Can the HIV-1 splicing machinery be targeted for drug discovery?

Abstract

HIV-1 is able to express multiple protein types and isoforms from a single 9 kb mRNA transcript. These proteins are also expressed at particular stages of viral development, and this is achieved through the control of alternative splicing and the export of these transcripts from the nucleus. The nuclear export is controlled by the HIV protein Rev being required to transport incompletely spliced and partially spliced mRNA from the nucleus where they are normally retained. This implies a close relationship between the control of alternate splicing and the nuclear export of mRNA in the control of HIV-1 viral proliferation. This review discusses both the processes. The specificity and regulation of splicing in HIV-1 is controlled by the use of specific splice sites as well as exonic splicing enhancer and exonic splicing silencer sequences. The use of these silencer and enhancer sequences is dependent on the serine arginine family of proteins as well as the heterogeneous nuclear ribonucleoprotein family of proteins that bind to these sequences and increase or decrease splicing. Since alternative splicing is such a critical factor in viral development, it presents itself as a promising drug target. This review aims to discuss the inhibition of splicing, which would stall viral development, as an anti-HIV therapeutic strategy. In this review, the most recent knowledge of splicing in human immunodeficiency viral development and the latest therapeutic strategies targeting human immunodeficiency viral splicing are discussed.

Keywords: Rev; SR proteins; Tat; Vpr; alternative splicing; exonic specific silencer; exonic splicing enhancer; hnRNP; splicing based therapies.

Figure 1

Organization of the HIV genome. Note: The 5′ ss (D1–4) and 3′ ss (A1–7) are indicated as well as the resulting mRNA transcripts with non-coding sequences marked in gray.

Figure 2

Position of splicing enhancers and silencers as well as the proteins that target these sites. Notes: Negative regulation sites are marked in orange, whereas positive regulators of splicing are marked in green. The sequences of the acceptor sites as well as their positions and the regulatory elements and factors associated with each site are given in the table below the figure. Abbreviations: ESS, exonic splicing silencer; ESE, exonic splicing enhancer; ESSV, exonic splicing silencer; hnRNP, heterogeneous nuclear ribonucleoprotein; ISS, intronic splicing silencer; GAR, guanosine–adenosine rich.

Figure 3

List of SR proteins involved in splicing and their domain structure. Note: The function of each SR protein and its HIV binding sites are given in the table below the figure. Abbreviations: ESE, exonic splicing enhancer; GAR, guanosine–adenosine rich.

Figure 4

Members of the hnRNP protein family and their domain structure. Note: The general function served by each of these domains in hnRNP protein family is given in table below the figure. Abbreviation: hnRNP, heterogeneous nuclear ribonucleoprotein.

Figure 5

A summary of the splicing pathways in HIV. Notes: During the early phase, unspliced RNA is exported through association with Rev, where it associates with the ribosome and is translated into Gagpol and Gag proteins. Partially spliced mRNAs are also exported and translated into proteins Env, Vpr, Vif, and Tat. During the late phase of viral infection, multiple spliced mRNAs are exported to the cytoplasm where they are translated into Tat, Vpu, Nef, and Rev.