Comparative genomic approach to elucidate the underlying capabilities of radio tolerance in the members of Genus Deinococcus

Abstract

newline vii newlineABSTRACT newlineRadioresistant bacteria (RRB) are an important class of extremophiles. RRB belong to several genera but almost all the members of Deinococcus genus have radioresistant property. This important class of organism is relatively less studied as compared to other extremophiles such as thermophiles Deinococcus radiodurans (D. radiodurans) is the most important RRB. Along with the evolutionary role, radioresistant organisms play important role in paper industries, bioremediation, vaccine development and possibility in anti-ageing and anti-cancer treatment. newlineThe most of the radioresistant mechanism present in organism known till date reside in cytosolic region e.g. DNA repair mechanisms, high antioxidant activity and cell cleansing system. The outer area of radioresistant bacteria cell has been relatively less studied in context to radioresistance (proteins/mechanism). Although the outer area is more exposed to radiation as cytosolic region. Novel localization based comparative study of proteome from RRB and non-radioresistant bacteria (NRRB) was carried out to identify proteins/mechanism present in outer area of RRB important in radioresistance (RR). In RRB 20 unique proteins have been identified. Further domain, structural, and pathway analysis of selected proteins were carried out. Out of 20 proteins, 8 proteins were found to have direct involvement in RR and literature study strengthens this, however, 1 proteins had assumed relation in RR. Selected radioresistant proteins may be helpful for optimal use of RRB in the industry and health care. newlineDeinococcus genus which is comprised of mostly RR bacteria and D. radiodurans are known to the toughest bacterium in terms of RR. Thermus are closely related with Deinococcus and thought to have a common ancestor but none of Thermus species are known to be RR while in Deinococcus most of the species are radioresistant in nature. The Deincoccus and Thermus have different extremophilic property that can be studied through pangenome approach and using comparative genomics which describes its ancestral relationship and their properties. newlineLimited comparative study between D. radiodurans and T. thermophilus had in literature but comparative study of different genomes of Deinococcus and Thermus have not studied. In current work, 11 species of Deinococcus and 7 species of Thermus were taken for pangenome analysis. Pangenome of Deinococcus species comprises of core genes, accessory genes, unique genes and exclusively absent genes. In pangenome analysis of Deinococcus species higher number of unique gene were present in D. peraridilitoris which suggest its acquisition of more newlineviii newlineunique genes due to the adaptive advantage to different environment. In case of D. proteolyticus exclusively absent genes were high and accessory genes were less in this species. D. proteolyticus undergo genome reduction and maintain relatively small size as compared to other RRB. Further comparative analysis revealed that Deinococcus gained 69 genes and lost 114 genes when they diverge from there common ancestor. newlineThe function-based comparison was performed on selected Deinococcus species according to their habitat. In pairwise comparison, D. radiodurans and D. geothermalis have more common genes in different metabolisms which revealed these bacteria are closely related to each other. In Escherichia coli (E.coli), unique genes were more in number in most of the metabolism which correlates bigger genome size as compared to other selected bacteria taken for the study. Iron acquisition metabolism was present in only soil species of Deinococcus whereas phosphorus metabolism was present in every species of radioresistant bacteria. newlinePangenome analysis would be helpful to understand the ancestral lineage of Deinococcus and Thermus. Pangenome analysis also provides the information related to unique and common genes according to habitat in different species. Through this analysis it also helpful to correlate function wise similarity in various important species. newlineKeywords: Subcellular localization, Comparative genomics, Radioresistant bacteria, Non-radioresistant bacteria, Conservation, Pangenome, Core genes, Accessory genes, Unique gene, Exclusively absent genes, Common genes.