A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes - PubMed

Affiliations

• PMID: 27485859
• DOI: 10.1080/07391102.2016.1194231

Review

A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes

Qi Qiao et al. J Biomol Struct Dyn. 2017 Jun.

Abstract

Programmed '-1' ribosomal frameshifting is necessary for expressing the pol gene overlapped from a gag of human immunodeficiency virus. A viral RNA structure that requires base pairing across the overlapping sequence region suggests a mechanism of regulating ribosome and helicase traffic during expression. To get precise roles of an element around the frameshift site, a review on architecture of the frameshifting RNA is performed in combination of reported information with augments of a representative set of 19 viral samples. In spite of a different length for the viral RNAs, a canonical comparison on the element sequence allocation is performed for viewing variability associations between virus genotypes. Additionally, recent and historical insights recognized in frameshifting regulation are looked back as for indel and single nucleotide polymorphism of RNA. As specially noted, structural changes at a frameshift site, the spacer sequence, and a three-helix junction element, as well as two Watson-Crick base pairs near a bulge and a C-G pair close a loop, are the most vital strategies for the virus frameshifting regulations. All of structural changes, which are dependent upon specific sequence variations, facilitate an elucidation about the RNA element conformation-dependent mechanism for frameshifting. These facts on disrupting base pair interactions also allow solving the problem of competition between ribosome and helicase on a same RNA template, common to single-stranded RNA viruses. In a broad perspective, each new insight of frameshifting regulation in the competition systems introduced by the RNA element construct changes will offer a compelling target for antiviral therapy.

Keywords: HIV phenotype and genotype; antiviral target discovery; frameshift stimulatory signal; gag-pol ribosomal frameshifting; proximal sequence element.

Similar articles

• Characterization of the frameshift stimulatory signal controlling a programmed -1 ribosomal frameshift in the human immunodeficiency virus type 1.

  Dulude D, Baril M, Brakier-Gingras L. Dulude D, et al. Nucleic Acids Res. 2002 Dec 1;30(23):5094-102. doi: 10.1093/nar/gkf657. Nucleic Acids Res. 2002. PMID: 12466532 Free PMC article.

• Stability of HIV Frameshift Site RNA Correlates with Frameshift Efficiency and Decreased Virus Infectivity.

  Garcia-Miranda P, Becker JT, Benner BE, Blume A, Sherer NM, Butcher SE. Garcia-Miranda P, et al. J Virol. 2016 Jul 11;90(15):6906-6917. doi: 10.1128/JVI.00149-16. Print 2016 Aug 1. J Virol. 2016. PMID: 27194769 Free PMC article.

• A -1 ribosomal frameshift element that requires base pairing across four kilobases suggests a mechanism of regulating ribosome and replicase traffic on a viral RNA.

  Barry JK, Miller WA. Barry JK, et al. Proc Natl Acad Sci U S A. 2002 Aug 20;99(17):11133-8. doi: 10.1073/pnas.162223099. Epub 2002 Jul 30. Proc Natl Acad Sci U S A. 2002. PMID: 12149516 Free PMC article.

• Programmed ribosomal frameshifting in HIV-1 and the SARS-CoV.

  Brierley I, Dos Ramos FJ. Brierley I, et al. Virus Res. 2006 Jul;119(1):29-42. doi: 10.1016/j.virusres.2005.10.008. Epub 2005 Nov 28. Virus Res. 2006. PMID: 16310880 Free PMC article. Review.

• Mechanisms and biomedical implications of -1 programmed ribosome frameshifting on viral and bacterial mRNAs.

  Korniy N, Samatova E, Anokhina MM, Peske F, Rodnina MV. Korniy N, et al. FEBS Lett. 2019 Jul;593(13):1468-1482. doi: 10.1002/1873-3468.13478. Epub 2019 Jun 20. FEBS Lett. 2019. PMID: 31222875 Free PMC article. Review.

Cited by

• Specific reverse transcriptase slippage at the HIV ribosomal frameshift sequence: potential implications for modulation of GagPol synthesis.

  Penno C, Kumari R, Baranov PV, van Sinderen D, Atkins JF. Penno C, et al. Nucleic Acids Res. 2017 Sep 29;45(17):10156-10167. doi: 10.1093/nar/gkx690. Nucleic Acids Res. 2017. PMID: 28973470 Free PMC article.

Publication types

MeSH terms

Substances

LinkOut - more resources

• Full Text Sources

  • Atypon

• Other Literature Sources

  • scite Smart Citations

• Research Materials

  • NCI CPTC Antibody Characterization Program