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Analysis of differential selective forces acting on the coat protein (P3) of the plant virus family Luteoviridae
Marina W. Torres1, Régis L. Corrêa2 and Carlos G. Schrago1
1Laboratório de Biodiversidade Molecular, Departamento de Genética, Instituto de Biologia,
2Laboratório de Virologia Molecular Vegetal, Departamento de Virologia,
Instituto de Microbiologia Prof. Paulo de Góes, Universidade Federal do Rio de Janeiro,
Ilha do Fundão, RJ, Brasil
Corresponding author: C.G. Schrago
E-mail: [email protected]
Genet. Mol. Res. 4 (4): 790-802 (2005)
Received March 17, 2005
Accepted November 16, 2005
Published December 27, 2005

ABSTRACT. The coat protein (CP) of the family Luteoviridae is directly associated with the success of infection. It participates in various steps of the virus life cycle, such as virion assembly, stability, systemic infection, and transmission. Despite its importance, extensive studies on the molecular evolution of this protein are lacking. In the present study, we investigate the action of differential selective forces on the CP coding region using maximum likelihood methods. We found that the protein is subjected to heterogeneous selective pressures and some sites may be evolving near neutrality. Based on the proposed 3-D model of the CP S-domain, we showed that nearly neutral sites are predominantly located in the region of the protein that faces the interior of the capsid, in close contact with the viral RNA, while highly conserved sites are mainly part of b-strands, in the protein’s major framework.

Key words: Neutral evolution, Maximum likelihood, PAML

 

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