Role of Viral Splicing Elements and Cellular RNA Binding Proteins in Regulation of HIV-1 Alternative RNA Splicing

Abstract

In HIV-1 infected cells, over 40 different mRNA species are produced by alternative splicing of the single HIV-1 primary RNA transcript. In addition, approximately half of the HIV-1 primary RNA transcripts are not spliced and are exported to the cytoplasm where they serve as mRNA and as genomic RNA. In this article, we will review current knowledge of the mechanisms by which the HIV-1 alternative splicing is regulated. Several negatively and positively-acting cis-acting elements have been detected within the viral genome that repress or facilitate viral RNA splicing by binding to cellular proteins. These include exonic splicing silencers (ESS) and an intronic splicing silencer (ISS) that are selectively bound either by members of the hnRNP A/B family (hnRNPs A1, A1(B), A2, and B1) or by hnRNP H. Exonic splicing enhancers (ESE) are also present within the HIV-1 genome and are selectively bound by members of the SR protein family. ESS and ISS repression mediated by hnRNP A/B proteins occurs at early steps of splicing, prior to formation of pre-spliceosome complexes. Current models propose that ESS elements promote cooperative binding of hnRNP A/B proteins to the exon and prevent efficient binding of essential cellular splicing factors to the 3' splice site. SR proteins bound to ESE elements that are juxtaposed or overlapping ESS elements may counteract this inhibition. We will review data indicating the importance of the HIV-1 splicing elements and their cognate binding proteins for efficient virus replication. Differences in cis-acting splicing elements between the group M (major) and group O (outlier) HIV-1 strains will also be discussed. Finally we will review evidence suggesting the possibility that there may be changes in regulation of HIV-1 alternative splicing in infected human T cells, human macrophages and rodent cells.

Serine- and Arginine-rich Proteins 55 and 75 (SRp55 and SRp75) Induce Production of HIV-1 vpr mRNA by Inhibiting the 5′-Splice Site of Exon 3

“…There are multiple splicing enhancer elements in exons 4 and 5 (16). Whereas SC35 binds to enhancer ESE2 (24), potential binding sites for ASF/SF2, SRp40, and SRp55 were identified in GAR (25).…”

“…Generally, the family of serine-and arginine-rich proteins (SR proteins) target enhancer sequences, and silencer sequences are targeted by heterogeneous nuclear ribonucleoproteins (15). There are several enhancers and silencers on HIV-1 pre-mRNA (16). A silencer in exon 3 called ESSV inhibits the vpr splice acceptor SA3 (10,17).…”

“…Recent studies have shown that the relative concentrations of SR proteins are of paramount importance for production of sufficient quantities of the various HIV-1 mRNAs (16). SR proteins have also been shown to be potential targets for novel therapy against HIV-1 infection (28).…”

Quantitative and evolutionary biology of alternative splicing: how changing the mix of alternative transcripts affects phenotypic plasticity and reaction norms

“…AS is not entirely restricted to eukaryotes, as retroviruses depend on AS for critical events in their life cycle (Pollard and Malim, 1998). Patterns of AS vary among viral strains, perhaps in functionally important ways (Stoltzfus and Madsen, 2006).…”

Quantitative analysis of clinically relevant mutations occurring in lymphoid cells harboring γ-retrovirus-encoded hsvtk suicide genes

“…20 Alternatively, these minute sequence changes may abrogate an intron splicing silencer in hsvtk2 otherwise present in hsvtk1 and 3. 21,22 It is noteworthy that the region of the hsvtk gene described to contain the SA 554 has been recently identified as an unusually short-sequence functioning as an internal ribosome entry site (IRES, 557-CCGUG CUGGCGU-568). 23 Although this IRES sequence is Rearrangements in retrovirally encoded hsvtk genes X Wang et al conserved between the three hsvtk variants discussed above, this secondary structure in conjunction with the nucleotide differences between the variants may be important in the appearance of a recombinogenic hot spot in hsvtk1.…”