Evolution of base composition in T-DNA genes from Agrobacterium

Résumé

T-DNA genes on Ti and Ri plasmids from Agrobacterium are replicated and repaired in bacteria but expressed in plant cells. Therefore, they can be useful tools to disclose the relative roles played by the two main mechanisms involved in the evolution of DNA base composition: (1) mutational bias along DNA replication/repair processes and (2) selective gene expression constraints. We compare the base-compositional features of 15 T-DNA genes with those of (1) other genes located on Ti or Ri plasmids but outside the T- DNA region (non-T-DNA genes) and (2) a sample of nuclear genes from a natural host plant species (tobacco). The similarity in G+C content found between T- DNA and plant genes at replacement sites, as well as the similar stronger avoidance of CpG at II-III codon positions, support an ancestral plant origin for T-DNA genes. When G+C content and codon usage are considered, T-DNA genes are more similar to non-T-DNA genes than to those of plants, indicating that the mutational bias along replication and repair processes in bacteria is the major factor driving the global compositional properties of T-DNA genes. However, when the reduction in the available CpG methylation targets and the distribution of these avoidances on the different codon positions are considered, T-DNA genes are more similar to those of plants than they are to the other plasmid genes. The requirements for expression of T-DNA genes in the plant cells would have modulated the compositional features of their sequences, mainly CpG avoidance.