Conservation of pathway
We next investigated the degree of conservation of DRR pathways. Conservation of DNA safeguarding pathways during evolution was calculated by the average conservation in amino acids and presence/absence of proteins belonging to a given pathway (Figure 1, Additional file 1). Component of different pathways have been defined according to KEGG pathway database. Pathway conservation was measured in three different categories: conservation between rice and human proteins (Figure 1a), conservation between Arabidopsis and human proteins (Figure 1b) and conservation between Arabidopsis and rice proteins (Figure 1c). Plants possess few prokaryotes and Saccharomyces cerevisiae specific DRR proteins also therefore E. coli and Saccharomyces cerevisiae specific proteins were used to compare the conservation level with its plants counterparts. Thus E. coli and Saccharomyces cerevisiae proteins replaced the human proteins in plant-human protein conservation categories and represented as white circles (Figure 1a and 1b). Proteins which are involved in several pathways were also included in each pathway to calculate the average conservation score. The best example was the MRN complex, classified in both NHEJ and HR pathway. In addition to the presence of several interconnections, pathway such as NER was more conserved than others in terms of amino acid identity. All genes of NER pathway revealed a high degree of sequence similarity with their counterparts present in other genomes (Figure 1). In human and plant pairs, NER, BER and HR pathways were very close in terms of identity of amino acid while in Arabidopsis-rice pair, NER and NHEJ pathways were closer to each other, while considering the characteristics of amino acid identity.
Figure 1  Conservation of different DNA repair pathways. Values of Smith-Waterman identity scores for conserved proteins in core DRR pathways. Each dot corresponds to a pairwise alignment between a protein and its orthologs. Eukaryotes specific proteins are represented by dark circles while prokaryotes specific proteins are represented by white circles (see text). Average identity of each pathway is indicated above the 100% line. In terms of absence or presence of a particular protein involved in a given pathway, NER and MMR were found to be most conserved pathways where merely all components were present while NHEJ and BER were least conserved pathways of genome maintenance. All components of both sub-pathways of NER, transcription-coupled repair (TCR) and global genome repair (GGR) pathways were well conserved in both genomes except the xeroderma pigmentosum complementation group A (XPA) gene which is involved in the damage-recognition step of the NER processes, while all genes which are reported to be involved in eukaryotic MMR pathway are present in plants. Difference in term of copy number of genes as seen in BER and NER pathway was not found in MMR specific proteins may suggest the universal and utmost functional importance of this pathway. It was also found that all subunit of a multimeric protein were not conserved with similar rate during evolution. For example, POLD1 subunit of Delta-type DNA polymerase holoenzymes (pold) was always more conserved (At-Hs -54.1%, Os-Hs-55.4%) than the other subunits while POLD3 subunit was always least conserved (At-Hs -25.1%, Os-Hs -21.4%) (Figure 1). Rbx1, an ubiquitin ligase, was the most conserved gene in plant DRR pathways. Plants Rbx1 genes showed more than 80% identity to its human homolog. PCNA, DMC and RAD51A were the other much conserved proteins which showed more than 60% identity at amino acid level in plant-human pair. POLD3, PRKDC, RPA3, XRCC4 and NBS1 proteins were the least conserved genes in plant-human pair which shared less than 25% amino acid. In terms of difference in number of paralogs, MMR and NHEJ were much conserved. In both pathways, similar number of paralogs was found in Arabidopsis and rice genomes except few exceptions like MRE11 and FEN1. This result may suggest that MMR and NHEJ pathway have been naturally preserved as such through out plant genome evolution. Our analysis suggested that plant DRR machinery is more closely related to human as compared to yeast because plants retain more mammalian homologs than the yeast counterparts.
Plants homologs of bacterial DRR gene have very low sequence similarity but retention of conserved domain probably suggested the functional conservation of those proteins. Bacterial homologs were found in all pathways except NHEJ. These prokaryotic and yeast specific genes are not well explored in plant genomes except the bacterial RecA gene. RecA, a gene central to general DNA repair and recombination in bacteria, was found to be most conserved bacterial homolog in plant which showed more than 40% amino acid identity in both genomes in comparison to RecA of E. coli. Arabidopsis encodes orthologs of bacterial RecA proteins which are targeted to chloroplasts [14,15] and mitochondria [16] and reported to be associated with DNA repair [16,17]. Complexes of different proteins plays pivotal role in DNA repair processes. We found that plants appeared to retain a partner of bacterial protein complexes while loose other partners. So, in the absence of partner how these bacterial proteins work would be an important question for further investigation.