Metabolic and translational efficiency in microbial organisms

Metabolic efficiency, as a selective force shaping proteomes, has been shown to exist in Escherichia coli and Bacillus subtilis and in a small number of organisms with photoautotrophic and thermophilic lifestyles. Earlier attempts at larger-scale analyses have utilized proxies (such as molecular weight) for biosynthetic cost, and did not consider lifestyle or auxotrophy. This study extends the analysis to all currently sequenced microbial organisms that are amenable to these analyses while utilizing lifestyle specific amino acid biosynthesis pathways (where possible) to determine protein production costs and compensating for auxotrophy. The tendency for highly expressed proteins (with adherence to codon usage bias as a proxy for expressivity) to utilize less biosynthetically expensive amino acids is taken as evidence of cost selection. A comprehensive analysis of sequenced genomes to identify those that exhibit strong translational efficiency bias (389 out of 1,700 sequenced organisms) is also presented.