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Journal of Virology, June 2006, p. 5833-5840, Vol. 80, No. 12
0022-538X/06/$08.00+0     doi:10.1128/JVI.00122-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Adaptive Covariation between the Coat and Movement Proteins of Prunus Necrotic Ringspot Virus

Francisco M. Codoñer,1 Mario A. Fares,2 and Santiago F. Elena1*

Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, 46022 València, Spain,1 Molecular Evolution and Bioinformatics Laboratory, Department of Biology, National University of Ireland, Maynooth, Ireland2

Received 18 January 2006/ Accepted 26 March 2006

The relative functional and/or structural importance of different amino acid sites in a protein can be assessed by evaluating the selective constraints to which they have been subjected during the course of evolution. Here we explore such constraints at the linear and three-dimensional levels for the movement protein (MP) and coat protein (CP) encoded by RNA 3 of prunus necrotic ringspot ilarvirus (PNRSV). By a maximum-parsimony approach, the nucleotide sequences from 46 isolates of PNRSV varying in symptomatology, host tree, and geographic origin have been analyzed and sites under different selective pressures have been identified in both proteins. We have also performed covariation analyses to explore whether changes in certain amino acid sites condition subsequent variation in other sites of the same protein or the other protein. These covariation analyses shed light on which particular amino acids should be involved in the physical and functional interaction between MP and CP. Finally, we discuss these findings in the light of what is already known about the implication of certain sites and domains in structure and protein-protein and RNA-protein interactions.

* Corresponding author. Mailing address: Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV), Avenida de los naranjos s/n, 46022 València, Spain. Phone: 34 963 877 895. Fax: 34 963 877 859. E-mail: sfelena{at}ibmcp.upv.es.

Journal of Virology, June 2006, p. 5833-5840, Vol. 80, No. 12
0022-538X/06/$08.00+0     doi:10.1128/JVI.00122-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Codoner, F. M., Elena, S. F. (2008). The promiscuous evolutionary history of the family Bromoviridae. J. Gen. Virol. 89: 1739-1747 [Abstract] [Full Text]  


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