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

Zheng, L.; Yang, T.; Guo, H.; Qi, C.; Lu, Y.; Xiao, H.; Gao, Y.; Liu, Y.; Yang, Y.; Zhou, M.; Nguyen, H.; Zhu, Y.; Sun, F.; Zhang, C.-Y.; Ji, X.

doi:10.1101/2023.09.25.559159

bioRxiv · 10.1101/2023.09.25.559159

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

Zheng, L.·Yang, T.·Guo, H.·Qi, C.·Lu, Y.·Xiao, H.·Gao, Y.·Liu, Y.·Yang, Y.·Zhou, M.·Nguyen, H.·Zhu, Y.·Sun, F.·Zhang, C.-Y.·Ji, X.

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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 {beta}-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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Zheng, L., Yang, T., Guo, H., Qi, C., Lu, Y., Xiao, H., Gao, Y., Liu, Y., Yang, Y., Zhou, M., Nguyen, H., Zhu, Y., Sun, F., Zhang, C.-Y., Ji, X.. 2023-09-26. Cryo-EM structures of human SID-1 transmembrane family proteins and implications for their low-pH-dependent RNA transport activity. https://doi.org/10.1101/2023.09.25.559159

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