Insights into the radiation and oxidative stress mechanisms in genus Deinococcus

Deinococcus species, noted for their exceptional resistance to DNA-damaging environmental stresses, have piqued scientists' interest for decades. This study dives into the complex mechanisms underpinning radiation resistance in the Deinococcus genus. We have examined the genomes of 82 Deinococcus species and classified radiation-resistance proteins manually into five unique curated categories: DNA repair, oxidative stress defense, Ddr and Ppr proteins, regulatory proteins, and miscellaneous resistance components. This classification reveals important information about the various molecular mechanisms used by these extremophiles which have been less explored so far. We also investigated the presence or lack of these proteins in the context of phylogenetic relationships, core, and pan-genomes, which offered light on the evolutionary dynamics of radiation resistance. This comprehensive study provides a deeper understanding of the genetic underpinnings of radiation resistance in the Deinococcus genus, with potential implications for understanding similar mechanisms in other organisms using an interactomics approach. Finally, this study reveals the complexities of radiation resistance mechanisms, providing a comprehensive understanding of the genetic components that allow Deinococcus species to flourish under harsh environments. The findings add to our understanding of the larger spectrum of stress adaption techniques in bacteria and may have applications in sectors ranging from biotechnology to environmental research.

Deinococcus detaillensis sp. nov., isolated from humus soil in Antarctica

A Gram-staining-positive, non-motile, coccus or short-rod-shaped bacterium, designated H1^T, was isolated from a humus soil sample in the Detaille Island of Antarctica. The 16S rRNA gene sequence result indicated that strain H1^T shared the highest 16S rRNA gene sequence identity with the type strain of Deinococcus alpinitundrae (96.2%). Growth of strain H1^T occurred at 4-25 °C, pH 6.0-8.0 and in the presence of 0-1.0% NaCl (w/v). The respiratory quinone was MK-8. The major fatty acids were C_16:0, C_17:0 cyclo and summed feature 3 (C_16:1 ω7c/C_16:1 ω6c). The polar lipids were aminoglycophospholipid, aminophospholipid, glycolipid and glycophospholipid. The cell wall peptidoglycan type was A3β. The genomic DNA G + C content was 61.3 mol%. The average nucleotide identity (ANI) between strain H1^T and the closely related Deinococcus members was below the cut-off level (95-96%) for species identification. Based on the above results, strain H1^T represents a novel species of the genus Deinococcus, for which the name Deinococcus detaillensis sp. nov. is proposed. Type strain is H1^T (= CGMCC 1.13938^T = JCM 33291^T).

The Aqueous Extract of Radio-Resistant Deinococcus actinosclerus BM2T Suppresses Lipopolysaccharide-Mediated Inflammation in RAW264.7 Cells

Deinococcus actinosclerus BM2^T (GenBank: KT448814) is a radio-resistant bacterium that is newly isolated from the soil of a rocky hillside in Seoul. As an extremophile, D. actinosclerus BM2^T may possess anti-inflammatory properties that may be beneficial to human health. In this study, we evaluated the anti-inflammatory effects of BM2U, an aqueous extract of D. actinosclerus BM2^T, on lipopolysaccharide (LPS)-mediated inflammatory responses in RAW264.7 macrophage cells. BM2U showed antioxidant capacity, as determined by the DPPH radical scavenging (IC₅₀ = 349.3 μg/ml) and ORAC (IC₅₀ = 50.24 μg/ml) assays. At 20 μg/ml, BM2U induced a significant increase in heme oxygenase-1 (HO-1) expression (p < 0.05). BM2U treatment (0.2-20 μg/ml) significantly suppressed LPS-induced increase in the mRNA expression of proinflammatory cytokines tumor necrosis factor-α (TNF-α), interleukin (IL)-1β, and IL-6 (p < 0.05). BM2U treatment also suppressed the expression of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2), which are involved in the production of inflammatory mediators. BM2U treatment also inhibited the activation of nuclear factor-κB (NF-κB) and mitogen-activated protein kinases (MAPKs): JNK, ERK, and p-38 (p < 0.05). Collectively, BM2U exhibited anti-inflammatory potential that can be exploited in attenuating inflammatory responses.

Draft genome sequence of Deinococcus sp. KR-1, a potential strain for palladium-leaching

Strain KR-1 was isolated from pond water collected in Japan. Because this strain was capable of adsorbing palladium particles in sterilized water, strain KR-1 will be a useful biocatalyst for palladium-leaching from metal waste. Here we present a draft genome sequence of Deinococcus sp. KR-1, which consists of a total of 7 contigs containing 4,556,772 bp with a GC content of 70.0% and comprises 4,450 predicted coding sequences. Based on the 16S rRNA gene sequence analysis, strain KR-1 was identified as Deinococcus sp. KR-1.

Shifts in microbial community composition in tannery-contaminated soil in response to increased gamma radiation

Purpose

Contaminated sites from man-made activities such as old-fashioned tanneries are inhabited by virulent microorganisms that exhibit more resistance against extreme and toxic environmental conditions. We investigated the effect of different Gamma radiation doses on microbial community composition in the sediment of an old-fashioned tannery.

Methods

Seven samples collected from the contaminated sites received different gamma radiation doses (I = 0.0, II = 5, III = 10, VI = 15, V = 20, VI = 25, and VII = 30 kGy) as an acute exposure. The shift in microbial community structure was assessed using the high throughput 454 pyrosequencing. Variations in diversity, richness, and the shift in operational taxonomic units (OTUs) were investigated using statistical analysis.

Result

Our results showed that the control sample (I) had the highest diversity, richness, and OTUs when compared with the irradiated samples. Species of Halocella, Parasporobacterium, and Anaerosporobacter had the highest relative abundance at the highest radiation dose of 30 kGy. Members of the Firmicutes also increased by 20% at the highest radiation dose when compared with the control sample (0.0 kGy). Representatives of Synergistetes decreased by 25% while Bacteroidetes retained a steady distribution across the range of gamma radiation intensities.

Conclusion

This study provides information about potential “radioresistant” and/or “radiotolerant” microbial species that are adapted to elevated level of chemical toxicity such as Cr and Sr in tannery. These species can be of a high biotechnological and environmental importance.

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.

Analysis of 1,000 Type-Strain Genomes Improves Taxonomic Classification of Bacteroidetes

Although considerable progress has been made in recent years regarding the classification of bacteria assigned to the phylum Bacteroidetes, there remains a need to further clarify taxonomic relationships within a diverse assemblage that includes organisms of clinical, piscicultural, and ecological importance. Bacteroidetes classification has proved to be difficult, not least when taxonomic decisions rested heavily on interpretation of poorly resolved 16S rRNA gene trees and a limited number of phenotypic features. Here, draft genome sequences of a greatly enlarged collection of genomes of more than 1,000 Bacteroidetes and outgroup type strains were used to infer phylogenetic trees from genome-scale data using the principles drawn from phylogenetic systematics. The majority of taxa were found to be monophyletic but several orders, families and genera, including taxa proposed long ago such as Bacteroides, Cytophaga, and Flavobacterium but also quite recent taxa, as well as a few species were shown to be in need of revision. According proposals are made for the recognition of new orders, families and genera, as well as the transfer of a variety of species to other genera. In addition, emended descriptions are given for many species mainly involving information on DNA G+C content and (approximate) genome size, both of which can be considered valuable taxonomic markers. We detected many incongruities when comparing the results of the present study with existing classifications, which appear to be caused by insufficiently resolved 16S rRNA gene trees or incomplete taxon sampling. The few significant incongruities found between 16S rRNA gene and whole genome trees underline the pitfalls inherent in phylogenies based upon single gene sequences and the impediment in using ordinary bootstrapping in phylogenomic studies, particularly when combined with too narrow gene selections. While a significant degree of phylogenetic conservation was detected in all phenotypic characters investigated, the overall fit to the tree varied considerably, which is one of the probable causes of misclassifications in the past, much like the use of plesiomorphic character states as diagnostic features.

Deinococcus fonticola sp. nov., isolated from a radioactive thermal spring in Hungary

A Gram-stain-negative, aerobic, non-motile and coccus-shaped bacterium, designated strain FeSDHB5-19^T, was isolated from a biofilm sample collected from a radioactive thermal spring (Budapest, Hungary), after exposure to 5 kGy gamma radiation. A polyphasic approach was used to study the taxonomic properties of strain FeSDHB5-19^T, which had highest 16S rRNA gene sequence similarity to Deinococcus antarcticus G3-6-20^T (96.5 %). The 16S rRNA gene sequence similarity to type strains of other Deinococcus species were 93.0 % or lower. The DNA G+C content of the draft genome sequence, consisting of 3.9 Mb, was 63.9 mol%. Strain FeSHDB5-19^T was found to grow at temperatures of 10-32 °C (optimum, 28 °C) and pH 5-10 (pH 6.5-7.5) and tolerated up to 1.5 % NaCl (w/v) with optimum growth at 0-0.5 % NaCl. The predominant fatty acids (>10 %) were C16 : 0 and C16 : 1ω7c. The cell-wall peptidoglycan type was A3β l-Orn-Gly1-2. The whole-cell sugars were glucose and low amounts of galactose. Strain FeSDHB5-19^T possessed MK-8 as the predominant respiratory quinone, typical of the genus Deinococcus. The polar lipid profile contained unidentified phosphoglycolipids and unidentified glycolipids. The isolate was found to be highly resistant to gamma (D10<8 kGy) and UV (D10~800 J m^-2) radiation. According to its genotypic, phenotypic and chemotaxonomic characteristics, strain FeSDHB5-19^T represents a novel species in the genus Deinococcus, for which the name Deinococcusfonticola sp. nov. is proposed. The type strain is FeSDHB5-19^T (=NCAIM B.02639^T=DSM 106917^T).

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.

Deinococcus terrigena sp. nov., a novel member of the family Deinococcaceae

A bacterial strain, S13-1-2-1^T, was isolated from a soil sample collected in Gyeongsangnam-do province, South Korea. Cells were observed to be Gram-stain negative, short rod-shaped and colonies to be pale pink in colour. Analysis of 16S rRNA gene sequences identified this strain as a member of the genus Deinococcus in the family Deinococcaceae, with high levels of sequence similarity with Deinococcus ficus CC-FR2-10^T (97.9%) and Deinococcus enclensis NIO-1023^T (95.4%). Growth of strain S13-1-2-1^T was observed at 10-42 °C, pH 6-8, and in the presence of 0-1.0% NaCl. The isolate was found to exhibit resistance to gamma radiation (D₁₀ 10.1 KGy) and UV-light (D₁₀ 612 J/m²). The major peptidoglycan amino acids were identified as D-glutamic acid, glycine, alanine and L-ornithine. The predominant respiratory quinone of the strain was identified as menaquinone-8, the major fatty acids were found to be C_16:1ω7c (31.4%), C_16:0 (18.4%), and C_17:1ω8c (17.4%) and the major polar lipids were observed to be an unidentified phosphoglycolipid and an unidentified glycolipid. The genomic DNA G + C content of the strain was determined to be 69.2 mol%. DNA-DNA hybridization with D. ficus showed a relatedness value of 31.5 ± 4.2%. The DNA-DNA hybridization result and the differentiating phenotypic properties clearly indicate that strain S13-1-2-1^T represents a novel species in the genus Deinococcus, for which the name Deinococcus terrigena sp. nov. is proposed. The type strain is S13-1-2-1^T (= KCTC 33939^T = JCM 32248^T).

Deinococcus lacus sp. nov., a gamma radiation-resistant bacterium isolated from an artificial freshwater pond

A Gram-stain-negative, pink-coloured, non-motile and gamma radiation-resistant bacterium, designated strain IMCC1711^T, was isolated from a freshwater sample collected from an artificial pond (Inkyong Pond). The 16S rRNA gene sequence analysis showed that strain IMCC1711^T was most closely related to Deinococcus piscis 3ax^T (94.2 %) and formed a robust phylogenetic clade with other species of the genus Deinococcus. Optimal growth of strain MCC1711^T was observed at 25 °C and pH 7.0 without NaCl. Strain IMCC1711^T exhibited high resistance to gamma radiation. The DNA G+C content of strain IMCC1711^T was 59.1 mol% and MK-8 was the predominant isoprenoid quinone. Major fatty acid constituents of the strain were C17 : 1ω8c, C16 : 0, summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c) and C15 : 1ω6c. The major polar lipids constituted phosphatidylethanolamine, one unidentified phosphoglycolipid and two unidentified glycolipids. On the basis of taxonomic data obtained in this study, it was concluded that strain IMCC1711^T represented a novel species of the genus Deinococcus, for which the name Deinococcus lacus sp. nov. is proposed. The type strain of Deinococcus lacus is IMCC1711^T (KCTC 52494^T=KACC 18979^T=NBRC 112440^T).

Deinococcus multiflagellatus sp. nov., isolated from a car air-conditioning system

A gamma radiation-resistant and pink-to-red pigmented bacterial strain, designated ID1504^T, was isolated from a car air-conditioning system sampled in Korea. The cells were observed to be Gram-stain negative, aerobic, motile with peritrichous flagella and short rod-shaped. Phylogenetically, the strain groups with the members of the genus Deinococcus and exhibits high 16S rRNA gene sequence similarities with Deinococcus arenae SA1^T (94.0%), Deinococcus actinosclerus BM2^T (93.9%) and Deinococcus soli N5^T (93.5%). The predominant fatty acids were identified as C_17:0, C_16:0, summed feature 3 (C_16:1 ω7c and/or C_16:1 ω6c) and iso-C_17:0. The major respiratory quinone was identified as MK-8. The polar lipids were found to be comprised of unidentified phospholipids, unidentified glycolipids, an unidentified aminophospholipid and an unidentified lipid. The DNA G+C content of the strain was determined to be 68.3 mol%. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain ID1504^T should be classified in a novel species in the genus Deinococcus, for which the name Deinococcus multiflagellatus sp. nov. (= KACC 19287^T = NBRC 112888^T) is proposed.

DrwH, a novel WHy domain-containing hydrophobic LEA5C protein from Deinococcus radiodurans, protects enzymatic activity under oxidative stress

Water stress and hypersensitive response (WHy) domain is typically found as a component of atypical late embryogenesis abundant (LEA) proteins closely associated with resistance to multiple stresses in numerous organisms. Several putative LEA proteins have been identified in Deinococcus bacteria; however their precise function remains unclear. This work reports the characterization of a Deinococcus-specific gene encoding a novel WHy domain-containing hydrophobic LEA5C protein (named DrwH) in D. radiodurans R1. The expression of the drwH gene was induced by oxidative and salinity stresses. Inactivation of this gene resulted in increased sensitivity to oxidative and salinity stresses as well as reduced activities of antioxidant enzymes. The WHy domain of the DrwH protein differs structurally from that of a previously studied bacterial LEA5C protein, dWHy1, identified as a gene product from an Antarctic desert soil metagenome library. Further analysis indicated that in E. coli, the function of DrwH is related to oxidative stress tolerance, whereas dWHy1 is associated with freezing-thawing stress tolerance. Under oxidative stress induced by H₂O₂, DrwH protected the enzymatic activities of malate dehydrogenase (MDH) and lactate dehydrogenase (LDH). These findings provide new insight into the evolutionary and survival strategies of Deinococcus bacteria under extreme environmental conditions.

Complete genome sequence of Deinococcus actinosclerus BM2(T), a bacterium with Gamma-radiation resistance isolated from soil in South Korea

A Gram-positive, short-rod shaped and non-motile bacterium Deinococcus actinosclerus BM2(T), resistant to gamma and UV radiation, was isolated from a soil sample collected in South Korea. Strain BM2(T) showed high resistance to gamma radiation with D10 value of 9 kGy. The complete genome of D. actinosclerus BM2(T) consists of a single chromosome (3,264,334bp). The genome features showed the presence of intracellular proteases that help to eliminate radiation-induced ROS during recovery from ionizing radiation damage.