Functional diversity of DRR genes
Many DRR proteins display a number of diverse activities unrelated to their DRR processes. Their role in normal plant growth and development is well established [28,29]. We have used DRR genes in plants to investigate functional diversity and complexity of genome maintenance pathways. To gain insight into the functional diversity of predicted rice and Arabidopsis DRR, Gene Ontology (GO) annotations (GO Consortium, 2001) were explored. This analysis has revealed that the largest number of DNA replication and repair genes, 21.51% and 18.84% for rice and Arabidopsis respectively, fall into the DNA binding molecular functional categories. As expected, relatively good number of genes (38.65% and 32.04% of total DRR genes of rice and Arabidopsis respectively) falls in DNA metabolic process biological process category (Figure 3). It was interesting to note that a large fraction, 25.46% of rice and 28.28% of Arabidopsis DRR pathway were found to respond against stress. However, a significantly large number of DRR genes fall into cell cycle, protein modification process and biosynthetic process biological process categories compared to total genes analyzed, indicating their crucial role in fundamental cellular processes. Although sixty nine genes of rice were found without any GO annotation but percentage of genes predicted under various molecular function and biological process categories were similar for both rice and Arabidopsis probably indicating towards the high conservation of DRR process.
Figure 3  Functional categorization of rice and Arabidopsis DRR genes: biological process (a, b) and molecular function (c, d) were determined for rice (a, c) and Arabidopsis (b, d) DRR genes and percentage of genes included in each category are given. Molecular functions are: DNA binding DB, transcription regulator activity TRA, hydrolase activity HA, protein binding PB, nucleotide binding NB, signal transducer activity TFA, kinase activity KA, receptor activity RA, enzyme regulator activity ERA, catalytic activity CA, nucleic acid binding NAB, nuclease activity NA, transferase activity TA. Biological processes are: cellular component organization CCO, DNA metabolic process DMP, biosynthetic process BP, metabolic process MP, signal transduction ST, nucleobase, nucleoside, nucleotide and nucleic acid metabolic process NAM, protein metabolic process PMP, response to stress RS, carbohydrate metabolic process CMP, protein modification process PMoP, catabolic process CP, cell cycle CCO.