Ultraviolet-B Radiation Stress-Induced Toxicity and Alterations in Proteome of Deinococcus radiodurans

Deinococcus radiodurans is a polyextremophilic bacterium capable to survive and grow at high doses of ionizing radiation. Besides resistance to ionizing radiation, the bacterium is also resistant to toxic chemicals and desiccation. This study deals with the effects of non-ionizing radiation (ultraviolet-B) on survival, alterations in proteomic profile, and gene expression in D. radiodurans. Exposure of culture to UV-B caused decrease in the percentage survival with increasing duration, complete killing occurred after 16 h. D. radiodurans also showed enhancement in the generation of reactive oxygen species and activities of antioxidative enzymes. Separation of proteins by 2-dimensional gel electrophoresis revealed major changes in number and abundance of different proteins. Twenty-eight differentially abundant protein spots were identified by MALDI-TOF MS/MS analysis and divided into 8 groups including unknown proteins. Gene expression of a few identified proteins was also analyzed employing qRT-PCR, which showed differential expression corresponding to the respective proteins. In silico analysis of certain hypothetical proteins (HPs) suggested that these are novel and as yet not reported from D. radiodurans subjected to UV-B stress. These HPs may prove useful in future studies especially for assessing their significance in the adaptation and management of stress responses against UV-B stress.

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Predicted highly expressed and putative alien genes of Deinococcus radiodurans and implications for resistance to ionizing radiation damage

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.081077598 ◽

2001 ◽

Vol 98 (9) ◽

pp. 5240-5245 ◽

Cited By ~ 39

Author(s):

S. Karlin ◽

J. Mrazek

Keyword(s):

Ionizing Radiation ◽

Radiation Damage ◽

Deinococcus Radiodurans ◽

Alien Genes ◽

Resistance To Ionizing Radiation

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Experimental Evolution of Extreme Resistance to Ionizing Radiation inEscherichia coliafter 50 Cycles of Selection

Journal of Bacteriology ◽

10.1128/jb.00784-18 ◽

2019 ◽

Vol 201 (8) ◽

Cited By ~ 9

Author(s):

Steven T. Bruckbauer ◽

Joseph D. Trimarco ◽

Joel Martin ◽

Brian Bushnell ◽

Katherine A. Senn ◽

...

Keyword(s):

Escherichia Coli ◽

Dna Repair ◽

Ionizing Radiation ◽

Experimental Evolution ◽

Deinococcus Radiodurans ◽

Bacterial Species ◽

Genomic Sequencing ◽

Novel Mutations ◽

Content Type ◽

Resistance To Ionizing Radiation

ABSTRACTIn previous work (D. R. Harris et al., J Bacteriol 191:5240–5252, 2009, https://doi.org/10.1128/JB.00502-09; B. T. Byrne et al., Elife 3:e01322, 2014, https://doi.org/10.7554/eLife.01322), we demonstrated thatEscherichia colicould acquire substantial levels of resistance to ionizing radiation (IR) via directed evolution. Major phenotypic contributions involved adaptation of organic systems for DNA repair. We have now undertaken an extended effort to generateE. colipopulations that are as resistant to IR asDeinococcus radiodurans. After an initial 50 cycles of selection using high-energy electron beam IR, four replicate populations exhibit major increases in IR resistance but have not yet reached IR resistance equivalent toD. radiodurans. Regular deep sequencing reveals complex evolutionary patterns with abundant clonal interference. Prominent IR resistance mechanisms involve novel adaptations to DNA repair systems and alterations in RNA polymerase. Adaptation is highly specialized to resist IR exposure, since isolates from the evolved populations exhibit highly variable patterns of resistance to other forms of DNA damage. Sequenced isolates from the populations possess between 184 and 280 mutations. IR resistance in one isolate, IR9-50-1, is derived largely from four novel mutations affecting DNA and RNA metabolism: RecD A90E, RecN K429Q, and RpoB S72N/RpoC K1172I. Additional mechanisms of IR resistance are evident.IMPORTANCESome bacterial species exhibit astonishing resistance to ionizing radiation, withDeinococcus radioduransbeing the archetype. As natural IR sources rarely exceed mGy levels, the capacity ofDeinococcusto survive 5,000 Gy has been attributed to desiccation resistance. To understand the molecular basis of true extreme IR resistance, we are using experimental evolution to generate strains ofEscherichia coliwith IR resistance levels comparable toDeinococcus. Experimental evolution has previously generated moderate radioresistance for multiple bacterial species. However, these efforts could not take advantage of modern genomic sequencing technologies. In this report, we examine four replicate bacterial populations after 50 selection cycles. Genomic sequencing allows us to follow the genesis of mutations in populations throughout selection. Novel mutations affecting genes encoding DNA repair proteins and RNA polymerase enhance radioresistance. However, more contributors are apparent.

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Genome of the Extremely Radiation-Resistant Bacterium Deinococcus radiodurans Viewed from the Perspective of Comparative Genomics

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.65.1.44-79.2001 ◽

2001 ◽

Vol 65 (1) ◽

pp. 44-79 ◽

Cited By ~ 452

Author(s):

Kira S. Makarova ◽

L. Aravind ◽

Yuri I. Wolf ◽

Roman L. Tatusov ◽

Kenneth W. Minton ◽

...

Keyword(s):

Dna Repair ◽

Ionizing Radiation ◽

Stress Responses ◽

Deinococcus Radiodurans ◽

Repetitive Sequences ◽

Comparative Sequence Analysis ◽

Phylogenetic Tree Analysis ◽

Chronic Radiation ◽

Clusters Of Orthologous Groups ◽

Radiation Resistant

SUMMARY The bacterium Deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, UV radiation, oxidizing agents, and electrophilic mutagens. D. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. These characteristics were the impetus for sequencing the genome of D. radiodurans and the ongoing development of its use for bioremediation of radioactive wastes. Although it is known that these multiple resistance phenotypes stem from efficient DNA repair processes, the mechanisms underlying these extraordinary repair capabilities remain poorly understood. In this work we present an extensive comparative sequence analysis of the Deinococcus genome. Deinococcus is the first representative with a completely sequenced genome from a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Phylogenetic tree analysis, combined with the identification of several synapomorphies between Thermus and Deinococcus, supports the hypothesis that it is an ancient group with no clear affinities to any of the other known bacterial lineages. Distinctive features of the Deinococcus genome as well as features shared with other free-living bacteria were revealed by comparison of its proteome to the collection of clusters of orthologous groups of proteins. Analysis of paralogs in Deinococcus has revealed several unique protein families. In addition, specific expansions of several other families including phosphatases, proteases, acyltransferases, and Nudix family pyrophosphohydrolases were detected. Genes that potentially affect DNA repair and recombination and stress responses were investigated in detail. Some proteins appear to have been horizontally transferred from eukaryotes and are not present in other bacteria. For example, three proteins homologous to plant desiccation resistance proteins were identified, and these are particularly interesting because of the correlation between desiccation and radiation resistance. Compared to other bacteria, the D. radiodurans genome is enriched in repetitive sequences, namely, IS-like transposons and small intergenic repeats. In combination, these observations suggest that several different biological mechanisms contribute to the multiple DNA repair-dependent phenotypes of this organism.

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Effects of Mn and Fe Levels onBacillus subtilisSpore Resistance and Effects of Mn2+, Other Divalent Cations, Orthophosphate, and Dipicolinic Acid on Protein Resistance to Ionizing Radiation

Applied and Environmental Microbiology ◽

10.1128/aem.01965-10 ◽

2010 ◽

Vol 77 (1) ◽

pp. 32-40 ◽

Cited By ~ 49

Author(s):

Amanda C. Granger ◽

Elena K. Gaidamakova ◽

Vera Y. Matrosova ◽

Michael J. Daly ◽

Peter Setlow

Keyword(s):

Ionizing Radiation ◽

Deinococcus Radiodurans ◽

Dipicolinic Acid ◽

Divalent Cations ◽

Wild Type ◽

Divalent Metal Ions ◽

Protein Resistance ◽

Wet Heat ◽

Resistance To Ionizing Radiation

ABSTRACTSpores ofBacillus subtilisstrains with (wild type) or without (α−β−) most DNA-binding α/β-type small, acid-soluble proteins (SASP) were prepared in medium with additional MnCl2concentrations of 0.3 μM to 1 mM. These haploid spores had Mn levels that varied up to 180-fold and Mn/Fe ratios that varied up to 300-fold. However, the resistance of these spores to desiccation, wet heat, dry heat, and in particular ionizing radiation was unaffected by their level of Mn or their Mn/Fe ratio; this was also the case for wild-type spore resistance to hydrogen peroxide (H2O2). However, α−β−spores were more sensitive to H2O2when they had high Mn levels and a high Mn/Fe ratio. These results suggest that Mn levels alone are not essential for wild-type bacterial spores' extreme resistance properties, in particular ionizing radiation, although high Mn levels sensitize α−β−spores to H2O2, probably by repressing expression of the auxiliary DNA-protective protein MrgA. Notably, Mn2+complexed with the abundant spore molecule dipicolinic acid (DPA) with or without inorganic phosphate was very effective at protecting a restriction enzyme against ionizing radiationin vitro, and Ca2+complexed with DPA and phosphate was also very effective in this regard. These latter data suggest that protein protection in spores against treatments such as ionizing radiation that generate reactive oxygen species may be due in part to the spores' high levels of DPA conjugated to divalent metal ions, predominantly Ca2+, much like high levels of Mn2+complexed with small molecules protect the bacteriumDeinococcus radioduransagainst ionizing radiation.

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