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BIOINFORMATICS

Evolutionary Dynamics of the DNA-Binding Domains in Putative R2R3-MYB Genes Identified from Rice Subspecies indica and japonica Genomes^1,[w]

Department of Biological Sciences, Wichita State University, Wichita, Kansas 67260 (L.J.); Departments of Botany and Plant Science (M.T.C.) and Computer Science (T.J.), University of California, Riverside, California 92521

The molecular evolution of the R2R3-MYB gene family is of great interest because it is one of the most important transcription factor gene families in the plant kingdom. Comparative analyses of a gene family may reveal important adaptive changes at the protein level and thereby provide insights that relate structure to function. We have performed a range of comparative and bioinformatics analyses on R2R3-MYB genes identified from the rice (Oryza sativa subsp. japonica and indica) and Arabidopsis genome sequences. The study provides an initial framework to investigate how different evolutionary lineages in a gene family evolve new functions. Our results reveal a remarkable excess of non-synonymous substitutions, an indication of adaptive selection on protein structure that occurred during the evolution of both helix1 and helix2 of rice R2R3-MYB DNA-binding domains. These flexible -helix regions associated with high frequencies of excess non-synonymous substitutions may play critical roles in the characteristic packing of R2R3-MYB DNA-binding domains and thereby modify the protein-DNA interaction process resulting in the recognition of novel DNA-binding sites. Furthermore, a co-evolutionary pattern is found between the second -helix of the R2 domain and the second -helix of the R3 domain by examining all the possible -helix pairings in both the R2 and R3 domains. This points to the functional importance of pairing interactions between related secondary structures.

¹ This work was supported in part by the National Science Foundation Information Technology Research (ITR); (grant no. ACI–0085910 to T.J. and M.T.C.), by the National Key Project for Basic Research (973; grant no. 2002CB512801 to T.J.), and by the National Institutes of Health (grant no. P20 RR16475 from the Biomedical Research Infrastructure Network Program of the National Center for Research Resources).

^[w] The online version of this article contains Web-only data.

^* Corresponding author; e-mail li.jia{at}wichita.edu; fax 316-978-3772.

Received May 22, 2003; returned for revision August 1, 2003; accepted November 8, 2003.

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