1887

Abstract

Human immunodeficiency virus type 1 (HIV-1) splicing has to be strictly controlled to ensure the balanced production of the unspliced and all differently spliced viral RNAs. Splicing at the major 5′ splice site (5′ss) that is used for the synthesis of all spliced RNAs is modulated by the local RNA structure and binding of regulatory SR proteins. Here, we demonstrate that the suboptimal sequence complementarity between this 5′ss and U1 small nuclear RNA (snRNA) also contributes to prevent excessive splicing. Analysis of a large set of HIV-1 sequences revealed that all three regulatory features of the 5′ss region (RNA structure, SR protein binding and sequence complementarity with U1 snRNA) are highly conserved amongst virus isolates, which supports their importance. Combined mutations that destabilize the local RNA structure, remove binding sites for inhibitory SR proteins and optimize the U1 snRNA complementarity resulted in almost complete splicing and accordingly reduced virus replication.

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2015-11-01
2019-12-13
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References

  1. Abbink T.E., Berkhout B.. ( 2008;). RNA structure modulates splicing efficiency at the human immunodeficiency virus type 1 major splice donor. J Virol 82: 3090–3098 [CrossRef] [PubMed].
    [Google Scholar]
  2. Asang C., Erkelenz S., Schaal H.. ( 2012;). The HIV-1 major splice donor D1 is activated by splicing enhancer elements within the leader region and the p17-inhibitory sequence. Virology 432: 133–145 [CrossRef] [PubMed].
    [Google Scholar]
  3. Cartegni L., Wang J., Zhu Z., Zhang M.Q., Krainer A.R.. ( 2003;). ESEfinder: a web resource to identify exonic splicing enhancers. Nucleic Acids Res 31: 3568–3571 [CrossRef] [PubMed].
    [Google Scholar]
  4. Das A.T., Verhoef K., Berkhout B.. ( 2004a;). A conditionally replicating virus as a novel approach toward an HIV vaccine. Methods Enzymol 388: 359–379 [CrossRef] [PubMed].
    [Google Scholar]
  5. Das A.T., Zhou X., Vink M., Klaver B., Verhoef K., Marzio G., Berkhout B.. ( 2004b;). Viral evolution as a tool to improve the tetracycline-regulated gene expression system. J Biol Chem 279: 18776–18782 [CrossRef] [PubMed].
    [Google Scholar]
  6. Freund M., Asang C., Kammler S., Konermann C., Krummheuer J., Hipp M., Meyer I., Gierling W., Theiss S., other authors. ( 2003;). A novel approach to describe a U1 snRNA binding site. Nucleic Acids Res 31: 6963–6975 [CrossRef] [PubMed].
    [Google Scholar]
  7. Mueller N., van Bel N., Berkhout B., Das A.T.. ( 2014;). HIV-1 splicing at the major splice donor site is restricted by RNA structure. Virology 468–470: 609–620 [CrossRef] [PubMed].
    [Google Scholar]
  8. Mueller N., Berkhout B., Das A.T.. ( 2015;). HIV-1 splicing is controlled by local RNA structure and binding of splicing regulatory proteins at the major 5′ splice site. J Gen Virol 96: 1906–1917 [CrossRef] [PubMed].
    [Google Scholar]
  9. Roca X., Krainer A.R., Eperon I.C.. ( 2013;). Pick one, but be quick: 5′ splice sites and the problems of too many choices. Genes Dev 27: 129–144 [CrossRef] [PubMed].
    [Google Scholar]
  10. Smith P.J., Zhang C., Wang J., Chew S.L., Zhang M.Q., Krainer A.R.. ( 2006;). An increased specificity score matrix for the prediction of SF2/ASF-specific exonic splicing enhancers. Hum Mol Genet 15: 2490–2508 [CrossRef] [PubMed].
    [Google Scholar]
  11. Zuker M.. ( 2003;). Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res 31: 3406–3415 [CrossRef] [PubMed].
    [Google Scholar]
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