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PreprintCited by 18RNA Interference and Gene DeliveryDrug Transport and Resistance MechanismsCellular transport and secretion

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Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity

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Zheng, Le, Yang, Tingting, Guo, Hangtian, Qi, Chen, Lu, Yuchi, Xiao, Haonan, Gao, Yan, Liu, Yue, Yang, Yixuan, Zhou, Mengru, Nguyen, Henry C., Zhu, Yun, Sun, Fei, Zhang, Chen-yu, Ji, Xiaoyun·2023·Cell Research
DOI 10.1101/2023.09.25.559159PMC PMC10770124

Preprint — published as 10.1038/s41422-023-00893-1

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Abstract

Human SIDT1 and SIDT2 are closely related members of the systemic RNA interference (RNAi)-defective (SID-1) transmembrane family. Both mediate RNA internalization and intracellular transport and are involved in various biological processes. However, the molecular basis of RNA uptake, especially for exogenous small RNAs, remains elusive. Here, we present the cryo-electron microscopy (cryo-EM) structures of human SIDT1 and SIDT2. Both structures reveal the overall architecture of a dimeric arrangement contributed by the β-strand-rich extracellular domain (ECD) and the transmembrane domain (TMD) with 11 passes, highlighting the remarkable structural congruence. The in situ assays confirm that SIDT1 and SIDT2 exist as dimers or higher-order oligomers. We demonstrate that for both SIDT1 and SIDT2, the ECD binds small RNAs, such as dietary plant-derived miRNA, only under acidic conditions. In addition, RNA binding under low pH can trigger higher-order assembly of the ECD dimer, suggesting the potential importance of oligomerization during RNA uptake. Our results illustrate the molecular features of the conserved SID-1 family proteins to elucidate the mechanism of the low pH-dependent activation of RNA uptake mediated by SIDT1 and SIDT2. This study provides a promising understanding of the molecular basis of the nucleic acid delivery platform, which may potentially open new avenues for the design and optimization of RNA-based therapies.

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Metadata

Authors
Zheng, L., Yang, T., Guo, H., Qi, C., Lu, Y., Xiao, H., Gao, Y., Liu, Y., Yang, Y., Zhou, M., Nguyen, H. C., Zhu, Y., Sun, F., Zhang, C.-Y., & Ji, X.
Affiliations
  • Nanjing University (CN)
  • ShanghaiTech University (CN)
  • Chinese Academy of Sciences (CN)
  • Ministry of Education of the People's Republic of China (CN)
Corresponding author
  • Guo, Hangtian
  • Zhu, Yun
  • Sun, Fei
  • Zhang, Chen-yu
  • Ji, Xiaoyun
ORCID
Venue
Cell Research
Publisher
openRxiv
Published
2023-09-26
Volume
34
Issue
1
Pages
80-83
ISSN
1001-0602 (ISSN-L)
DOI
10.1101/2023.09.25.559159
PMC
PMC10770124
OpenAlex
W4388421127
Cited by
18
References
1
Citations by year
2026: 3 · 2025: 6 · 2024: 8 · 2023: 1
FWCI
1.60
Type
journal article
Language
en
Open access
Licence
cc-by
Locations
  • Cell Research (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
Funders
  • Salt Science Research Foundation
  • National Natural Science Foundation of China (XDB37040102, 32270139, 32071187)
  • Chinese Academy of Sciences (XDB37040102)
  • Government of Jiangsu Province
  • Nanjing University
  • ShanghaiTech University
  • National Key Research and Development Program of China (2021YFA1301500, 2019YFA0904101, 2018YFA0507103)
  • Fundamental Research Funds for the Central Universities
  • Institute of Biophysics, Chinese Academy of Sciences (XDB37040102)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Interference and Gene Delivery
  • Health Sciences › Medicine › Oncology › Drug Transport and Resistance Mechanisms
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
Keywords
SIDT2, systemic RNA interference, RNA uptake, extracellular domain, transmembrane domain, protein dimerization, oligomerization, nucleic acid delivery
MeSH terms
Humans, Hydrogen-Ion Concentration, Cryoelectron Microscopy, RNA Transport

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