The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid.

Ashley York,Paul D Bieniasz,Sebla B Kutluay,Manel Errando,Bryan R Cullen

doi:10.1371/journal.ppat.1005833

Abstract

The APOBEC3 (A3) cytidine deaminases are antiretroviral proteins, whose targets include human immunodeficiency virus type-1 (HIV-1). Their incorporation into viral particles is critical for antiviral activity and is driven by interactions with the RNA molecules that are packaged into virions. However, it is unclear whether A3 proteins preferentially target RNA molecules that are destined to be packaged and if so, how. Using cross-linking immunoprecipitation sequencing (CLIP-seq), we determined the RNA binding preferences of the A3F, A3G and A3H proteins. We found that A3 proteins bind preferentially to RNA segments with particular properties, both in cells and in virions. Specifically, A3 proteins target RNA sequences that are G-rich and/or A-rich and are not scanned by ribosomes during translation. Comparative analyses of HIV-1 Gag, nucleocapsid (NC) and A3 RNA binding to HIV-1 RNA in cells and virions revealed the striking finding that A3 proteins partially mimic the RNA binding specificity of the HIV-1 NC protein. These findings suggest a model for A3 incorporation into HIV-1 virions in which an NC-like RNA binding specificity is determined by nucleotide composition rather than sequence. This model reconciles the promiscuity of A3 RNA binding that has been observed in previous studies with a presumed advantage that would accompany selective binding to RNAs that are destined to be packaged into virions.

Highlights

APOBEC3 (A3) proteins are a family of germline-encoded proteins that inhibit the replication of a broad range of viruses and retroelements
RNA Binding Specificity of APOBEC3 Proteins activity has been shown to be critical for virion incorporation, the mechanism by which packaged RNA molecules are targeted by A3 proteins has been unclear
We found that A3 proteins preferentially bind to particular types of RNA sequence in human immunodeficiency virus type-1 (HIV-1) and cellular RNAs

Summary

Introduction

APOBEC3 (A3) proteins are a family of germline-encoded proteins that inhibit the replication of a broad range of viruses and retroelements (reviewed in [1, 2]). A3 proteins exert their antiretroviral activity largely through their deoxycytosine deaminase activity, i.e. modification of dC-to-dU in single-stranded DNA retroviral reverse transcription intermediates, resulting in dG-to-dA hypermutation of the viral genome and error catastrophe [3,4,5,6]. There are seven members of the A3 protein family that are categorized by their possession of either a single zinc (Z)-containing deaminase domain (A3A, A3C and A3H), or two Z domains (A3B, A3D, A3F and A3G) (reviewed in [12]). The antiviral activity of some A3 proteins is antagonized by most lentiviruses, including human immunodeficiency virus type-1 (HIV-1) through the action of the virion infectivity factor (Vif) protein. In the absence of a functional Vif protein, some A3 proteins are efficiently incorporated into progeny HIV-1 virions, enabling them to exert their antiviral effects during subsequent infection of a target cell

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