Protomer alignment modulates specificity of RNA substrate recognition by Ire1
- University of California, San Francisco, United States
- Yale School of Medicine, United States
- Howard Hughes Medical Institute, University of California, San Francisco, United States
Abstract
The unfolded protein response (UPR) maintains protein folding homeostasis in the endoplasmic reticulum (ER). In metazoan cells, the Ire1 branch of the UPR initiates two functional outputs—non-conventional mRNA splicing and selective mRNA decay (RIDD). By contrast, Ire1 orthologs from Saccharomyces cerevisiae and Schizosaccharomyces pombe are specialized for only splicing or RIDD, respectively. Previously, we showed that the functional specialization lies in Ire1's RNase activity, which is either stringently splice-site specific or promiscuous (W. Li et al., 2018). Here, we developed an assay that reports on Ire1's RNase promiscuity. We found that conversion of two amino acids within the RNase domain of S. cerevisiae Ire1 to their S. pombe counterparts rendered it promiscuous. Using biochemical assays and computational modeling, we show that the mutations rewired a pair of salt bridges at Ire1 RNase domain's dimer interface, changing its protomer alignment. Thus, Ire1 protomer alignment affects its substrates specificity.
Data availability
All data generated or analysed during this study are included in the manuscript and supporting files.
Article and author information
Author details
Diego Garrido Ruiz
Funding
Howard Hughes Medical Institute
- R Dyche Mullins
- Peter Walter
Deutsche Forschungsgemeinschaft (Emmy Noether fellow)
- Jirka Peschek
UCSF-Zaffaroni Fellowship
- Weihan Li
Human Frontier Science Program
- Jirka Peschek
National Institute of Allergy and Infectious Diseases (2R37 AI066224)
- Anita Sil
National Institute of General Medical Sciences (R01 GM032384)
- Peter Walter
National Institute of General Medical Sciences (1R35 GM118119-01)
- R Dyche Mullins
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Nahum Sonenberg, McGill University, Canada
Publication history
- Received: February 12, 2021
- Accepted: April 27, 2021
- Accepted Manuscript published: April 27, 2021 (version 1)
- Accepted Manuscript updated: April 29, 2021 (version 2)
- Version of Record published: May 7, 2021 (version 3)
Copyright
© 2021, Li 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.
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Protomer alignment modulates specificity of RNA substrate recognition by Ire1
eLife 10:e67425.
https://doi.org/10.7554/eLife.67425
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