Conserved Stem-loop Structures in the HIV-1 RNA Region Containing the A3 3' Splice Site and Its Cis-regulatory Element: Possible Involvement in RNA Splicing

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2001 Jan 5

PMID 11139617

Citations 46

Authors

S Jacquenet

D Ropers

P S Bilodeau

L Damier

A Mougin

C M Stoltzfus

C Branlant

Affiliations

Soon will be listed here.

Abstract

The HIV-1 transcript is alternatively spliced to over 30 different mRNAs. Whether RNA secondary structure can influence HIV-1 RNA alternative splicing has not previously been examined. Here we have determined the secondary structure of the HIV-1/BRU RNA segment, containing the alternative A3, A4a, A4b, A4c and A5 3' splice sites. Site A3, required for tat mRNA production, is contained in the terminal loop of a stem-loop structure (SLS2), which is highly conserved in HIV-1 and related SIVcpz strains. The exon splicing silencer (ESS2) acting on site A3 is located in a long irregular stem-loop structure (SLS3). Two SLS3 domains were protected by nuclear components under splicing condition assays. One contains the A4c branch points and a putative SR protein binding site. The other one is adjacent to ESS2. Unexpectedly, only the 3' A residue of ESS2 was protected. The suboptimal A3 polypyrimidine tract (PPT) is base paired. Using site-directed mutagenesis and transfection of a mini-HIV-1 cDNA into HeLa cells, we found that, in a wild-type PPT context, a mutation of the A3 downstream sequence that reinforced SLS2 stability decreased site A3 utilization. This was not the case with an optimized PPT. Hence, sequence and secondary structure of the PPT may cooperate in limiting site A3 utilization.

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References

Nour M, Naimi A, Beck G, Branlant C . 16S-23S and 23S-5S intergenic spacer regions of Streptococcus thermophilus and Streptococcus salivarius, primary and secondary structure. Curr Microbiol. 1995; 31(5):270-8. DOI: 10.1007/BF00314579. View

Amendt B, Si Z, Stoltzfus C . Presence of exon splicing silencers within human immunodeficiency virus type 1 tat exon 2 and tat-rev exon 3: evidence for inhibition mediated by cellular factors. Mol Cell Biol. 1995; 15(11):6480. PMC: 230899. DOI: 10.1128/MCB.15.11.6480. View

OReilly M, McNally M, Beemon K . Two strong 5' splice sites and competing, suboptimal 3' splice sites involved in alternative splicing of human immunodeficiency virus type 1 RNA. Virology. 1995; 213(2):373-85. DOI: 10.1006/viro.1995.0010. View

Charpentier B, Rosbash M . Intramolecular structure in yeast introns aids the early steps of in vitro spliceosome assembly. RNA. 1996; 2(6):509-22. PMC: 1369391. View

Mougin A, Gregoire A, Banroques J, Segault V, Fournier R, Brule F . Secondary structure of the yeast Saccharomyces cerevisiae pre-U3A snoRNA and its implication for splicing efficiency. RNA. 1996; 2(11):1079-93. PMC: 1369438. View

Si Z, Amendt B, Stoltzfus C . Splicing efficiency of human immunodeficiency virus type 1 tat RNA is determined by both a suboptimal 3' splice site and a 10 nucleotide exon splicing silencer element located within tat exon 2. Nucleic Acids Res. 1997; 25(4):861-7. PMC: 146521. DOI: 10.1093/nar/25.4.861. View

Chabot B, Blanchette M, Lapierre I, La Branche H . An intron element modulating 5' splice site selection in the hnRNP A1 pre-mRNA interacts with hnRNP A1. Mol Cell Biol. 1997; 17(4):1776-86. PMC: 232024. DOI: 10.1128/MCB.17.4.1776. View

Shi H, Hoffman B, Lis J . A specific RNA hairpin loop structure binds the RNA recognition motifs of the Drosophila SR protein B52. Mol Cell Biol. 1997; 17(5):2649-57. PMC: 232115. DOI: 10.1128/MCB.17.5.2649. View

Damier L, Domenjoud L, Branlant C . The D1-A2 and D2-A2 pairs of splice sites from human immunodeficiency virus type 1 are highly efficient in vitro, in spite of an unusual branch site. Biochem Biophys Res Commun. 1997; 237(1):182-7. DOI: 10.1006/bbrc.1997.7091. View

10.

Frankel A, Young J . HIV-1: fifteen proteins and an RNA. Annu Rev Biochem. 1998; 67:1-25. DOI: 10.1146/annurev.biochem.67.1.1. View

11.

Swanson A, Stoltzfus C . Overlapping cis sites used for splicing of HIV-1 env/nef and rev mRNAs. J Biol Chem. 1998; 273(51):34551-7. DOI: 10.1074/jbc.273.51.34551. View

12.

Olive M, Gesnel M, Breathnach R . hnRNP A1 recruited to an exon in vivo can function as an exon splicing silencer. Mol Cell Biol. 1998; 19(1):251-60. PMC: 83883. DOI: 10.1128/MCB.19.1.251. View

13.

Gao F, Bailes E, Robertson D, Chen Y, Rodenburg C, Michael S . Origin of HIV-1 in the chimpanzee Pan troglodytes troglodytes. Nature. 1999; 397(6718):436-41. DOI: 10.1038/17130. View

14.

Muro A, Caputi M, Pariyarath R, Pagani F, Buratti E, Baralle F . Regulation of fibronectin EDA exon alternative splicing: possible role of RNA secondary structure for enhancer display. Mol Cell Biol. 1999; 19(4):2657-71. PMC: 84059. DOI: 10.1128/MCB.19.4.2657. View

15.

Handa N, Nureki O, Kurimoto K, Kim I, Sakamoto H, Shimura Y . Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein. Nature. 1999; 398(6728):579-85. DOI: 10.1038/19242. View

16.

Ding J, Hayashi M, Zhang Y, Manche L, Krainer A, Xu R . Crystal structure of the two-RRM domain of hnRNP A1 (UP1) complexed with single-stranded telomeric DNA. Genes Dev. 1999; 13(9):1102-15. PMC: 316951. DOI: 10.1101/gad.13.9.1102. View

17.

Caputi M, Mayeda A, Krainer A, Zahler A . hnRNP A/B proteins are required for inhibition of HIV-1 pre-mRNA splicing. EMBO J. 1999; 18(14):4060-7. PMC: 1171481. DOI: 10.1093/emboj/18.14.4060. View

18.

Bilodeau P, Domsic J, Stoltzfus C . Splicing regulatory elements within tat exon 2 of human immunodeficiency virus type 1 (HIV-1) are characteristic of group M but not group O HIV-1 strains. J Virol. 1999; 73(12):9764-72. PMC: 113023. DOI: 10.1128/JVI.73.12.9764-9772.1999. View

19.

Guth S, Martinez C, Gaur R, Valcarcel J . Evidence for substrate-specific requirement of the splicing factor U2AF(35) and for its function after polypyrimidine tract recognition by U2AF(65). Mol Cell Biol. 1999; 19(12):8263-71. PMC: 84910. DOI: 10.1128/MCB.19.12.8263. View

20.

Wu S, Romfo C, Nilsen T, Green M . Functional recognition of the 3' splice site AG by the splicing factor U2AF35. Nature. 2000; 402(6763):832-5. DOI: 10.1038/45590. View