Biopolym. Cell. 2003; 19(3):298-303.
Short Communications
Conservative structural motifs in the 3' untranslated region of SARS coronavirus
1Zarudnaya M. I., 1Potyahaylo A. L., 1Hovorun D. M.
  1. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680


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.


[1] Ksiazek TG, Erdman D, Goldsmith CS, Zaki SR, Peret T, Emery S, Tong S, Urbani C, Comer JA, Lim W, Rollin PE, Dowell SF, Ling AE, Humphrey CD, Shieh WJ, Guarner J, Paddock CD, Rota P, Fields B, DeRisi J, Yang JY, Cox N, Hughes JM, LeDuc JW, Bellini WJ, Anderson LJ; SARS Working Group. A novel coronavirus associated with severe acute respiratory syndrome. N Engl J Med. 2003;348(20):1953-66.
[2] Rota PA, Oberste MS, Monroe SS, Nix WA, Campagnoli R, Icenogle JP, Pe?aranda S, Bankamp B, Maher K, Chen MH, Tong S, Tamin A, Lowe L, Frace M, DeRisi JL, Chen Q, Wang D, Erdman DD, Peret TC, Burns C, Ksiazek TG, Rollin PE, Sanchez A, Liffick S, Holloway B, Limor J, McCaustland K, Olsen-Rasmussen M, Fouchier R, G?nther S, Osterhaus AD, Drosten C, Pallansch MA, Anderson LJ, Bellini WJ. Characterization of a novel coronavirus associated with severe acute respiratory syndrome. Science. 2003;300(5624):1394-9.
[3] Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, Khattra J, Asano JK, Barber SA, Chan SY, Cloutier A, Coughlin SM, Freeman D, Girn N, Griffith OL, Leach SR, Mayo M, McDonald H, Montgomery SB, Pandoh PK, Petrescu AS, Robertson AG, Schein JE, Siddiqui A, Smailus DE, Stott JM, Yang GS, Plummer F, Andonov A, Artsob H, Bastien N, Bernard K, Booth TF, Bowness D, Czub M, Drebot M, Fernando L, Flick R, Garbutt M, Gray M, Grolla A, Jones S, Feldmann H, Meyers A, Kabani A, Li Y, Normand S, Stroher U, Tipples GA, Tyler S, Vogrig R, Ward D, Watson B, Brunham RC, Krajden M, Petric M, Skowronski DM, Upton C, Roper RL. The Genome sequence of the SARS-associated coronavirus. Science. 2003;300(5624):1399-404.
[4] Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406-15.
[5] Sawicki SG, Sawicki DL. A new model for coronavirus transcription. Adv Exp Med Biol. 1998;440:215-9.
[6] Hsue B, Hartshorne T, Masters PS. Characterization of an essential RNA secondary structure in the 3' untranslated region of the murine coronavirus genome. J Virol. 2000;74(15):6911-21.
[7] Hsue B, Masters PS. A bulged stem-loop structure in the 3' untranslated region of the genome of the coronavirus mouse hepatitis virus is essential for replication. J Virol. 1997;71(10):7567-78.
[8] Williams GD, Chang RY, Brian DA. A phylogenetically conserved hairpin-type 3' untranslated region pseudoknot functions in coronavirus RNA replication. J Virol. 1999;73(10):8349-55.
[9] Liu Q, Johnson RF, Leibowitz JL. Secondary structural elements within the 3' untranslated region of mouse hepatitis virus strain JHM genomic RNA. J Virol. 2001;75(24):12105-13.
[10] Berkhout B, Ooms M, Beerens N, Huthoff H, Southern E, Verhoef K. In vitro evidence that the untranslated leader of the HIV-1 genome is an RNA checkpoint that regulates multiple functions through conformational changes. J Biol Chem. 2002;277(22):19967-75.
[11] Huthoff H, Berkhout B. Multiple secondary structure rearrangements during HIV-1 RNA dimerization. Biochemistry. 2002;41(33):10439-45.
[12] Jonassen CM, Jonassen TO, Grinde B. A common RNA motif in the 3' end of the genomes of astroviruses, avian infectious bronchitis virus and an equine rhinovirus. J Gen Virol. 1998;79 ( Pt 4):715-8.
[13] Lin YJ, Liao CL, Lai MM. Identification of the cis-acting signal for minus-strand RNA synthesis of a murine coronavirus: implications for the role of minus-strand RNA in RNA replication and transcription. J Virol. 1994;68(12):8131-40.
[14] Yu W, Leibowitz JL. Specific binding of host cellular proteins to multiple sites within the 3' end of mouse hepatitis virus genomic RNA. J Virol. 1995;69(4):2016-23.
[15] Liu Q, Yu W, Leibowitz JL. A specific host cellular protein binding element near the 3' end of mouse hepatitis virus genomic RNA. Virology. 1997;232(1):74-85.
[16] Yu W, Leibowitz JL. A conserved motif at the 3' end of mouse hepatitis virus genomic RNA required for host protein binding and viral RNA replication. Virology. 1995;214(1):128-38.
[17] Spagnolo JF, Hogue BG. Host protein interactions with the 3' end of bovine coronavirus RNA and the requirement of the poly(A) tail for coronavirus defective genome replication. J Virol. 2000;74(11):5053-65.
[18] Huang P, Lai MM. Heterogeneous nuclear ribonucleoprotein a1 binds to the 3'-untranslated region and mediates potential 5'-3'-end cross talks of mouse hepatitis virus RNA. J Virol. 2001;75(11):5009-17.