Journal of Microbiology

Journal Articles

Description of Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., novel bacteria isolated from the gut of three types of South Korean shellfish: Su-Won Jeong , Jeong Eun Han , June-Young Lee , Ji-Ho Yoo , Do-Yeon Kim , In Chul Jeong , Jee-Won Choi , Yun-Seok Jeong , Jae-Yun Lee , So-Yeon Lee , Euon Jung Tak , Hojun Sung , Hyun Sik Kim , Pil Soo Kim , Dong-Wook Hyun , Jin-Woo Bae; J. Microbiol. 2022;60(6):576-584. Published online April 18, 2022; DOI: https://doi.org/10.1007/s12275-022-1604-3

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Three aerobic, Gram-negative, and rod-shaped bacterial strains, designated strains G4M1T, SM13T, and L12M9T, were isolated from the gut of Batillaria multiformis, Cellana toreuma, and Patinopecten yessoensis collected from the Yellow Sea in South Korea. All the strains grew optimally at 25°C, in the presence of 2% (w/v) NaCl, and at pH 7. These three strains, which belonged to the genus Polaribacter in the family Flavobacteriaceae, shared < 98.8% in 16S rRNA gene sequence and < 86.68% in whole-genome sequence with each other. Compared with the type strains of Polaribacter, isolates showed the highest sequence similarity to P. haliotis KCTC 52418T (< 98.68%), followed by P. litorisediminis KCTC 52500T (< 98.13%). All the strains contained MK-6 as their predominant menaquinone and iso-C15:0 as their major fatty acid. Moreover, all the strains had phosphatidylethanolamine as their polar lipid component. In addition, strain G4M1T had two unidentified lipids and three unidentified aminolipids, strain SM13T had three unidentified lipids and three unidentified aminolipids, and strain L12M9T had three unidentified lipids and one unidentified aminolipid. The DNA G + C contents of strains G4M1T, SM13T, and L12M9T were 31.0, 30.4, and 29.7 mol%, respectively. Based on phenotypic, phylogenetic, chemotaxonomic, and genotypic findings, strains G4M1T (= KCTC 82388T = DSM 112372T), SM13T (= KCTC 82389T = DSM 112373T), and L12M9T (= KCTC 62751T = DSM 112374T) were classified into the genus Polaribacter as the type strains of novel species, for which the names Polaribacter batillariae sp. nov., Polaribacter cellanae sp. nov., and Polaribacter pectinis sp. nov., respectively, have been proposed.

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Unique skin microbiome: insights to understanding bacterial symbionts in octopuses
Chelsea O. Bennice, Lauren E. Krausfeldt, W. Randy Brooks, Jose V. Lopez
Frontiers in Marine Science.2024;[Epub] CrossRef
An update on novel taxa and revised taxonomic status of bacteria isolated from aquatic host species described in 2022–2023
Claire R. Burbick, Sara D. Lawhon, Brittany Bukouras, Giovanna Lazzerini, Erik Munson, Romney M. Humphries
Journal of Clinical Microbiology.2024;[Epub] CrossRef
Polaribacter ponticola sp. nov., isolated from seawater, reclassification of Polaribacter undariae as a later heterotypic synonym of Polaribacter sejongensis, and emended description of Polaribacter sejongensis Kim et al. 2013
Ju Hye Baek, Mahrukh Butt, Dong Min Han, Jeong Min Kim, Seohui Choi, Che Ok Jeon
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Rhodobacteraceae are Prevalent and Ecologically Crucial Bacterial Members in Marine Biofloc Aquaculture
Meora Rajeev, Jang-Cheon Cho
Journal of Microbiology.2024; 62(11): 985. CrossRef
Validation List no. 207. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, George Garrity
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Nocardioides palaemonis sp. nov. and Tessaracoccus palaemonis sp. nov., isolated from the gastrointestinal tract of lake prawn
Do-Yeon Kim, In-Chul Jeong, So-Yeon Lee, Yun-Seok Jeong, Jeong Eun Han, Euon Jung Tak, June-Young Lee, Pil Soo Kim, Dong-Wook Hyun, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef

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.

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Sonic-assisted antibacterial photodynamic therapy: a strategy for enhancing lateral canal disinfection
Yanhuang Wang, Lishan Lei, Jing Huang, Zhiyu Cai, Xiaojing Huang
BMC Oral Health.2024;[Epub] CrossRef
Unveiling the impact of antibiotic stress on biofilm formation and expression of toxin-antitoxin system genes in Clostridium difficile clinical isolates
Nasim Cheraghi, Saeed Khoshnood, Nourkhoda Sadeghifard, Niloufar Khodaei, Parisa Asadollahi, Saiyad Bastaminejad, Ebrahim Kouhsari, Nazanin Omidi, Behrooz Sadeghi Kalani
Molecular Biology Reports.2024;[Epub] CrossRef
Edwardsiella piscicida HigB: A type II toxin that is essential to oxidative resistance, biofilm formation, serum survival, intracellular propagation, and host infection
Jinhong Xie, Qianyun Zhao, Huiqin Huang, Zaiguang Fang, Yonghua Hu
Aquaculture.2021; 535: 736382. CrossRef

FgIlv3a is crucial in branched-chain amino acid biosynthesis, vegetative differentiation, and virulence in Fusarium graminearum: Xin Liu , Yichen Jiang , Yinghui Zhang , Mingzheng Yu , Hongjun Jiang , Jianhong Xu , Jianrong Shi; J. Microbiol. 2019;57(8):694-703. Published online May 11, 2019; DOI: https://doi.org/10.1007/s12275-019-9123-6

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Abstract

Dihydroxyacid dehydratase (DHAD), encoded by ILV3, catalyses the third step in the biosynthetic pathway of branchedchain amino acids (BCAAs), which include isoleucine (Ile), leucine (Leu), and valine (Val). Enzymes involved in BCAA biosynthesis exist in bacteria, plants, and fungi but not in mammals and are therefore attractive targets for antimicrobial or herbicide development. In this study, three paralogous ILV3 genes (FgILV3A, FgILV3B, and FgILV3C) were identified in the genome of Fusarium graminearum, the causal agent of Fusarium head blight (FHB). Deletion of FgILV3A alone or combined with FgILV3B or FgILV3C indicated an important role for FgILV3A in BCAA biosynthesis. FgILV3A deletion mutants lost the ability to grow on medium lacking amino acids. Exogenous supplementation of 1 mM Ile and Val rescued the auxotrophy of ΔFgIlv3A, though 5 mM was required to recover the growth defects in ΔFgIlv3AB and ΔFgIlv3AC strains, indicating that FgIlv3b and FgIlv3c exhibit redundant but accessory roles with FgIlv3a in BCAA biosynthesis. The auxotrophy of ΔFgIlv3A resulted in pleiotropic defects in aerial hyphal growth, in conidial formation and germination, and in aurofusarin accumulation. In addition, the mutants showed reduced virulence and deoxynivalenol production. Overall, our study demonstrates that FgIlv3a is crucial for BCAA biosynthesis in F. graminearum and a candidate fungicide target for FHB management.

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AflaILVB/G/I and AflaILVD are involved in mycelial production, aflatoxin biosynthesis, and fungal virulence in Aspergillus flavus
Yarong Zhao, Chulan Huang, Rui Zeng, Peirong Chen, Kaihang Xu, Xiaomei Huang, Xu Wang
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Histone H3 N-Terminal Lysine Acetylation Governs Fungal Growth, Conidiation, and Pathogenicity through Regulating Gene Expression in Fusarium pseudograminearum
Hang Jiang, Lifang Yuan, Liguo Ma, Kai Qi, Yueli Zhang, Bo Zhang, Guoping Ma, Junshan Qi
Journal of Fungi.2024; 10(6): 379. CrossRef
Identification and Characterization of an Antifungal Gene Mt1 from Bacillus subtilis by Affecting Amino Acid Metabolism in Fusarium graminearum
Pei Song, Wubei Dong
International Journal of Molecular Sciences.2023; 24(10): 8857. CrossRef
Branched-chain amino acid biosynthesis in fungi
Gary Jones, Jane Usher, Joel T. Steyer, Richard B. Todd
Essays in Biochemistry.2023; 67(5): 865. CrossRef
FgLEU1 Is Involved in Leucine Biosynthesis, Sexual Reproduction, and Full Virulence in Fusarium graminearum
Shaohua Sun, Mingyu Wang, Chunjie Liu, Yilin Tao, Tian Wang, Yuancun Liang, Li Zhang, Jinfeng Yu
Journal of Fungi.2022; 8(10): 1090. CrossRef
Acetolactate synthases regulatory subunit and catalytic subunit genes VdILVs are involved in BCAA biosynthesis, microscletotial and conidial formation and virulence in Verticillium dahliae
ShengNan Shao, Biao Li, Qi Sun, PeiRu Guo, YeJuan Du, JiaFeng Huang
Fungal Genetics and Biology.2022; 159: 103667. CrossRef
Molecular targets for antifungals in amino acid and protein biosynthetic pathways
Aleksandra Kuplińska, Kamila Rząd
Amino Acids.2021; 53(7): 961. CrossRef
MoCpa1-mediated arginine biosynthesis is crucial for fungal growth, conidiation, and plant infection of Magnaporthe oryzae
Osakina Aron, Min Wang, Anjago Wilfred Mabeche, Batool Wajjiha, Meiqin Li, Shuai Yang, Haixia You, Yan Cai, Tian Zhang, Yunxi Li, Baohua Wang, Dongmei Zhang, Zonghua Wang, Wei Tang
Applied Microbiology and Biotechnology.2021; 105(14-15): 5915. CrossRef
Metabolic, structural, and proteomic changes in Candida albicans cells induced by the protein-carbohydrate fraction of Dendrobaena veneta coelomic fluid
Marta J. Fiołka, Paulina Czaplewska, Sylwia Wójcik-Mieszawska, Aleksandra Lewandowska, Kinga Lewtak, Weronika Sofińska-Chmiel, Tomasz Buchwald
Scientific Reports.2021;[Epub] CrossRef
The pyruvate dehydrogenase kinase 2 (PDK2) is associated with conidiation, mycelial growth, and pathogenicity in Fusarium graminearum
Tao Gao, Dan He, Xin Liu, Fang Ji, Jianhong Xu, Jianrong Shi
Food Production, Processing and Nutrition.2020;[Epub] CrossRef
The Intermediates in Branched-Chain Amino Acid Biosynthesis Are Indispensable for Conidial Germination of the Insect-Pathogenic Fungus Metarhizium robertsii
Feifei Luo, Hongxia Zhou, Xue Zhou, Xiangyun Xie, You Li, Fenglin Hu, Bo Huang, Karyn N. Johnson
Applied and Environmental Microbiology.2020;[Epub] CrossRef

Metabolism-mediated induction of zinc tolerance in Brassica rapa by Burkholderia cepacia CS2-1: Sang-Mo Kang , Raheem Shahzad , Saqib Bilal , Abdul Latif Khan , Young-Hyun You , Won-Hee Lee , Hee-La Ryu , Ko-Eun Lee , In-Jung Lee; J. Microbiol. 2017;55(12):955-965. Published online December 7, 2017; DOI: https://doi.org/10.1007/s12275-017-7305-7

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Abstract

Brassica rapa (Chinese cabbage) is an essential component of traditional Korean food. However, the crop is often subject to zinc (Zn+) toxicity from contaminated irrigation water, which, as a result, compromises plant growth and production, as well as the health of human consumers. The present study investigated the bioaccumulation of Zn+ by Burkholderia cepacia CS2-1 and its effect on the heavy metal tolerance of Chinese cabbage. Strain CS2-1 was identified and characterized on the basis of 16S rRNA sequences and phylogenetic analysis. The strain actively produced indole-3-acetic acid (3.08 ± 0.21 μg/ml) and was also able to produce siderophore, solubilize minerals, and tolerate various concentrations of Zn+. The heavy metal tolerance of B. rapa plants was enhanced by CS2-1 inoculation, as indicated by growth attributes, Zn+ uptake, amino acid synthesis, antioxidant levels, and endogenous hormone (ABA and SA) synthesis. Without inoculation, the application of Zn+ negatively affected the growth and physiology of B. rapa plants. However, CS2-1 inoculation improved plant growth, lowered Zn+ uptake, altered both amino acid regulation and levels of flavonoids and phenolics, and significantly decreased levels of superoxide dismutase, endogenous abscisic acid, and salicylic acid. These findings indicate that B. cepacia CS2-1 is suitable for bioremediation against Zn+-induced oxidative stress.

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Assessing the health of climate-sensitive trees in a subalpine ecosystem through microbial community dynamics
Bo Ram Kang, Soo Bin Kim, Jin-Kyung Hong, Seok Hyun Ahn, Jinwon Kim, Nayeon Lee, Tae Kwon Lee
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Exploring the Phosphate Solubilising Rhizobacteria isolated from Wild Musa Rhizosphere and their Efficacy on Growth Promotion of Phaseolus vulgaris
Mum Tatung, Chitta Ranjan Deb
Journal of Experimental Biology and Agricultural Sciences.2024; 12(5): 742. CrossRef
Remediation of benzo[a]pyrene contaminated soils by moderate chemical oxidation coupled with microbial degradation
Bin Chen, Jiang Xu, Huijie Lu, Lizhong Zhu
Science of The Total Environment.2023; 871: 161801. CrossRef
Assessing the Involvement of Selected Phenotypes of Pseudomonas simiae PICF7 in Olive Root Colonization and Biological Control of Verticillium dahliae
Nuria Montes-Osuna, Carmen Gómez-Lama Cabanás, Antonio Valverde-Corredor, Roeland L. Berendsen, Pilar Prieto, Jesús Mercado-Blanco
Plants.2021; 10(2): 412. CrossRef
Ameliorative effect of indole-3-acetic acid- and siderophore-producing Leclercia adecarboxylata MO1 on cucumber plants under zinc stress
Sang-Mo Kang, Raheem Shahzad, Muhammad Aaqil Khan, Zuhair Hasnain, Ko-Eun Lee, Hee-Soon Park, Lee-Rang Kim, In-Jung Lee
Journal of Plant Interactions.2021; 16(1): 30. CrossRef
Cadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2–6
Xin Cheng, Bowen Yang, Jinfang Zheng, Hongyu Wei, Xuehuan Feng, Yanbin Yin
Computational and Structural Biotechnology Journal.2021; 19: 5678. CrossRef
Complete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions
Sang-Mo Kang, Sajjad Asaf, Abdul Latif Khan, Lubna, Adil Khan, Bong-Gyu Mun, Muhammad Aaqil Khan, Humaira Gul, In-Jung Lee
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The plant-growth promoting bacteria promote cadmium uptake by inducing a hormonal crosstalk and lateral root formation in a hyperaccumulator plant Sedum alfredii
Yingjie Wu, Luyao Ma, Qizhen Liu, Mette Vestergård, Olivera Topalovic, Qiong Wang, Qiyao Zhou, Lukuan Huang, Xiaoe Yang, Ying Feng
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Effect of Ammonia and Indole-3-acetic Acid Producing Endophytic Klebsiella pneumoniae YNA12 as a Bio-Herbicide for Weed Inhibition: Special Reference with Evening Primroses
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Potential role of plant growth-promoting bacteria in Miscanthus x giganteus phytotechnology applied to the trace elements contaminated soils
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Phytohormones enabled endophytic Penicillium funiculosum LHL06 protects Glycine max L. from synergistic toxicity of heavy metals by hormonal and stress-responsive proteins modulation
Saqib Bilal, Raheem Shahzad, Abdul Latif Khan, Ahmed Al-Harrasi, Chang Kil Kim, In-Jung Lee
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Amelioration of heavy metal stress by endophytic Bacillus amyloliquefaciens RWL-1 in rice by regulating metabolic changes: potential for bacterial bioremediation
Raheem Shahzad, Saqib Bilal, Muhammad Imran, Abdul Latif Khan, Areej Ahmed Alosaimi, Hussah Abdullah Al-Shwyeh, Hanan Almahasheer, Suriya Rehman, In-Jung Lee
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Identification of D-amino acid dehydrogenase as an upstream regulator of the autoinduction of a putative acyltransferase in Corynebacterium glutamicum: Jung-Hoon Lee , Yong-Jae Kim , Hee-Sung Shin , Heung-Shick Lee , Shouguang Jin , Un-Hwan Ha; J. Microbiol. 2016;54(6):432-439. Published online May 27, 2016; DOI: https://doi.org/10.1007/s12275-016-6046-3

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Abstract

Expression of a putative acyltransferase encoded by NCgl- 0350 of Corynebacterium glutamicum is induced by cell-free culture fluids obtained from stationary-phase growth of both C. glutamicum and Pseudomonas aeruginosa, providing evidence for interspecies communication. Here, we further confirmed that such communication occurs by showing that acyltransferase expression is induced by culture fluid obtained from diverse Gram-negative and -positive bacterial strains, including Escherichia coli, Salmonella Typhimurium, Bacillus subtilis, Staphylococcus aureus, Mycobacterium sp. strain JC1, and Mycobacterium smegmatis. A homologous acyltransferase encoded by PA5238 of P. aeruginosa was also induced by fluids obtained from P. aeruginosa as well as other bacterial strains, as observed for NCgl0350 of C. glutamicum. Because C. glutamicum is difficult to study using molecular approaches, the homologous gene PA5238 of P. aeruginosa was used to identify PA5309 as an upstream regulator of expression. A homologous D-amino acid dehydrogenase encoded by NCgl- 2909 of C. glutamicum was cloned based on amino acid similarity to PA5309, and its role in the regulation of NCgl0350 expression was confirmed. Moreover, NCgl2909 played positive roles in growth of C. glutamicum. Thus, we identified a D-amino acid dehydrogenase as an upstream regulator of the autoinduction of a putative acyltransferase in C. glutamicum.

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Enhanced Bacterial Growth and Gene Expression of D-Amino Acid Dehydrogenase With D-Glutamate as the Sole Carbon Source
Takeshi Naganuma, Yoshiakira Iinuma, Hitomi Nishiwaki, Ryota Murase, Kazuo Masaki, Ryosuke Nakai
Frontiers in Microbiology.2018;[Epub] CrossRef

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

Prevalence of Amino Acid Changes in the yvqF, vraSR, graSR, and tcaRAB Genes from Vancomycin Intermediate Resistant Staphylococcus aureus: Jae Il Yoo , Jung Wook Kim , Gi Su Kang , Hwa Su Kim , Jung Sik Yoo , Yeong Seon Lee; J. Microbiol. 2013;51(2):160-165. Published online April 27, 2013; DOI: https://doi.org/10.1007/s12275-013-3088-7

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Abstract: Vancomycin intermediate Staphylococcus aureus (VISA) strains are increasingly prevalent in the hospital setting, and are of major concern in the treatment of methicillin-resistant S. aureus infections. Multiple mutations in vancomycinsusceptible S. aureus (VSSA) strains likely led to the emergence of VISA, and point mutations in the agr, orf1, yvqF, vraSR, graSR, and tcaRAB genes of VISA strains have been shown to contribute to glycopeptide resistance. Therefore, we investigated point mutations in these genes from 87 VISA and 27 VSSA clinical strains isolated from Korean hospitals. All strains were assigned an agr type (I, II, or III) on the basis of multiplex PCR, with the majority of VISA strains belonging to agr groups I and II. Sequencing revealed amino acid changes in vraS from VISA strains which were not present in the VSSA strains. The E59D substitution in the vraR gene occurred in 36.3% of VSSA/agrI and 92.7% of VISA/agrI strains, suggesting that this mutation associated with emergence of VISA/agrI strains. VISA strains were classified into 31 mutation patterns according to mutations in the yvqF, vraSR, graSR, and tcaRAB genes. In addition, the mutation patterns were correlated with agr and sequence type (ST). The most prevalent pattern included agr type I (ST 72) strains with E59D (vraR), L26F and T224I (graS), D148Q (graR), and L218P, R283H and G312D (tcaA) amino acid substitutions. The minimum inhibitory concentration (MIC) range of mutation pattern 5 toward oxacillin and imipenem was much lower than that of patterns 6 and 24. These results improve our understanding of emergence of VISA strains.

NOTE] Detection of a Unique Fibrinolytic Enzyme in Aeromonas sp. JH1: Han-Young Cho , Min Jeong Seo , Jeong Uck Park , Byoung Won Kang , Gi-Young Kim , Woo Hong Joo , Young-Choon Lee , Yong Kee Jeong; J. Microbiol. 2011;49(6):1018-1021. Published online December 28, 2011; DOI: https://doi.org/10.1007/s12275-011-1376-7

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Abstract: A fibrinolytic enzyme was found in a Gram-negative bacterium, Aeromonas sp. JH1. SDS-PAGE and fibrinzymography showed that it was a 36 kDa, monomeric protein. Of note, the enzyme was highly specific for fibrinogen molecules and the hydrolysis rate of fibrinogen subunits was highest for α, β, and γ chains in that order. The first 15 amino acids of N-terminal sequence were X-D-A-T-G-P-G-G-N-V-X-T-G-K-Y, which was distinguishable from other fibrinolytic enzymes. The optimum pH and temperature of the enzyme were approximately 8.0 and 40°C, respectively. Therefore, these results provide a fibrinolytic enzyme with potent thrombolytic activity from the Aeromonas genus.

Biochemical Analysis of a Fibrinolytic Enzyme Purified from Bacillus subtilis Strain A1: Won Sik Yeo , Min Jeong Seo , Min Jeong Kim , Hye Hyeon Lee , Byoung Won Kang , Jeong Uck Park , Yung Hyun Choi , Yong Kee Jeong; J. Microbiol. 2011;49(3):376-380. Published online June 30, 2011; DOI: https://doi.org/10.1007/s12275-011-1165-3

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Abstract: A fibrinolytic enzyme from Bacillus subtilis strain A1 was purified by chromatographic methods, including DEAE Sephadex A-50 column chromatography and Sephadex G-50 column gel filtration. The purified enzyme consisted of a monomeric subunit and was estimated to be approximately 28 kDa in size by SDS-PAGE. The specific activity of the fibrinolytic enzyme was 1632-fold higher than that of the crude enzyme extract. The fibrinolytic activity of the purified enzyme was approximately 0.62 and 1.33 U/ml in plasminogen-free and plasminogen-rich fibrin plates, respectively. Protease inhibitors PMSF, DIFP, chymostatin, and TPCK reduced the fibrinolytic activity of the enzyme to 13.7, 35.7, 15.7, and 23.3%, respectively. This result suggests that the enzyme purified from B. subtilis strain A1 was a chymotrypsin-like serine protease. In addition, the optimum temperature and pH range of the fibrinolytic enzyme were 50°C and 6.0-10.0, respectively. The N-terminal amino acid sequence of the purified enzyme was identified as Q-T-G-G-S-I-I-D-P-I-N-G-Y-N, which was highly distinguished from other known fibrinolytic enzymes. Thus, these results suggest a fibrinolytic enzyme as a novel thrombolytic agent from B. subtilis strain A1.

Purification and Biochemical Characterization of a 17 kDa Fibrinolytic Enzyme from Schizophyllum commune: In Suk Park , Jeong Uck Park , Min Jeong Seo , Min Jeong Kim , Hye Hyeon Lee , Sung Ryeal Kim , Byoung Won Kang , Yung Hyun Choi , Woo Hong Joo , Yong Kee Jeong; J. Microbiol. 2010;48(6):836-841. Published online January 9, 2011; DOI: https://doi.org/10.1007/s12275-010-0384-3

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Abstract: A fibrinolytic enzyme of the mushroom, Schizophyllum commune was purified with chromatographic methods, including a DEAE-Sephadex A-50 ion-exchange column and gel filtrations with Sephadex G-75 and Sephadex G-50 columns. The analysis of fibrin-zymography and SDS-PAGE showed that the enzyme was a monomeric subunit that was estimated to be approximately 17 kDa in size. The fibrinolytic activity of the enzyme in plasminogen-rich and plasminogen-free fibrin plates was 1.25 and 0.44 U/ml, respectively. The N-terminal amino acid sequence of the purified enzyme was identified as HYNIXNSWSSFID, which was highly distinguished from known fibrinolytic enzymes. The relative activity of the purified enzyme with an addition of 5 mM EDTA, Phosphoramidon, and Bestatin was about 76, 64, and 52%, respectively, indicating that it is a metalloprotease. The optimum temperature for the purified enzyme was approximately 45°C, and over 87% of the enzymatic activity was maintained as a stable state in a pH range from 4.0 to 6.0. Therefore, our results suggest that the potential thrombolytic agent from S. commune is a unique type of fibrinolytic enzyme.

Studies on Synonymous Codon and Amino Acid Usage Biases in the Broad-Host Range Bacteriophage KVP40: Keya Sau , Sanjib Kumar Gupta , Subrata Sau , Subhas Chandra Mandal , Tapash Chandra Ghosh; J. Microbiol. 2007;45(1):58-63.; DOI: https://doi.org/2490 [pii]

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Abstract: In this study, the relative synonymous codon and amino acid usage biases of the broad-host range phage, KVP40, were investigated in an attempt to understand the structure and function of its proteins/proteincoding genes, as well as the role of its tRNAs. Synonymous codons in KVP40 were determined to be ATrich at the third codon positions, and their variations are dictated principally by both mutational bias and translational selection. Further analysis revealed that the RSCU of KVP40 is distinct from that of its Vibrio hosts, V. cholerae and V. parahaemolyticus. Interestingly, the expression of the putative highly expressed genes of KVP40 appear to be preferentially influenced by the abundant host tRNA species, whereas the tRNAs expressed by KVP40 may be required for the efficient synthesis of all its proteins in a diverse array of hosts. The data generated in this study also revealed that KVP40 proteins are rich in low molecular weight amino acid residues, and that these variations are influenced primarily by hydropathy, mean molecular weight, aromaticity, and cysteine content.

Journal Article

Regulation of Branched-Chain, and Sulfur-Containing Amino Acid Metabolism by Glutathione during Ultradian Metabolic Oscillation of Saccharomyces cerevisiae: Ho-Yong Sohn , Eun-Joo Kum , Gi-Seok Kwon , Ingnyol Jin , Hiroshi Kuriyama; J. Microbiol. 2005;43(4):375-380.; DOI: https://doi.org/2250 [pii]

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Abstract: Autonomous ultradian metabolic oscillation (T~=50 min) was detected in an aerobic chemostat culture of Saccharomyces cerevisiae. A pulse injection of GSH (a reduced form of glutathione) into the culture induced a perturbation in metabolic oscillation, with respiratory inhibition caused by H_2S burst production. As the production of H_2S in the culture was controlled by different amino acids, we attempted to characterize the effects of GSH on amino acid metabolism, particularly with regard to branched chain and sulfur-containing amino acids. During stable metabolic oscillation, concentrations of intracellular glutamate, aspartate, threonine, valine, leucine, isoleucine, and cysteine were observed to oscillate with the same periods of dissolved O_2 oscillation, although the oscillation amplitudes and maximal phases were shown to differ. The methionine concentration was stably maintained at 0.05 mM. When GSH (100 uM) was injected into the culture, cellular levels of branched chain amino acids increased dramatically with continuous H_2S production, whereas the cysteine and methionine concentrations were noticeably reduced. These results indicate that GSH-dependent perturbation occurs as the result of the promotion of branched chain amino acid synthesis and an attenuation of cysteine and methionine synthesis, both of which activate the generation of H_2S. In a low sulfate medium containing 2.5 mM sulfate, the GSH injections did not result in perturbations of dissolved O_2, NAD(P)H redox oscillations without burst H_2S production. This suggests that GSH-dependent perturbation is intimately linked with the metabolism of branched-chain amino acids and H_2S generation, rather than with direct GSH-GSSG redox control.

Research Support, Non-U.S. Gov't

Hydrogen Peroxide produced by Two Amino Acid Oxidases Mediates Antibacterial Actions: Hongmin Zhang , Qiuyue Yang , Mingxuan Sun , Maikun Teng , Liwen Niu; J. Microbiol. 2004;42(4):336-339.; DOI: https://doi.org/2102 [pii]

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Abstract: The antibacterial actions of two amino acid oxidases, a D-amino acid oxidase from hog kidney and a L-amino acid oxidase from the venom of Agkistrodon halys, were investigated, demonstrating that both enzymes were able to inhibit the growth of both Gram-positive and Gram-negative bacteria, and that hydrogen peroxide, a product of their enzymatic reactions, was the antibacterial factor. However, hydrogen peroxide generated in the enzymatic reactions was not sufficient to explain the degree to which bacterial growth was inhibited. A fluorescence labeling assay showed that both of these two enzymes could bind to the surfaces of bacteria. To the best of our knowledge, this is the first report regarding the antibacterial activity of the D-amino acid oxidases.

Characteristics of protease inhibitor produced by streptomyces fradiae SMF9: Kim, Hyoung Tae , Suh, Joo Won , Lee, Key Joon; J. Microbiol. 1995;33(2):103-108.

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Abstract: Streptomyces fradiae protease inhibitor (SFI) was purified effectively by preparative isoelectric focusing and hydroxyapatite chromatography. The molecular weight of SFI was estimated to be 1.7 kDa by SDS-PAGE and 1.8 kDa by molecular sieving HPLC. One hundred and sixty amino acid residues were determined from which molecular weight of SFI was calculated to be 17.054 Da and carbohydrate residue was not detected. SFI was calculated to be 17,064 Da and carbohydrate residue was not detected. SFI was a monomeric protein with two reactive sits, of which isoelectric point was pH 4.1. N-terminal amino acid sequence of SFI had homology with SSI (Streptomyces subsilisin inhibitor) and other protease inhibitors produced by Streptomyces.

Role of Amino Acids in Production of D-amino Acid Oxidase: Puneet Singh , Satwinder Singh Marwaha , Neelam Verma; J. Microbiol. 2001;39(3):229-231.

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Abstract: Different DL-amino acids were studied as inducers of D-amino acid oxidase (DAAO) and for their influence on the growth of Trigonopsis variabilis. DL-amino acids with non-polar side groups were found to be the best inducers of DAAO. Maximum increase in the growth of Trigonopsis variabilis (gram dry weight per liter culfure) was observed with DL-methionine (2.39 g/l) followed by DL-serine (2.22 g/l) and DL-alanine (2.21 g/l).

Kinetic Study on the Enzymatic Production of D-Alanine from D-Aspartic Acid: Jae-Heung Lee , Moon-Hee Sung , Yeong-Joong Jeon; J. Microbiol. 2002;40(1):33-37.

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Abstract: An enzymatic reaction for the production of D-alanine from D-aspartic acid and pyruvate as substrates by a thermostable D-amino acid aminotransferase (D-AAT) was investigated at various conditions in the temperature range of 40-70 C and pH range of 6.0-9.5. The D-AAT was produced with recombinant E. coli BL21, which hosted the chimeric plasmid pTLK2 harboring the D-AAT from the novel thermophilic Bacillus sp. LK-2. The enzyme reaction was shown to follow the Ping Pong Bi Bi mechanism. The K m values for D-aspartic acid and pyruvate were 4.38 mM and 0.72 mM, respectively. It was observed that competitive inhibition by D-alanine, the product of this reaction, was evident with the inhibition constant K i value of 0.1 mM. A unique feature of this reaction scheme is that the decarboxylation of oxaloacetic acid, one of the products, spontaneously produces pyruvate. Therefore, only a catalytic amount of pyruvate is necessary for the enzyme conversion reaction to proceed. A typical time-course kinetic study showed that D-alanine up to 88 mM could be produced from 100 mM of D-aspartic acid with a molar yield of 1.0.

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