Complete Genome Sequence of Hymenobacter sedentarius DG5BT, a Bacterium Resistant to Gamma Radiation

Myung Kyum Kim,Myung-Suk Kang,Sathiyaraj Srinivasan,Do Hee Lee,Seung-Yeol Lee,Hee-Young Jung,H Y. Jung 대한독성 유전단백체 학회 2017 Molecular & cellular toxicology Vol.13 No.2

The ionizing radiation toxicity becomes a primary concern of the world; several exceptional attention was given to the resistance mechanisms of the radiation-resistant bacteria. Hymenobacter sedentarius DG5BT strain isolated from the gamma ray-irradiated soil samples shows resistance against gamma and UV radiation; however, their level of resistance is lower than that of other radiation resistant bacteria. To gain insight of radiation resistance, we carried out the whole genome sequencing of this strain. The genome of DG5BT strain is comprised of 4,868,852 bp (G+C content of 60.96%) including 3,994 protein-coding genes and 55 RNA genes. When compared with other bacteria, there are differences in compositions and copy numbers of several genes involved in DNA repair pathways and defense mechanism against protein damages. In this study, we discuss the implication of such findings concerning other radiation resistant bacteria.

Molecular Pathogenesis of Radiation-Induced Cell Toxicity in Stem Cells

Hur, Wonhee,Yoon, Seung Kew MDPI 2017 INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES Vol.18 No.12

<P>Radiation therapy is an effective cancer therapy, but damage to normal tissues surrounding the tumor due to radiotherapy causes severe complications. The importance of the therapeutic area between tumor suppression and normal tissue injury has long been highlighted in radiation therapy. Recent advances in stem cell biology have shown that stem cell (SC) responses to genotoxic stresses of ionizing radiation can improve the therapeutic effect of radiation by repairing damaged cells. In contrast, cancer stem cells (CSCs), a small subpopulation of cells within tumors, are generally resistant to chemotherapy and radiotherapy and cause tumor recurrence. Although the underlying mechanisms are not clearly understood in detail, efforts are still underway to identify SC treatment or CSC resistant pathogenesis of DNA damage agents such as radiation therapy. In response to radiation, CSCs differ from normal SCs in their biological properties due to severe deregulation of the self-renewal ability in CSCs. Differences of cleavage mode, cell cycle characteristics, replication potential, and activation/inactivation of DNA damage treatment and cancer-specific molecular pathways between normal SCs and CSCs confer a malignant phenotype upon CSCs. However, further studies are needed to identify normal SC and CSC-specific targets. In this review, we summarize the current advances in research regarding how normal SCs and CSCs respond to ionizing radiation, with a special emphasis on cell toxicity, radiosensitivity, signaling networks, DNA damage response (DDR) and DNA repair. In addition, we discuss strategies to develop new diagnostic and therapeutic techniques for predicting responses to cancer treatment and overcoming radiation-related toxicity.</P>

Radiation-induced cathepsin S is involved in radioresistance

Seo, Haeng Ran,Bae, Sangwoo,Lee, Yun-Sil Wiley Subscription Services, Inc., A Wiley Company 2009 International journal of cancer: Journal internati Vol.124 No.8

<P>Previous studies have suggested that the production of cathepsin S (CatS), a cysteine protease, was specifically induced in radiation-induced rat mammary tumors. In this study, we further investigate the mechanism by which CatS is induced by radiation and its function. Radiation induced production of CatS at both the mRNA and protein level, and increased its protease activity. In addition, these radiation induced changes occurred in a dose and time-dependent fashion. Agents such as bleomycin, As<SUB>2</SUB>O<SUB>3</SUB> and H<SUB>2</SUB>O<SUB>2</SUB>, which produce reactive oxygen species (ROS), also induced CatS expression; however, other agents that damage DNA such as taxol and cisplatin did not. Additionally, treatment of the cells with the ROS scavengers, N-acetylcysteine and catalase, inhibited the radiation induced CatS expression. Furthermore, radiation-induced ROS was also involved in IFN-γ production, which was responsible for radiation-mediated CatS expression. Moreover, electrophoretic mobility shift assay (EMSA) data obtained using an IFN-stimulated response element (ISRE) oligonucleotide revealed that IFN regulatory factor-1 (IRF1) was the critical transcriptional mediator of IFN-γ-dependent CatS production after radiation. Finally, CatS overespression was found to induce radioresistance; however, knockdown of CatS resulted in the suppression of radioresistance. Taken together, the results of this study indicate that radiation induced CatS expression via ROS-IFN-γ pathways, and that this increased expression may be involved in radioresistance. © 2008 Wiley-Liss, Inc.</P>

Complete genome sequence of Methylobacterium sp. 17Sr1-43, a radiation-resistant bacterium

Myung-Suk Kang,Sathiyaraj Srinivasan 대한독성 유전단백체 학회 2018 Molecular & cellular toxicology Vol.14 No.4

Backgrounds: The genus Methylobacterium is composed of a variety of pink-pigmented and facultatively methylotrophic bacteria. Most of the species of these genera have been shown to be either gamma radiation resistant or UV radiation resistant or both. Strain Methylobacterium sp. 17Sr1-43 was isolated from a gamma- irradiated soil sample collected at Seoul Women’s University, South Korea. Methods: The complete genome of strain Methylobacterium sp. 17Sr1-43 was sequenced and assembled using Pacific Biosciences RS II system. The genome sequence was annotated using JGI GenePRIMP, Prodigal, and Genomes-Expert Review (IMG-ER) platform. The protein-coding genes were identified using Pfam and COG databases implemented in the IMG and NCBI systems. Results: The complete genome of strain Methylobacterium sp. 17Sr1-43 was found to comprise a complete circular chromosome of 5,539,695 bp, with 5,103 coding sequences (CDs) and 5,186 genes. Many identified genes involved either in DNA repair or the cellular response to ionization radiation. However, contributions by genes involved in cell wall structure/function, cell division, and intermediary metabolism were also evident. Some identified genes were previously have been associated with IR resistance or recovery from IR exposure, including the RecBCD pathway and UmuCD system. Conclusion: The new strains of Methylobacterium sp. 17Sr1-43 showed both gamma and UV-C irradiation resistance, and their complete genome sequence annotation features correspondingly showed the presence of the genes involved in the radiation-resistance.

Complete genome sequence of Microvirga sp. 17mud 1-3, a radiation-resistant bacterium

Gayathri Sathiyaraj,Myung Kyum Kim,Ju-Young Kim,Su Jeong Kim,장준휘,Soohyun Maeng,Myung-Suk Kang,Sathiyaraj Srinivasan 대한독성 유전단백체 학회 2018 Molecular & cellular toxicology Vol.14 No.3

Backgrounds: The genera Deinococcus Hymenobacter, Spirosoma, and Rubrobacter are renowned as an extremophilic bacteria. Most of the species of these genera have been shown to be either gamma radiation resistant or UV radiation resistant or both. Strain 17mud 1-3 was isolated from gamma-irradiated mud sample collected at Boryeong beach, South Korea. Methods: The genome of strain 17mud 1-3 was sequenced and assembled using Pacific Biosciences RS II system. The genome sequence was annotated using Genomes-Expert Review (IMG-ER) platform, Prodigal, and JGI GenePRIMP pipeline. The protein-coding genes were identified using Prodigal, Pfam and COG databases implemented in the IMG systems. Results: The complete genome consists of a circular chromosome (4,403,107 bp) encoding 4,368 coding sequences (CDs) and 4,301genes. Conclusion: The new strains showed both gamma and UV-C irradiation resistance and their complete genome sequence annotation features showed the presence of the genes involved in the radiation-resistance.

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

Sathiyaraj Srinivasan,Myung Kyum Kim,Eun Sun Joo,Seung-Yeol Lee,Dae Sung Lee,Hee-Young Jung,H.-Y. Jung 대한독성 유전단백체 학회 2015 Molecular & cellular toxicology Vol.11 No.4

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.

A Novel Radiation-Resistant Strain of Filobasidium sp. Isolated from the West Sea of Korea

Harinder Singh,Ha Ram Kim,Hyunpa Song,Min Ho Joe,Dong Ho Kim,Yong Sun Bahn,Jong Il Choi,Sangyong Lim 한국미생물생명공학회(구 한국산업미생물학회) 2013 Journal of microbiology and biotechnology Vol.23 No.11

A novel radiation-resistant Filobasidium sp. yeast strain was isolated from seawater. Along with this strain, a total of 656 yeast isolates were purified from seawater samples collected from three locations in the West Sea of Korea and assessed for their radiation tolerance. Among these isolates, five were found to survive a 5 kGy radiation dose. The most radiationresistant strain was classified as Filobasidium sp. based on 18S rDNA sequence analysis and hence was named Filobasidium RRY1 (Radiation-Resistant Yeast 1). RRY1 differed from F. elegans, which is closely related to RRY1, in terms of the optimal growth temperature and radiation resistance, and was resistant to high doses of γ-ionizing radiation (D10: 6-7 kGy). When exposed to a high dose of 3 kGy irradiation, the RRY1 cells remained intact and undistorted, with negligible cell death. When these irradiated cells were allowed to recover, the cells fully repaired their genomic DNA within 3 h of growth recovery. This is the first report in which a radiation-resistant response has been investigated at the physiological, morphological, and molecular levels in a strain of Filobasidium sp.

High expression of mTOR is associated with radiation resistance in cervical cancer

김민규,김태중,성창옥,최철훈,이정원,김병기,배덕수 대한부인종양학회 2010 Journal of Gynecologic Oncology Vol.21 No.3

Objective: Mammalian target of rapamycin (mTOR) is known to promote cell proliferation, survival, and resistance to radiation. The aim of this study was to determine whether mTOR expression was associated with survival and the response to radiation in patients with cervical cancer. Methods: After reviewing 119 patients treated by primary radiotherapy for stage IIB-IVA cervical cancer, a case-control study was performed. The cases (n=12) with local recurrence or radiation failure after primary radiation therapy were selected. For each case, two controls that had no recurrence were selected. Using pretreatment paraffin-embedded tissues, the cytoplasmic expression of phosphorylated-mTOR (p-mTOR) was evaluated by immunohistochemistry. Staining was scored based on intensity (intensity score [IS] 0-3) and proportion (proportion score [PS] 0-100). The progression free survival (PFS) was defined from the end of treatment to the day of recurrence by imaging studies or biopsy. The staining distribution and PFS were compared between the two groups. The results were analyzed by the Student t-test, Mann-Whitney U-test, Fisher's exact test, and Cox proportional hazards regression model. Results: The p-mTOR cytoplasmic expression was significantly associated with a poor response to radiotherapy (p <0.01). With respect to survival, a higher cytoplasmic expression of p-mTOR was associated with a worse outcome (p=0.02). The hazard ratio for recurrence or radiation failure was 6.18 for mTOR IS and 1.04 for mTOR PS (p<0.05for both), indicating that the degree of p-mTOR staining correlated with the recurrence risk. Conclusion: High expression of p-mTOR was associated with radiation resistance; therefore p-mTOR may be a prognostic marker for response to radiotherapy in patients with cervical cancer.

Increased expression of ICAM-3 is associated with radiation resistance in cervical cancer

Chung, Young Min,Kim, Byoung-Gie,Park, Chang-Soo,Huh, Seung Jae,Kim, Jhingook,Park, Jong Kuk,Cho, Sun Mi,Kim, Byung Soo,Kim, Jun Suk,Yoo, Young Do,Bae, Duk-Soo Wiley Subscription Services, Inc., A Wiley Company 2005 International journal of cancer: Journal internati Vol.117 No.2

<P>To search for a marker that predicts the efficacy of radiation therapy in human cervical cancer, gene expression profiles between parental SiHa cervical cancer cells and radiation-resistant SiHa/R cells have been compared by the microarray technique. Microarray and Northern blot analyses demonstrated that the ICAM-3 expression was upregulated in SiHa/R cells. This increased expression of ICAM-3 in SiHa cells enhanced cell survival by about 34.3% after a 2 Gy dosage of radiation. In addition, SiHa/ICAM-3 cells showed a 2.45-fold higher level of FAK phosphorylation than that of the control cells. In tumor specimens, ICAM-3 staining was restricted to tumor stromal endothelial cells and lymphocytes. The overexpression of ICAM-3 was significantly more frequent in radiation-resistant cervical cancer specimens when compared with radiation-sensitive specimens (83.3% vs. 35.3%; p = 0.015). With these observations, we can suggest that an increased expression of ICAM-3 is associated with radiation resistance in cervical cancer cells and the expression of ICAM-3 can be used as a valuable biomarker to predict the radiation resistance in cervical cancer that occurs during radiotherapy. © 2005 Wiley-Liss, Inc.</P>

한강물로부터 분리된 방사선 내성 세균들의 계통학적 다양성 및 UV 내성 분석

이재진,주은선,이도희,정희영,김명겸,Lee, Jae-Jin,Joo, Eun Sun,Lee, Do Hee,Jung, Hee-Young,Kim, Myung Kyum 한국미생물학회 2016 미생물학회지 Vol.52 No.1

이 논문은 서울 한강물에서 분리한 방사선 내성 세균군집과 분리된 신종 세균의 UV 내성 특성에 관한 내용이다. 세균은 R2A agar와 1/10 R2A agar를 사용하여 3 kGy가 조사된 한강물에서 분리되었다. 그 결과 방사선에 내성을 가지는 것으로 추측되는 균주를 60주 분리하였고, 본 연구 분석 자료로 사용하였다. 16S rRNA 유전자 염기서열 분석을 통해 분리균주 60개의 계통수를 파악한 결과, 3개의 문(4개의 속)이 확인되었고, Deinococcus-Thermus (Deinococcus)가 61.7%, Firmicutes(Exiguobacterium)는 15%, Bacteroidetes (Hymenobacter, Spirosoma)는 23.4%의 비중을 나타냈다. 분리균주 중 29개 균주가 Deinococcus, Hymenobacter, Spirosoma에 속하는 신종 또는 다른 신속으로 분류될 가능성을 보였으며, 앞으로 추가적인 신종 실험이 진행될 예정이다. 그리고 신종 예상균주를 9개 선정하여 UV 내성 실험을 진행한 결과, 9개 균주 모두 D. radiodurans $R1^T$ 균주 만큼 높은 UV 내성을 가지는 것으로 나타났다. 또한 분리된 Firmicutes (Exiguobacterium) 균주는 아직까지 방사선 내성 연구 보고가 되어 있지 않아서 추가적인 방사선 내성 연구가 필요하다. The aim of this study was to investigate the UV-resistance of radiation-resistant bacteria isolated from the water of Han River, South Korea. The water sample was irradiated with 3 kGy gamma radiation prior to isolation. Radiation-resistant bacterial strains were isolated by standard serial dilution method on R2A and 1/10 diluted R2A agar. The resulting purely isolated 60 cultures of bacteria were analysed for UV resistance and used in further studies. Based on the comparative analyses of 16S rRNA gene sequences, the bacterial isolates were divided into 3 phyla (4 genera): the phylum Deinococcus-Thermus (the genus Deinococcus) was 61.7%, Bacteroidetes (Hymenobacter and Spirosoma) was 23.4%, and Firmicutes (Exiguobacterium) was 15%. The results suggested that twenty-nine isolates are candidates new species belonging to Deinococcus, Hymenobacter, and Spirosoma, or other new genera. Nine bacterial strains were selected among the novel candidates and the UV-resistance analysis was conducted. All the candidate bacterial strains showed high UV resistance, similar to that of D. radiodurans R1.