title: Coronavirus cis-Acting RNA Elements.
abstract: Coronaviruses have exceptionally large RNA genomes of approximately 30 kilobases. Genome replication and transcription is mediated by a multisubunit protein complex comprised of more than a dozen virus-encoded proteins. The protein complex is thought to bind specific cis-acting RNA elements primarily located in the 5'- and 3'-terminal genome regions and upstream of the open reading frames located in the 3'-proximal one-third of the genome. Here, we review our current understanding of coronavirus cis-acting RNA elements, focusing on elements required for genome replication and packaging. Recent bioinformatic, biochemical, and genetic studies suggest a previously unknown level of conservation of cis-acting RNA structures among different coronavirus genera and, in some cases, even beyond genus boundaries. Also, there is increasing evidence to suggest that individual cis-acting elements may be part of higher-order RNA structures involving long-range and dynamic RNA-RNA interactions between RNA structural elements separated by thousands of nucleotides in the viral genome. We discuss the structural and functional features of these cis-acting RNA elements and their specific functions in coronavirus RNA synthesis.
authors.affiliation: Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany.
authors.forename: R
authors.initials: R
authors.lastname: Madhugiri
authors.affiliation: Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Fricke
authors.affiliation: Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany; FLI Leibniz Institute for Age Research, Jena, Germany.
authors.forename: M
authors.initials: M
authors.lastname: Marz
authors.affiliation: Institute of Medical Virology, Justus Liebig University Giessen, Giessen, Germany. Electronic address: john.ziebuhr@viro.med.uni-giessen.de.
authors.forename: J
authors.initials: J
authors.lastname: Ziebuhr
mesh_terms: D017934:Coronavirus / Q000235:genetics* / Q000378:metabolism; D018352:Coronavirus Infections / Q000821:virology; D004847:Epithelial Cells / Q000378:metabolism / Q000821:virology; D015967:Gene Expression Regulation, Viral; D059646:Genome Size; D016679:Genome, Viral; D054884:Host-Pathogen Interactions; D006801:Humans; D009690:Nucleic Acid Conformation; D012367:RNA, Viral / Q000096:biosynthesis / Q000235:genetics*; D050436:Regulatory Elements, Transcriptional; D014158:Transcription, Genetic; D014779:Virus Replication
chemical_list: D012367:RNA, Viral
keywords: Coronavirus; Genome packaging; RNA structure; RNA virus; Replication; cis-Acting element