JVI Accepts, published online ahead of print on 11 April 2007
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J. Virol. doi:10.1128/JVI.02231-06
Copyright (c) 2007, American Society for Microbiology and/or the Listed Authors/Institutions. All Rights Reserved.

A new structure model for the packaging signal in the genome of group IIa Coronaviruses

Shih-Cheng Chen, Erwin van den Born, Sjoerd H.E. van den Worm, Cornelis W.A. Pleij, Eric J. Snijder, and René C.L. Olsthoorn*

Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands, Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands

* To whom correspondence should be addressed. Email: olsthoor{at}chem.leidenuniv.nl.


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Abstract

A 190-nt packaging signal (PS) located in the 3' end of ORF1b in Mouse hepatitis virus (MHV), a group IIa coronavirus, was previously postulated to direct genome RNA packaging. Based on phylogenetic data and structure probing, we have identified a 95-nt hairpin within the 190-nt PS domain, which is conserved in all group IIa coronaviruses, but not in SARS-CoV (group IIb) or group I and III coronaviruses. The hairpin is composed of 6 copies of a repeating structural subunit that consists of 2-nt bulges and 5-bp stems. We propose that repeating AA-bulges are characteristic features of group IIa PSs.




This article has been cited by other articles:

  • Hurst, K. R., Koetzner, C. A., Masters, P. S. (2009). Identification of In Vivo-Interacting Domains of the Murine Coronavirus Nucleocapsid Protein. J. Virol. 83: 7221-7234 [Abstract] [Full Text]  


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