Interactions between the HIV-1 Unspliced mRNA and Host mRNA Decay Machineries

Abstract

The human immunodeficiency virus type-1 (HIV-1) unspliced transcript is used both as mRNA for the synthesis of structural proteins and as the packaged genome. Given the presence of retained introns and instability AU-rich sequences, this viral transcript is normally retained and degraded in the nucleus of host cells unless the viral protein REV is present. As such, the stability of the HIV-1 unspliced mRNA must be particularly controlled in the nucleus and the cytoplasm in order to ensure proper levels of this viral mRNA for translation and viral particle formation. During its journey, the HIV-1 unspliced mRNA assembles into highly specific messenger ribonucleoproteins (mRNPs) containing many different host proteins, amongst which are well-known regulators of cytoplasmic mRNA decay pathways such as up-frameshift suppressor 1 homolog (UPF1), Staufen double-stranded RNA binding protein 1/2 (STAU1/2), or components of miRNA-induced silencing complex (miRISC) and processing bodies (PBs). More recently, the HIV-1 unspliced mRNA was shown to contain N⁶-methyladenosine (m⁶A), allowing the recruitment of YTH N⁶-methyladenosine RNA binding protein 2 (YTHDF2), an m⁶A reader host protein involved in mRNA decay. Interestingly, these host proteins involved in mRNA decay were shown to play positive roles in viral gene expression and viral particle assembly, suggesting that HIV-1 interacts with mRNA decay components to successfully accomplish viral replication. This review summarizes the state of the art in terms of the interactions between HIV-1 unspliced mRNA and components of different host mRNA decay machineries.

Keywords: HIV-1 unspliced mRNA; REV; Staufen; UPF1; YTHDF2; m6A; mRNA decay.

Figure 1

Post-transcriptional control of gene expression in HIV-1. Upon RNA polymerase II-driven transcription, the capped and polyadenylated 9 kb full-length mRNA undergoes alternative splicing in order to generate the 2 kb fully spliced and the 4 kb partially spliced (omitted for simplicity) transcripts. Fully spliced transcripts follow the canonical pathway for mRNA metabolism, in which nuclear export and translation are ensured by the splicing-dependent recruitment of nuclear factors such as the exon junction complex (EJC) and the mRNA nuclear export factor NXF1. Once in the cytoplasm, fully spliced mRNA recruits the host translational machinery in order to synthesize viral proteins TAT, REV, and NEF and upon several rounds of translation they are degraded by the host RNA decay machinery. The viral protein REV enters the nucleus, allowing the accumulation of the 9 kb unspliced mRNA and its subsequent nuclear export through the chromosomal maintenance 1 (CRM1)-dependent pathway. This alternative nuclear export pathway allows the unspliced mRNA to evade surveillance and quality control mechanisms associated with the canonical nuclear export pathway. During its journey to the cytoplasm, the unspliced mRNA recruits several host proteins such as up-frameshift suppressor 1 homolog (UPF1) and the DEAD (Asp-Glu-Ala-Asp) box 3- (DDX3) RNA helicase that will ensure an efficient association with the host translational machinery in order to synthesize the major structural proteins GAG and GAG–POL. In contrast to fully spliced transcripts, the unspliced mRNA does not undergo mRNA turnover as it is used as the viral genome incorporated into viral particles. CA, capsid protein; DCP, decapping enzyme; IN, integrase; MA, matrix protein; MOV10; Moloney leukemia virus 10; Myr, N-terminally myristoylated; NC, nucleocapsid protein; Pan2/3, PAB-dependent poly(A)-specific ribonuclease; p6, p6 protein; Ran-GTP, ras-related nuclear protein GTP; RT, reverse transcriptase; XRN1, 5'-3' Exoribonuclease 1.

Figure 2

The HIV-1 unspliced mRNA has been shown to recruit components of different mRNA decay pathways including: (a) UPF1 (NMD, nonsense-mediated decay); (b) STAU1/2 (SMD, STAU-mediated mRNA decay); (c) RuvB-like 2 (RVB2) (NGD, No-Go decay); (d) HIV-1 trans-activating response (TAR) RNA-binding protein (TRBP) and Argonaute (Ago) (microRNA Machinery); (e) DDX6 (PBs, processing bodies); (f) eukaryotic elongation factor 2 (eEF2) and GTPase activating protein (GAP) SH3 domain-binding protein 1 (G3BP1) (SGs, stress granules); and (g) YTHDF2 (N⁶-methyladenosine (m⁶A)-dependent mRNA decay). Interestingly, most of these associations have been demonstrated to be beneficial for viral replication, suggesting that HIV-1 has evolved mechanisms to interact with these host factors in order to divert them from their functions in mRNA decay.