Journal Article

Functional anatomy of zinc finger antiviral protein complexes

Gonçalves-Carneiro, Daniel, Smith, Janet L., Bohn, Jennifer A., Takata, Matthew A., Meagher, Jennifer L., Bieniasz, Paul D., Yeoh, Zoe C., Ohi, Melanie D.

2024

Overview

ZAP is an antiviral protein that binds to and depletes viral RNA, which is often distinguished from vertebrate host RNA by its elevated CpG content. Two ZAP cofactors, TRIM25 and KHNYN, have activities that are poorly understood. Here, we show that functional interactions between ZAP, TRIM25 and KHNYN involve multiple domains of each protein, and that the ability of TRIM25 to multimerize via its RING domain augments ZAP activity and specificity. We show that KHNYN is an active nuclease that acts in a partly redundant manner with its homolog N4BP1. The ZAP N-terminal RNA binding domain constitutes a minimal core that is essential for antiviral complex activity, and we present a crystal structure of this domain that reveals contacts with the functionally required KHNYN C-terminal domain. These contacts are remote from the ZAP CpG binding site and would not interfere with RNA binding. Based on our dissection of ZAP, TRIM25 and KHNYN functional anatomy, we could design artificial chimeric antiviral proteins that reconstitute the antiviral function of the intact authentic proteins, but in the absence of protein domains that are otherwise required for activity. Together, these results suggest a model for the RNA recognition and action of ZAP-containing antiviral protein complexes. Structural and functional studies of Zinc finger antiviral protein and its cofactors, TRIM25 and KHYNYN, reveal the formation of complexes and suggest that multivalent recognition of CpG-rich RNA targets it for nucleolytic depletion.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 38/1 / 42 / 42/109 / 42/41 / 631/326/596/2557 / 631/337/1645 / 631/535/1266 / 82/80 / Anatomy / Antiviral activity / Antiviral drugs / Binding Sites / Cofactors / Crystal structure / Crystallography, X-Ray / Depletion / Endonucleases - chemistry / Endonucleases - metabolism / Functional anatomy / HEK293 Cells / Humanities and Social Sciences / Humans / Models, Molecular / multidisciplinary / Nuclease / Protein Binding / Protein Domains / Proteins / Recognition / Repressor Proteins / Ribonucleic acid / RNA / RNA, Viral - chemistry / RNA, Viral - genetics / RNA, Viral - metabolism / RNA-Binding Proteins - chemistry / RNA-Binding Proteins - metabolism / Science / Science (multidisciplinary) / Structure-function relationships / Transcription Factors - chemistry / Transcription Factors - metabolism / Tripartite Motif Proteins - chemistry / Tripartite Motif Proteins - genetics / Tripartite Motif Proteins - metabolism / Ubiquitin-Protein Ligases - chemistry / Ubiquitin-Protein Ligases - metabolism / Vertebrates / Zinc / Zinc finger proteins / Zinc Fingers