Radiation-resistant Bacterium Research Articles

Spirosoma fluminis sp. nov., a Gamma-Radiation Resistant Bacterium Isolated from Sediment of the Han River in South Korea.

A Gram-negative, long rod-shaped, and yellowish bacterium, designated as strain 15J17T(T), was isolated from sediment of the Han River in South Korea after exposure to 3kGy of gamma radiation. The strain was catalase- and oxidase-positive and showed resistance to gamma radiation-D10 value (i.e., the dose required to reduce the bacterial population by 10-fold) of>4kGy. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the strain belonged to the genus Spirosoma and showed moderate degrees of sequence similarity with related species (90.6-93.5%). Chemotaxonomic data revealed that the strain contained summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:1 ω5c, C16:0, C18:0, and C15:0 iso as the major fatty acids; phosphatidylethanolamine, an unidentified aminophospholipid, and an unidentified polar lipid as the major polar lipids; and menaquinone-7 (MK-7) as the major quinone. The genomic DNA G+C content of the new strain was 48.3mol%. Based on these data, type strain 15J17T(T) (=KCTC 52198(T)=JCM 31409(T)) should be classified as representing a new species, for which we propose the name Spirosoma fluminis sp. nov.

Complete genome sequence of Hymenobacter sp. strain PAMC26554, an ionizing radiation-resistant bacterium isolated from an Antarctic lichen

A Gram-negative, rod-shaped, red-pink in color, and UV radiation-resistant bacterium Hymenobacter sp. strain PAMC26554 was isolated from Usnea sp., an Antarctic lichen, and belongs to the class of Cytophagia and the phylum of Bacteroidetes. The complete genome of Hymenobacter sp. PAMC26554 consists of one chromosome (5,244,843bp) with two plasmids (199,990bp and 6421bp). The genomic sequence indicates that Hymenobacter sp. strain PAMC26554 possesses several genes involved in the nucleotide excision repair pathway that protects damaged DNA. This complete genome information will help us to understand its adaptation and novel survival strategy in the Antarctic extreme cold environment.

한강물로부터 분리된 방사선 내성 세균들의 계통학적 다양성 및 UV 내성 분석

한강물로부터 분리된 방사선 내성 세균들의 계통학적 다양성 및 UV 내성 분석

Draft Genome Sequence of Kocuria rhizophila RF, a Radiation-Resistant Soil Isolate.

Kocuria rhizophila RF, a soil isolate from Iran, is a radiation-resistant bacterium. Only a limited amount of genomic information for radiation-resistant bacteria is currently available. Here, we report the draft genome sequence of this bacterium, providing knowledge to aid in the discovery of the genomic basis of its resistance to radiation.

Complete genome sequence of Rufibacter sp. DG31D, a bacterium resistant to gamma and UV radiation toxicity

The ionizing radiation toxicity becomes a major concern for the modern world, recent years, several special interest has been given to the research for the radiation resistant and the mechanisms of which the radiation resistant bacteria survive after the irradiation. In the current study, we have isolated strain DG31D was isolated from gamma ray-irradiated soil sample and showed resistant to gamma and UV radiation. The aim of this study is to understanding the radiation resistant mechanisms and their genomic features of the strain DG31D, which can be potentially used for the biotechnological application to degrade harmful soil contamination near the nuclear power stations and other radiation-affected areas. Strain DG31D showed resistant to UV and gamma radiation with D10 value of 10 kGy. The genome comprised of 4,820,793 bp with the G+C content of 51.4%. It contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA.

Isolation of Radiation-Resistant Bacteria from Mars Analog Antarctic Dry Valleys by Preselection, and the Correlation between Radiation and Desiccation Resistance.

Extreme radiation-resistant microorganisms can survive doses of ionizing radiation far greater than are present in the natural environment. Radiation resistance is believed to be an incidental adaptation to desiccation resistance, as both hazards cause similar cellular damage. Desert soils are, therefore, promising targets to prospect for new radiation-resistant strains. This is the first study to isolate radiation-resistant microbes by using gamma-ray exposure preselection from the extreme cold desert of the Antarctic Dry Valleys (a martian surface analogue). Halomonads, identified by 16S rRNA gene sequencing, were the most numerous survivors of the highest irradiation exposures. They were studied here for the first time for both their desiccation and irradiation survival characteristics. In addition, the association between desiccation and radiation resistance has not been investigated quantitatively before for a broad diversity of microorganisms. Thus, a meta-analysis of scientific literature was conducted to gather a larger data set. A strong correlation was found between desiccation and radiation resistance, indicating that an increase in the desiccation resistance of 5 days corresponds to an increase in the room-temperature irradiation survival of 1 kGy. Irradiation at -79°C (representative of average martian surface temperatures) increases the microbial radiation resistance 9-fold. Consequently, the survival of the cold-, desiccation-, and radiation-resistant organisms isolated here has implications for the potential habitability of dormant or cryopreserved life on Mars. Extremophiles-Halomonas sp.-Antarctica-Mars-Ionizing radiation-Cosmic rays.

Complete genome sequence of Hymenobacter sp. DG25B, a novel bacterium with gamma-radiation resistance isolated from soil in South Korea

A Gram-negative, rod-shaped, non-motile, gamma and UV radiation resistant bacterium Hymenobacter radioresistens DG25B was isolated from a soil sample collected in South Korea. The complete genome sequence of H. radioresistens DG25B consists of one circular chromosome (3,874,646bp). The bacterium was isolated from gamma ray irradiated soil and contains the genomic features of enzymes involved in the nucleotide excision repair (NER) pathway that protect the damaged DNA. The genome also contains other genes involved in the efficient removal of double-strand breaks (DSB) caused by the ionizing radiations.

Surface (S)-layer proteins of Deinococcus radiodurans and their utility as vehicles for surface localization of functional proteins

The radiation resistant bacterium, Deinococcus radiodurans contains two major surface (S)-layer proteins, Hpi and SlpA. The Hpi protein was shown to (a) undergo specific in vivo cleavage, and (b) closely associate with the SlpA protein. Using a non-specific acid phosphatase from Salmonella enterica serovar Typhi, PhoN as a reporter, the Surface Layer Homology (SLH) domain of SlpA was shown to bind deinococcal peptidoglycan-containing cell wall sacculi. The association of SlpA with Hpi on one side and peptidoglycan on the other, localizes this protein in the ‘interstitial’ layer of the deinoccocal cell wall. Gene chimeras of hpi-phoN and slh-phoN were constructed to test efficacy of S-layer proteins, as vehicles for cell surface localization in D. radiodurans. The Hpi-PhoN protein localized exclusively in the membrane fraction, and displayed cell-based phosphatase activity in vivo. The SLH-PhoN, which localized to both cytosolic and membrane fractions, displayed in vitro activity but no cell-based in vivo activity. Hpi, therefore, emerged as an efficient surface localizing protein and can be exploited for suitable applications of this superbug.

CYP287A1 is a carotenoid 2-β-hydroxylase required for deinoxanthin biosynthesis in Deinococcus radiodurans R1.

The carotenoid deinoxanthin is a crucial resistance factor against various stresses in the radiation-resistant bacterium Deinococcus radiodurans. Disruption of the gene dr2473 encoding the cytochrome P450 CYP287A1 led to the accumulation of 2-deoxydeinoxanthin in D. radiodurans, demonstrating that CYP287A1 is a novel β-carotene 2-hydroxylase. The dr2473 knockout mutant was shown to be more sensitive to UV radiation and oxidative stress than the wild-type strain D. radiodurans R1, indicating that the C2 alcohol of deinoxanthin is important for antioxidant activity.

Spirosoma montaniterrae sp. nov., an ultraviolet and gamma radiation-resistant bacterium isolated from mountain soil.

A Gram-negative, yellow-pigmented, long-rod shaped bacterial strain designated DY10(T) was isolated from a soil sample collected at Mt. Deogyusan, Jeonbuk province, South Korea. Optimum growth observed at 30°C and pH 7. No growth was observed above 1% (w/v) NaCl. Comparative 16S rRNA gene sequence analysis showed that strain DY10(T) belonged to the genus Spirosoma and was distantly related to Spirosoma arcticum R2-35(T) (91.0%), Spirosoma lingual DSM 74(T) (90.8%), Spirosoma endophyticum EX36(T) (90.7%), Spirosoma panaciterrae DSM 21099(T) (90.5%), Spirosoma rigui WPCB118(T) (90.2%), Spirosoma spitsbergense DSM 19989(T) (89.8%), Spirosoma luteum DSM 19990(T) (89.6%), Spirosoma oryzae RHs22(T) (89.6%), and Spirosoma radiotolerans DG5A(T) (89.1%). Strain DY10(T) showed resistance to gamma and ultraviolet radiation. The chemotaxonomic characteristics of strain DY10(T) were consistent with those of the genus Spirosoma, with the quinone system with MK-7 as the predominant menaquinone, iso-C15:0, C16:1 ω5c, and summed feature3 (C16:1 ω7c/C16:1 ω6c), and phosphatidylethanolamine as the major polar lipid. The G+C content of the genomic DNA was 53.0 mol%. Differential phenotypic properties with the closely related type strains clearly distinguished strain DY10(T) from previously described members of the genus Spirosoma and represents a novel species in this genus, for which the name Spirosoma montaniterrae sp. nov. is proposed. The type strain is DY10(T) (=KCTC 23999(T) =KEMB 9004-162(T) =JCM 18492(T)).

Isolation and characterization of a new gamma and UV radiation resistant bacterium from soil samples of an iranian radioactive site and analysis of its pigment

Radiation resistance has been detected dispersedly among bacteria and some microorganisms growing in natural radioactive environments. Herein, we provide data of isolation and characterization of a new radiation resistant bacterium from a radioactive site in Mashhad, Iran. The soil samples were collected and serial dilution plating was performed in TGY agar. All distinct colonies were isolated and irradiated by gamma radiation. The radioresistant bacterium was characterized by its morphology, biochemistry properties and 16S rRNA gene sequencing. In addition, pigment of the isolate was analysed by spectroscopic properties and LC-MS system and its antioxidant activity was measured by DPPH activity. Among 20 pure colonies, a new gamma and ultraviolet violet radiation resistant bacterium was designated as F3 strain. The isolated bacterium was coccoid in shape, nonmotile, non-sporulating, aerobic and with yellow pigmentation. Phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain related most closely to Micrococcus lylae. The results of spectroscopic and LC-MS analysis of the pigment show that it was belonged to Astaxanthin. Moreover, the isolate was resistant to gamma radiation (15 kGy) and UV light (400 j m−2). The isolate is the first report on radioresistant bacteria belonged to the Micrococcus genus isolated from radioactive region. Due to its antioxidant activity, pigment production and radiation resistant properties, we supposed that this isolate could be a candidate in industrial and bioremediation applications.

Isolation and characterization of a novel strain of genus Dietzia capable of multiple-extreme resistance

An ultraviolet (UV) radiation resistant gram-positive bacterium, Dietzia sp. MG4 strain, was isolated from the Sirch Hot Spring (Kerman, Iran), then it was identified on the basis of morphological and biochemical characteristics, and 16S rRNA gene sequencing. The effects of temperature, pH, desiccation, different percentage of NaCl, hydrogen peroxide (H2O2), mitomycin C (MMC) and high levels of radiation on viability or growth rate of MG4 strain were investigated. Also heavy metal tolerance of MG4 strain was assayed. 16S rDNA sequence of the isolate exhibited 99.69% similarity with Dietzia sp. and this result was confirmed by phylogenetic analysis. Viability of this strain was obtained D91 according to D index after exposure to 25 J/cm2 UV radiation dose, and D30 after desiccation stress (for 28 days) using flow cytometery. The D10 value for a microorganism is defined as the stress dose necessary to provide 10% survivors. Therefore, this strain showed high resistance to UV-C radiation and moderate resistance to desiccation. Optimal growth of MG4 strain was observed at pH 9, temperature of 30°C and 5% (w/v) NaCl. Isolated Dietzia was resisted up to 3 mM of nickel and 0.2 mM of mercury ions. Also this strain could tolerate 1–4% (v/v) H2O2 and 8 µg/mL of MMC as oxidant agents. To the best of our knowledge, this is the first study on multiple extreme resistant Dietzia sp. MG4 strain.

Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans.

BackgroundDeinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution.ResultsThe sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution.ConclusionsThe structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.

Molecular investigation of the radiation resistance of edible cyanobacterium Arthrospira sp. PCC 8005.

The aim of this work was to characterize in detail the response of Arthrospira to ionizing radiation, to better understand its radiation resistance capacity. Live cells of Arthrospira sp. PCC 8005 were irradiated with 60Co gamma rays. This study is the first, showing that Arthrospira is highly tolerant to gamma rays, and can survive at least 6400 Gy (dose rate of 527 Gy h−1), which identified Arthrospira sp. PCC 8005 as a radiation resistant bacterium. Biochemical, including proteomic and transcriptomic, analysis after irradiation with 3200 or 5000 Gy showed a decline in photosystem II quantum yield, reduced carbon fixation, and reduced pigment, lipid, and secondary metabolite synthesis. Transcription of photo-sensing and signaling pathways, and thiol-based antioxidant systems was induced. Transcriptomics did show significant activation of ssDNA repair systems and mobile genetic elements (MGEs) at the RNA level. Surprisingly, the cells did not induce the classical antioxidant or DNA repair systems, such superoxide dismutase (SOD) enzyme and the RecA protein. Arthrospira cells lack the catalase gene and the LexA repressor. Irradiated Arthrospira cells did induce strongly a group of conserved proteins, of which the function in radiation resistance remains to be elucidated, but which are a promising novel routes to be explored. This study revealed the radiation resistance of Arthrospira, and the molecular systems involved, paving the way for its further and better exploitation.

自然干旱胁迫下IrrE基因对甘蓝型油菜生理生化变化的影响

以转IrrE基因与非转基因甘蓝型油菜为材料，在自然干旱条件下，比较研究了转基因与非转基因油菜植株的干旱耐受性情况。结果表明，在0-35 d的自然干旱情况下，随着盆土中土壤含水量的逐渐降低，转基因与非转基因油菜植株的叶片含水量(RWC)也逐渐下降，35 d后他们的含水量降到最低，恢复供水后，其含量均逐渐上升。而油菜叶片的叶绿素含量、可溶性蛋白含量、丙二醛(MDA)含量、SOD和POD酶活性却逐渐上升，恢复供水后，他们的含量和酶活性均逐渐下降，但在干旱胁迫和复水过程中，转基因油菜叶片的含水量、叶绿素含量、可溶性蛋白含量、SOD和POD酶活性均高于非转基因油菜，而丙二醛(MDA)含量始终低于非转基因的含量。说明来源于耐辐射奇球菌的转录调节因子IrrE，参与了油菜幼苗对干旱胁迫的耐受性应答过程，从而增强了植株的耐旱能力。 The tolerant responses to drought stress in IrrE-transgenic Brassica napus L. and non-transgenic Brassica napus L. were studied. The results showed that water content in IrrE-transgenic and non-transgenic leaves of rapeseed gradually decreased with the drop of soil water content in pots during 0 - 35 d and their contents reached the minimum value after 35 d under natural drought conditions and then increased gradually after the restoration of water supply. The content of chlorophyll, soluble protein and malondialdehyde (MDA), and the SOD and POD activity in leaves of Brassica napus L. were increased gradually during 0 - 35 d and their contents reached the maximal value after 35 d under natural drought conditions and then decreased gradually after the restoration of water supply. But the water content, chlorophyll content, soluble protein content and the activity of peroxidase (POD) and superoxide dismutase (SOD) in leaves of transgenic Brassica napus L were higher than those in non-transgenic Brassica napus L., while the content of ma-lonaldehyde (MDA) in transgenic Brassica napus L. was lower than non-transgenic Brassica napus L. during 0 - 35 d under drought stress and the restoration of water supply. Therefore, the results from above indicated that IrrE as the transcription regulation factor, which was derived from the radiation resistant bacteria, was involved in the tolerance response of rape seedling to drought stress, and then enhanced the ability of drought tolerance.

Deinococcus radioresistens sp. nov., a UV and gamma radiation-resistant bacterium isolated from mountain soil.

Two Gram-negative, non-motile, short rod-shaped bacterial strains, designated as 8A(T) and 28A, were isolated from Mount Deogyusan, Jeonbuk Province, South Korea. The isolates were analyzed by a polyphasic approach, revealing variations in their phenotypic characters but high DNA-DNA hybridisation values reciprocally, confirming that they belong to the same species. Both the isolates also showed a high resistance to UV compared with Deinococcus radiodurans, and a gamma-radiation resistance similar to other members of the genus Deinococcus. Phylogenetic analysis with the 16S rRNA gene sequences of closely related species indicated their similarities were below 97 %. Chemotaxonomic data showed the most abundant fatty acids to be C16:1ω7c and C16:0. The strains can be distinguished from closely related species by the production of esterase (C4) and α-galactosidase, and by their ability to assimilate L-alanine, L-histidine and N-acetyl-D-glucosamine. Based on the phenotypic, phylogenetic, and chemotaxonomic data, the isolates represent a novel species of the genus Deinococcus, for which the name Deinococcus radioresistens sp. nov. is proposed. The type strain is 8A(T) (KEMB 9004-109(T) = JCM 19777(T)), and a second strain is 28A (KEMB 9004-113 = JCM 19778).

Deep sequencing analysis of the Kineococcus radiotolerans transcriptome in response to ionizing radiation

Kineococcus radiotolerans is a gram-positive, radiation-resistant bacterium that was isolated from a radioactive environment. The synergy of several groups of genes is thought to contribute to the radio-resistance of this species of bacteria. Sequencing of the transcriptome, RNA sequencing (RNA-seq), using deep sequencing technology can reveal the genes that are differentially expressed in response to radiation in this bacterial strain. In this study, the transcriptomes of two samples (with and without irradiation treatment) were sequencing by deep sequencing technology. After the bioinformatics process, 143 genes were screened out by the differential expression (DE) analysis. In all 143 differentially expressed genes, 20 genes were annotated to be related to the radio-resistance based on the cluster analysis by the cluster of orthologous groups of proteins (COG) annotation which were validated by the quantitative RT-PCR. The pathway analysis revealed that these 20 validated genes were related to DNA damage repair, including recA, ruvA and ruvB, which were considered to be the key genes in DNA damage repair. This study provides the foundation to investigate the regulatory mechanism of these genes.

Isolation and characterization of a radiation-resistant bacterium from Taklamakan Desert showing potent ability to accumulate Lead (II) and considerable potential for bioremediation of radioactive wastes.

Radioactive wastes always contain radioactive substances and a lot of Pb compound and other heavy metals, which severely contaminate soils and groundwater. Thus, search for radiation-resistant microorganisms that are capable of sequestering Pb contaminants from the contaminated sites is urgently needed. However, very few such microorganisms have been found so far. In the present study, we discovered a novel Gram-negative bacterium from the arid Taklamakan desert, which can strongly resist both radiation and Pb(2+). Phylogenetic and phenotypic analysis indicated that this bacterial strain is closely affiliated with Microvirga aerilata, and was thus referred to as Microvirga aerilata LM (=CCTCC AB 208311). We found that M. aerilata LM can effectively accumulate Pb and form intracellular precipitations. It also keeps similar ability to remove Pb(2+) under radioactive stress. Our data suggest that M. aerilata LM may offer an effective and eco-friendly in situ approach to remove soluble Pb contaminants from radioactive wastes.

Radiation resistant of native Deinococcus spp. isolated from the Lout desert of Iran “the hottest place on Earth”

Two native ionizing radiation-resistant bacteria were isolated and identified from a soil sample collected from extreme conditions of the Lout desert in Iran. The hottest land surface temperature has been recorded in the Lout desert from 2004 to 2009. Also, it is categorized as a hyper arid place. Both ionizing radiation and desiccation may cause damage on genome. Soil sample was irradiated in order to eliminate sensitive bacteria then cultured in one-tenth-strength tryptic soy broth medium. Bacterial suspension used for radiation treatment. Morphological and physiological characterization and phylogenetic studies based on 16S rRNA gene sequence were used for identification. The cells were rod shape, non-motile, non-spore forming and gram positive. The 16S rRNA gene sequence showed 99.5 % of similarity to Deinococcus ficus. Phylogenetic dendrogram demonstrated that the isolates branched with D. xibeiensis, D. ficus and D. mumbaiensis. Both isolates were resistant to >15 kGy of gamma radiation and >600 J m2 of UV radiation. This is the first report on radiation resistant bacteria belonging to genus Deinococcus isolated from the Lout desert of Iran.

THE EFFECT OF Mn(II) ON THE AUTOINDUCING GROWTH INHIBITION FACTOR IN Deinococcus radiodurans

Decreases in cell division at the stationary phase in bacterial cultures are often due to the depletion of nutrients and/or accumulation of toxic waste products. Yet, during the stationary phase, the highly radiation-resistant bacterium Deinococcus radiodurans undergoes new rounds of cell division when Mn(II) is added to the medium in a phenomenon known as manganese-induced cell division (MnCD). When cells were cultured in medium without Mn(II)-enrichment, a heat-resistant, proteinase K-resistant factor (or factors) with a molecular mass less than 10 kD accumulated in the spent medium. Inclusion of the concentrated spent medium in fresh medium could inhibit the growth of D. radiodurans significantly, and the degree of inhibition was dose dependent. However, the relative stimulatory effect of MnCD was also dose dependent—the higher the inhibition, the stronger was the MnCD response. Previous studies have shown that nutrients were not limiting and deinococcal cells would continue metabolizing its nutrients at stationary phase. Cells became more sensitive to radiation when nutrients in the medium eventually became depleted. We speculated that D. radiodurans might produce this factor in the medium to control its population density. The reduction in cell population would conserve the nutrients that in turn might enhance the survival of the species.