Basal DNA repair machinery is subject to positive selection in ionizing-radiation-resistant bacteria

<p>Abstract</p> <p>Background</p> <p>Ionizing-radiation-resistant bacteria (IRRB) show a surprising capacity for adaptation to ionizing radiation and desiccation. Positive Darwinian selection is expected to play an important role in this trait, but no data are currently available regarding the role of positive adaptive selection in resistance to ionizing-radiation and tolerance of desiccation. We analyzed the four known genome sequences of IRRB (<it>Deinococcus geothermalis</it>, <it>Deinococcus radiodurans</it>, <it>Kineococcus radiotolerans</it>, and <it>Rubrobacter xylanophilus</it>) to determine the role of positive Darwinian selection in the evolution of resistance to ionizing radiation and tolerance of desiccation.</p> <p>Results</p> <p>We used the programs MultiParanoid and DnaSP to deduce the sets of orthologs that potentially evolved due to positive Darwinian selection in IRRB. We find that positive selection targets 689 ortholog sets of IRRB. Among these, 58 ortholog sets are absent in ionizing-radiation-sensitive bacteria (IRSB: <it>Escherichia coli </it>and <it>Thermus thermophilus</it>). The most striking finding is that all basal DNA repair genes in IRRB, unlike many of their orthologs in IRSB, are subject to positive selection.</p> <p>Conclusion</p> <p>Our results provide the first <it>in silico </it>prediction of positively selected genes with potential roles in the molecular basis of resistance to γ-radiation and tolerance of desiccation in IRRB. Identification of these genes provides a basis for future experimental work aimed at understanding the metabolic networks in which they participate.</p

The RadioP1 – An Integrative Web Resource for Radioresistant Prokaryotes

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

Insights into Ionizing-Radiation-Resistant Bacteria S-Layer Proteins and Nanobiotechnology for Bioremediation of Hazardous and Radioactive Waste

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

Ionizing-radiation-resistant Kocuria rhizophila PT10 isolated from the Tunisian Sahara xerophyte Panicum turgidum: Polyphasic characterization and proteogenomic arsenal

14 páginas, 5 tablas, 4 figurasA new strain belonging to the genus Kocuria, designed PT10, was isolated from irradiated roots of the xerophyte Panicum turgidum. Isolate PT10 is a Gram-positive, coccoid, aerobic and ionizing-radiation (IR)-resistant acti-nobacterium. PT10 has shown an ability to survive under extreme conditions, such as gamma irradiation, desiccation and high concentration of hydrogen peroxide. Phenotypic, chemotaxonomic and comparative genome analyses support the assignment of strain PT10 (LMG 31102 =DSM 108617) as Kocuria rhizophila. The complete genome sequence of PT10 consists of one chromosome (2,656,287 bps), with a 70.7% G +C content and comprises 2481 protein-coding sequences. A total of 1487 proteins were identified by LC-MS/MS profiling. In silico analyses revealed that the proteome of the oxidation-tolerant PT10 possesses several features explaining its IR-resistant phenotype and many adaptive pathways implicated in response to environmental pressures — desiccation, cold, reactive oxygen species and other stressors.This work was performed under the auspices of Université Lyon 1, UMR 5557, Ecologie Microbienne (France) and the National Center for Nuclear Sciences and Technologies CNSTN (MESRS, Tunisia) and in the ambit of the BIODESERT research program of the LR11-ES31 (BVBGR, ISBST, University of Manouba (MESRS, Tunisia). The LABGeM (CEA/ Genoscope & CNRS UMR8030), the France G ́enomique and French Bioinformatics Institute national infrastructures (funded as part of Investissement d’Avenir program managed by Agence Nationale pour la Recherche, contracts ANR-10-INBS-09 and ANR-11-INBS-0013) are acknowledged for support within the MicroScope annotation platform. We thank Betty Bigai, Corinne Sannaire and platform Genomique Environnementale PGE, UMR CNRS 5557 for technical supportPeer reviewe