Against all odds: the survival strategies of Deinococcus radiodurans

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

A 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 actinobacterium. 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.

N6-methyladenine and epigenetic immunity of Deinococcus radiodurans

DNA methylation is ubiquitously found in all three domains of life. This epigenetic modification on adenine or cytosine residues serves to regulate gene expression or to defend against invading DNA in bacteria. Here, we report the significance of N6-methyladenine (6mA) to epigenetic immunity in Deinococcus radiodurans. Putative protein encoded by DR_2267 ORF (Dam2_DR) contributed 35% of genomic 6mA in D. radiodurans but did not influence gene expression or radiation resistance. Dam2_DR was characterized to be a functional S-adenosyl methionine (SAM)-dependent N6-adenine DNA methyltransferase (MTase) but with no endonuclease activity. Adenine methylation from Dam2_DR or Dam1_DR (N6-adenine MTase encoded by DR_0643) improved DNA uptake during natural transformation. To the contrary, methylation from Escherichia coli N6-adenine MTase (Dam_EC that methylates adenine in GATC sequence) on donor plasmid drastically reduced DNA uptake in D. radiodurans, even in presence of Dam2_DR or Dam1_DR methylated adenines. With these results, we conclude that self-type N6-adenine methylation on donor DNA had a protective effect in absence of additional foreign methylation, a separate methylation-dependent Restriction Modification (R-M) system effectively identifies and limits uptake of G6mATC sequence containing donor DNA. This is the first report demonstrating presence of epigenetic immunity in D. radiodurans.

Single-Molecule Insights into ATP-Dependent Conformational Dynamics of Nucleoprotein Filaments of Deinococcus radiodurans RecA

Deinococcus radiodurans (Dr) has one of the most robust DNA repair systems, which is capable of withstanding extreme doses of ionizing radiation and other sources of DNA damage. DrRecA, a central enzyme of recombinational DNA repair, is essential for extreme radioresistance. In the presence of ATP, DrRecA forms nucleoprotein filaments on DNA, similar to other bacterial RecA and eukaryotic DNA strand exchange proteins. However, DrRecA catalyzes DNA strand exchange in a unique reverse pathway. Here, we study the dynamics of DrRecA filaments formed on individual molecules of duplex and single-stranded DNA, and we follow conformational transitions triggered by ATP hydrolysis. Our results reveal that ATP hydrolysis promotes rapid DrRecA dissociation from duplex DNA, whereas on single-stranded DNA, DrRecA filaments interconvert between stretched and compressed conformations, which is a behavior shared by E. coli RecA and human Rad51. This indicates a high conservation of conformational switching in nucleoprotein filaments and suggests that additional factors might contribute to an inverse pathway of DrRecA strand exchange.

Purification from Deinococcus radiodurans of a 66 kDa ABC transporter acting on peptides containing at least 3 amino acids

Deinococcus radiodurans is a Gram positive bacterium the capability of which to withstand high doses of ionizing radiations is well known. Physiologically speaking, D. radiodurans is a proteolytic prokaryote able to express and secrete quite a number of proteases, and to use amino acids as an energy source. When considering this, it is surprising that little information is available on the biochemical components responsible for the uptake of peptides in D. radiodurans. Here we report on the purification and characterization of an ABC peptide transporter, isolated from D. radiodurans cells grown in tryptone-glucose-yeast extract (TGY) medium. In particular, we show here that the action of this transporter (denoted DR1571, SwissProt data bank accession number Q9RU24 UF71_DEIRA) is exerted on peptides containing at least 3 amino acids. Further, using tetra-peptides as model systems, we were able to observe that the DR1571 protein does not bind to peptides containing phenylalanine or valine, but associates with high efficiency to tetra-glycine, and with moderate affinity to tetra-peptides containing arginine or aspartate.

Deinococcus terrestris sp. nov., a gamma ray- and ultraviolet-resistant bacterium isolated from soil

Strain SDU3-2^T was isolated from a soil sample collected in Shandong Province, PR China. Cells of SDU3-2^T were spherical, Gram-stain-positive, aerobic and non-motile. Cellular growth of the strain occurred at 25-45 °C, pH 5.5-8.5 and with 0-1.5 % (w/v) of NaCl. Phylogenetic analysis based on the 16S rRNA gene sequences showed that strain SDU3-2^T was closest to the type strain Deinococcus murrayi ALT-1b^T with a similarity of 95.2 %. The draft genome was 3.49 Mbp long with 69.2 mol% G+C content. Strain SDU3-2^T exhibited high resistance to gamma radiation (D₁₀ >12 kGy) and UV (D₁₀ >900 J m^-2). The strain encoded many genes for resistance to radiation and oxidative stress, which were highly conserved with other Deinococcus species, but possessed interspecific properties. The major fatty acids of SDU3-2^T cells were C_15 : 1  ω6c, C_16 : 1  ω7c/C_16 : 1  ω6c, and C_17 : 1  ω8c, the major menaquinone was menaquinone-8, and the major polar lipids were an unidentified phosphoglycolipid, four unidentified glycolipids and an unidentified phospholipid. The average nucleotide identity and DNA-DNA hybridization results further indicated that strain SDU3-2^T represents a new species in the genus Deinococcus, for which the name Deinococcus terrestris sp. nov. is proposed. The type strain is SDU3-2^T (=CGMCC 1.17147^T=KCTC 43098^T).

Does solar irradiation drive community assembly of vulture plumage microbiotas?

BACKGROUND

Stereotyped sunning behaviour in birds has been hypothesized to inhibit keratin-degrading bacteria but there is little evidence that solar irradiation affects community assembly and abundance of plumage microbiota. The monophyletic New World vultures (Cathartiformes) are renowned for scavenging vertebrate carrion, spread-wing sunning at roosts, and thermal soaring. Few avian species experience greater exposure to solar irradiation. We used 16S rRNA sequencing to investigate the plumage microbiota of wild individuals of five sympatric species of vultures in Guyana.

RESULTS

The exceptionally diverse plumage microbiotas (631 genera of Bacteria and Archaea) were numerically dominated by bacterial genera resistant to ultraviolet (UV) light, desiccation, and high ambient temperatures, and genera known for forming desiccation-resistant endospores (phylum Firmicutes, order Clostridiales). The extremophile genera Deinococcus (phylum Deinococcus-Thermus) and Hymenobacter (phylum, Bacteroidetes), rare in vertebrate gut microbiotas, accounted for 9.1% of 2.7 million sequences (CSS normalized and log2 transformed). Five bacterial genera known to exhibit strong keratinolytic capacities in vitro (Bacillus, Enterococcus, Pseudomonas, Staphylococcus, and Streptomyces) were less abundant (totaling 4%) in vulture plumage.

CONCLUSIONS

Bacterial rank-abundance profiles from melanized vulture plumage have no known analog in the integumentary systems of terrestrial vertebrates. The prominence of UV-resistant extremophiles suggests that solar irradiation may play a significant role in the assembly of vulture plumage microbiotas. Our results highlight the need for controlled in vivo experiments to test the effects of UV on microbial communities of avian plumage.

Structural and Functional Characterization of a Unique AP Endonuclease From Deinococcus radiodurans

Various endogenous and exogenous agents cause DNA damage, including apurinic/apyrimidinic (AP) sites. Due to their cytotoxic effects, AP sites are usually cleaved by AP endonuclease through the base excision repair (BER) pathway. Deinococcus radiodurans, an extraordinary radiation-resistant bacterium, is known as an ideal model organism for elucidating DNA repair processes. Here, we have investigated a unique AP endonuclease (DrXth) from D. radiodurans and found that it possesses AP endonuclease, 3'-phosphodiesterase, 3'-phosphatase, and 3'-5' exonuclease but has no nucleotide incision repair (NIR) activity. We also found that Mg²⁺ and Mn²⁺ were the preferred divalent metals for endonuclease and exonuclease activities, respectively. In addition, DrXth were crystallized and the crystals diffracted to 1.5 Å. Structural and biochemical analyses demonstrated that residue Gly198 is the key residue involved in the substrate DNA binding and cleavage. Deletion of the drxth gene in D. radiodurans caused elevated sensitivity to DNA damage agents and increased spontaneous mutation frequency. Overall, our results indicate that DrXth is an important AP endonuclease involved in BER pathway and functions in conjunction with other DNA repair enzymes to maintain the genome stability.

The Novel ncRNA OsiR Positively Regulates Expression of katE2 and Is Required for Oxidative Stress Tolerance in Deinococcus radiodurans

Deinococcus radiodurans is a polyextremophilic bacterium well known for its extreme resistance to irradiation, oxidative stress, and other damaging conditions. Many small noncoding RNAs (ncRNAs) in D. radiodurans have been identified by deep sequencing analysis and computational predictions. However, the precise roles of ncRNAs and their target genes in the oxidative stress response have not been investigated. Here, we report the identification and characterization of a novel ncRNA named OsiR (for oxidative stress-induced ncRNA). Oxidative stress tolerance analysis showed that deleting osiR significantly decreased viability, total antioxidant capacity, and catalase activity in D. radiodurans under oxidative stress conditions. Comparative phenotypic and qRT-PCR analyses of an osiR mutant identify a role of OsiR in regulating the expression of the catalase gene katE2. Microscale thermophoresis and genetic complementation showed that a 21-nt sequence in the stem–loop structure of OsiR (204–244 nt) directly base pairs with its counterpart in the coding region of katE2 mRNA (843–866 nt) via a 19 nt region. In addition, deletion of katE2 caused a significant reduction of catalase activity and oxidative stress tolerance similar to that observed in an osiR mutant. Our results show that OsiR positively regulates oxidative stress tolerance in D. radiodurans by increasing the mRNA stability and translation efficiency of katE2. This work provides a new regulatory pathway mediated by ncRNA for the oxidative stress response that most likely contributes to the extreme tolerances of D. radiodurans.

Single-molecule observation of ATP-independent SSB displacement by RecO in Deinococcus radiodurans

Deinococcus radiodurans (DR) survives in the presence of hundreds of double-stranded DNA (dsDNA) breaks by efficiently repairing such breaks. RecO, a protein that is essential for the extreme radioresistance of DR, is one of the major recombination mediator proteins in the RecA-loading process in the RecFOR pathway. However, how RecO participates in the RecA-loading process is still unclear. In this work, we investigated the function of drRecO using single-molecule techniques. We found that drRecO competes with the ssDNA-binding protein (drSSB) for binding to the freely exposed ssDNA, and efficiently displaces drSSB from ssDNA without consuming ATP. drRecO replaces drSSB and dissociates it completely from ssDNA even though drSSB binds to ssDNA approximately 300 times more strongly than drRecO does. We suggest that drRecO facilitates the loading of RecA onto drSSB-coated ssDNA by utilizing a small drSSB-free space on ssDNA that is generated by the fast diffusion of drSSB on ssDNA.

Space Radiation Biology for "Living in Space"

Space travel has advanced significantly over the last six decades with astronauts spending up to 6 months at the International Space Station. Nonetheless, the living environment while in outer space is extremely challenging to astronauts. In particular, exposure to space radiation represents a serious potential long-term threat to the health of astronauts because the amount of radiation exposure accumulates during their time in space. Therefore, health risks associated with exposure to space radiation are an important topic in space travel, and characterizing space radiation in detail is essential for improving the safety of space missions. In the first part of this review, we provide an overview of the space radiation environment and briefly present current and future endeavors that monitor different space radiation environments. We then present research evaluating adverse biological effects caused by exposure to various space radiation environments and how these can be reduced. We especially consider the deleterious effects on cellular DNA and how cells activate DNA repair mechanisms. The latest technologies being developed, e.g., a fluorescent ubiquitination-based cell cycle indicator, to measure real-time cell cycle progression and DNA damage caused by exposure to ultraviolet radiation are presented. Progress in examining the combined effects of microgravity and radiation to animals and plants are summarized, and our current understanding of the relationship between psychological stress and radiation is presented. Finally, we provide details about protective agents and the study of organisms that are highly resistant to radiation and how their biological mechanisms may aid developing novel technologies that alleviate biological damage caused by radiation. Future research that furthers our understanding of the effects of space radiation on human health will facilitate risk-mitigating strategies to enable long-term space and planetary exploration.

Novel Genes Involved in Resistance to Both Ultraviolet Radiation and Perchlorate From the Metagenomes of Hypersaline Environments

Microorganisms that thrive in hypersaline environments on the surface of our planet are exposed to the harmful effects of ultraviolet radiation. Therefore, for their protection, they have sunscreen pigments and highly efficient DNA repair and protection systems. The present study aimed to identify new genes involved in UV radiation resistance from these microorganisms, many of which cannot be cultured in the laboratory. Thus, a functional metagenomic approach was used and for this, small-insert libraries were constructed with DNA isolated from microorganisms of high-altitude Andean hypersaline lakes in Argentina (Diamante and Ojo Seco lakes, 4,589 and 3,200 m, respectively) and from the Es Trenc solar saltern in Spain. The libraries were hosted in a UV radiation-sensitive strain of Escherichia coli (recA mutant) and they were exposed to UVB. The resistant colonies were analyzed and as a result, four clones were identified with environmental DNA fragments containing five genes that conferred resistance to UV radiation in E. coli. One gene encoded a RecA-like protein, complementing the mutation in recA that makes the E. coli host strain more sensitive to UV radiation. Two other genes from the same DNA fragment encoded a TATA-box binding protein and an unknown protein, both responsible for UV resistance. Interestingly, two other genes from different and remote environments, the Ojo Seco Andean lake and the Es Trenc saltern, encoded two hypothetical proteins that can be considered homologous based on their significant amino acid similarity (49%). All of these genes also conferred resistance to 4-nitroquinoline 1-oxide (4-NQO), a compound that mimics the effect of UV radiation on DNA, and also to perchlorate, a powerful oxidant that can induce DNA damage. Furthermore, the hypothetical protein from the Es Trenc salterns was localized as discrete foci possibly associated with damaged sites in the DNA in cells treated with 4-NQO, so it could be involved in the repair of damaged DNA. In summary, novel genes involved in resistance to UV radiation, 4-NQO and perchlorate have been identified in this work and two of them encoding hypothetical proteins that could be involved in DNA damage repair activities not previously described.

Antioxidative and Radioprotective Properties of Glycosylated Flavonoid, Xanthorhamnin from Radio-Resistant Bacterium Bacillus indicus Strain TMC-6

A radio-resistant bacterium labeled as strain TMC-6 was isolated from Thal desert, Pakistan and identified through 16S rRNA gene sequencing as Bacillus indicus strain TMC-6 (MN721293). The isolate was found to be resistant to UV radiation dose of 6.780 × 10³ J/m² and showed 50% survivability to mitomycin C (6 μg/ml) and H₂O₂ (30 mM). The bacterium showed yellowish orange coloration when grown on tryptone yeast glucose (TGY) medium. The cellular metabolite was extracted in methanol and purified through solid phase extraction with C18 column cartridge. The compound was characterized through UV/Visible spectrophotometry, Fourier Transform Infra-Red (FT-IR) spectroscopy and Liquid Chromatography Mass Spectrometry (LC-MS). The LC-MS analysis of the compound revealed a molar mass of 769 [m/z]^- that matched the chemical formula C₃₄H₄₂O₂₀ and identified as a glycosylated flavonoid xanthorhamnin. The compound showed significant antioxidant (77.05%) and metal chelation (79.80%) activities. Xanthorhamnin showed promising oxidative damage inhibitory actions in bovine serum albumin (65.32%) and mice liver lipids (71.61%) and prevented DNA strand breaks from oxidative stress. Cytotoxicity in brine shrimp larvae was observed when compared with mitomycin C indicating its effect toward cancerous cells. These findings concluded that xanthorhamnin from radio-resistant Bacillus indicus strain TMC-6 has high antioxidant, radioprotective, and antitumor properties against UV-mediated oxidative damages.

Photophysics of deinoxanthin, the keto-carotenoid bound to the main S-layer unit of Deinococcus radiodurans

An ultrafast transient absorption experiment on the SDBC, which binds the carotenoid deinoxanthin, reveals a non-specific binding site that loosely binds the carotenoid, but protects the carotenoid from the outer environment.

Molecular response of Deinococcus radiodurans to simulated microgravity explored by proteometabolomic approach

Regarding future space exploration missions and long-term exposure experiments, a detailed investigation of all factors present in the outer space environment and their effects on organisms of all life kingdoms is advantageous. Influenced by the multiple factors of outer space, the extremophilic bacterium Deinococcus radiodurans has been long-termly exposed outside the International Space Station in frames of the Tanpopo orbital mission. The study presented here aims to elucidate molecular key components in D. radiodurans, which are responsible for recognition and adaptation to simulated microgravity. D. radiodurans cultures were grown for two days on plates in a fast-rotating 2-D clinostat to minimize sedimentation, thus simulating reduced gravity conditions. Subsequently, metabolites and proteins were extracted and measured with mass spectrometry-based techniques. Our results emphasize the importance of certain signal transducer proteins, which showed higher abundances in cells grown under reduced gravity. These proteins activate a cellular signal cascade, which leads to differences in gene expressions. Proteins involved in stress response, repair mechanisms and proteins connected to the extracellular milieu and the cell envelope showed an increased abundance under simulated microgravity. Focusing on the expression of these proteins might present a strategy of cells to adapt to microgravity conditions.

RNA-Seq-Based Comparative Transcriptome Analysis Highlights New Features of the Heat-Stress Response in the Extremophilic Bacterium Deinococcus radiodurans

Deinococcus radiodurans is best known for its extraordinary resistance to diverse environmental stress factors, such as ionizing radiation, ultraviolet (UV) irradiation, desiccation, oxidation, and high temperatures. The heat response of this bacterium is considered to be due to a classical, stress-induced regulatory system that is characterized by extensive transcriptional reprogramming. In this study, we investigated the key functional genes involved in heat stress that were expressed and accumulated in cells (R48) following heat treatment at 48 °C for 2 h. Considering that protein degradation is a time-consuming bioprocess, we predicted that to maintain cellular homeostasis, the expression of the key functional proteins would be significantly decreased in cells (RH) that had partly recovered from heat stress relative to their expression in cells (R30) grown under control conditions. Comparative transcriptomics identified 15 genes that were significantly downregulated in RH relative to R30, seven of which had previously been characterized to be heat shock proteins. Among these genes, three hypothetical genes (dr_0127, dr_1083, and dr_1325) are highly likely to be involved in response to heat stress. Survival analysis of mutant strains lacking DR_0127 (a DNA-binding protein), DR_1325 (an endopeptidase-like protein), and DR_1083 (a hypothetical protein) showed a reduction in heat tolerance compared to the wild-type strain. These results suggest that DR_0127, DR_1083, and DR_1325 might play roles in the heat stress response. Overall, the results of this study provide deeper insights into the transcriptional regulation of the heat response in D. radiodurans.

Cell morphology and nucleoid dynamics in dividing Deinococcus radiodurans

Our knowledge of bacterial nucleoids originates mostly from studies of rod- or crescent-shaped bacteria. Here we reveal that Deinococcus radiodurans, a relatively large spherical bacterium with a multipartite genome, constitutes a valuable system for the study of the nucleoid in cocci. Using advanced microscopy, we show that D. radiodurans undergoes coordinated morphological changes at both the cellular and nucleoid level as it progresses through its cell cycle. The nucleoid is highly condensed, but also surprisingly dynamic, adopting multiple configurations and presenting an unusual arrangement in which oriC loci are radially distributed around clustered ter sites maintained at the cell centre. Single-particle tracking and fluorescence recovery after photobleaching studies of the histone-like HU protein suggest that its loose binding to DNA may contribute to this remarkable plasticity. These findings demonstrate that nucleoid organization is complex and tightly coupled to cell cycle progression in this organism.

Amino Acid-Dependent Alterations in Cell Wall and Cell Morphology of Deinococcus indicus DR1

Deinococcus radiodurans exhibits growth medium-dependent morphological variation in cell shape, but there is no evidence whether this phenomenon is observed in other members of the Deinococcaceae family. In this study, we isolated a red-pigmented, aerobic, Deinococcus indicus strain DR1 from Dadri wetland, India. This D. indicus strain exhibited cell–morphology transition from rod-shaped cells to multi-cell chains in a growth-medium-dependent fashion. In response to addition of 1% casamino acids in the minimal growth medium, rod-shaped cells formed multi-cell chains. Addition of all 20 amino acids to the minimal medium was able to recapitulate the phenotype. Specifically, a combination of L-methionine, L-lysine, L-aspartate, and L-threonine caused morphological alterations. The transition from rod shape to multi-cell chains is due to delay in daughter cell separation after cell division. Minimal medium supplemented with L-ornithine alone was able to cause cell morphology changes. Furthermore, a comparative UPLC analysis of PG fragments isolated from D. indicus cells propagated in different growth media revealed alterations in the PG composition. An increase in the overall cross-linkage of PG was observed in muropeptides from nutrient-rich TSB and NB media versus PYE medium. Overall our study highlights that environmental conditions influence PG composition and cell morphology in D. indicus.

The Role of Iron and Copper on the Oligomerization Dynamics of DR_2577, the Main S-Layer Protein of Deinococcus radiodurans

Surface (S)-layers are cryptic structures that coat the external surface of the bacterial cell in many species. The paracrystalline regularity of the S-layer is due to the self-assembling of one or more protein units. The property of self-assembling seems to be mediated by specific topologies of the S-layer proteins as well as the presence of specific ions that provide support in building and stabilizing the bi-dimensional S-layer organization. In the present study, we have investigated the self-assembling mechanism of the main S-layer protein of Deinococcus radiodurans (DR_2577) finding an unusual role played by Fe³⁺ and Cu²⁺ in the oligomerization of this protein. These findings may trace a structural and functional metallo-mediated convergence between the role of these metals in the assembling of the S-layer and their well-known roles in protecting against oxidative stress in D. radiodurans.

Combined pre-treatments effects on zucchini (Cucurbita pepo L.) squash microbial load reduction

Freezing vegetables requires pre-treatments to reduce microbial load and destroy enzymes that impair the frozen product quality. So far blanching has been the most effective pre-treatment, preferred by the food industry, despite its severity: heating up to temperatures close to 100 °C for 1-3 min causes sensory and texture changes in most horticultural products. Alternative blanching treatments, using UV-C radiation combined with milder thermal treatments or with thermosonication, may improve the quality of the final frozen vegetables. Zucchini (Cucurbita pepo L.), the vegetable under study, has an availability in fresh restricted to a season, needing therefore to be often frozen to be used throughout the year. In this study, its surface was first inoculated with two vegetable contaminants, Enterococcus faecalis and Deinococcus radiodurans cells, which are resistant, respectively, to high temperatures and to radiation and then submitted to several blanching treatments, single or combined, and the effect on these microorganisms reduction was evaluated. As single treatments, water blanching (the control treatment, as it is the blanching treatment traditionally used) was applied up to 180 s at temperatures ranging from 65 to 90 °C, and UV-irradiation applied in continuous. As combined pre-treatments, water blanching combined with UV-C (continuous or in pulses), and thermosonication (20 kHz at 50% of power) combined with UV-C pulses were also studied. The continuous UV-C radiation incident irradiance was 11 W/m² up to 180 s, and the pulses at incident radiance of 67 W/m², lasting 3.5 s each (35 pulses). Mathematical modeling of bacterial reduction data was carried out using the Bigelow, the Weibull and Weibull modified models, and estimation of their respective kinetic parameters proved that the latter models presented a better fit below 75 °C. The best results proved to be the combination of water blanching at temperatures as low as 85 °C during <2 min with 25 pulses of UV-C (incident irradiance of 67 W/m²) or thermosonication at 90 °C also combined with UV-C pulses, both resulting in 3 log reductions of both microorganisms under study. These results proved to overcome what industry is requiring so far (a 2 log microbial reduction in 3 min), hence minimizing quality changes of frozen zucchini.

Changes in soil taxonomic and functional diversity resulting from gamma irradiation

Little is known of the effects of ionizing radiation exposure on soil biota. We exposed soil microcosms to weekly bursts of ⁶⁰Co gamma radiation over six weeks, at three levels of exposure (0.1 kGy/hr/wk [low], 1 kGy/hr/wk [medium] and 3 kGy/hr/wk [high]). Soil DNA was extracted, and shotgun metagenomes were sequenced and characterised using MG-RAST. We hypothesized that with increasing radiation exposure there would be a decrease in both taxonomic and functional diversity. While bacterial diversity decreased, diversity of fungi and algae unexpectedly increased, perhaps because of release from competition. Despite the decrease in diversity of bacteria and of biota overall, functional gene diversity of algae, bacteria, fungi and total biota increased. Cycles of radiation exposure may increase the range of gene functional strategies viable in soil, a novel ecological example of the effects of stressors or disturbance events promoting some aspects of diversity. Moreover, repeated density-independent population crashes followed by population expansion may allow lottery effects, promoting coexistence. Radiation exposure produced large overall changes in community composition. Our study suggests several potential novel radiation-tolerant groups: in addition to Deinococcus-Thermus, which reached up to 20% relative abundance in the metagenome, the phyla Chloroflexi (bacteria), Chytridiomycota (fungi) and Nanoarcheota (archaea) may be considered as radiation-tolerant.

Phosphorylation of deinococcal RecA affects its structural and functional dynamics implicated for its roles in radioresistance of Deinococcus radiodurans

Deinococcus RecA (DrRecA) protein is a key repair enzyme and contributes to efficient DNA repair of Deinococcus radiodurans. Phosphorylation of DrRecA at Y77 (tyrosine 77) and T318 (threonine 318) residues modifies the structural and conformational switching that impart the efficiency and activity of DrRecA. Dynamics comparisons of DrRecA with its phosphorylated analogues support the idea that phosphorylation of Y77 and T318 sites could change the dynamics and conformation plasticity of DrRecA. Furthermore, docking studies showed that phosphorylation increases the binding preference of DrRecA towards dATP versus ATP and for double-strand DNA versus single-strand DNA. This work supporting the idea that phosphorylation can modulate the crucial functions of this protein and having good concordance with the experimental data. AbbreviationsDrRecADeinococcus RecADSBDNA double-strand breakshDNAheteroduplex DNASTYPKserine/threonine/tyrosine protein kinaseT318threonine 318Y77tyrosine 77Communicated by Ramaswamy H. Sarma.

Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species

Deinococcus bacteria are famous for their extreme resistance to ionising radiation and other DNA damage- and oxidative stress-generating agents. More than a hundred genes have been reported to contribute to resistance to radiation, desiccation and/or oxidative stress in Deinococcus radiodurans. These encode proteins involved in DNA repair, oxidative stress defence, regulation and proteins of yet unknown function or with an extracytoplasmic location. Here, we analysed the conservation of radiation resistance-associated proteins in other radiation-resistant Deinococcus species. Strikingly, homologues of dozens of these proteins are absent in one or more Deinococcus species. For example, only a few Deinococcus-specific proteins and radiation resistance-associated regulatory proteins are present in each Deinococcus, notably the metallopeptidase/repressor pair IrrE/DdrO that controls the radiation/desiccation response regulon. Inversely, some Deinococcus species possess proteins that D. radiodurans lacks, including DNA repair proteins consisting of novel domain combinations, translesion polymerases, additional metalloregulators, redox-sensitive regulator SoxR and manganese-containing catalase. Moreover, the comparisons improved the characterisation of several proteins regarding important conserved residues, cellular location and possible protein–protein interactions. This comprehensive analysis indicates not only conservation but also large diversity in the molecular mechanisms involved in radiation resistance even within the Deinococcus genus.

A Model for Manganese interaction with Deinococcus radiodurans proteome network involved in ROS response and defense

A complex network of regulatory proteins takes part in the mechanism underlying the radioresistance of Deinoccocus radiodurans bacterium (DR). The interaction of Mn(II) ions with DR-proteins and peptides seems to be responsible for proteins protection from oxidative damage induced by Reactive Oxygen Species during irradiation. In the present work we describe a combined approach of bioinformatic strategies based on structural data and annotation to predict the Mn(II)-binding proteins encoded by the genome of DR and, in parallel, the same predictions for other bacteria were performed; the comparison revealed that, in most of the cases, the content of Mn(II)-binding proteins is significantly higher in radioresistant than in radiosensitive bacteria. Moreover, we report the in silico protein-protein interaction network of the putative Mn(II)-proteins, remodeled in order to enhance the knowledge about the impact of Mn-binding proteins in DR ability to protect also DNA from various damaging agents such as ionizing radiation, UV radiation and oxidative stress.

Pleiotropic effects of a cold shock protein homolog PprM on the proteome of Deinococcus radiodurans

An extremophile D. radiodurans encodes a non-cold shock inducible cold shock protein homolog DR_0907 (also known as PprM). The DR_0907 ORF was deleted by knockout mutagenesis and the resultant deletion mutant (ΔpprM D. radiodurans) displayed growth defect as well as gamma-radiation sensitivity (D₁₀ values = ΔpprM D. radiodurans: 12.1 kGy versus wild type (WT) D. radiodurans: 14 kGy). 2D gel based comparative proteomics revealed a comparable induction of DNA repair proteins in ΔpprM D. radiodurans and WT D. radiodurans recovering from 5 kGy gamma irradiation (⁶⁰Co gamma source, dose rate: 2 kGy/h), suggesting that pprM does not cause radiation sensitivity through modulation of DdrO-regulated DNA repair genes. However, deletion of pprM did result in repression of several proteins that belonged to vital housekeeping pathways such as metabolism and protein homeostasis that might contribute to slow growth phenotype. These deficiencies intrinsic to ΔpprM D. radiodurans might also contribute to its radiation sensitivity.

MALDI-TOF MS Affords Discrimination of Deinococcus aquaticus Isolates Obtained From Diverse Biofilm Habitats

Matrix-assisted Laser Desorption Ionization-Time of Flight Mass Spectroscopy (MALDI-TOF MS) has been used routinely over the past decade in clinical microbiology laboratories to rapidly characterize diverse microorganisms of medical importance both at the genus and species levels. Currently, there is keen interest in applying MALDI-TOF MS at taxonomic levels beyond species and to characterize environmental isolates. We constructed a model system consisting of 19 isolates of Deinococcus aquaticus obtained from biofilm communities indigenous to diverse substrates (concrete, leaf tissue, metal, and wood) in the Fox River - Lake Winnebago system of Wisconsin to: (1) develop rapid sample preparation methods that produce high quality, reproducible MALDI-TOF spectra and (2) compare the performance of MALDI-TOF MS-based profiling to common DNA-based approaches including 16S rRNA sequencing and genomic diversity by BOX-A1R fingerprinting. Our results suggest that MALDI-TOF MS can be used to rapidly and reproducibly characterize environmental isolates of D. aquaticus at the subpopulation level. MALDI-TOF MS provided higher taxonomic resolution than either 16S rRNA gene sequence analysis or BOX-A1R fingerprinting. Spectra contained features that appeared to permit characterization of isolates into two co-occurring subpopulations. However, reliable strain-level performance required rigorous and systematic standardization of culture conditions and sample preparation. Our work suggests that MALDI-TOF MS offers promise as a rapid, reproducible, and high-resolution approach to characterize environmental isolates of members of the genus Deinococcus. Future work will focus upon application of methods described here to additional members of this ecologically diverse and ubiquitous genus.

Bacterial cell wall nanoimaging by autoblinking microscopy

Spurious blinking fluorescent spots are often seen in bacteria during single-molecule localization microscopy experiments. Although this 'autoblinking' phenomenon is widespread, its origin remains unclear. In Deinococcus strains, we observed particularly strong autoblinking at the periphery of the bacteria, facilitating its comprehensive characterization. A systematic evaluation of the contributions of different components of the sample environment to autoblinking levels and the in-depth analysis of the photophysical properties of autoblinking molecules indicate that the phenomenon results from transient binding of fluorophores originating mostly from the growth medium to the bacterial cell wall, which produces single-molecule fluorescence through a Point Accumulation for Imaging in Nanoscale Topography (PAINT) mechanism. Our data suggest that the autoblinking molecules preferentially bind to the plasma membrane of bacterial cells. Autoblinking microscopy was used to acquire nanoscale images of live, unlabeled D. radiodurans and could be combined with PALM imaging of PAmCherry-labeled bacteria in two-color experiments. Autoblinking-based super-resolved images provided insight into the formation of septa in dividing bacteria and revealed heterogeneities in the distribution and dynamics of autoblinking molecules within the cell wall.

Desiccation and radiation stress tolerance in cyanobacteria

Cyanobacteria are among the oldest living organisms on this planet, existing since more than 3 billion years. They are ideal organisms for investigating biological processes such as photosynthesis, respiration, circadian rhythm, photoregulation of gene expression, developmental gene rearrangements, and specialized cell differentiation. They are nearly ubiquitous in distribution, have colonized a wide range of ecosystems including soil, air, dry rock, and aquatic systems, and even occupy extreme niches that are inaccessible to other organisms. Such wide ecological distribution reflects their capacity to acclimate to extreme environments. They show great adaptive abilities and have survived various adverse physiological growth conditions like desiccation, high temperatures, extreme pH, cold, osmosis, salt, light, nitrogen, and high salinity. Their ancient origin and surviving through numerous stresses during evolution indicates their remarkable capabilities to survive and prevail under different environmental and man-made stresses. It has been hypothesized that similar and overlap stress response mechanisms help them to survive different stresses. It has been stated that responses against stresses like radiation has been accidental-exhibited because of similar response against desiccation stress, which has prevailed more during evolution. These overlaps and similarities in stress responses have been instrumental in making these organisms a large class of biological entities today. Present review discuss about stress tolerance in cyanobacteria against two extreme stresses - desiccation and gamma radiation. It also discuss the commonality and underlying molecular mechanisms in these two stress responses.

Responses exhibited by various microbial groups relevant to uranium exposure

There is a strong interest in knowing how various microbial systems respond to the presence of uranium (U), largely in the context of bioremediation. There is no known biological role for uranium so far. Uranium is naturally present in rocks and minerals. The insoluble nature of the U(IV) minerals keeps uranium firmly bound in the earth's crust minimizing its bioavailability. However, anthropogenic nuclear reaction processes over the last few decades have resulted in introduction of uranium into the environment in soluble and toxic forms. Microbes adsorb, accumulate, reduce, oxidize, possibly respire, mineralize and precipitate uranium. This review focuses on the microbial responses to uranium exposure which allows the alteration of the forms and concentrations of uranium within the cell and in the local environment. Detailed information on the three major bioprocesses namely, biosorption, bioprecipitation and bioreduction exhibited by the microbes belonging to various groups and subgroups of bacteria, fungi and algae is provided in this review elucidating their intrinsic and engineered abilities for uranium removal. The survey also highlights the instances of the field trials undertaken for in situ uranium bioremediation. Advances in genomics and proteomics approaches providing the information on the regulatory and physiologically important determinants in the microbes in response to uranium challenge have been catalogued here. Recent developments in metagenomics and metaproteomics indicating the ecologically relevant traits required for the adaptation and survival of environmental microbes residing in uranium contaminated sites are also included. A comprehensive understanding of the microbial responses to uranium can facilitate the development of in situ U bioremediation strategies.

A novel bacterial class V dye-decolourizing peroxidase from the extremophile Deinococcus radiodurans: cloning, expression optimization, purification, crystallization, initial characterization and X-ray diffraction analysis

Deinococcus radiodurans is a bacterium with extreme resistance to desiccation and radiation. The resistance mechanism is unknown, but an efficient reactive oxygen species (ROS) scavenging system and DNA-repair and DNA-protection mechanisms are believed to play important roles. Here, the cloning and small- and medium-scale expression tests of a novel dye-decolourizing peroxidase from D. radiodurans (DrDyP) using three different Escherichia coli strains and three different temperatures in order to identify the optimum conditions for the expression of recombinant DrDyP are presented. The best expression conditions were used for large-scale expression and yielded ∼10 mg recombinant DrDyP per litre of culture after purification. Initial characterization experiments demonstrated unusual features with regard to the haem spin state, which motivated the crystallization experiment. The obtained crystals were used for data collection and diffracted to 2.2 Å resolution. The crystals belonged to the trigonal space group P31 or P32, with unit-cell parameters a = b = 64.13, c = 111.32 Å, and are predicted to contain one DrDyP molecule per asymmetric unit. Structure determination by molecular replacement using previously determined structures of dye-decolourizing peroxidases with ∼30% sequence identity at ∼2 Å resolution as templates are ongoing.

Deinococcus koreensis sp. nov., a gamma radiation-resistant bacterium isolated from river water

A gamma radiation-resistant, Gram-stain-negative, rod-shaped bacterial strain, designated SJW1-2^T, was isolated from freshwater samples collected from the Seomjin River, Republic of Korea. The 16S rRNA gene sequence analyses showed that strain SJW1-2^T was most closely related to Deinococcus metalli 1PNM-19^T (94.3 % sequence similarity) and formed a robust phylogenetic clade with other species of the genus Deinococcus. The optimum growth pH and temperature for the isolate were pH 7.0-7.5 and 25 °C, respectively. Strain SJW1-2^T exhibited high resistance to gamma radiation. The predominant respiratory quinone was MK-8. The polar lipid profile consisted of different unidentified glycolipids, two unidentified lipids, two unidentified phospholipids and an unidentified phosphoglycolipid. The major peptidoglycan amino acids were alanine, d-glutamic acid, glycine and l-ornithine. The predominant fatty acids (>10 %) were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) (25.2 %) and C16 : 0 (21.2 %), and the DNA G+C content was 69.5 mol%. On the basis of phenotypic, genotypic and phylogenetic analyses, strain SJW1-2^T (=KACC 19332^T=NBRC 112908^T) represents a novel species of the genus Deinococcus, for which the name Deinococcus koreensis sp. nov. is proposed.

Novel Sequence Features of DNA Repair Genes/Proteins from Deinococcus Species Implicated in Protection from Oxidatively Generated Damage

Deinococcus species display a high degree of resistance to radiation and desiccation due to their ability to protect critical proteome from oxidatively generated damage; however, the underlying mechanisms are not understood. Comparative analysis of DNA repair proteins reported here has identified 22 conserved signature indels (CSIs) in the proteins UvrA1, UvrC, UvrD, UvsE, MutY, MutM, Nth, RecA, RecD, RecG, RecQ, RecR, RuvC, RadA, PolA, DnaE, LigA, GyrA and GyrB, that are uniquely shared by all/most Deinococcus homologs. Of these CSIs, a 30 amino acid surface-exposed insert in the Deinococcus UvrA1, which distinguishes it from all other UvrA homologs, is of much interest. The uvrA1 gene in Deinococcus also exhibits specific genetic linkage (predicted operonic arrangement) to genes for three other proteins including a novel Deinococcus-specific transmembrane protein (designated dCSP-1) and the proteins DsbA and DsbB, playing central roles in protein disulfide bond formation by oxidation-reduction of CXXC (C represents cysteine, X any other amino acid) motifs. The CXXC motifs provide important targets for oxidation damage and they are present in many DNA repair proteins including five in UvrA, which are part of Zinc-finger elements. A conserved insert specific for Deinococcus is also present in the DsbA protein. Additionally, the uvsE gene in Deinococcus also shows specific linkage to the gene for a membrane-associated protein. To account for these novel observations, a model is proposed where specific interaction of the Deinococcus UvrA1 protein with membrane-bound dCSP-1 enables the UvrA1 to receive electrons from DsbA-DsbB oxido-reductase machinery to ameliorate oxidation damage in the UvrA1 protein.

Draft Whole-Genome Sequence of Deinococcus sp. UR1, a Putative Novel Species Isolated from an External Stainless Steel Surface in the Canadian Prairies

Deinococcus sp. strain UR1, a resilient bacterium isolated from the surface of a stainless steel sign located on the University of Regina campus in Saskatchewan, Canada, was sequenced to 56-fold coverage to produce 73 contigs with a consensus length of 4,472,838 bp and a G+C content of 69.37%.

Coexisting properties of thermostability and ultraviolet radiation resistance in the main S-layer complex of Deinococcus radiodurans

Deinococcus radiodurans is well known for its unusual resistance to different environmental stresses.

Rapid and Selective Screening Method for Isolation and Identification of Carotenoid-Producing Bacteria

Carotenoids are naturally occurring yellow to red pigments with many biological activities including antioxidant, anticancer, anti-inflammatory, membrane stabilizers, and precursors for vitamin A. These biological activities are linked with many health benefits (e.g., anticarcinogenic activity, prevention of chronic diseases, etc.), which grew the interest of several industrial sectors especially in food, feed, nutraceuticals, cosmetics, and pharmaceutical industries. The production of natural carotenoids from microbial sources such as bacteria can help meet the growing global market of carotenoids estimated at $1.5 billion in 2014 and is expected to reach 1.8 billion in 2019. This chapter demonstrates, step-by-step, the development of a rapid and selective screening method for isolation and identification of carotenoid-producing microorganisms and their carotenoid analysis. This method involves three main procedures: UV treatment, sequencing analysis of 16S rRNA genes, and carotenoids analysis using rapid and effective HPLC-diode array-MS methods.

Regulation of potassium dependent ATPase (kdp) operon of Deinococcus radiodurans

The genome of D. radiodurans harbors genes for structural and regulatory proteins of Kdp ATPase, in an operon pattern, on Mega plasmid 1. Organization of its two-component regulatory genes is unique. Here we demonstrate that both, the structural as well as regulatory components of the kdp operon of D. radiodurans are expressed quickly as the cells experience potassium limitation but are not expressed upon increase in osmolarity. The cognate DNA binding response regulator (RR) effects the expression of kdp operon during potassium deficiency through specific interaction with the kdp promoter. Deletion of the gene encoding RR protein renders the mutant D. radiodurans (ΔRR) unable to express kdp operon under potassium limitation. The ΔRR D. radiodurans displays no growth defect when grown on rich media or when exposed to oxidative or heat stress but shows reduced growth following gamma irradiation. The study elucidates the functional and regulatory aspects of the novel kdp operon of this extremophile, for the first time.

Deinococcus radiodurans pprI expression enhances the radioresistance of eukaryotes

PprI accelerates radiation-induced DNA damage repair via regulating the expression of DNA repair genes and enhances antioxidative enzyme activity in Deinococcus radiodurans after radiation. The main aim of our study was to determine whether the expression of pprI gene could fulfil its DNA repair function in eukaryotes and enhance the radioresistance of eukaryotic organism or not. In this study, we constructed pEGFP-c1-pprI eukaryotic expression vector and established a human lung epithelial cell line BEAS-2B with stable integration of pprI gene. We found that pprIexpression enhanced radioresistance of BEAS-2B cells, decreased γ-H2AX foci formation and apoptosis in irradiated BEAS-2B cells and alleviated radiation induced G2/M arrest of BEAS-2B cells. Moreover, we transferred pEGFP-c1-pprI vector into muscle of BALB/c mice by in vivo electroporation and studied the protective effect of prokaryotic pprI gene in irradiated mice. We found that pprI expression alleviated acute radiation induced hematopoietic system, lung, small intestine and testis damage and increased survival rate of irradiated mice via regulating Rad51 expression in different organs. These findings suggest that prokaryotic pprI gene expression in mammalian cells could enhance radioresistance in vitro and in vivo.

On the possibility of galactic cosmic ray-induced radiolysis-powered life in subsurface environments in the Universe

Photosynthesis is a mechanism developed by terrestrial life to utilize the energy from photons of solar origin for biological use. Subsurface regions are isolated from the photosphere, and consequently are incapable of utilizing this energy. This opens up the opportunity for life to evolve alternative mechanisms for harvesting available energy. Bacterium Candidatus Desulforudis audaxviator, found 2.8 km deep in a South African mine, harvests energy from radiolysis, induced by particles emitted from radioactive U, Th and K present in surrounding rock. Another radiation source in the subsurface environments is secondary particles generated by galactic cosmic rays (GCRs). Using Monte Carlo simulations, it is shown that it is a steady source of energy comparable to that produced by radioactive substances, and the possibility of a slow metabolizing life flourishing on it cannot be ruled out. Two mechanisms are proposed through which GCR-induced secondary particles can be utilized for biological use in subsurface environments: (i) GCRs injecting energy in the environment through particle-induced radiolysis and (ii) organic synthesis from GCR secondaries interacting with the medium. Laboratory experiments to test these hypotheses are also proposed. Implications of these mechanisms on finding life in the Solar System and elsewhere in the Universe are discussed.

On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets

Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX) project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets.

Active microorganisms thrive among extremely diverse communities in cloud water

Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~10³−10⁴ bacteria and archaea mL^-1 and ~10²−10³ eukaryote cells mL^-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.

A Prototype Ice-Melting Probe for Collecting Biological Samples from Cryogenic Ice at Low Pressure

In the Solar System, the surface of an icy moon is composed of irregular ice formations at cryogenic temperatures (<200 K), with an oxidized surface layer and a tenuous atmosphere at very low pressure (<10^-6 atm). A lander mission, whose aim is to collect and analyze biological samples from the surface ice, must contain a device that collects samples without refreezing liquid and without sublimation of ice. In addition, if the samples are biological in nature, then precautions must be taken to ensure the samples do not overheat or mix with the oxidized layer. To achieve these conditions, the collector must maintain temperatures close to maintenance or growth conditions of the organism (<293 K), and it must separate or neutralize the oxidized layer and be physically gentle. Here, we describe a device that addresses these requirements and is compatible with low atmospheric pressure while using no pumps. The device contains a heated conical probe with a central orifice, which is forced into surface ice and directs the meltwater upward into a reservoir. The force on the probe is proportional to the height of meltwater (pressure) obtained in the system and allows regulation of the melt rate and temperature of the sample. The device can collect 5-50 mL of meltwater from the surface of an ice block at 233-208 K with an environmental pressure of less than 10^-2 atm while maintaining a sample temperature between 273 and 293 K. These conditions maintain most biological samples in a pristine state and maintain the integrity of most organisms' structure and function. Key Words: Europa-Icy moon-Microbe-Eukaryote-Spacecraft. Astrobiology 17, 709-720.

Understanding low radiation background biology through controlled evolution experiments

Biological experiments conducted in underground laboratories over the last decade have shown that life can respond to relatively small changes in the radiation background in unconventional ways. Rapid changes in cell growth, indicative of hormetic behaviour and long-term inheritable changes in antioxidant regulation have been observed in response to changes in the radiation background that should be almost undetectable to cells. Here, we summarize the recent body of underground experiments conducted to date, and outline potential mechanisms (such as cell signalling, DNA repair and antioxidant regulation) that could mediate the response of cells to low radiation backgrounds. We highlight how multigenerational studies drawing on methods well established in studying evolutionary biology are well suited for elucidating these mechanisms, especially given these changes may be mediated by epigenetic pathways. Controlled evolution experiments with model organisms, conducted in underground laboratories, can highlight the short- and long-term differences in how extremely low-dose radiation environments affect living systems, shining light on the extent to which epimutations caused by the radiation background propagate through the population. Such studies can provide a baseline for understanding the evolutionary responses of microorganisms to ionizing radiation, and provide clues for understanding the higher radiation environments around uranium mines and nuclear disaster zones, as well as those inside nuclear reactors.

Proteome dynamics during post-desiccation recovery reveal convergence of desiccation and gamma radiation stress response pathways in Deinococcus radiodurans

Deinococcus radiodurans is inherently resistant to both ionizing radiation and desiccation. Fifteen months of desiccation was found to be the LD₅₀ dose for D. radiodurans. Desiccated cells of D. radiodurans entered 6h of growth arrest during post-desiccation recovery (PDR). Proteome dynamics during PDR were mapped by resolving cellular proteins by 2-dimensional gel electrophoresis coupled with mass spectrometry. At least 41 proteins, represented by 51 spots on proteome profiles, were differentially expressed throughout PDR. High upregulation in expression was observed for DNA repair proteins involved in single strand annealing (DdrA and DdrB), nucleotide excision repair (UvrA and UvrB), homologous recombination (RecA) and other vital proteins that contribute to DNA replication, recombination and repair (Ssb, GyrA and GyrB). Expression of CRP/FNR family transcriptional regulator (Crp) remained high throughout PDR. Other pathways such as cellular detoxification, protein homeostasis and metabolism displayed both, moderately induced and repressed proteins. Functional relevance of proteomic modulations to surviving desiccation stress is discussed in detail. Comparison of our data with the published literature revealed convergence of radiation and desiccation stress responses of D. radiodurans. This is the first report that substantiates the hypothesis that the radiation stress resistance of D. radiodurans is incidental to its desiccation stress resistance.

DNA Protection Protein, a Novel Mechanism of Radiation Tolerance: Lessons from Tardigrades

Genomic DNA stores all genetic information and is indispensable for maintenance of normal cellular activity and propagation. Radiation causes severe DNA lesions, including double-strand breaks, and leads to genome instability and even lethality. Regardless of the toxicity of radiation, some organisms exhibit extraordinary tolerance against radiation. These organisms are supposed to possess special mechanisms to mitigate radiation-induced DNA damages. Extensive study using radiotolerant bacteria suggested that effective protection of proteins and enhanced DNA repair system play important roles in tolerability against high-dose radiation. Recent studies using an extremotolerant animal, the tardigrade, provides new evidence that a tardigrade-unique DNA-associating protein, termed Dsup, suppresses the occurrence of DNA breaks by radiation in human-cultured cells. In this review, we provide a brief summary of the current knowledge on extremely radiotolerant animals, and present novel insights from the tardigrade research, which expand our understanding on molecular mechanism of exceptional radio-tolerability.

Survival of Deinococcus geothermalis in Biofilms under Desiccation and Simulated Space and Martian Conditions

Biofilm formation represents a successful survival strategy for bacteria. In biofilms, cells are embedded in a matrix of extracellular polymeric substances (EPS). As they are often more stress-tolerant than single cells, biofilm cells might survive the conditions present in space and on Mars. To investigate this topic, the bacterium Deinococcus geothermalis was chosen as a model organism due to its tolerance toward desiccation and radiation. Biofilms cultivated on membranes and, for comparison, planktonically grown cells deposited on membranes were air-dried and exposed to individual stressors that included prolonged desiccation, extreme temperatures, vacuum, simulated martian atmosphere, and UV irradiation, and they were exposed to combinations of stressors that simulate space (desiccation + vacuum + UV) or martian (desiccation + Mars atmosphere + UV) conditions. The effect of sulfatic Mars regolith simulant on cell viability during stress was investigated separately. The EPS produced by the biofilm cells contained mainly polysaccharides and proteins. To detect viable but nonculturable (VBNC) cells, cultivation-independent viability indicators (membrane integrity, ATP, 16S rRNA) were determined in addition to colony counts. Desiccation for 2 months resulted in a decrease of culturability with minor changes of membrane integrity in biofilm cells and major loss of membrane integrity in planktonic bacteria. Temperatures between -25°C and +60°C, vacuum, and Mars atmosphere affected neither culturability nor membrane integrity in both phenotypes. Monochromatic (254 nm; ≥1 kJ m^-2) and polychromatic (200-400 nm; >5.5 MJ m^-2 for planktonic cells and >270 MJ m^-2 for biofilms) UV irradiation significantly reduced the culturability of D. geothermalis but did not affect cultivation-independent viability markers, indicating the induction of a VBNC state in UV-irradiated cells. In conclusion, a substantial proportion of the D. geothermalis population remained viable under all stress conditions tested, and in most cases the biofilm form proved advantageous for surviving space and Mars-like conditions. Key Words: Biofilms-Desiccation-UV radiation-Mars-Lithopanspermia. Astrobiology 17, 431-447.

A tamB homolog is involved in maintenance of cell envelope integrity and stress resistance of Deinococcus radiodurans

The translocation and assembly module (TAM) in bacteria consists of TamA and TamB that form a complex to control the transport and secretion of outer membrane proteins. Herein, we demonstrated that the DR_1462-DR_1461-DR_1460 gene loci on chromosome 1 of Deinococcus radiodurans, which lacks tamA homologs, is a tamB homolog (DR_146T) with two tamB motifs and a DUF490 motif. Mutation of DR_146T resulted in cell envelope peeling and a decrease in resistance to shear stress and osmotic pressure, as well as an increase in oxidative stress resistance, consistent with the phenotype of a surface layer (S-layer) protein SlpA (DR_2577) mutant, demonstrating the involvement of DR_146T in maintenance of cell envelope integrity. The 123 kDa SlpA was absent and only its fragments were present in the cell envelope of DR_146T mutant, suggesting that DR_146T might be involved in maintenance of the S-layer. A mutant lacking the DUF490 motif displayed only a slight alteration in phenotype compared with the wild type, suggesting DUF490 is less important than tamB motif for the function of DR_146T. These findings enhance our understanding of the properties of the multilayered envelope in extremophilic D. radiodurans, as well as the diversity and functions of TAMs in bacteria.

In situ real-time evaluation of radiation-responsive promoters in the extremely radioresistant microbe Deinococcus radiodurans

A third generation promoter probe shuttle vector pKG was constructed, using the green fluorescent protein as a reporter, for in situ evaluation of Deinococcal promoter activity in Escherichia coli or Deinococcus radiodurans. The construct yielded zero background fluorescence in both the organisms, in the absence of promoter sequences. Fifteen Deinococcal promoters, either harbouring Radiation and Desiccation Response Motif (RDRM) or not, were cloned in vector pKG. Only the RDRM-promoter constructs displayed (i) gamma radiation inducible GFP expression in D. radiodurans, following gamma irradiation, (ii) DdrO-mediated repression of GFP expression in heterologous E. coli, or (iii) abolition in GFP induction following gamma irradiation, in pprI mutant of D. radiodurans. Utility of pKG vector for real-time in situ assessment of Deinococcal promoter function was, thus, successfully demonstrated.

Repair of oxidatively induced DNA damage by DNA glycosylases: Mechanisms of action, substrate specificities and excision kinetics

Endogenous and exogenous reactive species cause oxidatively induced DNA damage in living organisms by a variety of mechanisms. As a result, a plethora of mutagenic and/or cytotoxic products are formed in cellular DNA. This type of DNA damage is repaired by base excision repair, although nucleotide excision repair also plays a limited role. DNA glycosylases remove modified DNA bases from DNA by hydrolyzing the glycosidic bond leaving behind an apurinic/apyrimidinic (AP) site. Some of them also possess an accompanying AP-lyase activity that cleaves the sugar-phosphate chain of DNA. Since the first discovery of a DNA glycosylase, many studies have elucidated the mechanisms of action, substrate specificities and excision kinetics of these enzymes present in all living organisms. For this purpose, most studies used single- or double-stranded oligodeoxynucleotides with a single DNA lesion embedded at a defined position. High-molecular weight DNA with multiple base lesions has been used in other studies with the advantage of the simultaneous investigation of many DNA base lesions as substrates. Differences between the substrate specificities and excision kinetics of DNA glycosylases have been found when these two different substrates were used. Some DNA glycosylases possess varying substrate specificities for either purine-derived lesions or pyrimidine-derived lesions, whereas others exhibit cross-activity for both types of lesions. Laboratory animals with knockouts of the genes of DNA glycosylases have also been used to provide unequivocal evidence for the substrates, which had previously been found in in vitro studies, to be the actual substrates in vivo as well. On the basis of the knowledge gained from the past studies, efforts are being made to discover small molecule inhibitors of DNA glycosylases that may be used as potential drugs in cancer therapy.