Role of Cellular RNA Processing Factors in Human Immunodeficiency Virus Type 1 mRNA Metabolism, Replication, and Infectivity

Jablonski, Joseph; Caputi, Massimo

doi:10.1128/jvi.01801-08

Cited by 98 publications

(115 citation statements)

References 42 publications

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“…In line with this, knockdown of these splicing factors with small interfering RNA shows an inverse effect and results in mRNAs in which exon 3 skips, indicating that these proteins drive splicing toward 3=ss A2 (47,48). Similarly, the ESS2p silencer downstream of 3=ss A3 (49) and the interaction of U1 snRNP with exon 6D 5=ss are regulated by hnRNPs F and H (50).…”

mentioning

confidence: 74%

An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of vif mRNA

Widera

Erkelenz

Hillebrand

et al. 2013

J Virol

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Within target T lymphocytes, human immunodeficiency virus type I (HIV-1) encounters the retroviral restriction factor APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), which is counteracted by the HIV-1 accessory protein Vif. Vif is encoded by intron-containing viral RNAs that are generated by splicing at 3= splice site (3=ss) A1 but lack splicing at 5=ss D2, which results in the retention of a large downstream intron. Hence, the extents of activation of 3=ss A1 and repression of D2, respectively, determine the levels of vif mRNA and thus the ability to evade A3G-mediated antiviral effects. The use of 3=ss A1 can be enhanced or repressed by splicing regulatory elements that control the recognition of downstream 5=ss D2. Here we show that an intronic G run (G I2 -1) represses the use of a second 5=ss, termed D2b, that is embedded within intron 2 and, as determined by RNA deep-sequencing analysis, is normally inefficiently used. Mutations of G I2 -1 and activation of D2b led to the generation of transcripts coding for Gp41 and Rev protein isoforms but primarily led to considerable upregulation of vif mRNA expression. We further demonstrate, however, that higher levels of Vif protein are actually detrimental to viral replication in A3G-expressing T cell lines but not in A3G-deficient cells. These observations suggest that an appropriate ratio of Vifto-A3G protein levels is required for optimal virus replication and that part of Vif level regulation is effected by the novel G run identified here. R eplication of human immunodeficiency virus type 1 (HIV-1) is counteracted by four major classes of host-encoded restriction factors: APOBEC3G (apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3G; A3G), TRIM5␣ (tripartite motif 5␣), tetherin (BST-2, CD317, or HM1.24), and SAMHD1 (1-4). A3G (5) belongs to a family of cytidine deaminases that includes seven members (A3A to A3D and A3F to A3H) located in a gene cluster on chromosome 22 (6-8). It is encapsidated into newly assembled virions and introduces C-to-U substitutions during minus-strand synthesis, resulting in G-to-A hypermutations and aberrant DNA ends in the HIV-1 genome. Furthermore, A3G, independent of its deaminase activity, inhibits reverse transcriptase-mediated minus-strand elongation by direct binding to the viral RNA (9). This leads to massive impairment of viral replication (10). However, the HIV-1-encoded accessory protein Vif counteracts A3G by direct interaction, by inducing proteasomal degradation, and by repression of mRNA synthesis (10). Whereas HIV-1 is able to replicate efficiently in A3G-expressing cells, Vifdeficient virus strains are completely suppressed (5). Nevertheless, a narrowly restricted level of Vif is crucial for optimal HIV-1 replication since proteolytic processing of the Gag precursor at the p2/nucleocapsid processing site is inhibited by high levels of Vif (11).During the course of infection, the HIV-1 9-kb single-sense pre-mRNA is processed into more than 40 alternatively spliced m...

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mentioning

confidence: 74%

An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of vif mRNA

Widera

Erkelenz

Hillebrand

et al. 2013

J Virol

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“…In HIV-1-infected cells, levels of various SR proteins may change during the infection (44), or HIV-1 has adapted to the intracellular levels of SR proteins in T cells and monocyte/ macrophages to optimize production of sufficient quantities of each alternatively spliced HIV-1 mRNA. Nevertheless, it is clear that HIV-1 alternative splicing and virus production are sensitive to minor changes in intracellular concentrations of various SR proteins (40,45).…”

Section: Discussionmentioning

confidence: 99%

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

Tranell

Fenyõ

Schwartz

2010

Journal of Biological Chemistry

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HIV-1 non-coding exon 3 can either be spliced to exons 4, 4a, 4b, 4c, and 5 to generate tat, rev, and nef mRNAs or remain unspliced to produce the 13a7 vpr mRNA. Here we show that serine-and arginine-rich proteins 55 and 75 (SRp55 and SRp75) inhibit splicing from the 5-splice site of exon 3 thereby causing an accumulation of the partially unspliced 13a7 vpr mRNA. In contrast, serineand arginine-rich protein 40 (SRp40) induces splicing from exon 3 to exon 4, thereby promoting the production of the 1347 tat mRNA. We demonstrate that SRp55 stimulates vpr mRNA production by interacting with the previously identified HIV-1 splicing enhancer named GAR and inhibiting its function. This inhibition requires both serine arginine-rich and RNA-binding domains of SRp55, indicating that production of HIV-1 vpr mRNA depends on the interaction of SRp55 with an unknown factor.To produce all the mRNAs that are needed for HIV-1 to be infectious it uses alternative splicing. The full-length 9-kb transcript contains several splice sites, including four 5Ј-splice sites, also called splice donors (SD1-4) 2 and eight 3Ј-splice sites, also called splice acceptors (SA2-3, -4a-c, -5, and -7) (supplemental Fig. 1A), which can all be used in different combinations to create more than 35 differently spliced mRNAs (supplemental Fig. 1, B and C) (1-6). Cloning and expression of individual HIV-1 mRNAs have revealed that mRNAs spliced to SA3 produce Vpr, those spliced to SA4 produce Tat, those spliced to SA4a and -4b produce Rev and Nef, and those spliced to SA5 produce Nef (1,2,7,8). mRNAs spliced to SA2 are believed to produce Vif (5, 7). Two additional mRNAs that are believed to produce Rev and Nef are spliced to SA4c or to SA7, respectively (4). To produce the correct amounts of all mRNAs, the splice acceptors in HIV-1 are sub-optimal because of short and interrupted polypyrimidine tracts, non-canonical branch points, and inhibitory sequences that down-regulate the usage of several splice sites (6, 9 -13).Enhancer or silencer sequences regulate alternative splicing by up-regulating or down-regulating the usage of a splice site (14). 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). Two silencers in exon 4, named ESS2 and ESS2p, inhibit splicing into exon 4 thereby inhibiting the production of tat mRNA (18,19). SA7 is used by all mRNAs in the 2-kb class. In exon 7 a silencer called ESS3 blocks U2 small nuclear ribonucleoprotein, thereby suppressing SA7 (19 -21). An intronic silencer that blocks SA7 is located in the intron, directly upstream of exon 7 (22). An enhancer element called ESE3 that activates SA7 is located close to ESS3 in exon 7 (9, 21, 23). An enhancer in exon 4 has been named ESE2, because it attenuates ESS2 and thereby enhances splicing into SA4 (24)...

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“…23 Additional roles for hnRNP A1 and other hnRNPs in retroviral splicing regulation rely largely on their ability to bind sequences adjacent to and within splicing enhancer and negative splicing regulatory sequences. 18,24,25 These roles in retroviral RNA splicing and nucleocytoplasmic ReseARch PAPeR trafficking might also be functionally linked 26 a notion that is supported by newer work that shows that several functionally distinct hnRNPs interact with Rev. 27 Although principally nuclear, several hnRNPs indeed have cytoplasmic functions that contribute to the localization, the utilization, and fate of RNA in the cell.…”

Section: Introductionmentioning

confidence: 77%

Depletion of hnRNP A2/B1 overrides the nuclear retention of the HIV-1 genomic RNA

et al. 2013

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hnRNP A2 is a cellular protein that is important for nucleocytoplasmic and cytosolic trafficking of the hIV-1 genomic RNA. Both hnRNP A2's interaction with hIV-1 RNA and its expression levels influence the activities of Rev in mediating nucleocytoplasmic export of the hIV-1 genomic RNA. While the lack of Rev expression during hIV-1 gene expression results in nuclear retention of hIV-1 genomic RNA, we show here by fluorescence in situ hybridization and fractionation studies that the genomic RNA translocates to the cytoplasm when hnRNP A2/B1 are depleted from cells. Polyribosome analyses revealed that the genomic RNA was shunted into a cytoplasmic, dense polyribosomal fraction. This fraction contained several RNA-binding proteins involved in viral gene expression and RNA trafficking but did not contain the translation initiation factor, eIF4G1. Amino acid incorporation into nascent polypeptides in this fraction was also greatly reduced, demonstrating that this fraction contains mRNAs that are poorly translated. These results demonstrate that hnRNP A2/B1 expression plays roles in the nuclear retention of the hIV-1 genomic RNA in the absence of Rev and in the release of the genomic RNA from translationally inactive, cytoplasmic RNP complexes.

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Role of Cellular RNA Processing Factors in Human Immunodeficiency Virus Type 1 mRNA Metabolism, Replication, and Infectivity

Cited by 98 publications

References 42 publications

An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of vif mRNA

An Intronic G Run within HIV-1 Intron 2 Is Critical for Splicing Regulation of vif mRNA

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

Depletion of hnRNP A2/B1 overrides the nuclear retention of the HIV-1 genomic RNA

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