryo-EM 3D reconstruction, as well as cross-linking and mass spectrometry (XL-MS) analysis, we provide a complete picture of the subunit organization and full molecular architecture of yeast COMPASS
To obtain a sufficient quantity of COMPASS for cryo-EM study, we developed a strategy for overexpressing S. cerevisiae COMPASS in yeast

Summary

Introduction

The yeast COMPASS complex consists of seven distinct subunits, including Set[1], Cps60/Bre[2], Cps50/Swd[1], Cps40/Spp[1], Cps35/Swd[2], Cps30/Swd[3], and Cps25/Sdc[14]. Cps[50] and Cps[30], two WD40 repeat-containing proteins, can stably associate with each other to form a heterodimer and are required for the integrity of the complex, which is critical for maintaining global levels of H3K4 methylation[7]. Cps[35], another WD40 repeat-containing protein, is essential in budding yeast[10,11] and is required for maintaining proper levels of H3K4me[2] and H3K4me[35,8,9,12]. Many of these findings for yeast COMPASS complex hold true for human COMPASS family. This study could facilitate our understanding of the COMPASS machinery and its functionality

Methods

Results

Conclusion