title: Group-specific structural features of the 5'-proximal sequences of coronavirus genomic RNAs.
abstract: Global predictions of the secondary structure of coronavirus (CoV) 5' untranslated regions and adjacent coding sequences revealed the presence of conserved structural elements. Stem loops (SL) 1, 2, 4, and 5 were predicted in all CoVs, while the core leader transcription-regulating sequence (L-TRS) forms SL3 in only some CoVs. SL5 in group I and II CoVs, with the exception of group IIa CoVs, is characterized by the presence of a large sequence insertion capable of forming hairpins with the conserved 5'-UUYCGU-3' loop sequence. Structure probing confirmed the existence of these hairpins in the group I Human coronavirus-229E and the group II Severe acute respiratory syndrome coronavirus (SARS-CoV). In general, the pattern of the 5' cis-acting elements is highly related to the lineage of CoVs, including features of the conserved hairpins in SL5. The function of these conserved hairpins as a putative packaging signal is discussed.
authors.affiliation: Leiden Institute of Chemistry, Department of Molecular Genetics, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands.
authors.forename: Shih-Cheng
authors.initials: SC
authors.lastname: Chen
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
mesh_terms: D020121:5' Untranslated Regions / Q000235:genetics*; D001483:Base Sequence; D016679:Genome, Viral / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D045473:Severe acute respiratory syndrome-related coronavirus / Q000145:classification / Q000235:genetics*
chemical_list: D020121:5' Untranslated Regions; D012367:RNA, Viral