Molecular evolution and positive Darwinian selection of the gymnosperm photosynthetic Rubisco enzyme

摘要

Although it was found that gymnosperm rbcL of three orders evolves under Darwinian positive selection, it is not clear whether rbcL in other gymnosperm lineages is also subject to positive selection. In this study, eleven gymnosperm groups, representing 393 species at various evolutionary levels, were used to illustrate the molecular adaptation and evolutionary dynamics of gene divergence in rbchs. rbcL sequences were amplified from 21 Taxaceae and 10 Cephalotaxaceae species. rbcL sequences of otherspecies were retrieved from GenBank. Selective influences were investigated using standard dN/dS ratio methods and more sensitive techniques investigating the amino acid property changes resulting from nonsynonymous replacements in a phylogenetic context. Analyses revealed the presence of positive selection in rbcLs of all gymnosperm groups. Twenty most often positively selected amino acid sites were characterized. In Taxaceae and Cephalotaxaceae, seven amino acid properties, equilibrium constant of ionization -COOH as the most significant, were found to be influenced by destabilizing positive selection. Some amino acid sites relating to these properties were found to be involved in active site, intradimer interaction, dimer-dimer interaction, and interactions with Rubisco small subunits. Moreover, removing amino acid sites that are under positive selection has significant effect on the bootstrap values of phylogenetic reconstruction. Our results suggest that the conservative rbcL evolves under positive selection in gymnosperm lineages. Several regions of rbcL have experienced molecular adaptation which fine-tunes photosynthetic Rubisco performance.