Journal of Microbiology

Journal Articles

Effects of tryptophan and phenylalanine on tryptophol production in Saccharomyces cerevisiae revealed by transcriptomic and metabolomic analyses: Xiaowei Gong , Huajun Luo , Liu Hong , Jun Wu , Heng Wu , Chunxia Song , Wei Zhao , Yi Han , Ya Dao , Xia Zhang , Donglai Zhu , Yiyong Luo; J. Microbiol. 2022;60(8):832-842. Published online May 27, 2022; DOI: https://doi.org/10.1007/s12275-022-2059-2

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Abstract: Tryptophol (TOL) is a metabolic derivative of tryptophan (Trp) and shows pleiotropic effects in humans, plants and microbes. In this study, the effect of Trp and phenylalanine (Phe) on TOL production in Saccharomyces cerevisiae was determined, and a systematic interpretation of TOL accumulation was offered by transcriptomic and metabolomic analyses. Trp significantly promoted TOL production, but the output plateaued (231.02−266.31 mg/L) at Trp concentrations ≥ 0.6 g/L. In contrast, Phe reduced the stimulatory effect of Trp, which was strongly dependent on the Phe concentration. An integrated genomic, transcriptomic, and metabolomic analysis revealed that the effect of Trp and Phe on TOL production was mainly related to the transamination and decarboxylation of the Ehrlich pathway. Additionally, other genes, including thiamine regulon genes (this), the allantoin catabolic genes dal1, dal2, dal4, and the transcriptional activator gene aro80, may play important roles. These findings were partly supported by the fact that the thi4 gene was involved in TOL production, as shown by heterologous expression analysis. To the best of our knowledge, this novel biological function of thi4 in S. cerevisiae is reported here for the first time. Overall, our findings provide insights into the mechanism of TOL production, which will contribute to TOL production using metabolic engineering strategies.

The role of Jacalin-related lectin gene AOL_s00083g511 in the development and pathogenicity of the nematophagous fungus Arthrobotrys oligospora: Xinyuan Dong , Jiali Si , Guanghui Zhang , Zhen Shen , Li Zhang , Kangliang Sheng , Jingmin Wang , Xiaowei Kong , Xiangdong Zha , Yongzhong Wang; J. Microbiol. 2021;59(8):736-745. Published online July 5, 2021; DOI: https://doi.org/10.1007/s12275-021-1029-4

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Abstract: Arthrobotrys oligospora is a model species of nematophagous fungi and has great potential for the biological control of nematode diseases. Lectin is a protein that binds to carbohydrates and their complexes with high specificity, which mediates recognition events in various physiological and pathological processes. This study aimed to investigate the role of the Jacalin-related lectin (JRL) gene, AOL_s00083g511, in A. oligospora development. Through a homology recombination approach, we obtained the AOL_s00083g511 knockout mutant strain (Δg511). Next, the biological characteristics of the Δg511 mutant strain, including growth rate, conidia germination rate, adaptation to environmental stresses, and nematocidal activity, were compared with those of the wild-type (WT) strain. The results showed that the JRL gene AOL_ s00083g511 did not affect fungal growth, conidia germination, 3D-trap formation, and the ability of A. oligospora to prey on nematodes significantly. We speculate that this phenomenon may be caused by a loss of the key β1–β2 loops in the AOL_ s00083g511-encoded JRL domain and an intrinsic genetic compensation of AOL_s00083g511 in this fungus. The growth rates of both strains on high salt or surfactant media were similar; however, in the strong oxidation medium, the growth rate of the Δg511 mutant was significantly lower than that of the WT strain, indicating that AOL_s00083g511 might play a role in oxidative stress resistance. These findings provide a basis for further analysis of the related functions of the JRL gene in A. oligospora and their potential roles in the biological control of nematodes in the future.

The effect of the HRB linker of Newcastle disease virus fusion protein on the fusogenic activity: Yaqing Liu , Ying Liu , Yanan Huang , Hongling Wen , Li Zhao , Yanyan Song , Zhiyu Wang; J. Microbiol. 2021;59(5):513-521. Published online March 29, 2021; DOI: https://doi.org/10.1007/s12275-021-0539-4

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5 Citations

Abstract: Newcastle disease, designated a class A disease of poultry by the Office international des epizooties (OIE), is an acute infection caused by Newcastle disease virus (NDV). The merging of the envelope of NDV with the membrane of a target host cell is the key step in the infection pathway, which is driven by the concerted action of two glycoproteins: haemagglutinin- neuraminidase (HN) and fusion (F) protein. When the HN protein binds to the host cell surface receptor, the F protein is activated to mediate fusion. The three-dimensional structure of the F protein has been reported to have low electron density between the DIII domain and the HRB domain, and this electron-poor region is defined as the HRB linker. To clarify the contributing role of the HRB linker in the NDV F protein-mediated fusion process, 6 single amino acid mutants were obtained by site-directed mutagenesis of the HRB linker. The expression of the mutants and their abilities to mediate fusion were analysed, and the key amino acids in the HRB linker were identified as L436, E439, I450, and S453, as they can modulate the fusion ability or expression of the active form to a certain extent. The data shed light on the crucial role of the F protein HRB linker in the acquisition of a normal fusogenic phenotype.

Characteristic and role of chromosomal type II toxin-antitoxin systems locus in Enterococcus faecalis ATCC29212: Zhen Li , Chao Shi , Shanjun Gao , Xiulei Zhang , Di Lu , Guangzhi Liu; J. Microbiol. 2020;58(12):1027-1036. Published online October 23, 2020; DOI: https://doi.org/10.1007/s12275-020-0079-3

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Abstract: The Gram-positive bacterium Enterococcus faecalis is currently one of the major pathogens of nosocomial infections. The lifestyle of E. faecalis relies primarily on its remarkable capacity to face and survive in harsh environmental conditions. Toxin-antitoxin (TA) systems have been linked to the growth control of bacteria in response to adverse environments but have rarely been reported in Enterococcus. Three functional type II TA systems were identified among the 10 putative TA systems encoded by E. faecalis ATCC29212. These toxin genes have conserved domains homologous to MazF (DR75_ 1948) and ImmA/IrrE family metallo-endopeptidases (DR75_ 1673 and DR75_2160). Overexpression of toxin genes could inhibit the growth of Escherichia coli. However, the toxin DR75_1673 could not inhibit bacterial growth, and the bacteriostatic effect occurred only when it was coexpressed with the antitoxin DR75_1672. DR75_1948–DR75_1949 and DR75_ 160–DR75_2161 could maintain the stable inheritance of the unstable plasmid pLMO12102 in E. coli. Moreover, the transcription levels of these TAs showed significant differences when cultivated under normal conditions and with different temperatures, antibiotics, anaerobic agents and H2O2. When DR75_2161 was knocked out, the growth of the mutant strain at high temperature and oxidative stress was limited. The experimental characterization of these TAs loci might be helpful to investigate the key roles of type II TA systems in the physiology and environmental stress responses of Enterococcus.

Sequence analysis of the first B5 subgenogroup strain of enterovirus 71 isolated in Korea: Yu Jung Won , Lae Hyung Kang , Ah Ra Lee , Bomina Paik , Hyun Kim , Sung Geun Lee , Seung Won Park , Seung Jin Hong , Soon Young Paik; J. Microbiol. 2020;58(5):422-429. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9539-z

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Abstract: Enterovirus A71 (EV71), the main etiological agent of handfoot- mouth disease (HFMD), circulates in many areas of the world and has caused large epidemics since 1997, especially in the Asia-Pacific region. In this study, we determined the full-genome sequence of CMC718, a newly isolated EV71 strain in Korea. The CMC718 genome was 7,415 nucleotides in length and was confirmed by whole-genome phylogenetic analysis to belong to the B5 genotype. In particular, CMC718 demonstrated maximum identity with strain M988 of the B5 genotype and numerous amino acid variants were detected in the 3D domain of the viral protein P3, which is consistent with the mutation pattern of a B5 strain isolated in 2012–2013. Comparison of the CMC718 sequence with other EV71 reference strains confirmed the relationship and genetic variation of CMC718. Our study was a full-genome sequence analysis of the first EV71 strain of the B5 genotype isolated in South Korea. This information will be a valuable reference for the development of methods for the detection of recombinant viruses, the tracking of infections, and the diagnosis of EV71.

Methylobacterium terrae sp. nov., a radiation-resistant bacterium isolated from gamma ray-irradiated soil: Jiyoun Kim , Geeta Chhetri , Inhyup Kim , Hyungdong Kim , Myung Kyum Kim , Taegun Seo; J. Microbiol. 2019;57(11):959-966. Published online August 28, 2019; DOI: https://doi.org/10.1007/s12275-019-9007-9

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21 Citations

Abstract: A Gram-stain-negative, asporogenous, aerobic rods, motile by means of a single polar flagellum, catalase- and oxidase-positive, methylotrophic bacterium, designated 17Sr1-28T, was isolated from gamma ray-irradiated soil. The 16S rRNA gene sequence analysis showed that strain 17Sr1-28T was phylogenetically related to Methylobacterium currus PR1016AT (96.8%), Methylobacterium platani PMB02T (96.2%), Methylobacterium aquaticum DSM 16371T (96.3%), Methylobacterium tarhaniae N4211T (96.4%), Methylobacterium frigidaeris IER25-16T (95.8%), and Methylobacterium organophilum JCM 2833T (92.7%). The G+C content calculated based on genome sequence was 71.6%. The average nucleotide identity and in silico DNA-DNA hybridization values between strain 17Sr1- 28T and M. currus, M. platani, M. aquaticum, M. tarhaniae, M. frigidaeris, and M. organophilum were 77.7–90.4% and 22–39.6%, respectively. The major fatty acids of strain 17Sr1- 28T were summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant quinone was ubiquinone 10 and the major polar lipids were diphosphatidylglycerol, phosphatidylcholine, phosphatidylethanolamine, and phosphatidylglycerol. On the basis of the data from phenotypic tests and genotypic differences between strain 17Sr1-28T and its close phylogenetic relatives, strain 17Sr1-28T represents a new species belonging to the genus Methylobacterium, for which the name Methylobacterium terrae sp. nov. (= KCTC 52904T = NBRC 112873T) is proposed.

Review

[MINIREVIEW] Phylogenetic comparison of Epstein-Barr virus genomes: Su Jin Choi , Seok Won Jung , Sora Huh , Hyosun Cho , Hyojeung Kang; J. Microbiol. 2018;56(8):525-533. Published online June 14, 2018; DOI: https://doi.org/10.1007/s12275-018-8039-x

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13 Citations

Abstract: Technologies used for genome analysis and whole genome sequencing are useful for us to understand genomic characterization and divergence. The Epstein-Barr virus (EBV) is an oncogenic virus that causes diverse diseases such as Burkitt’s lymphoma (BL), nasopharyngeal carcinoma (NPC), Hodgkin’s lymphoma (HL), and gastric carcinoma (GC). EBV genomes found in these diseases can be classified either by phases of EBV latency (type-I, -II, and -III latency) or types of EBNA2 sequence difference (type-I EBV, type-II EBV or EBV-1, EBV-2). EBV from EBV-transformed lymphoblastoid cell line (LCL) establishes type-III latency, EBV from NPC establishes type-II latency, and EBV from GC establishes type-I latency. However, other important factors play key roles in classifying numerous EBV strains because EBV genomes are highly diverse and not phylogenetically related to types of EBV-associated diseases. Herein, we first reviewed previous studies to describe molecular characteristics of EBV genomes. Then, using comparative and phylogenetic analyses, we phylogenetically analyzed molecular variations of EBV genomes and proteins. The review of previous studies and our phylogenetic analysis showed that EBV genomes and proteins were highly diverse regardless of types of EBV-associated diseases. Other factors should be considered in determining EBV taxonomy. This review will be helpful to understand complicated phylogenetic relationships of EBV genomes.

Journal Articles

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction: Seong-In Na , Yeong Ouk Kim , Seok-Hwan Yoon , Sung-min Ha , Inwoo Baek , Jongsik Chun; J. Microbiol. 2018;56(4):280-285. Published online February 28, 2018; DOI: https://doi.org/10.1007/s12275-018-8014-6

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965 Citations

Abstract: Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/ tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer, respectively.

A New record of four Penicillium species isolated from Agarum clathratum in Korea: Myung Soo Park , Seobihn Lee , Young Woon Lim; J. Microbiol. 2017;55(4):237-246. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6405-8

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8 Citations

Abstract: Agarum clathratum, brown algae, play important ecological roles in marine ecosystem, but can cause secondary environ-ment pollution when they pile up on the beach. In order to resolve the environment problem by A. clathratum, we focus to isolate and identify Penicillium because many species are well known to produce extracellular enzymes. A total of 32 Penicillium strains were isolated from A. clathratum sam-ples that collected from 13 sites along the mid-east coast of Korea in summer. They were identified based on morpho-logical characters and phylogenetic analysis using β-tubulin DNA sequences as well as a combined dataset of β-tubulin and calmodulin. A total of 32 strains were isolated and they were identified to 13 Penicillium species. The commonly iso-lated species were Penicillium citrinum, P. roseomaculatum, and Penicillium sp. Among 13 Penicillium species, four spe-cies – P. bilaiae, P. cremeogriseum, P. madriti, and P. rose-omaculatum – have not been previously recorded in Korea. For these four new species records to Korea, we provide mor-phological characteristics of each strain.

Research Support, Non-U.S. Gov'ts

Luteimonas dalianensis sp. nov., an Obligate Marine Bacterium Isolated from Seawater: Yanjuan Xin , Xupeng Cao , Peichun Wu , Song Xue; J. Microbiol. 2014;52(9):729-733. Published online August 2, 2014; DOI: https://doi.org/10.1007/s12275-014-3610-6

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16 Citations

Abstract: A marine bacterial strain, designated OB44-3T, was isolated from a crude oil-contaminated seawater sample collected near Dalian Bay, China. Cells of strain OB44-3T were Gramnegative, aerobic, rod-shaped, and oxidase- and catalasepositive. The major fatty acids were branched-chain saturated iso-C15:0 (27.9%) and unsaturated iso-C17:1 ω9c (14.8%). The DNA G+C content was 64.6 mol%. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that strain OB44-3T was a member of the genus Luteimonas (95–96% 16S rRNA gene sequence similarity); its closest neighbors were the type strains of Luteimonas terricola (96% sequence similarity), Luteimonas mephitis (96%), and Luteimonas lutimaris (96%). On the basis of phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain OB44-3T was considered to represent a novel species of the genus Luteimonas. The name Luteimonas dalianensis sp. nov. is proposed, with strain OB44-3T (=CGMCC 1.12191T =JCM 18136T) as the type strain.

Molecular Serotyping of Salmonella enterica by Complete rpoB Gene Sequencing: Won-Jin Seong , Hyuk-Joon Kwon , Tae-Eun Kim , Deog-Yong Lee , Mi-Sun Park , Jae-Hong Kim; J. Microbiol. 2012;50(6):962-969. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2547-x

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18 Citations

Abstract: Serotyping has been the gold standard for identifying Salmonella, but it requires large amounts of standard antisera. Multilocus sequence typing (MLST) has been applied to identify Salmonella serovars, but the recombination of 4–7 housekeeping genes and multiple analytic steps diminish its applicability. In the present study, we determined the complete sequences of the RNA polymerase beta subunit gene (rpoB) and 7 housekeeping genes (aroC, dnaN, hemD, hisD, purE, sucA, and thrA) for 76 strains of 33 Salmonella enterica serovars and conducted phylogenetic analyses together with the corresponding gene sequences of 24 reference strains registered in the GenBank database. Based on the phylogenetic analyses, 100 strains from 40 serovars and 91 strains from 37 serovars were classified into 60 rpoB (RST) and 49 multilocus sequence types (ST), respectively. The nucleotide similarities were 98.8–100% and 96.9–100% for the complete rpoB gene and the seven concatenated housekeeping genes, respectively. The strains of 35 and 30 serovars formed serovar-specific branches or clusters in the rpoB and housekeeping gene phylogenetic trees, respectively. Therefore, complete rpoB gene sequencing and phylogenetic analysis may be a useful method for identifying Salmonella serovars that is a simpler, more cost-effective, and less time-consuming alternative or complementary method to MLST and conventional serotyping.

Journal Articles

Flavobacterium cheonhonense sp. nov., Isolated from a Freshwater Reservoir: Siwon Lee , Jung-Hwan Oh , Hang-Yeon Weon , Tae-Young Ahn; J. Microbiol. 2012;50(4):562-566. Published online July 21, 2012; DOI: https://doi.org/10.1007/s12275-012-1229-z

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12 Citations

Abstract: A novel bacterium, designated strain ARSA-15T, was isolated from a freshwater sample collected from the Cheonho reservoir, Cheonan, Republic of Korea. The isolate was deepyellow pigment, Gram-negative, rod-shaped, non-motile, and catalase- and oxidase-positive. Phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate belongs to the genus Flavobacterium, and shared less than 97% sequence similarity with recognized Flavobacterium species. The novel species was able to grow at 10–37°C, pH 6.5–10.0, and in 0–0.5% (w/v) NaCl concentrations. Chemotaxonomically, iso-C15:1, iso-C15:0, and iso-C16:0 were observed to be the predominant cellular fatty acid, and menaquinone-6 (MK-6) was the predominant respiratory quinone. The major polar lipid patterns of strain ARSA-19T was phosphatidylethanolamine, unknown aminolipid (AL1 and AL2), and unidentified polar lipids (L1, L2, and L3). The genomic DNA G+C content of the isolate was 39.2 mol%. On the basis of polyphasic approach, strain ARSA-15T represents a novel species of the genus Flavobacterium, for which the name Flavobacterium cheonhonense sp. nov. is proposed. The type strain is ARSA-15T (=KACC 14967T =KCTC 23180T =JCM 17064T).

NOTE] Sawadaea koelreuteriae comb. nov., a Powdery Mildew of Koelreuteria paniculata: Hyeon-Dong Shin , Mi-Jeong Park; J. Microbiol. 2011;49(5):862-866. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1479-1

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6 Citations

Abstract: A powdery mildew parasitizing Koelreuteria spp. was first described under the name Uncinula koelreuteriae Miyake and later transferred to the genus Typhulochaeta. Based on morphological and molecular data of several herbarium specimens collected from Korea, the generic placement of Typhulochaeta is discussed and T. koelreuteriae is combined in the genus Sawadaea. Redescription and epitypification of this species is provided hereby.

Research Support, Non-U.S. Gov'ts

Rapid Discrimination of Potato Scab-Causing Streptomyces Species Based on the RNase P RNA Gene Sequences: Hang-Yeon Weon , Jaekyeong Song , Byung-Yong Kim , On-Suk Hur , In-Cheol Park , Joo-Won Suh; J. Microbiol. 2011;49(5):791-796. Published online November 9, 2011; DOI: https://doi.org/10.1007/s12275-011-1279-7

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Abstract: Scab disease significantly damages potatoes and other root crops. Some Streptomyces species have been reported as potato-scab pathogens. Identification of the phytopathogenic Streptomyces is mainly done on the basis of the 16S rRNA gene, but use of this gene has some limitations for discriminating these strains because they share high similarities of 16S rRNA gene sequences. We tested the RNase P RNA (rnpB) gene as a taxonomic marker to clarify the relationship among closely related scab-causing Streptomyces strains. The rnpB genes were analyzed for 41 strains including 9 isolates from Jeju, Korea. There were 4 highly variable regions including nucleotide gaps in the rnpB genes. Interspecies similarity of the rnpB gene in tested Streptomyces strains was lower than about 97%, while the intraspecies similarity was higher than about 98%. Phylogenetic analysis demonstrated that the rnpB tree has similar topology to the 16S rRNA gene tree, but produces a more divergent phyletic lineage. These results revealed that the rnpB gene could be used as a powerful taxonomic tool for rapid differentiation of closely related Streptomyces species. In addition, it was also suggested that the variable regions marked as α, β, γ, and δ in the rnpB gene could be useful markers for the detection of specific Streptomyces species.

Genome Sequence Analysis of H5N1 Influenza A Virus Isolated from a Vietnamese in 2007: Dieu Linh Tran , Kangmo Kim , Jae Yoo Choi , Hyun Dong Paik , Si-Woo Choi , Jin Yeul Ma , Sung-Soon Kim , Sung Joon Ahn , Young Bong Kim; J. Microbiol. 2011;49(2):274-279. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0311-2

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Abstract: Highly pathogenic H5N1 avian influenza A virus (AIV) crossed the species barrier and caused a number of deaths in humans in Vietnam and 14 other countries. Since the last report of human H5N1 infection in November 2005, the first documented H5N1 human infection was reported in June 2007 in Vietnam and was followed by 7 more cases, including 5 fatalities. In this study, we isolated and analyzed the full length of the H5N1 genome from a sample from the first patient in 2007. Phylogenetic analysis of eight genomic segments of the H5N1 virus strain (A/Vietnam/HN/2007, VNH07) revealed that this strain appears to be of genotype V and contains the HA gene, which is classified into clade 2.3.4. The deduced amino acid sequence of the HA protein has a typical affinity sequence for α2,3 linkage (SAα2,3-Gal) receptors and typical multibasic cleavage sequences. Compared with other H5N1 isolates, VNH07 showed that the possible reassortments for the NA and NP segments occurred between A/goose/Guangxi/3017/2005-like isolates (2.3.2) and A/human/Zhejiang/16/2006-like isolates (2.3.4).

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