Structural and functional conservation of cis-acting RNA elements in coronavirus 5'-terminal genome regions

Virology. 2018 Apr:517:44-55. doi: 10.1016/j.virol.2017.11.025. Epub 2017 Dec 6.


Structure predictions suggest a partial conservation of RNA structure elements in coronavirus terminal genome regions. Here, we determined the structures of stem-loops (SL) 1 and 2 of two alphacoronaviruses, human coronavirus (HCoV) 229E and NL63, by RNA structure probing and studied the functional relevance of these putative cis-acting elements. HCoV-229E SL1 and SL2 mutants generated by reverse genetics were used to study the effects on viral replication of single-nucleotide substitutions predicted to destabilize the SL1 and SL2 structures. The data provide conclusive evidence for the critical role of SL1 and SL2 in HCoV-229E replication and, in some cases, revealed parallels with previously characterized betacoronavirus SL1 and SL2 elements. Also, we were able to rescue viable HCoV-229E mutants carrying replacements of SL2 with equivalent betacoronavirus structural elements. The data obtained in this study reveal a remarkable degree of structural and functional conservation of 5'-terminal RNA structural elements across coronavirus genus boundaries.

Keywords: Coronavirus; Coronavirus phylogeny; RNA structure; Replication; Stem-loop; cis-acting RNA element.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Cell Line
  • Coronavirus 229E, Human / genetics*
  • Coronavirus NL63, Human / genetics*
  • Genome, Viral*
  • Humans
  • Nucleic Acid Conformation
  • RNA, Viral / chemistry
  • RNA, Viral / genetics
  • Regulatory Sequences, Nucleic Acid / physiology*
  • Virus Replication / physiology


  • RNA, Viral