title: A review on architecture of the gag-pol ribosomal frameshifting RNA in human immunodeficiency virus: a variability survey of virus genotypes.
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.
authors.affiliation: a School of Pharmaceutical Sciences, Xiamen University , Fujian 361102 , P.R. China.
authors.forename: Qi
authors.initials: Q
authors.lastname: Qiao
authors.affiliation: b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Yanhua
authors.initials: Y
authors.lastname: Yan
authors.affiliation: c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Jinmei
authors.initials: J
authors.lastname: Guo
authors.affiliation: c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Shuqiang
authors.initials: S
authors.lastname: Du
authors.affiliation: b Department of Bioscience , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Jiangtao
authors.initials: J
authors.lastname: Zhang
authors.affiliation: c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Ruyue
authors.initials: R
authors.lastname: Jia
authors.affiliation: c Department of Chemistry & Chemical Engineering , Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Haimin
authors.initials: H
authors.lastname: Ren
authors.affiliation: d Graduate Institute of Pharmaceutical Chemistry, Luliang University , Shanxi 033001 , P.R. China.
authors.forename: Yuanbiao
authors.initials: Y
authors.lastname: Qiao
authors.affiliation: e School of Pharmaceutical Sciences , Shanxi Medical University , Shanxi 030001 , P.R. China.
authors.forename: Qingshan
authors.initials: Q
authors.lastname: Li
mesh_terms: D020029:Base Pairing; D001483:Base Sequence; D018965:Frameshifting, Ribosomal; D015967:Gene Expression Regulation, Viral; D005807:Genes, Overlapping; D015750:Genes, gag; D015751:Genes, pol; D005838:Genotype; D057809:HEK293 Cells; D015497:HIV-1 / Q000235:genetics* / Q000378:metabolism; D006801:Humans; D009690:Nucleic Acid Conformation; D020365:RNA Helicases / Q000235:genetics / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D012367:RNA, Viral / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012270:Ribosomes / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment
chemical_list: D012367:RNA, Viral; D012343:RNA, Transfer; D020365:RNA Helicases
keywords: HIV phenotype and genotype; antiviral target discovery; frameshift stimulatory signal; gag-pol ribosomal frameshifting; proximal sequence element