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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10 Citations

Abstract: 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.

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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8 Citations

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.

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).

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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17 Citations

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.

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.

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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49 Citations

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.

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.

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.

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.

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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