Mechanistic Insights into the Collaboration of Dicer, RIG-I-like Helicase, and dsRNA Binding Protein in Antiviral Defense in C. elegans

Core Concepts

The C. elegans antiviral complex comprising Dicer (DCR-1), the RIG-I-like helicase DRH-1, and the dsRNA binding protein RDE-4 cooperate to cleave viral dsRNA in an ATP-dependent and terminus-specific manner, with DRH-1 playing a dominant role in ATP hydrolysis and processive cleavage.

Abstract

The content provides mechanistic insights into how the C. elegans antiviral complex, comprising the endoribonuclease Dicer (DCR-1), the RIG-I-like helicase DRH-1, and the dsRNA binding protein RDE-4, functions to cleave viral dsRNA during antiviral defense.

Key highlights:

1. The complex exhibits ATP-dependent and terminus-specific cleavage of dsRNA, similar to the Drosophila Dicer-2 (dmDcr2), but with notable differences.
2. DRH-1, the RIG-I ortholog, plays a dominant role in ATP hydrolysis, while the helicase domain of DCR-1 contributes to an ATP-dependent measuring step.
3. RDE-4 is critical for both ATP-independent and ATP-dependent cleavage activities, likely by positioning the dsRNA substrate for catalysis.
4. Cryo-EM structures reveal that DRH-1's N-terminal domain interacts with DCR-1's helicase domain, suggesting this interaction relieves DRH-1's autoinhibition and allows it to translocate along dsRNA to promote processive cleavage.
5. The study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways (RNAi and interferon response) to achieve antiviral defense in C. elegans.

Stats

The single-turnover cleavage rate of the wildtype antiviral complex with 106 BLT dsRNA in the presence of ATP is 0.14 min-1.
The single-turnover cleavage rate of the wildtype antiviral complex with 106 3'ovr dsRNA in the presence of ATP is 0.006 min-1.
The ATP hydrolysis rate of the wildtype antiviral complex with 106 BLT dsRNA is 0.11 min-1.
The ATP hydrolysis rate of the wildtype antiviral complex with 106 3'ovr dsRNA is 0.03 min-1.

Quotes

"DRH-1 plays the dominant role in ATP hydrolysis, and like mammalian RLRs, has an N-terminal domain that functions in autoinhibition."
"RDE-4 is critical for both ATP-independent and ATP-dependent cleavage activities, likely by positioning the dsRNA substrate for catalysis."
"The study unravels the mechanistic basis of the collaboration between two helicases from typically distinct innate immune defense pathways (RNAi and interferon response) to achieve antiviral defense in C. elegans."

Key Insights Distilled From

C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA

by Consalvo,C. ... at www.biorxiv.org 09-21-2023

https://www.biorxiv.org/content/10.1101/2023.09.21.558868v3

Deeper Inquiries

How might the insights from the C. elegans antiviral complex inform our understanding of antiviral defense mechanisms in other invertebrate species?

The insights gained from studying the C. elegans antiviral complex can provide valuable information about the mechanisms of antiviral defense in other invertebrate species. By understanding how Dicer, DRH-1, and RDE-4 collaborate to cleave dsRNA and trigger an antiviral response in C. elegans, we can extrapolate similar mechanisms to other invertebrates that rely on RNAi for antiviral defense. The role of ATP-dependent and ATP-independent cleavage, the interactions between the helicase domains of Dicer and DRH-1, and the involvement of a dsRNA binding protein like RDE-4 can shed light on common strategies used by invertebrates to combat viral infections.

What are the potential implications of the autoinhibitory role of DRH-1's N-terminal domain for the regulation of the antiviral response in C. elegans?

The autoinhibitory role of DRH-1's N-terminal domain has significant implications for the regulation of the antiviral response in C. elegans. The interaction of the NTD with DCR-1's helicase domain suggests a mechanism by which DRH-1 is kept in an inactive state until it encounters its substrate, dsRNA. This autoinhibition ensures that ATP hydrolysis and subsequent cleavage are tightly regulated and only occur when needed. The relief of autoinhibition upon binding to dsRNA allows DRH-1 to translocate along the dsRNA and promote processive cleavage, enhancing the efficiency of the antiviral response. Understanding this regulatory mechanism can provide insights into how the antiviral response is finely tuned and controlled in C. elegans.

Could the collaboration between Dicer and RIG-I-like helicases observed in C. elegans provide clues about the evolutionary origins of the distinct innate immune pathways in vertebrates and invertebrates?

The collaboration between Dicer and RIG-I-like helicases observed in C. elegans could indeed provide clues about the evolutionary origins of the distinct innate immune pathways in vertebrates and invertebrates. The conservation of key domains and functional interactions between Dicer and RIG-I-like helicases suggests a common ancestry and shared evolutionary history of these proteins in antiviral defense mechanisms. The presence of an N-terminal domain that functions in autoinhibition in DRH-1, similar to the autoinhibitory role of CARD domains in RIG-I, hints at a conserved regulatory mechanism that has been adapted in different ways in vertebrates and invertebrates. By studying the collaboration between these proteins in C. elegans, we can gain insights into the evolutionary processes that led to the divergence of innate immune pathways in different species.