DNA repair and recombination in higher plants: insights from comparative genomics of arabidopsis and rice

Abstract

BackgroundThe DNA repair and recombination (DRR) proteins protect organisms against genetic damage, caused by environmental agents and other genotoxic agents, by removal of DNA lesions or helping to abide them.ResultsWe identified genes potentially involved in DRR mechanisms in Arabidopsis and rice using similarity searches and conserved domain analysis against proteins known to be involved in DRR in human, yeast and E. coli. As expected, many of DRR genes are very similar to those found in other eukaryotes. Beside these eukaryotes specific genes, several prokaryotes specific genes were also found to be well conserved in plants. In Arabidopsis, several functionally important DRR gene duplications are present, which do not occur in rice. Among DRR proteins, we found that proteins belonging to the nucleotide excision repair pathway were relatively more conserved than proteins needed for the other DRR pathways. Sub-cellular localization studies of DRR gene suggests that these proteins are mostly reside in nucleus while gene drain in between nucleus and cell organelles were also found in some cases.ConclusionsThe similarities and dissimilarities in between plants and other organisms' DRR pathways are discussed. The observed differences broaden our knowledge about DRR in the plants world, and raises the potential question of whether differentiated functions have evolved in some cases. These results, altogether, provide a useful framework for further experimental studies in these organisms.

An efficient gene targeting system using homologous recombination in plants

“…1). 모든 진핵생물에서 Ku70, Ku80, Lig4는 NHEJ에 주요하게 관여한다고 보고되어 있 다 (Singh et al 2010;Symington and Gautier 2011). 애기장대 에서 AtLig4의 결손으로 AGL4 유전자의 GT 빈도가 증가 되었으며 (Tanaka et al 2010), 벼에서는 Ku70/80과 Lig4의 억제로 HR의 빈도가 증가되었다(Nishizawa-Yokoi et al 2012).…”

UV Damaged DNA Repair & Tolerance in Plants

“…In plants genes encoding CPD photolyases have been identified in Arabidopsis thaliana (Ahmed et al, 1997), cucumber (Takahashi et al, 2002), rice (Hirouchi et al, 2003), spinach (Yoshihara et al, 2005), and soybean (Yamamoto et al, 2008). Genes encoding 6-4 PP photolyases have been identified in Arabidopsis and rice (Chen et al, 1994;Singh et al, 2010). In Arabidopsis, the highest levels of both photolyases are associated with floral tissues, which may presumably serve to minimize lesions in germline cells.…”

“…Bioinformatic analysis of the plant NER protein machinery suggests the molecular mechanisms are largely but not entirely conserved with that of the extensively studied yeast S. cerevisiae and mammalian cells Kunz et al, 2005Kunz et al, , 2006. NER in plants has been studied primarily in rice and Arabidopsis (Singh et al, 2010). Many Arabidopsis NER related genes were initially isolated by analysis of UV hypersensitive (uvh) and UV repair defective (uvr) mutants which were subsequently mapped to homologues of the human XP genes (Table 1).…”

Recognition and Repair Pathways of Damaged DNA in Higher Plants

“…One strategy plants seem to have adopted to manage the higher demands on DNA repair is redundancy. For instance, genes of every pathway discussed here were found to be duplicated in Arabidopsis or rice (Singh et al, 2010). Additionally the existence of both 8-oxo-guanine glycosylases, OGG1, as well as MutM/Fpg in Arabidopsis demonstrate functional redundancy of independent, alternative repair pathways, which may have originated from the incorporation of chloroplast and mitochondrial genes into the nuclear genome (Boesch et al, 2009;Singh et al, 2010;Rowan et al, 2010).…”

“…For instance, genes of every pathway discussed here were found to be duplicated in Arabidopsis or rice (Singh et al, 2010). Additionally the existence of both 8-oxo-guanine glycosylases, OGG1, as well as MutM/Fpg in Arabidopsis demonstrate functional redundancy of independent, alternative repair pathways, which may have originated from the incorporation of chloroplast and mitochondrial genes into the nuclear genome (Boesch et al, 2009;Singh et al, 2010;Rowan et al, 2010). Probably because of these gene duplications, functional redundancies, and more efficient or alternative pathways in comparison to animals, plants often have greater flexibilities in how they can respond to and potentially tolerate damaged DNA and mutations.…”