Research Article: The RNA Binding Specificity of Human APOBEC3 Proteins Resembles That of HIV-1 Nucleocapsid

Date Published: August 19, 2016

Publisher: Public Library of Science

Author(s): Ashley York, Sebla B. Kutluay, Manel Errando, Paul D. Bieniasz, Bryan R. Cullen.


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.

Partial Text

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 [3–6]. In addition to inflicting genetic damage, alternative deamination-independent antiretroviral mechanisms have also been reported [7–11].

The RNA binding activity of A3 proteins is essential for incorporation into HIV-1 virions and restriction of virus replication. Our data confirm previous studies in that A3 proteins are promiscuous in the RNA molecules that they bind. Importantly however, our findings also argue that A3 proteins exhibit significant RNA binding selectivity that could facilitate their incorporation into nascent HIV-1 virions and thus contribute to their antiviral activity.




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