Journal of Microbiology

Volume 58(2); February 2020

Review

Functional interplay between the oxidative stress response and DNA damage checkpoint signaling for genome maintenance in aerobic organisms: Ji Eun Choi , Woo-Hyun Chung; J. Microbiol. 2020;58(2):81-91. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9520-x

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The DNA damage checkpoint signaling pathway is a highly conserved surveillance mechanism that ensures genome integrity by sequential activation of protein kinase cascades. In mammals, the main pathway is orchestrated by two central sensor kinases, ATM and ATR, that are activated in response to DNA damage and DNA replication stress. Patients lacking functional ATM or ATR suffer from ataxia-telangiectasia (A-T) or Seckel syndrome, respectively, with pleiotropic degenerative phenotypes. In addition to DNA strand breaks, ATM and ATR also respond to oxidative DNA damage and reactive oxygen species (ROS), suggesting an unconventional function as regulators of intracellular redox status. Here, we summarize the multiple roles of ATM and ATR, and of their orthologs in Saccharomyces cerevisiae, Tel1 and Mec1, in DNA damage checkpoint signaling and the oxidative stress response, and discuss emerging ideas regarding the possible mechanisms underlying the elaborate crosstalk between those pathways. This review may provide new insights into the integrated cellular strategies responsible for maintaining genome stability in eukaryotes with a focus on the yeast model organism.

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DSB-induced oxidative stress: Uncovering crosstalk between DNA damage response and cellular metabolism
Xinyu Li, Caini Yang, Hengyu Wu, Hongran Chen, Xing Gao, Sa Zhou, Tong-Cun Zhang, Wenjian Ma
DNA Repair.2024; 141: 103730. CrossRef
Effects of Stress on Biological Characteristics and Metabolism of Periodontal Ligament Stem Cells of Deciduous Teeth
Zhengyang Li, Jinyi Li, Shanshan Dai, Xuelong Su, Meiyue Ren, Shuyang He, Qingyu Guo, Fei Liu
International Dental Journal.2024;[Epub] CrossRef
Signification and Application of Mutator and Antimutator Phenotype-Induced Genetic Variations in Evolutionary Adaptation and Cancer Therapeutics
Woo-Hyun Chung
Journal of Microbiology.2023; 61(12): 1013. CrossRef
Metabolic Stress and Mitochondrial Dysfunction in Ataxia-Telangiectasia
Goutham Narayanan Subramanian, Abrey Jie Yeo, Magtouf Hnaidi Gatei, David John Coman, Martin Francis Lavin
Antioxidants.2022; 11(4): 653. CrossRef
The Rad9–Rad1–Hus1 DNA Repair Clamp is Found in Microsporidia
Anne Caroline Mascarenhas dos Santos, Alexander Thomas Julian, Jean-François Pombert, Emmanuelle Lerat
Genome Biology and Evolution.2022;[Epub] CrossRef
Novel insights into the mechanism of cell cycle kinases Mec1(ATR) and Tel1(ATM)
Elias A. Tannous, Peter M. Burgers
Critical Reviews in Biochemistry and Molecular Biology.2021; 56(5): 441. CrossRef
DNA damage checkpoint and repair: From the budding yeast Saccharomyces cerevisiae to the pathogenic fungus Candida albicans
Shuangyan Yao, Yuting Feng, Yan Zhang, Jinrong Feng
Computational and Structural Biotechnology Journal.2021; 19: 6343. CrossRef
Acute Toxicity and DNA Instability Induced by Exposure to Low Doses of Triclosan and Phthalate DEHP, and Their Combinations, in vitro
Nathalia de Assis Aguilar Duarte, Lindiane Eloisa de Lima, Flora Troina Maraslis, Michael Kundi, Emilene Arusievicz Nunes, Gustavo Rafael Mazzaron Barcelos
Frontiers in Genetics.2021;[Epub] CrossRef
The mechanism and prevention of mitochondrial injury after exercise
Mingzhe Li, Baoan Ning, Tianhui Wang
Journal of Physiology and Biochemistry.2021; 77(2): 215. CrossRef

Journal Articles

Parahaliea maris sp. nov., isolated from surface seawater and emended description of the genus Parahaliea: Yang Liu , Juan Du , Jun Zhang , Qiliang Lai , Zongze Shao , Honghui Zhu; J. Microbiol. 2020;58(2):92-98. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9405-z

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Abstract

A Gram-stain-negative, strictly aerobic, short-rod-shaped, and non-motile bacterial strain designated HSLHS9T was isolated from surface seawater collected from the South China Sea. Strain HSLHS9T could grow at 15–41°C (optimum 28°C), at pH 5.0–9.0 (optimum 6.0–7.0), and in 0–7% (w/v) NaCl (optimum 2–3%). Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain HSLHS9T shared high identities with the closely related Parahaliea aestuarii S2-26T (98.6%) and Parahaliea mediterranea 7SM29T (97.8%) and formed a distinct lineage within the genus Parahaliea. Wholegenome sequencing of strain HSLHS9T revealed the size of 4.8 Mbp and DNA G + C content of 61.8 mol%. Strain HSLHS9T shared the digital DNA-DNA hybridization values of 22.4% and 23.0%, and the average nucleotide identities of 79.7% and 79.9%, respectively, with the two type strains above. The predominant cellular fatty acids of the strain were summed feature 8 (C18:1 ω6c and/or C18:1 ω7c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C17:1 ω8c, and C16:0. The sole isoprenoid quinone was identified as Q-8. The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, aminolipid, and two glycolipids. Based on taxonomic data obtained in this study, it is suggested that strain HSLHS9T represents a novel species of the genus Parahaliea, for which the name Parahaliea maris sp. nov. is proposed. The type strain is HSLHS9T (= MCCC 1A06717T = KCTC 52307T). An emended description of the genus Parahaliea is also provided.

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A comparative analysis of the microbial communities and functional genes of the nitrogen cycling in mangroves of China, Indian and Malaysia
Zhihui Qian, Yuyang Li, Amit Pratush, Jie Kan, Ji-Dong Gu, Tao Peng, Tongwang Huang, Zhong Hu
International Biodeterioration & Biodegradation.2024; 190: 105767. CrossRef
Phylogenomic evaluation of Mangrovimicrobium sediminis gen. nov. sp. nov., the first nitrogen fixing member of the family Halieaceae adapted to mangrove habitat and reclassification of Halioglobus pacificus to Pseudohaliglobus pacificus comb. nov.
Pravin Kumar, Ashish Verma, Pooja Yadav, Joyasree Das, Lalit Kumar, Srinivasan Krishnamurthi
Science of The Total Environment.2024; 933: 172995. CrossRef
Abundant and rare bacteria in anthropogenic estuary: Community co-occurrence and assembly patterns
Ziyue Shi, Lili Ma, Yingying Wang, Jie Liu
Ecological Indicators.2023; 146: 109820. CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
Sediminihaliea albiluteola gen. nov., sp. nov., a new member of the family Halieaceae, isolated from marine sediment
Shan Jiang, Feng-Bai Lian, You-Yang Sun, Xiao-Kui Zhang, Zong-Jun Du
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2020; 70(5): 2960. CrossRef
Notification of changes in taxonomic opinion previously published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2020; 70(7): 4061. CrossRef
Aequoribacter fuscus gen. nov., sp. nov., a new member of the family Halieaceae, isolated from coastal seawater
Shan-Hui Li, Jaeho Song, Ilnam Kang, Juchan Hwang, Jang-Cheon Cho
Journal of Microbiology.2020; 58(6): 463. CrossRef

Sutterella faecalis sp. nov., isolated from human faeces: Byeong Seob Oh , Ji-Sun Kim , Seung Yeob Yu , Seoung Woo Ryu , Seung-Hwan Park , Se Won Kang , Jam-Eon Park , Seung-Hyeon Choi , Kook-Il Han , Keun Chul Lee , Mi Kyung Eom , Min Kuk Suh , Han Sol Kim , Dong Ho Lee , Hyuk Yoon , Byung-Yong Kim , Je Hee Lee , Jung-Sook Lee , Ju Huck Lee; J. Microbiol. 2020;58(2):99-104. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9396-9

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Abstract

An obligately anaerobic, Gram-stain-negative, non-motile, non-spore-forming, and coccobacilli-shaped bacterial strain, designated KGMB03119T, was isolated from human faeces from a Korean. Phylogenetic analysis based on the 16S rRNA gene sequence revealed that the isolate was a member of the genus Sutterella and most closely related to Sutterlla wadsworthensis KCTC 15691T (96.8% 16S rRNA gene sequence similarity). The DNA G + C content of strain KGMB03119T was 58.3 mol% as determined from its whole genome sequence. Strain KGMB03119T was asaccharolytic, catalase-positive, oxidase- and urease-negative. Furthermore, the isolate was positive for alkaline phosphatase, leucine arylamidase, acid phosphatase, arginine arylamidase, alanine arylamidase, and glycine arylamidase. The major cellular fatty acids (> 10%) of the isolate were C18:1ω9c and C16:0. Methylmenaquinone-5 (MMK-5, 100%) was the predominant isoprenoid quinone in the isolate. Based on the phylogenetic, physiological, and chemotaxonomic characteristics, strain KGMB03119T represents a novel species, for which the name Sutterella faecalis sp. nov. is proposed. The type strain is KGMB03119T (= KCTC 15823T = NBRC 114254T).

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In vitro gastrointestinal digestion and colonic fermentation of Mangiferin: Impacts on gut microbiota and metabolite profiles
Huilin Deng, Yaozhong Zheng, Qiongyao Wang, Jiaqi Peng, Weibin Bai, Lingmin Tian, Zouyan He, Rui Jiao
Journal of Functional Foods.2025; 124: 106667. CrossRef
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Jose Bellver, Marta Gonzalez-Monfort, Sandra González, Bruno Toson, Elena Labarta, Gemma Castillón, Giulia Mariani, Carmina Vidal, Juan Giles, Fabio Cruz, Agustin Ballesteros, Marcos Ferrando, Juan Antonio García-Velasco, Diana Valbuena, Felipe Vilella, M
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Arianna Carella, Karen C. Carroll, Erik Munson, Romney M. Humphries
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Lauryn Langford, Dhara D. Shah
International Journal of Molecular Sciences.2024; 25(5): 2983. CrossRef
Validation List no. 212. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Longitudinal Study of the Effects of Flammulina velutipes Stipe Wastes on the Cecal Microbiota of Laying Hens
Jiali Wei, Huanwei Xiao, Yingbo Wei, Ivan Stève Nguepi Tsopmejio, Chang Sun, Haoyuan Wu, Zhouyu Jin, Hui Song, Suzanne Lynn Ishaq, Yunhe Xu
mSystems.2023;[Epub] CrossRef

Natronorubrum halophilum sp. nov. isolated from two inland salt lakes: Cong-Qi Tao , Yi Ding , Yang-Jie Zhao , Heng-Lin Cui; J. Microbiol. 2020;58(2):105-112. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9514-8

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Abstract

Two halophilic archaeal strains, SHR37T and NEN6, were isolated from salt lakes located in the Tibet and Xinjiang regions of China. The two strains were found to form a single cluster (99.9% and 99.3% similarity, respectively) separating them from the six current members of Natronorubrum (94.7– 96.9% and 86.1–90.8% similarity, respectively) on the basis of the 16S rRNA and rpoB􍿁 gene sequence similarities and phylogenetic analysis. Diverse phenotypic characteristics differentiate strains SHR37T and NEN6 from current Natronorubrum members. Their polar lipids are C20C20 and C20C25 glycerol diether derivatives of PG, PGP-Me, and a major glycolipid chromatographically identical to disulfated mannosyl glucosyl diether (S2-DGD). Four minor unidentified glycolipids are also present. The OrthoANI and in silico DDH values of the two strains were 97.3% and 76.1%, respectively, which were much higher than the threshold values proposed as a species boundary (ANI 95–96% and in silico DDH 70%), which revealed that the two strains represent one species; the two values (ANI 79.0–81.9% and in silico DDH 23.5– 25.7%) of the strains examined in this study and the current members of Natronorubrum are much lower than the recommended threshold values, suggesting that strains SHR37T and NEN6 represent a genomically different species of Natronorubrum. These results showed that strains SHR37T (= CGMCC 1.15233T = JCM 30845T) and NEN6 (= CGMCC 1.17161) represent a novel species of Natronorubrum, for which the name Natronorubrum halophilum sp. nov. is proposed.

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Genome-based taxonomy of genera Haloarcula and Halomicroarcula, and description of six novel species of Haloarcula
Xue Ma, Yao Hu, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef
Genome-based classification of the family Haloferacaceae and description of five novel species of Halobaculum
Shun Tan, Ling-Rui Zhu, Qing-Ke Zhang, Xin-Yue Dong, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef
Halobacterium yunchengense sp. nov., Natronomonas amylolytica sp. nov., Halorientalis halophila sp. nov., Halobellus salinisoli sp. nov., halophilic archaea isolated from a saline lake and inland saline soil
Ling Cui, Yao Hu, Xin-Xin Li, Xue Ma, Mu Cheng, Shun Tan, Jing Hou, Heng-Lin Cui
Extremophiles.2024;[Epub] CrossRef
Prokaryotic Community Structure, Abundances, and Potential Ecological Functions in a Mars Analog Salt Lake
Wenqi Cai, Ke Yu, Wanting Yang, Rong Mu, Chunang Lian, Luhua Xie, Yan Yan, Shibin Liao, Fan Wang
Astrobiology.2023; 23(5): 550. CrossRef
Halocatena marina sp. nov., a novel filamentous halophilic archaeon isolated from marine tidal flat and emended description of the genus Halocatena
Zhang-Ping Wu, Xi-Wen Zheng, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui
Extremophiles.2023;[Epub] CrossRef
Halomicroarcula laminariae sp. nov. and Halomicroarcula marina sp. nov., extremely halophilic archaea isolated from salted brown alga Laminaria and coastal saline-alkali lands
Xue Ma, Yao Hu, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Natrinema caseinilyticum sp. nov., Natrinema gelatinilyticum sp. nov., Natrinema marinum sp. nov., Natrinema zhouii sp. nov., extremely halophilic archaea isolated from marine environments and a salt mine
Yao Hu, Xue Ma, Xin-Xin Li, Shun Tan, Mu Cheng, Jing Hou, Heng-Lin Cui
Extremophiles.2023;[Epub] CrossRef
Halobacterium wangiae sp. nov. and Halobacterium zhouii sp. nov., two extremely halophilic archaea isolated from sediment of a salt lake and saline soil of an inland saltern
Bei-Bei Wang, Chen-Xi Bao, Ya-Ping Sun, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Halocatena salina sp. nov., a filamentous halophilic archaeon isolated from Aiding Salt Lake
Zhang-Ping Wu, Xi-Wen Zheng, Ya-Ping Sun, Bei-Bei Wang, Jing Hou, Heng-Lin Cui
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Correlating bacterial and archaeal community with efficiency of a coking wastewater treatment plant employing anaerobic-anoxic-oxic process in coal industry
Qiaoying Ban, Liguo Zhang, Jianzheng Li
Chemosphere.2022; 286: 131724. CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
Haloprofundus salilacus sp. nov., Haloprofundus halobius sp. nov. and Haloprofundus salinisoli sp. nov.: three extremely halophilic archaea isolated from salt lake and saline soil
Si-Ya Li, Yu-Jie Xin, Chen-Xi Bao, Jing Hou, Heng-Lin Cui
Extremophiles.2022;[Epub] CrossRef
Natronorubrum halalkaliphilum sp. nov., a haloalkaliphilic archaeon isolated from soda lake in Inner Mongolia Autonomous Region, China
Qiong Xue, Dahe Zhao, Zhenqiang Zuo, Jian Zhou, Hua Xiang
Archives of Microbiology.2021; 203(5): 2335. CrossRef
Phylogenomics of Haloarchaea: The Controversy of the Genera Natrinema-Haloterrigena
Rafael R. de la Haba, Hiroaki Minegishi, Masahiro Kamekura, Yasuhiro Shimane, Antonio Ventosa
Frontiers in Microbiology.2021;[Epub] CrossRef
Salinadaptatus halalkaliphilus gen. nov., sp. nov., a haloalkaliphilic archaeon isolated from salt pond in Inner Mongolia Autonomous Region, China
Qiong Xue, Zhenqiang Zuo, Heng Zhou, Jian Zhou, Shengjie Zhang, Jing Han, Dahe Zhao, Hua Xiang
International Journal of Systematic and Evolutionary Microbiology .2021;[Epub] CrossRef
Cultivation of halophilic archaea (class Halobacteria) from thalassohaline and athalassohaline environments
Heng-Lin Cui, Mike L. Dyall-Smith
Marine Life Science & Technology.2021; 3(2): 243. CrossRef
List of new names and new combinations previously effectively, but not validly, published
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology.2020; 70(5): 2960. CrossRef

Comparative genomic analysis of selenium utilization traits in different marine environments: Muhammad Farukh; J. Microbiol. 2020;58(2):113-122. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9250-0

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Abstract

Selenium (Se) is an essential trace element for many organisms, which is required in the biosynthesis of proteins with selenocysteine, tRNAs with selenouridine, and certain enzymes with Se as a cofactor. Recent large-scale metagenomics projects provide a unique opportunity for studying the global trends of Se utilization in marine environments. Here, we analyzed samples from different marine microbial communities, revealed by the Tara Oceans project, to characterize the Se utilization traits. We found that the selenophosphate synthetase gene, which defines the overall Se utilization, and Se utilization traits are present in all samples. Regions with samples rich and poor in Se utilization traits were categorized. From the analysis of environmental factors, the mesopelagic zone and high temperature (> 15°C) of water are favorable, while geographical location has little influence on Se utilization. All Se utilization traits showed a relatively independent occurrence. The taxonomic classification of Se traits shows that most of the sequences corresponding to Se utilization traits belong to the phylum Proteobacteria. Overall, our study provides useful insights into the general features of Se utilization in ocean samples and may help to understand the evolutionary dynamics of Se utilization in different marine environments.

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The selenophosphate synthetase family: A review
Bruno Manta, Nadezhda E Makarova, Marco Mariotti
Free Radical Biology and Medicine.2022; 192: 63. CrossRef
Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Uses of Selenium Nanoparticles in the Plant Production
Iqra Bano, Sylvie Skalickova, Hira Sajjad, Jiri Skladanka, Pavel Horky
Agronomy.2021; 11(11): 2229. CrossRef

Exploring the antibiotic resistome in activated sludge and anaerobic digestion sludge in an urban wastewater treatment plant via metagenomic analysis: Keunje Yoo , Hyunji Yoo , Jangho Lee , Eun Joo Choi , Joonhong Park; J. Microbiol. 2020;58(2):123-130. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9309-y

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Abstract

Antibiotic resistance genes (ARGs) are emerging contaminants that pose a potential threat to human health worldwide. Urban wastewater treatment plants (WWTPs) are a main source of both antibiotic-resistant bacteria and ARGs released into the environment. Nevertheless, the propagation of ARGs and their underlying mechanisms and the dynamics of mobile genetic elements (MGEs) in WWTPs have rarely been investigated in South Korea. In this study, shotgun metagenomic analysis was used to identify comprehensive ARGs and their mechanisms, bacterial communities, and MGEs from 4 configurations with 2 activated sludge (AS) and 2 anaerobic digestion sludge (ADS) samples. A total of 181 ARG subtypes belonging to 22 ARG types were broadly detected, and the ARG abundances in the AS samples were 1.3–2.0 orders of magnitude higher than in the ADS samples. Multidrug and bacitracin resistance genes were the predominant ARG types in AS samples, followed by ARGs against sulfonamide, tetracycline, and β-lactam. However, the composition of ARG types in ADS samples was significantly changed. The abundance of multidrug and β-lactam resistance genes was drastically reduced in the ADS samples. The resistance genes of MLS were the predominant, followed by ARGs against sulfonamide and tetracycline in the ADS samples. In addition, plasmids were the dominant MGEs in the AS samples, while integrons (intI1) were the dominant MGEs in the ADS samples. These results provide valuable information regarding the prevalence of ARG types and MGEs and the difference patterns between the AS and ADS systems.

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Gihan Lee, Keunje Yoo
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Maoxia Chen, Jiali Chang, Tao Jiang, Shiqian Wei, Jiawei Zou, Juan Yang, Xuguang Ma
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Ranjith Kumar Manoharan, Fahmida Ishaque, Young-Ho Ahn
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Connor L. Brown, James Mullet, Fadi Hindi, James E. Stoll, Suraj Gupta, Minyoung Choi, Ishi Keenum, Peter Vikesland, Amy Pruden, Liqing Zhang, Hideaki Nojiri
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Qian Ping, Zhipeng Zhang, Liping Ma, Tingting Yan, Lin Wang, Yongmei Li
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Sonia Gupta, T.R. Sreekrishnan, Shaikh Ziauddin Ahammad
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Hafeez Ul Haq, Wei Huang, Ye Li, Ting Zhang, Shaocheng Ma, Yajing Zhang, Yongkang Song, Daiyan Lin, Baoyu Tian
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Yu-Xi Gao, Xing Li, Xiao-Yan Fan, Jun-Ru Zhao, Zhong-Xing Zhang
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Wiktor Zieliński, Jakub Hubeny, Martyna Buta-Hubeny, Damian Rolbiecki, Monika Harnisz, Łukasz Paukszto, Ewa Korzeniewska
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Impact of Anthropogenic Activities on the Dissemination of ARGs in the Environment—A Review
Małgorzata Czatzkowska, Izabela Wolak, Monika Harnisz, Ewa Korzeniewska
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Ana R. Cardoso, Liliana P.T. Carneiro, Gustavo Cabral-Miranda, Martin F. Bachmann, M. Goreti F. Sales
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Anh Q. Nguyen, Hang P. Vu, Luong N. Nguyen, Qilin Wang, Steven P. Djordjevic, Erica Donner, Huabing Yin, Long D. Nghiem
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Agricultural Soils Amended With Thermally-Dried Anaerobically-Digested Sewage Sludge Showed Increased Risk of Antibiotic Resistance Dissemination
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Improved tolerance of Escherichia coli to oxidative stress by expressing putative response regulator homologs from Antarctic bacteria: Seo-jeong Park , Sangyong Lim , Jong-il Choi; J. Microbiol. 2020;58(2):131-141. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9290-5

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Abstract

Response regulator (RR) is known a protein that mediates cell’s response to environmental changes. The effect of RR from extremophiles was still under investigation. In this study, response regulator homologs were mined from NGS data of Antarctic bacteria and overexpressed in Escherichia coli. Sixteen amino acid sequences were annotated corresponding to response regulators related to the two-component regulatory systems; of these, 3 amino acid sequences (DRH632, DRH1601 and DRH577) with high homology were selected. These genes were cloned in pRadGro and expressed in E. coli. The transformant strains were subjected to various abiotic stresses including oxidative, osmotic, thermal stress, and acidic stress. There was found that the robustness of E. coli to abiotic stress was increased in the presence of these response regulator homologs. Especially, recombinant E. coli overexpressing drh632 had the highest survival rate in oxidative, hypothermic, osmotic, and acidic conditions. Recombinant E. coli overexpressing drh1601 showed the highest tolerance level to osmotic stress. These results will be applicable for development of recombinant strains with high tolerance to abiotic stress.

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Deionococcus proteotlycius Genomic Library Exploration Enhances Oxidative Stress Resistance and Poly-3-hydroxybutyrate Production in Recombinant Escherichia coli
Seul-Ki Yang, Soyoung Jeong, Inwoo Baek, Jong-il Choi, Sangyong Lim, Jong-Hyun Jung
Microorganisms.2023; 11(9): 2135. CrossRef
Bacterial redox response factors in the management of environmental oxidative stress
Sudharsan M, Rajendra Prasad N, Saravanan Rajendrasozhan
World Journal of Microbiology and Biotechnology.2023;[Epub] CrossRef
Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli
Sadika Dkhili, Miguel Ribeiro, Salma Ghariani, Houssem Ben Yahia, Mélanie Hillion, Patricia Poeta, Karim Ben Slama, Michel Hébraud, Gilberto Igrejas
OMICS: A Journal of Integrative Biology.2021; 25(10): 626. CrossRef
Regulator of ribonuclease activity modulates the pathogenicity of Vibrio vulnificus
Jaejin Lee, Eunkyoung Shin, Jaeyeong Park, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(12): 1133. CrossRef

Mitochondrial genome and diverse inheritance patterns in Pleurotus pulmonarius: Li-Yun Ye+ , You-Jin Deng+ , Irum Mukhtar , Guo-Liang Meng , Yan-Jiao Song , Bing Cheng , Jin-bing Hao , Xiao-Ping Wu; J. Microbiol. 2020;58(2):142-152. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9318-x

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Abstract

Pleurotus pulmonarius, a member of the Pleurotaceae family in Basidiomycota, is an edible, economically important mushroom in most Asian countries. In this study, the complete mitochondrial genomes (mtDNA) of three P. pulmonarius strains – two monokaryotic commercial (J1-13 and ZA3) and one wild (X1-15) – were sequenced and analyzed. In ZA3 and X1-15, the mtDNA molecule was found to be a single circle of 68,305 bp and 73,435 bp, respectively. Both strains contain 14 core protein-coding genes and two ribosomal RNA (rRNA) subunit genes. The ZA3 strain has 22 transfer RNA (tRNA) genes and nine introns: eight in cytochrome c oxidase subunit 1 (cox1), and one in the rRNA large subunit (rnl). Monokaryotic J1-13 and ZA3 mtDNAs were found to be similar in their structure. However, the wild strain X1-15 contains 25 tRNA genes and only seven introns in cox1. Open reading frames (ORFs) of ZA3/J1-13 and X1-15 encode LAGLIDADG, ribosomal protein S3, and DNA polymerase II. In addition, mtDNA inheritance in J1-13, ZA3, and X1-15 was also studied.
Results
showed that the mtDNA inheritance pattern was uniparental and closely related to dikaryotic hyphal location with respect to the parent. Results also show that mtDNA inheritance is influenced by both the parental nuclear genome and mitogenome in the zone of contact between two compatible parents. In summary, this analysis provides valuable information and a basis for further studies to improve our understanding of the inheritance of fungal mtDNA.

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Comparative analyses of Pleurotus pulmonarius mitochondrial genomes reveal two major lineages of mini oyster mushroom cultivars
Yang Yu, Tianhai Liu, Yong Wang, Lixu Liu, Xiaolan He, Jianwei Li, Francis M. Martin, Weihong Peng, Hao Tan
Computational and Structural Biotechnology Journal.2024; 23: 905. CrossRef
Intraspecific and interspecific variations in the synonymous codon usage in mitochondrial genomes of 8 pleurotus strains
Wei Gao, Xiaodie Chen, Jing He, Ajia Sha, Yingyong Luo, Wenqi Xiao, Zhuang Xiong, Qiang Li
BMC Genomics.2024;[Epub] CrossRef
Identification of s9ap used as an endogenous reference gene in qualitative and real-time quantitative PCR detection of Pleurotus eryngii
Yuanmiao Wei, Yao Liu, Ling Li, Shuna Xiang, Hanyue Zhang, Ying Shang
Molecular Biology Reports.2023; 50(1): 621. CrossRef
Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Auricularia villosula, an edible wild mushroom in China
Xiaoguo Wang, Shiyan Wei, Shengjin Wu, Jun Tang, Jiaojun Wei, Zengliang Liu, Liangliang Qi
Biologia.2023; 78(12): 3713. CrossRef
The Effect of Mitochondria on Ganoderma lucidum Growth and Bioactive Components Based on Transcriptomics
Liyun Ye, Xiaofang He, Congbao Su, Haiying Feng, Guoliang Meng, Bingzhi Chen, Xiaoping Wu
Journal of Fungi.2022; 8(11): 1182. CrossRef
Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602
Thomas Schafhauser, Daniel Wibberg, Antonia Binder, Christian Rückert, Tobias Busche, Wolfgang Wohlleben, Jörn Kalinowski
Journal of Fungi.2022; 8(8): 862. CrossRef

The discovery of potent immunostimulatory CpG-ODNs widely distributed in bacterial genomes: Juan Liu , Yan Wei , Yongling Lu , Yangyuling Li , Qian Chen , Yan Li; J. Microbiol. 2020;58(2):153-162. Published online December 23, 2019; DOI: https://doi.org/10.1007/s12275-020-9289-y

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Abstract

Oligodeoxynucleotides containing unmethylated CpG dinucleotides (CpG-ODN) can be specifically recognized by Toll-like receptor 9 (TLR9), provoking innate immune responses. Designed according to this structural feature, many synthetic phosphorothioate CpG-ODNs successfully activate macrophages. However, it is difficult to find potent stimulatory CpG-DNA fragments in microbial genomes. Therefore, whether microbial CpG-DNA substantially contributes to infectious and immune diseases remains controversial. In this study, high-throughput scanning was carried out for thousands of bacterial genomes with bioinformatics tools to comprehensively evaluate the distribution of CpG-DNA fragments. A random sampling test was then performed to verify their immunostimulatory properties by experiments in vitro and in vivo. Natural TLR9-dependent and potent stimulatory CpG-DNA fragments were found in microbial genomes. Interestingly, highly conserved stimulatory CpG-DNA fragments were found in 16S and 23S rDNA sequences with multiple copies, while others were species-specific. Additionally, we found that the reported active motifs were mostly nonstimulatory in natural CpG fragments. This evidence indicates that the previous structural descriptions of functional CpG-ODNs are incomplete. Our study has assessed the distribution of microbial CpG-DNA fragments, and identified natural stimulatory CpG-DNA fragments. These findings provide a deeper understanding of CpG-ODN structures and new evidence for microbial DNA inflammatory function and pathogenicity.

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Advances in protein subunit vaccines against H1N1/09 influenza
Yu Zhang, Jingyao Gao, Wenqi Xu, Xingyu Huo, Jingyan Wang, Yirui Xu, Wenting Ding, Zeliang Guo, Rongzeng Liu
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Development of a strategy for the screening of α-glucosidase-producing microorganisms: Bo Zhou+ , Nan Huang+ , Wei Zeng+ , Hao Zhang , Guiguang Chen , Zhiqun Liang; J. Microbiol. 2020;58(2):163-172. Published online January 29, 2020; DOI: https://doi.org/10.1007/s12275-020-9267-4

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Abstract

α-Glucosidase is a crucial enzyme for the production of isomaltooligosaccharide. In this study, a novel method comprising eosin Y (EY) and α-D-methylglucoside (AMG) in glass plates was tested for the primary screening of α-glucosidaseproducing strains. First, α-glucosidase-producing Aspergillus niger strains were selected on plates containing EY and AMG based on transparent zone formation resulting from the solubilization of EY by the hydrolyzed product. Conventional
methods
that use trypan blue (TB) and p-nitrophenyl-α-Dglucopyranoside (pPNP) as indicators were then compared with the new strategy. The results showed that EY-containing plates provide the advantages of low price and higher specificity for the screening of α-glucosidase-producing strains. We then evaluated the correlation between the hydrolytic activity of α-glucosidase and diffusion distance, and found that good linearity could be established within a 6–75 U/ml enzyme concentration range. Finally, the hydrolytic and transglycosylation activities of α-glucosidase obtained from the target isolates were determined by EY plate assay and 3,5- dinitrosalicylic acid-Saccharomyces cerevisiae assay, respectively. The results showed that the diameter of the transparent zone varied among isolates was positively correlated with α-glucosidase hydrolytic activity, while good linearity could also be established between α-glucosidase transglycosylation activity and non-fermentable reducing sugars content. With this strategy, 7 Aspergillus niger mutants with high yield of α-glucosidase from 200 obvious single colonies on the primary screen plate were obtained.

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Purification, characterization of a novel α-glucosidase from Debaryomyces hansenii strain MCC 0202 and chromatographic separation for high purity isomalto-oligosaccharides production
Saravanan Rengarajan, Rameshthangam Palanivel
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Biocatalysis and Agricultural Biotechnology.2020; 30: 101837. CrossRef

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