Genetic and mechanistic basis for APOBEC3H alternative splicing, retrovirus restriction, and counteraction by HIV-1 protease

Diako Ebrahimi,Christopher M Richards,Gabriel J Starrett,William L Brown,Terumasa Ikeda,Jennifer L Mccann,Jiayi Wang,Jordan T Becker,Jeongsik Yong,Adam Z Cheng,Michael A Carpenter,Reuben S Harris,Nadine M Shaban,Jairam R Lingappa,Daniel J Salamango

doi:10.1038/s41467-018-06594-3

Abstract

Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1. Seven haplotypes (I–VII) and four splice variants (SV154/182/183/200) with differing antiviral activities and geographic distributions have been described, but the genetic and mechanistic basis for variant expression and function remains unclear. Using a combined bioinformatic/experimental analysis, we find that SV200 expression is specific to haplotype II, which is primarily found in sub-Saharan Africa. The underlying genetic mechanism for differential mRNA splicing is an ancient intronic deletion [del(ctc)] within A3H haplotype II sequence. We show that SV200 is at least fourfold more HIV-1 restrictive than other A3H splice variants. To counteract this elevated antiviral activity, HIV-1 protease cleaves SV200 into a shorter, less restrictive isoform. Our analyses indicate that, in addition to Vif-mediated degradation, HIV-1 may use protease as a counter-defense mechanism against A3H in >80% of sub-Saharan African populations.

Highlights

Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1
The hallmark biochemical activity of this family is single-stranded DNA cytosine-to-uracil deamination, the family namesake (APOBEC1) and at least one A3 enzyme (A3A) have the capability to edit RNA cytosines[4,5]. These enzymes have diverse functions in biology ranging from transcriptome editing (APOBEC1 and A3A), antibody gene diversification (AID), and restriction of a broad number of DNAbased parasites (APOBEC1, AID, and A3A-H)
It is not surprising that HIV-1 and related lentiviruses have an A3 counter-defense mechanism governed by the viral protein Vif, which nucleates the formation of an E3 ubiquitin ligase complex to degrade cellular A3 enzymes and prevent access to susceptible viral replication intermediates

Summary

Introduction

Human APOBEC3H (A3H) is a single-stranded DNA cytosine deaminase that inhibits HIV-1. Most humans have seven APOBEC3 (apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3, A3) genes organized in tandem on chromosome 22 and located between conserved chromobox genes CBX6 and CBX71 These genes, A3A-D and A3F-H, encode members of the APOBEC family of polynucleotide cytosine deaminases The hallmark biochemical activity of this family is single-stranded DNA cytosine-to-uracil deamination, the family namesake (APOBEC1) and at least one A3 enzyme (A3A) have the capability to edit RNA cytosines[4,5] These enzymes have diverse functions in biology ranging from transcriptome editing (APOBEC1 and A3A), antibody gene diversification (AID), and restriction of a broad number of DNAbased parasites (APOBEC1, AID, and A3A-H) The global frequency of the A3H haplotype II is 20.9%, the allele frequency in HIV-1 pandemic areas of sub-Saharan Africa is 57%, which means 82% of this population has at least one allele of this HIV-1 restrictive haplotype

Methods

Results

Conclusion