title: New structure model for the packaging signal in the genome of group IIa coronaviruses.
abstract: A 190-nucleotide (nt) packaging signal (PS) located in the 3' end of open reading frame 1b in the mouse hepatitis virus, a group IIa coronavirus, was previously postulated to direct genome RNA packaging. Based on phylogenetic data and structure probing, we have identified a 95-nt hairpin within the 190-nt PS domain which is conserved in all group IIa coronaviruses but not in the severe acute respiratory syndrome coronavirus (group IIb), group I coronaviruses, or group III coronaviruses. The hairpin is composed of six copies of a repeating structural subunit that consists of 2-nt bulges and 5-bp stems. We propose that repeating AA bulges are characteristic features of group IIa PSs.
authors.affiliation: Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands. olsthoor@chem.leidenuniv.nl.
authors.forename: Shih-Cheng
authors.initials: SC
authors.lastname: Chen
authors.forename: Erwin
authors.initials: E
authors.lastname: van den Born
authors.forename: Sjoerd H E
authors.initials: SH
authors.lastname: van den Worm
authors.forename: Cornelis W A
authors.initials: CW
authors.lastname: Pleij
authors.forename: Eric J
authors.initials: EJ
authors.lastname: Snijder
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
mesh_terms: D001483:Base Sequence; D017934:Coronavirus / Q000235:genetics*; D030562:Databases, Protein; D016679:Genome, Viral; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016366:Open Reading Frames; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012328:RNA Viruses / Q000235:genetics; D045473:Severe acute respiratory syndrome-related coronavirus / Q000235:genetics; D017422:Sequence Analysis, DNA; D013045:Species Specificity