Biopolymers and cell. 2003; 19 (3): 298 - 303

Conservative structural motifs in the 3' untranslated region of SARS coronavirus

M. I. Zarudnaya, A. L. Potyahaylo, D. M. Hovorun

Signal elements in the 3' untranslated region (UTR) of «plus»-RNA viruses function as control elements in RNA replication, transcription and translation. Here we performed computer-assisted (Zuker, 2003) secondary structure analysis and prediction of tertiary structure of 3' UTR of SARS coronavirus. We found that this region contains a sequence potentially able to form a pseudoknot which was earlier observed in 3' UTR of every coronavirus genome that was sequenced. The SARS-CoV pseudoknot structure is similar to the pseudoknot structure of the group 1 coronaviruses. As in the case of other coronaviruses the formation of the SARS-CoV pseudoknot interferes with the formation of a bulged stem-loop structure with high negative free energy value located in the most upstream part of 3' UTR. Besides the SARS-CoV 3' UTR, like the same region of 1BV coronavirus, contains the s2m motif which is absent in 3' UTR of a number of group 1 and 2 coronaviruses. Other structural motifs in 3' UTR of SARS-CoV has been discussed as well. As a result, the SARS-CoV 3' UTR structure established supports the present opinion on a unique character of this virus which cannot be assigned to any of three known groups of coronaviruses.