Abstract
The bacterium Deinococcus deserti is well known for their higher radiation-resistance properties. Their mode of interactions with radiation is poorly explored. However, no attempt has been made on radiation-specific protein–protein interaction network construction for their radiation-resistance property. This investigation aimed to establish the radiation-specific RNA-seq co-expression network along with an experimentally validated protein (deletion or site-specific mutation analysis, 2D gel electrophoresis, followed by mass spectroscopy and qPCR analysis)-based network of D. deserti to explore the radiation-specific global protein interactome, biological processes, and metabolic pathways. Furthermore, topologically important proteins from each network have been predicted to identify the centrally important radiation-specific biological responses using Gene Ontology and KEGG: Kyoto Encyclopedia of Genes and Genomes. Along with the DNA repair processes, we decipher that the nucleoid and/or chromosome structure maintenance, cellular cleansing system, production of secondary metabolites and antioxidants are the major biological processes involved in radiation-related stress responses. This study also predicted a few topologically important uncharacterized proteins. Amongst them, Deide_20140 and Deide_19830 are common from both the networks that could potentially be involved in the regulation of radiation stress responsive pathways of D. deserti, which needs further study. So the radiation survival property of D. deserti is a multidimensional phenomenon where proposed proteins and their biological processes might give a global picture with higher resolution. The molecular modules identified hare provide new directions for further validation and understanding of the stress resistance phenotype, which have tremendous applications on radiation exposure mitigation.
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The authors are thankful to the Department of Life Science and Biotechnology, Jadavpur University, for carrying the research. The authors also acknowledge the Department of Biotechnology (DBT), India, for providing student fellowship (Grant No. DBT/2016/JU/732).
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Conceptualization: TN and PKD. Data curation: TN. Formal analysis: TN. Writing—review and editing: TN and PKD. Investigation: PKD. Data availability statement.
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Nayak, T., Dhal, P.K. Global protein interactome of Deinococcus deserti reveals their strategies for radiation resistance. Netw Model Anal Health Inform Bioinforma 12, 27 (2023). https://doi.org/10.1007/s13721-023-00422-5
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DOI: https://doi.org/10.1007/s13721-023-00422-5