A phylogenomic study of DNA repair genes, proteins, and processes

Abstract

The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extreme environments). Unfortunately, while repair processes have been studied in quite a few species, the ecological and evolutionary diversity of such studies has been limited. Complete genome sequences can provide potential sources of new information about repair in different species. In this paper, we present a global comparative analysis of DNA repair proteins and processes based upon the analysis of available complete genome sequences. We use a new form of analysis that combines genome sequence information and phylogenetic studies into a composite analysis we refer to as phylogenomics. We use this phylogenomic analysis to study the evolution of repair proteins and processes and to predict the repair phenotypes of those species for which we now know the complete genome sequence.

Figure 1. Demonstration of using evolutionary distribution patterns to trace gene gain and loss

An evolutionary tree of the relationships among some representatives of the bacteria, Archaea, and eukaryotes is shown. Presence of genes in these species is indicated by a colored box at the tip of the terminal branches of the tree. Gain and loss of the gene is inferred through parsimony reconstruction techniques. Within the bacterial part of the tree, we divide the species into major phyla but have collapsed the branches joining the different phyla to indicate that the relationships among these phyla are ambiguous.

Figure 2

Schematic diagram of an alignment of alkyltransferase genes.

Figure 3. Evolutionary gain and loss of DNA repair genes

The gain and loss of repair genes is traced onto an evolutionary tree of the species for which complete genome sequences were analyzed. Gain and loss were inferred by methods described in the main text. Origins of repair genes (+) are indicated on the branches while loss of genes (−) is indicated along side the branches. Gene duplication events are indicated by a “d” while possible lateral transfers are indicated by a “t”.