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Project Progress

A major goal of Astrobiology is to understand the circumstances and processes underlying the evolution of life on Earth. The development of early life and multicellular complexity depended upon close genome-genome interactions among microbial symbionts, ranging from commensal associations within populations to the extreme genomic integration represented by obligate endosymbiosis and organelles. Among bacteria, the acquisition of a strictly endosymbiotic lifestyle has resulted in gene loss, elevated mutational biases, and increased rates of protein evolution. We aim to decipher the molecular and evolutionary processes that drive this so-called genome "degradation" in endosymbionts, and to examine their phenotypic effects on the host and symbiont alike. To date, we have focused on Buchnera aphidicola, the obligate bacterial mutualists of aphids, as a model system to explore genome changes that are coupled with an intracellular lifestyle.

Availability of the complete genome sequence of Buchnera allows comparisons with its close free-living relatives in the enterobacteria (e.g. E. coli). To elucidate factors shaping genome-wide patterns of protein evolution, we compared patterns of amino acid and codon usage across the Buchnera and E. coli genomes (Palacios and Wernegreen 2002). We performed correspondence analysis (COA) to identify the major biological factors shaping protein evolution at 479 loci from Buchnera and 2,919 loci from E. coli. Across the AT-rich Buchnera genome, we found a strong effect of mutational bias on amino acid composition, indicating that biased DNA replication errors and/or DNA repair severely affect protein evolution in this endosymbiont, with important implications for protein structure and stability. Furthermore, we found distinct amino acid profiles at high and low expression genes in Buchnera. High expression Buchnera genes are biased toward amino acids that use relatively GC-rich codons, suggesting relatively strong selection against AT-rich codons. We also found significant evidence for selection on hydrophobicity of integral membrane proteins, and selection against aromatic amino acids at high expression Buchnera loci. Therefore, selection in Buchnera is sufficient to drive variation in amino acid content of proteins with different expression levels. Further comparisons of other endosymbiont genomes will provide a comparative framework to determine whether bacterial species with similar lifestyles show parallel modes of evolution, and whether processes shaping amino acid usage in Buchnera extend to other endosymbiont species.