Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding

Wataru Kobayashi; Yoshimasa Takizawa; Maya Aihara; Lumi Negishi; Hajime Ishii; Hitoshi Kurumizaka

doi:10.1038/s42003-019-0385-7

Structural and biochemical analyses of the nuclear pore complex component ELYS identify residues responsible for nucleosome binding

Commun Biol. 2019 May 3:2:163. doi: 10.1038/s42003-019-0385-7. eCollection 2019.

Authors

Wataru Kobayashi^{1

2}, Yoshimasa Takizawa¹, Maya Aihara², Lumi Negishi¹, Hajime Ishii², Hitoshi Kurumizaka^{1

2}

Affiliations

¹ 1Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-0032 Japan.
² 2Graduate School of Advanced Science and Engineering, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo, 162-8480 Japan.

Abstract

The nuclear pore complex embedded within the nuclear envelope is the essential architecture for trafficking macromolecules, such as proteins and RNAs, between the cytoplasm and nucleus. The nuclear pore complex assembly occurs on chromatin in the post-mitotic phase of the cell cycle. ELYS (MEL-28/AHCTF1) binds to the nucleosome, which is the basic chromatin unit, and promotes assembly of the complex around the chromosomes in cells. Here we show that the Arg-Arg-Lys (RRK) stretch of the C-terminal ELYS region plays an essential role in the nucleosome binding. The cryo-EM structure and the crosslinking mass spectrometry reveal that the ELYS C-terminal region directly binds to the acidic patch of the nucleosome. These results provide mechanistic insight into the ELYS-nucleosome interaction, which promotes the post-mitotic nuclear pore complex formation around chromosomes in cells.

Keywords: Cryoelectron microscopy; Nucleosomes.

Publication types

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

MeSH terms

Active Transport, Cell Nucleus / genetics
Animals
Binding Sites
Cell Cycle / genetics
Cloning, Molecular
Cryoelectron Microscopy
DNA-Binding Proteins / chemistry*
DNA-Binding Proteins / genetics
DNA-Binding Proteins / metabolism
Escherichia coli / genetics
Escherichia coli / metabolism
Gene Expression
Genetic Vectors / chemistry
Genetic Vectors / metabolism
Histones / chemistry*
Histones / genetics
Histones / metabolism
Humans
Models, Molecular
Nuclear Pore / chemistry*
Nuclear Pore / metabolism
Nuclear Pore / ultrastructure
Nuclear Pore Complex Proteins / chemistry*
Nuclear Pore Complex Proteins / genetics
Nuclear Pore Complex Proteins / metabolism
Nucleosomes / chemistry*
Nucleosomes / metabolism
Nucleosomes / ultrastructure
Protein Binding
Protein Interaction Domains and Motifs
Protein Structure, Secondary
Recombinant Fusion Proteins / chemistry
Recombinant Fusion Proteins / genetics
Recombinant Fusion Proteins / metabolism
Transcription Factors / chemistry*
Transcription Factors / genetics
Transcription Factors / metabolism
Xenopus Proteins / chemistry*
Xenopus Proteins / genetics
Xenopus Proteins / metabolism
Xenopus laevis / genetics
Xenopus laevis / metabolism

Substances

AHCTF1 protein, Xenopus
DNA-Binding Proteins
Histones
Nuclear Pore Complex Proteins
Nucleosomes
Recombinant Fusion Proteins
Transcription Factors
Xenopus Proteins