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Journal of Virology, October 1999, p. 8349-8355, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.

A Phylogenetically Conserved Hairpin-Type 3' Untranslated Region Pseudoknot Functions in Coronavirus RNA Replication

Gwyn D. Williams, Ruey-Yi Chang,dagger and David A. Brian*

Department of Microbiology, University of Tennessee, Knoxville, Tennessee 37996-0845

Received 12 April 1999/Accepted 2 July 1999

Secondary and tertiary structures in the 3' untranslated region (UTR) of plus-strand RNA viruses have been postulated to function as control elements in RNA replication, transcription, and translation. Here we describe a 54-nucleotide (nt) hairpin-type pseudoknot within the 288-nt 3' UTR of the bovine coronavirus genome and show by mutational analysis of both stems that the pseudoknotted structure is required for the replication of a defective interfering RNA genome. The pseudoknot is phylogenetically conserved among coronaviruses both in location and in shape but only partially in nucleotide sequence, and evolutionary covariation of bases to maintain G · U pairings indicates that it functions in the plus strand. RNase probing of synthetic transcripts provided additional evidence of its tertiary structure and also identified the possible existence of two conformational states. These results indicate that the 3' UTR pseudoknot is involved in coronavirus RNA replication and lead us to postulate that it functions as a regulatory control element.

* Corresponding author. Mailing address: Department of Microbiology, University of Tennessee, M409 Walters Life Sciences Building, Knoxville, TN 37996-0845. Phone: (423) 974-4030. Fax: (423) 974-4007. E-mail: dbrian{at}utk.edu.

dagger Present address: National Dong-Hwa University, Hualien, Taiwan.

Journal of Virology, October 1999, p. 8349-8355, Vol. 73, No. 10
0022-538X/99/$04.00+0
Copyright © 1999, American Society for Microbiology. All rights reserved.


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Copyright © 1999 by the American Society for Microbiology. All rights reserved.