Abstract
Herpes simplex virus type 1 latent infection in sensory neurons is characterized by the highly restricted transcription of viral genes. The latency-associated transcripts (LAT) family members are the only transcripts that can be identified in large amounts in latently infected cells. The most abundant LAT species is a 2-kb RNA that results from splicing of a rare primary transcript. Analysis of a LAT mutant virus (TB1) in cell culture revealed an aberrant splicing pattern and production of a stable small (0.95-kb) LAT intron. A panel of deletion constructs expressing truncated LAT in transiently transfected cells mapped the region influencing stability to the 3' end of the LAT intron. This region encompasses the branch point and a putative stable stem-loop hairpin structure immediately upstream of the splice acceptor consensus polypyrimidine tract. Mutagenic analysis of the sequence in this region confirmed our hypothesis that the stem-loop structure is important for efficient splicing by influencing the selection of a nonconsensus branch point. Changes in this structure correlate with changes in branch point selection and production of an unstable 2-kb LAT.
Full Text
The Full Text of this article is available as a PDF (728.6 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Arenas J., Hurwitz J. Purification of a RNA debranching activity from HeLa cells. J Biol Chem. 1987 Mar 25;262(9):4274–4279. [PubMed] [Google Scholar]
- Block T. M., Deshmane S., Masonis J., Maggioncalda J., Valyi-Nagi T., Fraser N. W. An HSV LAT null mutant reactivates slowly from latent infection and makes small plaques on CV-1 monolayers. Virology. 1993 Feb;192(2):618–630. doi: 10.1006/viro.1993.1078. [DOI] [PubMed] [Google Scholar]
- Block T. M., Spivack J. G., Steiner I., Deshmane S., McIntosh M. T., Lirette R. P., Fraser N. W. A herpes simplex virus type 1 latency-associated transcript mutant reactivates with normal kinetics from latent infection. J Virol. 1990 Jul;64(7):3417–3426. doi: 10.1128/jvi.64.7.3417-3426.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bloom D. C., Hill J. M., Devi-Rao G., Wagner E. K., Feldman L. T., Stevens J. G. A 348-base-pair region in the latency-associated transcript facilitates herpes simplex virus type 1 reactivation. J Virol. 1996 Apr;70(4):2449–2459. doi: 10.1128/jvi.70.4.2449-2459.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Carter K. L., Roizman B. Alternatively spliced mRNAs predicted to yield frame-shift proteins and stable intron 1 RNAs of the herpes simplex virus 1 regulatory gene alpha 0 accumulate in the cytoplasm of infected cells. Proc Natl Acad Sci U S A. 1996 Oct 29;93(22):12535–12540. doi: 10.1073/pnas.93.22.12535. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Castanotto D., Rossi J. J. Small sequence insertions within the branch point region dictate alternative sites of lariat formation in a yeast intron. Nucleic Acids Res. 1992 Dec 25;20(24):6649–6655. doi: 10.1093/nar/20.24.6649. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chapman K. B., Boeke J. D. Isolation and characterization of the gene encoding yeast debranching enzyme. Cell. 1991 May 3;65(3):483–492. doi: 10.1016/0092-8674(91)90466-c. [DOI] [PubMed] [Google Scholar]
- Deatly A. M., Spivack J. G., Lavi E., Fraser N. W. RNA from an immediate early region of the type 1 herpes simplex virus genome is present in the trigeminal ganglia of latently infected mice. Proc Natl Acad Sci U S A. 1987 May;84(10):3204–3208. doi: 10.1073/pnas.84.10.3204. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Deatly A. M., Spivack J. G., Lavi E., O'Boyle D. R., 2nd, Fraser N. W. Latent herpes simplex virus type 1 transcripts in peripheral and central nervous system tissues of mice map to similar regions of the viral genome. J Virol. 1988 Mar;62(3):749–756. doi: 10.1128/jvi.62.3.749-756.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Devi-Rao G. B., Goodart S. A., Hecht L. M., Rochford R., Rice M. K., Wagner E. K. Relationship between polyadenylated and nonpolyadenylated herpes simplex virus type 1 latency-associated transcripts. J Virol. 1991 May;65(5):2179–2190. doi: 10.1128/jvi.65.5.2179-2190.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dobson A. T., Sederati F., Devi-Rao G., Flanagan W. M., Farrell M. J., Stevens J. G., Wagner E. K., Feldman L. T. Identification of the latency-associated transcript promoter by expression of rabbit beta-globin mRNA in mouse sensory nerve ganglia latently infected with a recombinant herpes simplex virus. J Virol. 1989 Sep;63(9):3844–3851. doi: 10.1128/jvi.63.9.3844-3851.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Doerig C., Pizer L. I., Wilcox C. L. An antigen encoded by the latency-associated transcript in neuronal cell cultures latently infected with herpes simplex virus type 1. J Virol. 1991 May;65(5):2724–2727. doi: 10.1128/jvi.65.5.2724-2727.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Dominski Z., Kole R. Identification and characterization by antisense oligonucleotides of exon and intron sequences required for splicing. Mol Cell Biol. 1994 Nov;14(11):7445–7454. doi: 10.1128/mcb.14.11.7445. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Estes P. A., Cooke N. E., Liebhaber S. A. A native RNA secondary structure controls alternative splice-site selection and generates two human growth hormone isoforms. J Biol Chem. 1992 Jul 25;267(21):14902–14908. [PubMed] [Google Scholar]
- Farrell M. J., Dobson A. T., Feldman L. T. Herpes simplex virus latency-associated transcript is a stable intron. Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):790–794. doi: 10.1073/pnas.88.3.790. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Fraser N. W., Block T. M., Spivack J. G. The latency-associated transcripts of herpes simplex virus: RNA in search of function. Virology. 1992 Nov;191(1):1–8. doi: 10.1016/0042-6822(92)90160-q. [DOI] [PubMed] [Google Scholar]
- Fraser N. W., Spivack J. G., Wroblewska Z., Block T., Deshmane S. L., Valyi-Nagy T., Natarajan R., Gesser R. M. A review of the molecular mechanism of HSV-1 latency. Curr Eye Res. 1991;10 (Suppl):1–13. doi: 10.3109/02713689109020352. [DOI] [PubMed] [Google Scholar]
- Gaur R. K., Valcárcel J., Green M. R. Sequential recognition of the pre-mRNA branch point by U2AF65 and a novel spliceosome-associated 28-kDa protein. RNA. 1995 Jun;1(4):407–417. [PMC free article] [PubMed] [Google Scholar]
- Goguel V., Wang Y., Rosbash M. Short artificial hairpins sequester splicing signals and inhibit yeast pre-mRNA splicing. Mol Cell Biol. 1993 Nov;13(11):6841–6848. doi: 10.1128/mcb.13.11.6841. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hara T., Ichihara M., Takagi M., Miyajima A. Interleukin-3 (IL-3) poor-responsive inbred mouse strains carry the identical deletion of a branch point in the IL-3 receptor alpha subunit gene. Blood. 1995 May 1;85(9):2331–2336. [PubMed] [Google Scholar]
- Hill J. M., Sedarati F., Javier R. T., Wagner E. K., Stevens J. G. Herpes simplex virus latent phase transcription facilitates in vivo reactivation. Virology. 1990 Jan;174(1):117–125. doi: 10.1016/0042-6822(90)90060-5. [DOI] [PubMed] [Google Scholar]
- Jacquier A., Rosbash M. RNA splicing and intron turnover are greatly diminished by a mutant yeast branch point. Proc Natl Acad Sci U S A. 1986 Aug;83(16):5835–5839. doi: 10.1073/pnas.83.16.5835. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kuivenhoven J. A., Weibusch H., Pritchard P. H., Funke H., Benne R., Assmann G., Kastelein J. J. An intronic mutation in a lariat branchpoint sequence is a direct cause of an inherited human disorder (fish-eye disease). J Clin Invest. 1996 Jul 15;98(2):358–364. doi: 10.1172/JCI118800. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Leib D. A., Bogard C. L., Kosz-Vnenchak M., Hicks K. A., Coen D. M., Knipe D. M., Schaffer P. A. A deletion mutant of the latency-associated transcript of herpes simplex virus type 1 reactivates from the latent state with reduced frequency. J Virol. 1989 Jul;63(7):2893–2900. doi: 10.1128/jvi.63.7.2893-2900.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol. 1988 Jul;69(Pt 7):1531–1574. doi: 10.1099/0022-1317-69-7-1531. [DOI] [PubMed] [Google Scholar]
- McGeoch D. J., Dalrymple M. A., Davison A. J., Dolan A., Frame M. C., McNab D., Perry L. J., Scott J. E., Taylor P. The complete DNA sequence of the long unique region in the genome of herpes simplex virus type 1. J Gen Virol. 1988 Jul;69(Pt 7):1531–1574. doi: 10.1099/0022-1317-69-7-1531. [DOI] [PubMed] [Google Scholar]
- Mitchell W. J., Lirette R. P., Fraser N. W. Mapping of low abundance latency-associated RNA in the trigeminal ganglia of mice latently infected with herpes simplex virus type 1. J Gen Virol. 1990 Jan;71(Pt 1):125–132. doi: 10.1099/0022-1317-71-1-125. [DOI] [PubMed] [Google Scholar]
- Nam K., Hudson R. H., Chapman K. B., Ganeshan K., Damha M. J., Boeke J. D. Yeast lariat debranching enzyme. Substrate and sequence specificity. J Biol Chem. 1994 Aug 12;269(32):20613–20621. [PubMed] [Google Scholar]
- Norton P. A. Polypyrimidine tract sequences direct selection of alternative branch sites and influence protein binding. Nucleic Acids Res. 1994 Sep 25;22(19):3854–3860. doi: 10.1093/nar/22.19.3854. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Perng G. C., Ghiasi H., Slanina S. M., Nesburn A. B., Wechsler S. L. The spontaneous reactivation function of the herpes simplex virus type 1 LAT gene resides completely within the first 1.5 kilobases of the 8.3-kilobase primary transcript. J Virol. 1996 Feb;70(2):976–984. doi: 10.1128/jvi.70.2.976-984.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Qian L., Vu M. N., Carter M., Wilkinson M. F. A spliced intron accumulates as a lariat in the nucleus of T cells. Nucleic Acids Res. 1992 Oct 25;20(20):5345–5350. doi: 10.1093/nar/20.20.5345. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Query C. C., Strobel S. A., Sharp P. A. Three recognition events at the branch-site adenine. EMBO J. 1996 Mar 15;15(6):1392–1402. [PMC free article] [PubMed] [Google Scholar]
- Ris-Stalpers C., Verleun-Mooijman M. C., de Blaeij T. J., Degenhart H. J., Trapman J., Brinkmann A. O. Differential splicing of human androgen receptor pre-mRNA in X-linked Reifenstein syndrome, because of a deletion involving a putative branch site. Am J Hum Genet. 1994 Apr;54(4):609–617. [PMC free article] [PubMed] [Google Scholar]
- Roizman B., Sears A. E. An inquiry into the mechanisms of herpes simplex virus latency. Annu Rev Microbiol. 1987;41:543–571. doi: 10.1146/annurev.mi.41.100187.002551. [DOI] [PubMed] [Google Scholar]
- Roscigno R. F., Weiner M., Garcia-Blanco M. A. A mutational analysis of the polypyrimidine tract of introns. Effects of sequence differences in pyrimidine tracts on splicing. J Biol Chem. 1993 May 25;268(15):11222–11229. [PubMed] [Google Scholar]
- Rødahl E., Haarr L. Analysis of the 2-kilobase latency-associated transcript expressed in PC12 cells productively infected with herpes simplex virus type 1: evidence for a stable, nonlinear structure. J Virol. 1997 Feb;71(2):1703–1707. doi: 10.1128/jvi.71.2.1703-1707.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Saini K. S., Summerhayes I. C., Thomas P. Molecular events regulating messenger RNA stability in eukaryotes. Mol Cell Biochem. 1990 Jul 17;96(1):15–23. doi: 10.1007/BF00228449. [DOI] [PubMed] [Google Scholar]
- Sawtell N. M., Thompson R. L. Herpes simplex virus type 1 latency-associated transcription unit promotes anatomical site-dependent establishment and reactivation from latency. J Virol. 1992 Apr;66(4):2157–2169. doi: 10.1128/jvi.66.4.2157-2169.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schang L. M., Hossain A., Jones C. The latency-related gene of bovine herpesvirus 1 encodes a product which inhibits cell cycle progression. J Virol. 1996 Jun;70(6):3807–3814. doi: 10.1128/jvi.70.6.3807-3814.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Solnick D. Alternative splicing caused by RNA secondary structure. Cell. 1985 Dec;43(3 Pt 2):667–676. doi: 10.1016/0092-8674(85)90239-9. [DOI] [PubMed] [Google Scholar]
- Spivack J. G., Fraser N. W. Detection of herpes simplex virus type 1 transcripts during latent infection in mice. J Virol. 1987 Dec;61(12):3841–3847. doi: 10.1128/jvi.61.12.3841-3847.1987. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spivack J. G., Fraser N. W. Expression of herpes simplex virus type 1 (HSV-1) latency-associated transcripts and transcripts affected by the deletion in avirulent mutant HFEM: evidence for a new class of HSV-1 genes. J Virol. 1988 Sep;62(9):3281–3287. doi: 10.1128/jvi.62.9.3281-3287.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spivack J. G., Fraser N. W. Expression of herpes simplex virus type 1 latency-associated transcripts in the trigeminal ganglia of mice during acute infection and reactivation of latent infection. J Virol. 1988 May;62(5):1479–1485. doi: 10.1128/jvi.62.5.1479-1485.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Spivack J. G., Woods G. M., Fraser N. W. Identification of a novel latency-specific splice donor signal within the herpes simplex virus type 1 2.0-kilobase latency-associated transcript (LAT): translation inhibition of LAT open reading frames by the intron within the 2.0-kilobase LAT. J Virol. 1991 Dec;65(12):6800–6810. doi: 10.1128/jvi.65.12.6800-6810.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Staffa A., Cochrane A. The tat/rev intron of human immunodeficiency virus type 1 is inefficiently spliced because of suboptimal signals in the 3' splice site. J Virol. 1994 May;68(5):3071–3079. doi: 10.1128/jvi.68.5.3071-3079.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Steiner I., Spivack J. G., Lirette R. P., Brown S. M., MacLean A. R., Subak-Sharpe J. H., Fraser N. W. Herpes simplex virus type 1 latency-associated transcripts are evidently not essential for latent infection. EMBO J. 1989 Feb;8(2):505–511. doi: 10.1002/j.1460-2075.1989.tb03404.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Steiner I., Spivack J. G., O'Boyle D. R., 2nd, Lavi E., Fraser N. W. Latent herpes simplex virus type 1 transcription in human trigeminal ganglia. J Virol. 1988 Sep;62(9):3493–3496. doi: 10.1128/jvi.62.9.3493-3496.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stevens J. G. Human herpesviruses: a consideration of the latent state. Microbiol Rev. 1989 Sep;53(3):318–332. doi: 10.1128/mr.53.3.318-332.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Stevens J. G., Wagner E. K., Devi-Rao G. B., Cook M. L., Feldman L. T. RNA complementary to a herpesvirus alpha gene mRNA is prominent in latently infected neurons. Science. 1987 Feb 27;235(4792):1056–1059. doi: 10.1126/science.2434993. [DOI] [PubMed] [Google Scholar]
- Trousdale M. D., Steiner I., Spivack J. G., Deshmane S. L., Brown S. M., MacLean A. R., Subak-Sharpe J. H., Fraser N. W. In vivo and in vitro reactivation impairment of a herpes simplex virus type 1 latency-associated transcript variant in a rabbit eye model. J Virol. 1991 Dec;65(12):6989–6993. doi: 10.1128/jvi.65.12.6989-6993.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wagner E. K., Devi-Rao G., Feldman L. T., Dobson A. T., Zhang Y. F., Flanagan W. M., Stevens J. G. Physical characterization of the herpes simplex virus latency-associated transcript in neurons. J Virol. 1988 Apr;62(4):1194–1202. doi: 10.1128/jvi.62.4.1194-1202.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wagner E. K., Flanagan W. M., Devi-Rao G., Zhang Y. F., Hill J. M., Anderson K. P., Stevens J. G. The herpes simplex virus latency-associated transcript is spliced during the latent phase of infection. J Virol. 1988 Dec;62(12):4577–4585. doi: 10.1128/jvi.62.12.4577-4585.1988. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wu T. T., Su Y. H., Block T. M., Taylor J. M. Evidence that two latency-associated transcripts of herpes simplex virus type 1 are nonlinear. J Virol. 1996 Sep;70(9):5962–5967. doi: 10.1128/jvi.70.9.5962-5967.1996. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zabolotny J. M., Krummenacher C., Fraser N. W. The herpes simplex virus type 1 2.0-kilobase latency-associated transcript is a stable intron which branches at a guanosine. J Virol. 1997 Jun;71(6):4199–4208. doi: 10.1128/jvi.71.6.4199-4208.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Zwaagstra J. C., Ghiasi H., Slanina S. M., Nesburn A. B., Wheatley S. C., Lillycrop K., Wood J., Latchman D. S., Patel K., Wechsler S. L. Activity of herpes simplex virus type 1 latency-associated transcript (LAT) promoter in neuron-derived cells: evidence for neuron specificity and for a large LAT transcript. J Virol. 1990 Oct;64(10):5019–5028. doi: 10.1128/jvi.64.10.5019-5028.1990. [DOI] [PMC free article] [PubMed] [Google Scholar]