Protomer alignment modulates specificity of RNA substrate recognition by Ire1
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 c...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
eLife Sciences Publications Ltd
2021-04-01
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| Series: | eLife |
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| Online Access: | https://elifesciences.org/articles/67425 |
| _version_ | 1811201243051196416 |
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| author | Weihan Li Kelly Crotty Diego Garrido Ruiz Mark Voorhies Carlos Rivera Anita Sil R Dyche Mullins Matthew P Jacobson Jirka Peschek Peter Walter |
| author_facet | Weihan Li Kelly Crotty Diego Garrido Ruiz Mark Voorhies Carlos Rivera Anita Sil R Dyche Mullins Matthew P Jacobson Jirka Peschek Peter Walter |
| author_sort | Weihan Li |
| collection | DOAJ |
| description | 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 (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. |
| first_indexed | 2024-04-12T02:18:51Z |
| format | Article |
| id | doaj.art-51c4c86e6d97423886be2d4ad90f74de |
| institution | Directory Open Access Journal |
| issn | 2050-084X |
| language | English |
| last_indexed | 2024-04-12T02:18:51Z |
| publishDate | 2021-04-01 |
| publisher | eLife Sciences Publications Ltd |
| record_format | Article |
| series | eLife |
| spelling | doaj.art-51c4c86e6d97423886be2d4ad90f74de2022-12-22T03:52:11ZengeLife Sciences Publications LtdeLife2050-084X2021-04-011010.7554/eLife.67425Protomer alignment modulates specificity of RNA substrate recognition by Ire1Weihan Li0https://orcid.org/0000-0003-4718-1884Kelly Crotty1Diego Garrido Ruiz2https://orcid.org/0000-0002-2441-385XMark Voorhies3https://orcid.org/0000-0001-8815-7384Carlos Rivera4Anita Sil5R Dyche Mullins6Matthew P Jacobson7Jirka Peschek8https://orcid.org/0000-0001-8158-9301Peter Walter9https://orcid.org/0000-0002-6849-708XDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States; Howard Hughes Medical Institute, San Francisco, United StatesDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States; Howard Hughes Medical Institute, San Francisco, United StatesDepartment of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, United StatesDepartment of Microbiology and Immunology, University of California at San Francisco, San Francisco, United StatesDepartment of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, United StatesDepartment of Microbiology and Immunology, University of California at San Francisco, San Francisco, United StatesHoward Hughes Medical Institute, San Francisco, United States; Department of Cellular and Molecular Pharmacology, University of California at San Francisco, San Francisco, United StatesDepartment of Pharmaceutical Chemistry, University of California at San Francisco, San Francisco, United StatesDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States; Howard Hughes Medical Institute, San Francisco, United StatesDepartment of Biochemistry and Biophysics, University of California San Francisco, San Francisco, United States; Howard Hughes Medical Institute, San Francisco, United StatesThe 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 (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.https://elifesciences.org/articles/67425unfolded protein responseenzymatic substrate specificityRNA biologyIre1 |
| spellingShingle | Weihan Li Kelly Crotty Diego Garrido Ruiz Mark Voorhies Carlos Rivera Anita Sil R Dyche Mullins Matthew P Jacobson Jirka Peschek Peter Walter Protomer alignment modulates specificity of RNA substrate recognition by Ire1 eLife unfolded protein response enzymatic substrate specificity RNA biology Ire1 |
| title | Protomer alignment modulates specificity of RNA substrate recognition by Ire1 |
| title_full | Protomer alignment modulates specificity of RNA substrate recognition by Ire1 |
| title_fullStr | Protomer alignment modulates specificity of RNA substrate recognition by Ire1 |
| title_full_unstemmed | Protomer alignment modulates specificity of RNA substrate recognition by Ire1 |
| title_short | Protomer alignment modulates specificity of RNA substrate recognition by Ire1 |
| title_sort | protomer alignment modulates specificity of rna substrate recognition by ire1 |
| topic | unfolded protein response enzymatic substrate specificity RNA biology Ire1 |
| url | https://elifesciences.org/articles/67425 |
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