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Journal of Virology, April 2008, p. 3882-3893, Vol. 82, No. 8
0022-538X/08/$08.00+0     doi:10.1128/JVI.02622-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Identification of a Coronavirus Transcription Enhancer{triangledown}

José L. Moreno, Sonia Zúñiga, Luis Enjuanes,* and Isabel Sola

Centro Nacional de Biotecnología, CSIC, Department of Molecular and Cell Biology, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain

Received 10 December 2007/ Accepted 1 February 2008

Coronavirus (CoV) transcription includes a discontinuous mechanism during the synthesis of sub-genome-length minus-strand RNAs leading to a collection of mRNAs in which the 5' terminal leader sequence is fused to contiguous genome sequences. It has been previously shown that transcription-regulating sequences (TRSs) preceding each gene regulate transcription. Base pairing between the leader TRS (TRS-L) and the complement of the body TRS (cTRS-B) in the nascent RNA is a determinant factor during CoV transcription. In fact, in transmissible gastroenteritis CoV, a good correlation has been observed between subgenomic mRNA (sg mRNA) levels and the free energy ({Delta}G) of TRS-L and cTRS-B duplex formation. The only exception was sg mRNA N, the most abundant sg mRNA during viral infection in spite of its minimum {Delta}G associated with duplex formation. We postulated that additional factors should regulate transcription of sg mRNA N. In this report, we have described a novel transcription regulation mechanism operating in CoV by which a 9-nucleotide (nt) sequence located 449 nt upstream of the N gene TRS core sequence (CS-N) interacts with a complementary sequence just upstream of CS-N, specifically increasing the accumulation of sg mRNA N. Alteration of this complementarity in mutant replicon genomes showed a correlation between the predicted stability of the base pairing between 9-nt sequences and the accumulation of sg mRNA N. This interaction is exclusively conserved in group 1a CoVs, the only CoV subgroup in which the N gene is not the most 3' gene in the viral genome. This is the first time that a long-distance RNA-RNA interaction regulating transcriptional activity specifically enhancing the transcription of one gene has been described to occur in CoVs.

* Corresponding author. Mailing address: Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, CSIC, C/Darwin 3, Cantoblanco, 28049 Madrid, Spain. Phone: 34-91-585 4555. Fax: 34-91-585 4915. E-mail: L.Enjuanes{at}cnb.uam.es

{triangledown} Published ahead of print on 13 February 2008.

Journal of Virology, April 2008, p. 3882-3893, Vol. 82, No. 8
0022-538X/08/$08.00+0     doi:10.1128/JVI.02622-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.





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