HIV-1 virus cycle replication: a review of RNA polymerase II transcription, alternative splicing and protein synthesis

TL;DR

This review details the HIV-1 replication cycle focusing on RNA polymerase II transcription, splicing, and protein synthesis, highlighting recent sequencing and simulation methods to understand viral protein production and potential vaccine targets.

Contribution

It introduces a comprehensive analysis combining long-read sequencing and simulation software to elucidate HIV-1 RNA processing and protein synthesis, identifying novel ORFs and regulatory mechanisms.

Findings

Identification of variable length Tat and Rev proteins

Localization of small polypeptides and unknown proteins

Application of long-read sequencing and simulation tools

Abstract

HIV virus replication is a time-related process that includes several stages. Focusing on the core steps, RNA polymerase II transcripts in an early stage pre-mRNA containing regulator proteins (i.e nef,tat,rev,vif,vpr,vpu), which are completely spliced by the spliceosome complex (0.9kb and 1.8kb) and exported to the ribosome for protein synthesis. These splicing and export processes are regulated by tat protein, which binds on Trans-activation response (TAR) element, and by rev protein, which binds to the Rev-responsive Element (RRE). As long as these regulators are synthesized, splicing is progressively inhibited (from 4.0kb to 9.0kb) and mRNAs are translated into structural and enzymatic proteins (env, gag-pol). During this RNAPII scanning and splicing, around 40 different multi-cystronic mRNA have been produced. Long-read sequencing has been applied to the HIV-1 virus genome (type HXB2CG) with the HIV.pro software, a fortran 90 code for simulating the virus replication cycle, specially RNAPII transcription, exon/intron splicing and ribosome protein synthesis, including the frameshift at gag/pol gene and the ribosome pause at env gene. All HIV-1 virus proteins have been identified as far as other ORFs. As observed, tat/rev protein regulators have different length depending on the splicing cleavage site: tat protein varies from 224aa to a final state of 72aa, whereas rev protein from 25aa to 27aa, with a maximum of 119aa. Furthermore, several ORFs coding for small polypeptides sPEP (less than 10 amino acids) and for other unidentified proteins have been localised with unknown functionality. The detailed analysis of the HIV virus replication and the virus proteomics are important for identifying which antigens are presented by macrophages to CD4 cells, for localizing reactive epitopes or for creating transfer vectors to develop new HIV vaccines and effective therapies.