Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
- University of Dundee, United Kingdom
- The Australian National University, Australia
- University of St Andrews, United Kingdom
- European Molecular Biology Laboratory, Germany
- Max Planck Institute for Evolutionary Anthropolgy, Germany
- Ulm University, Germany
- Universitat Würzburg, Germany
Abstract
The yeast Chd1 protein acts to position nucleosomes across genomes. Here we model the structure of the Chd1 protein in solution and when bound to nucleosomes. In the apo state the DNA binding domain contacts the edge of the nucleosome while in the presence of the non-hydrolyzable ATP analog, ADP-beryllium fluoride, we observe additional interactions between the ATPase domain and the adjacent DNA gyre 1.5 helical turns from the dyad axis of symmetry. Binding in this conformation involves unravelling the outer turn of nucleosomal DNA and requires substantial reorientation of the DNA binding domain with respect to the ATPase domains. The orientation of the DNA-binding domain is mediated by sequences in the N-terminus and mutations to this part of the protein have positive and negative effects on Chd1 activity. These observations indicate that the unfavourable alignment of C-terminal DNA binding region in solution contributes to an auto-inhibited state.
Data availability
-
Chd1-nuc-engagedPublicly available at the Electron Microscopy Data Bank (accession no. EMDB-3502).
-
Chd1 Nuc SeqPublicly available at the EMBL European Archive (accession no: PRJEB15701).
-
Chd1-nuc apoPublicly available at the Electron Microscopy Data Bank (accession no. EMDB-3517).
-
Data from: Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomesAvailable at Dryad Digital Repository under a CC0 Public Domain Dedication.
-
SAXSPublicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBU7).
-
SAXSPublicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBV7).
-
SAXSPublicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBW7).
-
SAXSPublicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBX7).
-
SAXSPublicly available at the Small Angle Scattering Biological Data Bank (accession no. SASDBY7).
Article and author information
Author details
Funding
Wellcome (95062)
- Ramasubramanian Sundaramoorthy
- Amanda L Hughes
- Vijender Singh
- Nicola Wiechens
- Tom Owen-Hughes
Wellcome (097945/B/11/Z)
- Ramasubramanian Sundaramoorthy
- Amanda L Hughes
- Vijender Singh
- Nicola Wiechens
- Tom Owen-Hughes
Wellcome (099149/Z/12/Z)
- Ramasubramanian Sundaramoorthy
- Hassane El-Mkami
- David G Norman
- Tom Owen-Hughes
Wellcome (97945)
- Ramasubramanian Sundaramoorthy
- Amanda L Hughes
- Nicola Wiechens
- Daniel P Ryan
- David G Norman
- Tom Owen-Hughes
European Molecular Biology Organization (ALTF 380-2015)
- Amanda L Hughes
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2017, Sundaramoorthy et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
Metrics
-
- 3,137
- views
-
- 761
- downloads
-
- 51
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
Structural reorganization of the chromatin remodeling enzyme Chd1 upon engagement with nucleosomes
eLife 6:e22510.
https://doi.org/10.7554/eLife.22510
Further reading
-
- Chromosomes and Gene Expression
- Structural Biology and Molecular Biophysics
Type II nuclear receptors (T2NRs) require heterodimerization with a common partner, the retinoid X receptor (RXR), to bind cognate DNA recognition sites in chromatin. Based on previous biochemical and overexpression studies, binding of T2NRs to chromatin is proposed to be regulated by competition for a limiting pool of the core RXR subunit. However, this mechanism has not yet been tested for endogenous proteins in live cells. Using single-molecule tracking (SMT) and proximity-assisted photoactivation (PAPA), we monitored interactions between endogenously tagged RXR and retinoic acid receptor (RAR) in live cells. Unexpectedly, we find that higher expression of RAR, but not RXR, increases heterodimerization and chromatin binding in U2OS cells. This surprising finding indicates the limiting factor is not RXR but likely its cadre of obligate dimer binding partners. SMT and PAPA thus provide a direct way to probe which components are functionally limiting within a complex TF interaction network providing new insights into mechanisms of gene regulation in vivo with implications for drug development targeting nuclear receptors.
-
- Biochemistry and Chemical Biology
- Structural Biology and Molecular Biophysics
The SARS-CoV-2 main protease (Mpro or Nsp5) is critical for production of viral proteins during infection and, like many viral proteases, also targets host proteins to subvert their cellular functions. Here, we show that the human tRNA methyltransferase TRMT1 is recognized and cleaved by SARS-CoV-2 Mpro. TRMT1 installs the N2,N2-dimethylguanosine (m2,2G) modification on mammalian tRNAs, which promotes cellular protein synthesis and redox homeostasis. We find that Mpro can cleave endogenous TRMT1 in human cell lysate, resulting in removal of the TRMT1 zinc finger domain. Evolutionary analysis shows the TRMT1 cleavage site is highly conserved in mammals, except in Muroidea, where TRMT1 is likely resistant to cleavage. TRMT1 proteolysis results in reduced tRNA binding and elimination of tRNA methyltransferase activity. We also determined the structure of an Mpro-TRMT1 peptide complex that shows how TRMT1 engages the Mpro active site in an uncommon substrate binding conformation. Finally, enzymology and molecular dynamics simulations indicate that kinetic discrimination occurs during a later step of Mpro-mediated proteolysis following substrate binding. Together, these data provide new insights into substrate recognition by SARS-CoV-2 Mpro that could help guide future antiviral therapeutic development and show how proteolysis of TRMT1 during SARS-CoV-2 infection impairs both TRMT1 tRNA binding and tRNA modification activity to disrupt host translation and potentially impact COVID-19 pathogenesis or phenotypes.
