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MBE Advance Access published online on September 8, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msj007
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted August 30, 2005

Research Article

Coevolution of DNA-Interacting Proteins and Genome "Dialect"

A. Paz 1, V. Kirzhner 1, E. Nevo 1, and A. Korol 1*

1 Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel

* To whom correspondence should be addressed.
A. Korol, E-mail: korol{at}esti.haifa.ac.il


  Abstract

Several species-specific characteristics of genome organization that are superimposed on its coding aspects were proposed earlier, including genome signature, genome accent and compositional spectrum. These notions could be considered as representatives of genome dialect. We measured within the proteobacteria some genome dialect representatives: The relative abundance of dinucleotides, or genome signature; the profiles of occurrence of 10 nucleotide words" (compositional spectra), and the profiles of occurrence of 20 nucleotide words, using a degenerate two letter alphabet (purine-pyrimidine compositional spectra). Here, we show that the evolutionary distances between DNA repair and recombination orthologous enzymes (especially those of the nucleotide excision repair system) are highly correlated with purine-pyrimidine compositional spectra and genome signature distances. Orthologous proteins involved in structural or metabolic processes (control group), have significantly lower correlations of their evolutionary distances with the purine-pyrimidine compositional spectra and genome signature distances. We hypothesize that the high correlation of the evolutionary distances of the DNA repair orthologous enzymes with their genome's dialect is a result of the coevolution of the DNA repair enzymes structures and genome dialects. Species genome dialects could be substantially influenced by the function of DNA polymerase I (the bacterial major DNA repair polymerase). This might cause the correlation of species genome dialects differentiation with evolutionary changes of species DNA polymerase I. Simultaneously, the structures of DNA repair-recombination enzymes might be evolutionary sensitive and responsive to changes in the structure of their substrate - the DNA (including those that are represented by genome dialect differentiation). We further discuss the rationale and mechanisms of the hypothesized coevolution. We suggest that stress might be an important cause of changes in the repair-recombination genes and the genome dialect, and the trigger of the aforementioned coevolution process. Other triggers might be massive horizontal gene transfer and ecological selection.

Keywords: Genome dialect; genome signature; compositional spectrum; DNA repair; stress.
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