MBE Advance Access published online on September 22, 2008
Molecular Biology and Evolution, doi:10.1093/molbev/msn210
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Research Article |
The Proteomic Constraint and its role in molecular evolution
Molecular Biology Department, University of Wyoming
Current affiliation: Biology Department, University of Puerto Rico, PO Box 23360, San Juan PR 00931, Fax: 787 7643875
E-mail: smassey{at}hpcf.upr.edu
Received for publication August 11, 2008. Accepted for publication August 26, 2008.
Recently, the concept of a ‘Proteomic Constraint’ was introduced to explain the frequency of genetic code deviations in mitochondrial genomes. The Proteomic Constraint was proposed to be proportional to the size of the mitochondrially encoded proteome, hence small proteomes are expected to experience smaller numbers of errors (genetic code deviations). The concept is now extended to encompass several other aspects of the genetic information system. When the Proteomic Constraint is small it is proposed that there is little selective pressure to evolve or maintain error correction mechanisms, as a result of the smaller total number of errors that accumulate. Conversely, a large Proteomic Constraint is proposed to result in a correspondingly large selective pressure to evolve or maintain error correction mechanisms. Differences in the size of the Proteomic Constraint can help to explain differences in replicational, transcriptional and translational fidelities between genomes. A key piece of evidence is the existence of negative power law relationships between proteome size and error rates; these are demonstrated to be diagnostic of the action of the Proteomic Constraint. The Proteomic Constraint is argued to be a major factor determining mutation rates in a diverse range of DNA genomes, implying that mutation rates are clock-like. A small Proteomic Constraint partly explains why RNA viruses possess high mutation rates. A reduced Proteomic Constraint in intracellular pathogenic bacteria predicts a drift upwards in mutation rates. Differences in the Proteomic Constraint also appear to be linked to differences in recombination rates between eukaryotes. In addition, a reduced Proteomic Constraint may explain features of resident genomes, such as loss of DNA repair pathways, increased substitution rates and AT-biases, in addition to the occurrence of genetic code deviations. Thus, it is argued that the Proteomic Constraint is a universal factor that influences a wide range of properties of the genetic information system.
Key Words: proteomic constraint • error rate • mutation rate • codon reassignment • resident genome