Background
The integrity of genomes of all living organisms is continuously being challenged by different environmental agents and metabolic by-products. Consequently, evolution has provided organisms with several DNA repair and recombination (DRR) pathways to remove or to tolerate lesions in their genetic material and maintain the integrity of genome. Thus DRR is not only a fundamental cellular process for protecting cells against the damage, but is also indispensable to ensure faithful transmission of genetic information from one generation to the next. In fact, these partly redundant machineries have at least two important contrasting roles in evolution, escorting the genome, and allowing for a certain level of mutations during evolution. The decisive balance of these two activities is perhaps the best reason for the high levels of conservation observed in DRR related proteins, even across the three domains, Bacteria, Archaea and Eukarya [1-3].
The effect of environmental change on ecosystem scales responses and on the life processes of individual organisms has been a major environmental issue for the last three decades. Understanding of how species may evolve in response to environmental changes remains relatively unclear, particularly for plants. Plants, because of their intrinsic immobility, are constantly exposed to various environmental agents and endogenous processes that impose damage to DNA and cause genotoxic stress, which can reduce plant genome stability, growth and productivity. Like any other organisms plants employ a wide variety of strategies to either reverse, excise, or tolerate the presence of DNA damage products. Although repair and damage tolerance mechanisms have been thoroughly described in E. coli, Saccharomyces cerevisiae, rodents and human, surprisingly little is known about these processes in plants. However, in recent years, there has been increased interest in plant DRR and in using plants as models for understanding the under lying mechanism of DRR [4].
Our research interest lies mainly with understanding the coordination between replication and repair machinery in higher plant genome with special emphasis on the role of single subunit, short gap- filling family-X DNA polymerase orthologues in plant DNA replication and repair (DNA polymerase λ) [5-9]. Previously few attempts have been made to study the different repair pathway in plants at genome level but they were limited to either gene identification or single pathway only [10,11]. Recent study has reported in detail about the core DNA replication machinery in rice and Arabidopsis [12]. Previously, we carried out an in silico analysis to study the sequential, structural and phylogenetic features of BRCT (breast cancer susceptibility C-terminus) domain in higher plant genome and investigated the distribution of this module in various proteins in higher plants in relation to the functional significance of these proteins in plant DNA damage and repair [13]. However detailed knowledge about the sequential, structural and evolutionary properties of the genes involved in plant DRR events is still very limited.
In this article, we have made an attempt to systemically analyze the genomes of the two fully sequenced and well explored plants, Arabidopsis (a dicot) and rice (a monocot), to investigate the presence and evolution of genes known to be involved in DRR in other organisms. We have found that some repair machinery is very well conserved in plant genomes whereas others have diverged more rapidly. In addition, several genes involved in different repair pathways are found to be duplicated in both the genomes. To further gain insight into plant DRR components, we have combined published experimental information with our own bioinformatics analysis of genomic sequence data. We observed that the genes involved in DRR are, in general, part of the cell core metabolic pathways and showed significant similarity in different genomes while intriguing differences indicating biological diversity in plant responses to DNA damage. Overall this in silico study provides important information regarding DRR pathways in plants and represents a useful starting place for further research on the functional characterization of the proteins involved in plant DNA metabolism and the evolution of DRR genes in higher plant genomes.