Kaïs Ghedira

By Cherif Benhamda, Alia Benkahla, Slimane Ben Miled, Houria Ouled- Haddar, María del Carmen Montero-Calasanz, Maher Gtari, Ameur Cherif, Benjamin Hofner, Kaïs Ghedira and Haïtham Sghaier

The extremely radioresistant eubacterium Deinococcus radiodurans and the phenotypically related prokaryotes, whose genomes have been completely sequenced, are presently used as model species in several laboratories to study the lethal effects of DNA-damaging and protein-oxidizing agents, particularly the effects of ionizing radiation (IR). Unfortunately, providing relevant information about radioresistant prokaryotes (RP) in a neatly centralized and organized manner still remains a need. In this study, we designed RadioP1 Web resource (www.radiop.org.tn) to gather information about RP defined by the published literature with specific emphasis on (i) predicted genes that produce and protect against oxidative stress, (ii) predicted proteins involved in DNA repair mechanisms and (iii) potential uses of RP in biotechnology. RadioP1 allows the complete RP proteogenomes to be queried using various patterns in a user-friendly and interactive manner. The output data can be saved in plain text, Excel or HyperText Markup Language (HTML) formats for subsequent analyses. Moreover, RadioP1 provides for users a tool “START ANALYSIS”, including the previously described R-packages “drc” and “lethal”, to generate exponential or sigmoid survival curves with D10 and D50 values. Furthermore, when accessible, links to external databases are provided. Supplementary data will be included in the future when the sequences of other RP genomes will become available.

Part of the book: Evolution of Ionizing Radiation Research

By Kaïs Ghedira, Houcemeddine Othman, Taieb Saied, Zouhair Majdi Baccar, Faouzi Hosni, Ahmed Hichem Hamzaoui, Kaliannan Thamaraiselvi, Hafedh Abdelmelek, Najet Srairi-Abid, Maria Clara Costa and Haïtham Sghaier

S-layers are crystalline arrays formed by proteinaceous subunits that cover the outer surface of many different kinds of microorganisms. This “proteinaceous cover” is particularly important in the case of ionizing-radiation-resistant bacteria (IRRB) that might be used in bioremediating hazardous and radioactive wastes (HRW). Despite the exponential growth in the number of comparative studies and solved proteic crystal structures, the proteic networks, diversity, and bioremediation-useful structural properties of IRRB S-layers remain unknown. Here, aided by literature, a tentative model of Deinococcus radiodurans R1 S-layer proteins (SLPs) and the network of its main constituents were proposed. The domain analysis of this network was performed. Moreover, to show the diversity of IRRB S-layers, comparative genomics and computer modeling experiments were carried out. In addition, using in silico modeling, assisted by previously published data, the outermost exposed segments of D. radiodurans SlpA (surface layer protein A) that were predicted to interact with uranium were mapped. The combination of data and results pointed to various prospective applications of IRRB S-layers in nanobiotechnology for bioremediation of radioactive waste.

Part of the book: Management of Hazardous Wastes