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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. Life Sci Alliance 2024; 7:e202402624. [PMID: 38925866 PMCID: PMC11208740 DOI: 10.26508/lsa.202402624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Revised: 06/10/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
In Caenorhabditis elegans, inter-cellular transport of the small non-coding RNA causing systemic RNAi is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNAi defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the ChUP family. Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products-hSIDT1 and hSIDT2-mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain exists as two modules-a flexible lipid binding domain and a rigid transmembrane domain core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in ChUP family members.
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Affiliation(s)
- Vikas Navratna
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | | | - Jaimin K Rana
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Shyamal Mosalaganti
- https://ror.org/00jmfr291 Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- https://ror.org/00jmfr291 Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, MI, USA
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Wang R, Cong Y, Qian D, Yan C, Gong D. Structural basis for double-stranded RNA recognition by SID1. Nucleic Acids Res 2024; 52:6718-6727. [PMID: 38742627 PMCID: PMC11194109 DOI: 10.1093/nar/gkae395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 04/23/2024] [Accepted: 04/30/2024] [Indexed: 05/16/2024] Open
Abstract
The nucleic acid transport properties of the systemic RNAi-defective (SID) 1 family make them attractive targets for developing RNA-based therapeutics and drugs. However, the molecular basis for double-stranded (ds) RNA recognition by SID1 family remains elusive. Here, we report the cryo-EM structures of Caenorhabditis elegans (c) SID1 alone and in complex with dsRNA, both at a resolution of 2.2 Å. The dimeric cSID1 interacts with two dsRNA molecules simultaneously. The dsRNA is located at the interface between β-strand rich domain (BRD)1 and BRD2 and nearly parallel to the membrane plane. In addition to extensive ionic interactions between basic residues and phosphate backbone, several hydrogen bonds are formed between 2'-hydroxyl group of dsRNA and the contact residues. Additionally, the electrostatic potential surface shows three basic regions are fitted perfectly into three major grooves of dsRNA. These structural characteristics enable cSID1 to bind dsRNA in a sequence-independent manner and to distinguish between DNA and RNA. The cSID1 exhibits no conformational changes upon binding dsRNA, with the exception of a few binding surfaces. Structural mapping of dozens of loss-of-function mutations allows potential interpretation of their diverse functional mechanisms. Our study marks an important step toward mechanistic understanding of the SID1 family-mediated dsRNA uptake.
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Affiliation(s)
- Runhao Wang
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Ye Cong
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Dandan Qian
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
| | - Chuangye Yan
- School of Life Sciences, Tsinghua University, Beijing, 100084, China. Tsinghua-Peking Joint Center for Life Sciences, Tsinghua University, Beijing, 100084, China. Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, 100084, China. State Key Laboratory of Membrane Biology, Tsinghua University, Beijing 100084, China
| | - Deshun Gong
- State Key Laboratory of Medicinal Chemical Biology and College of Life Sciences, Nankai University, Tianjin 300350, China
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Navratna V, Kumar A, Rana JK, Mosalaganti S. Structure of the human systemic RNAi defective transmembrane protein 1 (hSIDT1) reveals the conformational flexibility of its lipid binding domain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.21.572875. [PMID: 38187772 PMCID: PMC10769365 DOI: 10.1101/2023.12.21.572875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
In C. elegans, inter-cellular transport of the small non-coding RNA causing systemic RNA interference (RNAi) is mediated by the transmembrane protein SID1, encoded by the sid1 gene in the systemic RNA interference-defective (sid) loci. SID1 shares structural and sequence similarity with cholesterol uptake protein 1 (CHUP1) and is classified as a member of the cholesterol uptake family (ChUP). Although systemic RNAi is not an evolutionarily conserved process, the sid gene products are found across the animal kingdom, suggesting the existence of other novel gene regulatory mechanisms mediated by small non-coding RNAs. Human homologs of sid gene products - hSIDT1 and hSIDT2 - mediate contact-dependent lipophilic small non-coding dsRNA transport. Here, we report the structure of recombinant human SIDT1. We find that the extra-cytosolic domain (ECD) of hSIDT1 adopts a double jelly roll fold, and the transmembrane domain (TMD) exists as two modules - a flexible lipid binding domain (LBD) and a rigid TMD core. Our structural analyses provide insights into the inherent conformational dynamics within the lipid binding domain in cholesterol uptake (ChUP) family members.
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Affiliation(s)
- Vikas Navratna
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Arvind Kumar
- Thermo Fisher Scientific, Waltham, Massachusetts, 02451, United States
| | - Jaimin K. Rana
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
| | - Shyamal Mosalaganti
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Cell and Developmental Biology, University of Michigan, Ann Arbor, Michigan, 48109, United States
- Department of Biophysics, College of Literature, Science and the Arts, University of Michigan, Ann Arbor, Michigan, 48109, United States
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