Mutations in the U5 Region Adjacent to the Primer Binding Site Affect TRNA Cleavage by Human Immunodeficiency Virus Type 1 Reverse Transcriptase in Vivo

Overview

Journal J Virol

Publisher American Society for Microbiology

Date 2007 Nov 9

PMID 17989171

Citations 12

Authors

Jangsuk Oh

Mary Jane McWilliams

John G Julias

Stephen H Hughes

Affiliations

Soon will be listed here.

Abstract

In retroviruses, the first nucleotide added to the tRNA primer defines the end of the U5 region in the right long terminal repeat, and the subsequent removal of this tRNA primer by RNase H exactly defines the U5 end of the linear double-stranded DNA. In most retroviruses, the entire tRNA is removed by RNase H cleavage at the RNA/DNA junction. However, the RNase H domain of human immunodeficiency virus type 1 (HIV-1) reverse transcriptase cleaves the tRNA 1 nucleotide from the RNA/DNA junction at the U5/primer binding site (PBS) junction, which leaves an rA residue at the U5 terminus. We made sequence changes at the end of the U5 region adjacent to the PBS in HIV-1 to determine whether such changes affect the specificity of tRNA primer cleavage by RNase H. In some of the mutants, RNase H usually removed the entire tRNA, showing that the cleavage specificity was shifted by 1 nucleotide. This result suggests that the tRNA cleavage specificity of the HIV-1 RNase domain H depends on sequences in U5.

Citing Articles

Developing and Evaluating Inhibitors against the RNase H Active Site of HIV-1 Reverse Transcriptase.

Boyer P, Smith S, Zhao X, Das K, Gruber K, Arnold E J Virol. 2018; 92(13).

PMID: 29643235 PMC: 6002700. DOI: 10.1128/JVI.02203-17.

Drug resistant integrase mutants cause aberrant HIV integrations.

Varadarajan J, McWilliams M, Mott B, Thomas C, Smith S, Hughes S Retrovirology. 2016; 13(1):71.

PMID: 27682062 PMC: 5041404. DOI: 10.1186/s12977-016-0305-6.

Structural basis of genomic RNA (gRNA) dimerization and packaging determinants of mouse mammary tumor virus (MMTV).

Aktar S, Vivet-Boudou V, Ali L, Jabeen A, Kalloush R, Richer D Retrovirology. 2014; 11:96.

PMID: 25394412 PMC: 4264320. DOI: 10.1186/s12977-014-0096-6.

Treatment with suboptimal doses of raltegravir leads to aberrant HIV-1 integrations.

Varadarajan J, McWilliams M, Hughes S Proc Natl Acad Sci U S A. 2013; 110(36):14747-52.

PMID: 23959861 PMC: 3767498. DOI: 10.1073/pnas.1305066110.

HIV-1 Ribonuclease H: Structure, Catalytic Mechanism and Inhibitors.

Beilhartz G, Gotte M Viruses. 2011; 2(4):900-926.

PMID: 21994660 PMC: 3185654. DOI: 10.3390/v2040900.

References

Gao H, Sarafianos S, Arnold E, Hughes S . Similarities and differences in the RNase H activities of human immunodeficiency virus type 1 reverse transcriptase and Moloney murine leukemia virus reverse transcriptase. J Mol Biol. 1999; 294(5):1097-113. DOI: 10.1006/jmbi.1999.3325. View

Whitcomb J, Hughes S . The sequence of human immunodeficiency virus type 2 circle junction suggests that integration protein cleaves the ends of linear DNA asymmetrically. J Virol. 1991; 65(7):3906-10. PMC: 241426. DOI: 10.1128/JVI.65.7.3906-3910.1991. View

Whitcomb J, Kumar R, Hughes S . Sequence of the circle junction of human immunodeficiency virus type 1: implications for reverse transcription and integration. J Virol. 1990; 64(10):4903-6. PMC: 247980. DOI: 10.1128/JVI.64.10.4903-4906.1990. View

Ding J, Nanni R, Clark Jr A, Lu X, Tantillo C, Williams R . Crystal structure of human immunodeficiency virus type 1 reverse transcriptase complexed with double-stranded DNA at 3.0 A resolution shows bent DNA. Proc Natl Acad Sci U S A. 1993; 90(13):6320-4. PMC: 46920. DOI: 10.1073/pnas.90.13.6320. View

Huber H, Richardson C . Processing of the primer for plus strand DNA synthesis by human immunodeficiency virus 1 reverse transcriptase. J Biol Chem. 1990; 265(18):10565-73. View

Sarafianos S, Das K, Tantillo C, Clark Jr A, Ding J, Whitcomb J . Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J. 2001; 20(6):1449-61. PMC: 145536. DOI: 10.1093/emboj/20.6.1449. View

Artzi H, Shemesh J, Zeelon E, Amit B, Kleiman L, Gorecki M . Ribonuclease H activity during initiation of reverse transcription using tRNA(lys)/RNA primer/template of human immunodeficiency virus. Arch Biochem Biophys. 1996; 325(2):209-16. DOI: 10.1006/abbi.1996.0026. View

Ghosh M, Howard K, Cameron C, Benkovic S, Hughes S, Le Grice S . Truncating alpha-helix E' of p66 human immunodeficiency virus reverse transcriptase modulates RNase H function and impairs DNA strand transfer. J Biol Chem. 1995; 270(13):7068-76. DOI: 10.1074/jbc.270.13.7068. View

Bartz S, Vodicka M . Production of high-titer human immunodeficiency virus type 1 pseudotyped with vesicular stomatitis virus glycoprotein. Methods. 1997; 12(4):337-42. DOI: 10.1006/meth.1997.0487. View

10.

Pullen K, Ishimoto L, Champoux J . Incomplete removal of the RNA primer for minus-strand DNA synthesis by human immunodeficiency virus type 1 reverse transcriptase. J Virol. 1992; 66(1):367-73. PMC: 238296. DOI: 10.1128/JVI.66.1.367-373.1992. View

11.

Arnold E, Ding J, Hughes S, Hostomsky Z . Structures of DNA and RNA polymerases and their interactions with nucleic acid substrates. Curr Opin Struct Biol. 1995; 5(1):27-38. DOI: 10.1016/0959-440x(95)80006-m. View

12.

Youvan D, Hearst J . Reverse transcriptase pauses at N2-methylguanine during in vitro transcription of Escherichia coli 16S ribosomal RNA. Proc Natl Acad Sci U S A. 1979; 76(8):3751-4. PMC: 383911. DOI: 10.1073/pnas.76.8.3751. View

13.

Gotte M, Fackler S, Hermann T, Perola E, Cellai L, Gross H . HIV-1 reverse transcriptase-associated RNase H cleaves RNA/RNA in arrested complexes: implications for the mechanism by which RNase H discriminates between RNA/RNA and RNA/DNA. EMBO J. 1995; 14(4):833-41. PMC: 398150. DOI: 10.1002/j.1460-2075.1995.tb07061.x. View

14.

Zhou H, Rainey G, Wong S, Coffin J . Substrate sequence selection by retroviral integrase. J Virol. 2001; 75(3):1359-70. PMC: 114042. DOI: 10.1128/JVI.75.3.1359-1370.2001. View

15.

Kulkosky J, KATZ R, Skalka A . Terminal nucleotides of the preintegrative linear form of HIV-1 DNA deduced from the sequence of circular DNA junctions. J Acquir Immune Defic Syndr (1988). 1990; 3(9):852-8. View

16.

Yee J, Friedmann T, Burns J . Generation of high-titer pseudotyped retroviral vectors with very broad host range. Methods Cell Biol. 1994; 43 Pt A:99-112. DOI: 10.1016/s0091-679x(08)60600-7. View

17.

Oh J, Chang K, Hughes S . Mutations in the U5 sequences adjacent to the primer binding site do not affect tRNA cleavage by rous sarcoma virus RNase H but do cause aberrant integrations in vivo. J Virol. 2005; 80(1):451-9. PMC: 1317513. DOI: 10.1128/JVI.80.1.451-459.2006. View

18.

Masuda T, Kuroda M, Harada S . Specific and independent recognition of U3 and U5 att sites by human immunodeficiency virus type 1 integrase in vivo. J Virol. 1998; 72(10):8396-402. PMC: 110226. DOI: 10.1128/JVI.72.10.8396-8402.1998. View

19.

Julias J, McWilliams M, Sarafianos S, Alvord W, Arnold E, Hughes S . Effects of mutations in the G tract of the human immunodeficiency virus type 1 polypurine tract on virus replication and RNase H cleavage. J Virol. 2004; 78(23):13315-24. PMC: 524982. DOI: 10.1128/JVI.78.23.13315-13324.2004. View

20.

Leavitt A, Rose R, Varmus H . Both substrate and target oligonucleotide sequences affect in vitro integration mediated by human immunodeficiency virus type 1 integrase protein produced in Saccharomyces cerevisiae. J Virol. 1992; 66(4):2359-68. PMC: 289031. DOI: 10.1128/JVI.66.4.2359-2368.1992. View