title: The posttranscriptional control element of the simian retrovirus type 1 forms an extensive RNA secondary structure necessary for its function.
abstract: It was previously shown that a 240-nucleotide (nt) RNA element (cis-acting transactivation element [CTE]) located between the env gene and the 3' long terminal repeat of simian retrovirus type 1 (SRV-1) can functionally replace posttranscriptional activation directed by Rev and the Rev-responsive element (RRE) when inserted into a Rev- and RRE-deficient molecular clone of human immunodeficiency virus type 1, resulting in efficient virus replication. Here, we analyze the molecular and structural requirements for function of this RNA element. Deletion mutagenesis demonstrated that the core element spans 173 nt. SRV-2 and Mason-Pfizer monkey virus have highly homologous elements, which function similarly when inserted into the Rev/RRE-deficient human immunodeficiency virus type 1. Computer prediction indicated that the core CTEs of all three viruses have similar extensive secondary structures. Mutagenesis of the SRV-1 CTE revealed that both sequence and secondary structure are essential for function. Nuclease probing of the SRV-1 CTE further supported the genetic analysis and confirmed the predicted structural features of the RNA element. Sequence analysis of the 240-nt SRV-1 CTE, after continuous long-term propagation of the Rev-independent viruses, revealed that the genetically defined core element remained unchanged, while regions outside the core CTE underwent deletions or duplications. These data further support our in vitro mutagenesis data and demonstrate the importance of the sequence and structure of the SRV-1 CTE for appropriate function.
authors.affiliation: Human Retrovirus Pathogenesis Group, ABL-Basic Research Program, National Cancer Institute-Frederick Cancer Research and Development Center, Maryland 21702-1201, USA.
authors.forename: C
authors.initials: C
authors.lastname: Tabernero
authors.forename: A S
authors.initials: AS
authors.lastname: Zolotukhin
authors.forename: A
authors.initials: A
authors.lastname: Valentin
authors.forename: G N
authors.initials: GN
authors.lastname: Pavlakis
authors.forename: B K
authors.initials: BK
authors.lastname: Felber
mesh_terms: D001483:Base Sequence; D017931:DNA Primers; D015694:Gene Products, rev / Q000378:metabolism*; D015752:Genes, env; D016655:HIV Core Protein p24 / Q000096:biosynthesis; D016325:HIV Long Terminal Repeat; D015497:HIV-1 / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D007700:Kinetics; D008969:Molecular Sequence Data; D016296:Mutagenesis; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D012323:RNA Processing, Post-Transcriptional; D012367:RNA, Viral / Q000737:chemistry / Q000378:metabolism; D012091:Repetitive Sequences, Nucleic Acid; D015183:Restriction Mapping; D015301:Retroviruses, Simian / Q000235:genetics / Q000378:metabolism / Q000502:physiology*; D017384:Sequence Deletion; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D015534:Trans-Activators / Q000096:biosynthesis / Q000737:chemistry / Q000378:metabolism*; D014162:Transfection; D014779:Virus Replication; D054321:rev Gene Products, Human Immunodeficiency Virus
chemical_list: D017931:DNA Primers; D015694:Gene Products, rev; D016655:HIV Core Protein p24; D012367:RNA, Viral; D015534:Trans-Activators; D054321:rev Gene Products, Human Immunodeficiency Virus