RIG-I Uses an ATPase-Powered Translocation-Throttling Mechanism for Kinetic Proofreading of RNAs and Oligomerization

Overview

Journal Mol Cell

Publisher Cell Press

Specialty Cell Biology

Date 2018 Oct 2

PMID 30270105

Citations 44

Authors

Swapnil C Devarkar

Brandon Schweibenz

Chen Wang

Joseph Marcotrigiano

Smita S Patel

Affiliations

Soon will be listed here.

Abstract

RIG-I has a remarkable ability to specifically select viral 5'ppp dsRNAs for activation from a pool of cytosolic self-RNAs. The ATPase activity of RIG-I plays a role in RNA discrimination and activation, but the underlying mechanism was unclear. Using transient-state kinetics, we elucidated the ATPase-driven "kinetic proofreading" mechanism of RIG-I activation and RNA discrimination, akin to DNA polymerases, ribosomes, and T cell receptors. Even in the autoinhibited state of RIG-I, the C-terminal domain kinetically discriminates against self-RNAs by fast off rates. ATP binding facilitates dsRNA engagement but, interestingly, makes RIG-I promiscuous, explaining the constitutive signaling by Singleton-Merten syndrome-linked mutants that bind ATP without hydrolysis. ATP hydrolysis dissociates self-RNAs faster than 5'ppp dsRNA but, more importantly, drives RIG-I oligomerization through translocation, which we show to be regulated by helicase motif IVa. RIG-I translocates directionally from the dsRNA end into the stem region, and the 5'ppp end "throttles" translocation to provide a mechanism for threading and building a signaling-active oligomeric complex.

Citing Articles

Biochemical and structural basis of Dicer helicase function unveiled by resurrecting ancient proteins.

Aderounmu A, Maus-Conn J, Consalvo C, Shen P, Bass B bioRxiv. 2025; .

PMID: 39990435 PMC: 11844470. DOI: 10.1101/2025.02.15.638221.

Regulation and mechanisms of action of RNA helicases.

Lang N, Jagtap P, Hennig J RNA Biol. 2024; 21(1):24-38.

PMID: 39435974 PMC: 11498004. DOI: 10.1080/15476286.2024.2415801.

Sterile activation of RNA-sensing pathways in autoimmunity.

Li J, Zhu J, Yang H, Hou F J Mol Cell Biol. 2024; 16(7).

PMID: 39143032 PMC: 11659683. DOI: 10.1093/jmcb/mjae029.

Recent developments in understanding RIG-I's activation and oligomerization.

Sikorska J, Wyss D Sci Prog. 2024; 107(3):368504241265182.

PMID: 39091074 PMC: 11297509. DOI: 10.1177/00368504241265182.

Proofreading mechanisms of the innate immune receptor RIG-I: distinguishing self and viral RNA.

Solotchi M, Patel S Biochem Soc Trans. 2024; 52(3):1131-1148.

PMID: 38884803 PMC: 11346460. DOI: 10.1042/BST20230724.

References

Luo D, Ding S, Vela A, Kohlway A, Lindenbach B, Pyle A . Structural insights into RNA recognition by RIG-I. Cell. 2011; 147(2):409-22. PMC: 3222294. DOI: 10.1016/j.cell.2011.09.023. View

Lu C, Ranjith-Kumar C, Hao L, Kao C, Li P . Crystal structure of RIG-I C-terminal domain bound to blunt-ended double-strand RNA without 5' triphosphate. Nucleic Acids Res. 2010; 39(4):1565-75. PMC: 3045611. DOI: 10.1093/nar/gkq974. View

Morris P, Tackett A, Raney K . Biotin-streptavidin-labeled oligonucleotides as probes of helicase mechanisms. Methods. 2001; 23(2):149-59. DOI: 10.1006/meth.2000.1116. View

Jiang X, Kinch L, Brautigam C, Chen X, Du F, Grishin N . Ubiquitin-induced oligomerization of the RNA sensors RIG-I and MDA5 activates antiviral innate immune response. Immunity. 2012; 36(6):959-73. PMC: 3412146. DOI: 10.1016/j.immuni.2012.03.022. View

Myong S, Cui S, Cornish P, Kirchhofer A, Gack M, Jung J . Cytosolic viral sensor RIG-I is a 5'-triphosphate-dependent translocase on double-stranded RNA. Science. 2009; 323(5917):1070-4. PMC: 3567915. DOI: 10.1126/science.1168352. View

Tomko E, Fischer C, Lohman T . Ensemble methods for monitoring enzyme translocation along single stranded nucleic acids. Methods. 2010; 51(3):269-76. PMC: 2900532. DOI: 10.1016/j.ymeth.2010.03.010. View

Bamming D, Horvath C . Regulation of signal transduction by enzymatically inactive antiviral RNA helicase proteins MDA5, RIG-I, and LGP2. J Biol Chem. 2009; 284(15):9700-12. PMC: 2665091. DOI: 10.1074/jbc.M807365200. View

Banerjee K, Kolomeisky A, Igoshin O . Accuracy of Substrate Selection by Enzymes Is Controlled by Kinetic Discrimination. J Phys Chem Lett. 2017; 8(7):1552-1556. DOI: 10.1021/acs.jpclett.7b00441. View

Schlee M, Roth A, Hornung V, Hagmann C, Wimmenauer V, Barchet W . Recognition of 5' triphosphate by RIG-I helicase requires short blunt double-stranded RNA as contained in panhandle of negative-strand virus. Immunity. 2009; 31(1):25-34. PMC: 2824854. DOI: 10.1016/j.immuni.2009.05.008. View

10.

Lassig C, Matheisl S, Sparrer K, de Oliveira Mann C, Moldt M, Patel J . ATP hydrolysis by the viral RNA sensor RIG-I prevents unintentional recognition of self-RNA. Elife. 2015; 4. PMC: 4733034. DOI: 10.7554/eLife.10859. View

11.

Willemsen J, Wicht O, Wolanski J, Baur N, Bastian S, Haas D . Phosphorylation-Dependent Feedback Inhibition of RIG-I by DAPK1 Identified by Kinome-wide siRNA Screening. Mol Cell. 2017; 65(3):403-415.e8. DOI: 10.1016/j.molcel.2016.12.021. View

12.

Devarkar S, Wang C, Miller M, Ramanathan A, Jiang F, Khan A . Structural basis for m7G recognition and 2'-O-methyl discrimination in capped RNAs by the innate immune receptor RIG-I. Proc Natl Acad Sci U S A. 2016; 113(3):596-601. PMC: 4725518. DOI: 10.1073/pnas.1515152113. View

13.

Yoneyama M, Fujita T . Function of RIG-I-like receptors in antiviral innate immunity. J Biol Chem. 2007; 282(21):15315-8. DOI: 10.1074/jbc.R700007200. View

14.

Peisley A, Wu B, Xu H, Chen Z, Hur S . Structural basis for ubiquitin-mediated antiviral signal activation by RIG-I. Nature. 2014; 509(7498):110-4. PMC: 6136653. DOI: 10.1038/nature13140. View

15.

Rehwinkel J, Tan C, Goubau D, Schulz O, Pichlmair A, Bier K . RIG-I detects viral genomic RNA during negative-strand RNA virus infection. Cell. 2010; 140(3):397-408. DOI: 10.1016/j.cell.2010.01.020. View

16.

Zheng J, Yong H, Panutdaporn N, Liu C, Tang K, Luo D . High-resolution HDX-MS reveals distinct mechanisms of RNA recognition and activation by RIG-I and MDA5. Nucleic Acids Res. 2014; 43(2):1216-30. PMC: 4333383. DOI: 10.1093/nar/gku1329. View

17.

Poeck H, Bscheider M, Gross O, Finger K, Roth S, Rebsamen M . Recognition of RNA virus by RIG-I results in activation of CARD9 and inflammasome signaling for interleukin 1 beta production. Nat Immunol. 2009; 11(1):63-9. DOI: 10.1038/ni.1824. View

18.

Schuberth-Wagner C, Ludwig J, Bruder A, Herzner A, Zillinger T, Goldeck M . A Conserved Histidine in the RNA Sensor RIG-I Controls Immune Tolerance to N1-2'O-Methylated Self RNA. Immunity. 2015; 43(1):41-51. PMC: 7128463. DOI: 10.1016/j.immuni.2015.06.015. View

19.

Dillingham M, Wigley D, Webb M . Demonstration of unidirectional single-stranded DNA translocation by PcrA helicase: measurement of step size and translocation speed. Biochemistry. 2000; 39(1):205-12. DOI: 10.1021/bi992105o. View

20.

McKeithan T . Kinetic proofreading in T-cell receptor signal transduction. Proc Natl Acad Sci U S A. 1995; 92(11):5042-6. PMC: 41844. DOI: 10.1073/pnas.92.11.5042. View