• Journal of Microbiology and Biotechnology
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• v.21 no.4
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• pp.438-447
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• 2011

Deinococcus radiodurans is extremely resistant to various genotoxic conditions and chemicals. In this study, we characterized the effect of a sublethal concentration (100 ${\mu}M$) of cadmium (Cd) on D. radiodurans using a whole-genome DNA microarray. Time-course global gene expression profiling showed that 1,505 genes out of 3,116 total ORFs were differentially expressed more than 2-fold in response to Cd treatment for at least one timepoint. The majority of the upregulated genes are related to iron uptake, cysteine biosynthesis, protein disulfide stress, and various types of DNA repair systems. The enhanced upregulation of genes involved in cysteine biosynthesis and disulfide stress indicate that Cd has a high affinity for sulfur compounds. Provocation of iron deficiency and growth resumption of Cd-treated cells by iron supplementation also indicates that CdS forms in iron-sulfur-containing proteins such as the [Fe-S] cluster. Induction of base excision, mismatch, and recombinational repair systems indicates that various types of DNA damage, especially base excision, were enhanced by Cd. Exposure to sublethal Cd stress reduces the growth rate, and many of the downregulated genes are related to cell growth, including biosynthesis of cell membrane, translation, and transcription. The differential expression of 52 regulatory genes suggests a dynamic operation of complex regulatory networks by Cd-induced stress. These results demonstrate the effect of Cd exposure on D. radiodurans and how the related genes are expressed by this stress.

• Microbiology and Biotechnology Letters
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• v.45 no.3
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• pp.271-275
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• 2017

The expression of Deinococcus radiodurans dr1558 and pprM genes was examined for enhanced lysine production in recombinant Corynebacterium glutamicum. These genes are known to confer high tolerance to pH and osmotic shock in Escherichia coli. D. radiodurans dr1558 and pprM genes were expressed in C. glutamicum by using 6 synthetic promoters of different strengths, to evaluate the effect of expression efficiency on lysine production. Recombinant C. glutamicum expressing DR1558 under the L26 and I64 promoters showed higher lysine production than that expressing DR1558 under other promoters. Similarly, recombinant C. glutamicum expressing PprM under same promoters (L26 and I64) showed a higher increase in lysine production compared to that expressing PprM under other promoters. In the absence of $CaCO_3$ in the medium, the expression of DR1558 or PprM also increased lysine concentration in C. glutamicum depending on the promoter used. Together, these results suggest that genes involved in radiation tolerance in D. radiodurans can be used to enhance production of amino acids and their derivatives.

• Journal of Microbiology and Biotechnology
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• v.28 no.10
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• pp.1691-1699
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• 2018

A metabolically-engineered Deinococcus radiodurans R1 strain capable of producing phytoene, a colorless $C_{40}$ carotenoid and a promising antioxidant, has been developed. To make this base strain, first, the crtI gene encoding phytoene desaturase was deleted to block the conversion of phytoene to other carotenoids such as lycopene and ${\gamma}$-carotene. This engineered strain produced $0.413{\pm}0.023mg/l$ of phytoene from 10 g/l of fructose. Further enhanced production of phytoene up to $4.46{\pm}0.19mg/l$ was achieved by overexpressing the crtB gene encoding phytoene synthase and the dxs genes encoding 1-deoxy-$\text\tiny{D}$-xylulose-5-phosphate synthase gene, and by deleting the crtD gene. High cell-density culture of our final engineered strain allowed production of $10.3{\pm}0.85mg/l$ of phytoene with the yield and productivity of $1.04{\pm}0.05mg/g$ and $0.143{\pm}0.012mg/l/h$, respectively, from 10 g/l of fructose. Furthermore, the antioxidant potential of phytoene produced by the final engineered strain was confirmed by in vitro DPPH radical-scavenging assay.

• Korean Journal of Microbiology
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• v.44 no.3
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• pp.169-177
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• 2008

Global gene expression of Deinococcus radiodurans, a highly radiation resistant bacterium, in response to excess copper was analyzed by using oligonucleotide microarray chip. Among 3,187 open reading frames of D. radiodurans, seventy genes showed a statistically significant expression ratio of at least 2-fold changes under growth conditions of excess copper; 64 genes were induced and 6 genes were reduced. Especially, two operons ($DRB0014{\sim}DRB0017$ and $DRB0125{\sim}DRB0121$) presumably involved in the iron transport and utilization were the most highly induced genes by excess copper. A quantitative real-time PCR assay revealed that DRB00l4 and DRB0125 are highly transcribed responding to excess copper and 2,2'-dipyridyl, an iron chelator. In addition, the transcription of both genes was not changed by excess iron and bathocuproine disulphonate, a copper chelator. These results suggested that the copper metabolism may be closely connected with the iron transport and utilization in D. radiodurans. However, the disruption of each gene, DRB00l4 and DRB0125, did not affect the copper and radiation resistance, the most well-known character of this organism.

• Journal of Microbiology and Biotechnology
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• v.32 no.7
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• pp.835-843
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• 2022

Deinococcus radiodurans is an extremophilic bacterium that can thrive in harsh environments. This property can be attributed to its unique metabolites that possess strong antioxidants and other pharmacological properties. To determine the potential of D. radiodurans R1 lysate (DeinoLys) as a pharmacological candidate for inflammatory bowel disease (IBD), we investigated the antiinflammatory activity of DeinoLys in bone marrow-derived dendritic cells (BMDCs) and a colitis mice model. Lipopolysaccharide (LPS)-stimulated BMDCs treated with DeinoLys exhibited alterations in their phenotypic and functional properties by changing into tolerogenic DCs, including strongly inhibited proinflammatory cytokines (TNF-α and IL-12p70) and surface molecule expression and activated DC-induced T cell proliferation/activation with high IL-10 production. These phenotypic and functional changes in BMDCs induced by DeinoLys in the presence of LPS were abrogated by IL-10 neutralization. Furthermore, oral administration of DeinoLys significantly reduced clinical symptoms against dextran sulfate sodium-induced colitis, including body weight loss, disease activity index, histological severity in colon tissue, and lower myeloperoxidase level in mice. Our results establish DeinoLys as a potential anti-inflammatory candidate for IBD therapy.

• Journal of Microbiology and Biotechnology
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• v.20 no.12
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• pp.1637-1646
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• 2010

The bacterium Deinococcus radiodurans is one of the most resistant organisms to ionizing radiation and other DNA-damaging agents. Although, at present, 30 Deinococcus species have been identified, the whole-genome sequences of most species remain unknown, with the exception of D. radiodurans (DRD), D. geothermalis, and D. deserti. In this study, comparative genomic hybridization (CGH) microarray analysis of three Deinococcus species, D. radiopugnans (DRP), D. proteolyticus (DPL), and D. radiophilus (DRPH), was performed using oligonucleotide arrays based on DRD. Approximately 28%, 14%, and 15% of 3,128 open reading frames (ORFs) of DRD were absent in the genomes of DRP, DPL, and DRPH, respectively. In addition, 162 DRD ORFs were absent in all three species. The absence of 17 randomly selected ORFs was confirmed by a Southern blot. Functional classification showed that the absent genes spanned a variety of functional categories: some genes involved in amino acid biosynthesis, cell envelope, cellular processes, central intermediary metabolism, and DNA metabolism were not present in any of the three deinococcal species tested. Finally, comparative genomic data showed that 120 genes were Deinococcus-specific, not the 230 reported previously. Specifically, ddrD, ddrO, and ddrH genes, previously identified as Deinococcus-specific, were not present in DRP, DPL, or DRPH, suggesting that only a portion of ddr genes are shared by all members of the genus Deinococcus.

• BMB Reports
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• v.33 no.5
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• pp.412-416
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• 2000

The obligate aerobic Deinococcus are highly resistant against lethal effect of UV-and ionizing-radiation. Only five mesophilic Deinococcus species, i. e. D. radiodurans, D. radiophilus, D. proteolyticus, D. radiopugnans, and D. grandis are known. Since an indispensable role of catalase has been suggested in protecting cells against oxidative stress and UV radiation, Deinococcal catalase activity of each species and electrophoretic profiles of catalases were investigated on gel. Total catalase activity was varied among the species in the aerobically grown culture at stationary phase. The occurrence of multiple forms of catalases with different molecular weights in four species of Deinococcus and of a single catalase in D. radiopugnans suggests that each species shows the unique catalase profiles on gel. Some Deinococcal catalases also exhibit peroxidase activity. Since Deinococcus spp. are less-distinct to each other in their morphology, biochemical and physiological properties, the catalase profiles on PAGE would be useful in identifying the species of Deinococcus.

• Journal of Microbiology and Biotechnology
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• v.25 no.12
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• pp.2125-2134
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• 2015

IrrE is a highly conserved global regulator in the Deinococcus genus and contributes to survival from high doses of UV radiation, ionizing radiation, and desiccation. Drad-IrrE and Dgob-IrrE from Deinococcus radiodurans and Deinococcus gobiensis I-0 each share 66% sequence identity. However, Dgob-IrrE showed a stronger protection phenotype against UV radiation than Drad-IrrE in the D. radiodurans irrE-deletion mutant (ΔirrE), which may be due to amino acid residues differences around the DNA-binding HTH domain. Site-directed mutagenesis was used to generate a Drad-IrrE A184S single mutant, which has been characterized and compared with the ΔirrE mutant complemented strain with Drad-irrE, designated ΔirrE-E. The effects of the A184S mutation following UV radiation and mitomycin C (MMC) shock were determined. The A184S mutant displayed significantly increased resistance to UV radiation and MMC shock. The corresponding A184 site in Dgob-IrrE was inversely mutated, generating the S131A mutant, which exhibited a loss of resistance against UV radiation, MMC shock, and desiccation. qPCR analysis revealed that critical genes in the DNA repair system, such as recA, pprA, uvrA, and ddrB, were remarkably induced after UV radiation and MMC shock in the ΔirrE-IE and A184S mutants. These data suggested that A184S improves the ability against UV radiation and MMC shock, providing new insights into the modification of IrrE. We speculated that the serine residue may determine the efficiency of DNA binding, leading to the increased expression of IrrE-dependent genes important for protection against DNA damage.

• Journal of Microbiology and Biotechnology
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• v.22 no.9
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• pp.1296-1300
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• 2012

The feasibility of using Deinococcus showing strong resistance to both desiccation and ionizing radiation as a dose indicator of gamma radiation exposure was evaluated. Three Deinococcus strains having different levels of radiation resistance, Deinococcus radiodurans (DRD), Deinococcus radiopugnans (DRP), and the DRD pprI mutant (DRM), were selected to develop an appropriate dose indicator for a broad range of exposures. DRD, DRP, and DRM cultures with different numbers of cells [${\sim}10^7$ to $10^3$ colony forming units (CFU)/$100{\mu}l$] were lyophilized and subjected to various doses of gamma radiation to determine a critical dose that inhibited bacterial growth completely. Finally, a combination of DRD at ${\sim}10^7$ and ${\sim}10^6$ CFU, DRP at ${\sim}10^5$ CFU, and DRM at ${\sim}10^4$ CFU successfully indicated exposure to 5, 10, 20, and 30 kGy of gamma radiation, respectively. This study shows the possibility of developing a qualitative indicator of radiation exposure using Deinococcus.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2863-2866
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• 2014