Journal of Microbiology

Journal Articles

Biosynthesis of Chryseno[2,1,c]oxepin‑12‑Carboxylic Acid from Glycyrrhizic Acid in Aspergillus terreus TMZ05‑2, and Analysis of Its Anti‑inflammatory Activity: Liangliang Chen , Lin Zhao , Ju Han , Ping Xiao , Mingzhe Zhao , Sen Zhang , Jinao Duan; J. Microbiol. 2024;62(2):113-124. Published online February 27, 2024; DOI: https://doi.org/10.1007/s12275-024-00105-4

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Glycyrrhizic acid, glycyrrhetinic acid, and their oxo, ester, lactone, and other derivatives, are known for their anti-inflammatory, anti-oxidant, and hypoglycemic pharmacological activities. In this study, chryseno[2,1-c]oxepin-12-carboxylic acid (MG) was first biosynthesized from glycyrrhizic acid through sequential hydrolysis, oxidation, and esterification using Aspergillus terreus TMZ05-2, providing a novel in vitro biosynthetic pathway for glycyrrhizic acid derivatives. Assessing the influence of fermentation conditions and variation of strains during culture under stress-induction strategies enhanced the final molar yield to 88.3% (5 g/L glycyrrhizic acid). CCK8 assays showed no cytotoxicity and good cell proliferation, and anti-inflammatory experiments demonstrated strong inhibition of NO release (36.3%, low-dose MG vs. model), transcriptional downregulation of classical effective cellular factors tumor necrosis factor-α (TNF-α; 72.2%, low-dose MG vs. model), interleukin-6 (IL-6; 58.3%, low-dose MG vs. model) and interleukin-1β (IL-1β; 76.4%, low-dose MG vs. model), and decreased abundance of P-IKK-α, P-IKB-α, and P-P65 proteins, thereby alleviating inflammatory responses through the NF-κB pathway in LPS-induced RAW264.7 cells. The findings provide a reference for the biosynthesis of lactone compounds from medicinal plants.

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Effect of different crosslinking agents on carboxymethyl chitosan-glycyrrhizic acid hydrogel: Characterization and biological activities comparison
Yinbing Wu, Zimin Gu, Tingting Chen, Duntao Zu, Yuhui Gan, Honglin Chen, Jianni Yang, Xin Yu, Huaihong Cai, Pinghua Sun, Jianying Ning, Haibo Zhou, Junxia Zheng
International Journal of Biological Macromolecules.2025; 298: 139977. CrossRef
New oxepin and dihydrobenzofuran derivatives from Bauhinia saccocalyx roots and their anti-inflammatory, cytotoxic, and antioxidant activities
Lueacha Tabtimmai, Thanyathon Phonchan, Natrinee Thongprik, Sutin Kaennakam, Nuttapon Yodsin, Kiattawee Choowongkomon, Chanikan Sonklin, Supachai Jadsadajerm, Awat Wisetsai
Journal of Natural Medicines.2025;[Epub] CrossRef
Efficient directional biosynthesis of isoquercitrin from quercetin by Bacillus subtilis CD-2 and its anti-inflammatory activity
Ju Han, Jingru Ma, Ruiqi He, Fan Yang, Jingyi Meng, Jiaqi Liu, Fanxing Shi, Jinao Duan, Liangliang Chen, Sen Zhang
Natural Product Research.2024; : 1. CrossRef

Comparative genomic analysis of Geosporobacter ferrireducens and its versatility of anaerobic energy metabolism: Man-Young Jung , So-Jeong Kim , Jong-Geol Kim , Heeji Hong , Joo-Han Gwak , Soo-Je Park , Yang-Hoon Kim , Sung-Keun Rhee; J. Microbiol. 2018;56(5):365-371. Published online May 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7451-6

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Abstract

Members of the family Clostridiaceae within phylum Firmicutes are ubiquitous in various iron-reducing environments. However, genomic data on iron-reducing bacteria of the family Clostridiaceae, particularly regarding their environmental distribution, are limited. Here, we report the analysis and comparison of the genomic properties of Geosporobacter ferrireducens IRF9, a strict anaerobe that ferments sugars and degrades toluene under iron-reducing conditions, with those of the closely related species, Geosporobacter subterraneus DSM 17957. Putative alkyl succinate synthase-encoding genes were observed in the genome of strain IRF9 instead of the typical benzyl succinate synthase-encoding genes. Canonical genes associated with iron reduction were not observed in either genome. The genomes of strains IRF9 and DMS 17957 harbored genes for acetogenesis, that encode two types of Rnf complexes mediating the translocation of H+ and Na+ ions, respectively. Strain IRF9 harbored two different types of ATPases (Na+-dependent F-type ATPase and H+- dependent V-type ATPase), which enable full exploitation of ion gradients. The versatile energy conservation potential of strain IRF9 promotes its survival in various environmental conditions.

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Promoting effects and mechanisms of common iron oxides on corrosion of carbon steel induced by methanogenic microbiota
Jianping Wu, Weidong Zhang, Shanyu Xie, Zhaoshou Wang, Yuanpeng Wang
Journal of Environmental Chemical Engineering.2025; : 115769. CrossRef
Co-exposure of microplastics and polychlorinated biphenyls strongly influenced the cycling processes of typical biogenic elements in anoxic soil
Guangxue Xie, Qian Hou, Lianzhen Li, Yan Xu, Shaochong Liu, Xilin She
Journal of Hazardous Materials.2024; 465: 133277. CrossRef
A review on microbial diversity and genetic markers involved in methanogenic degradation of hydrocarbons: futuristic prospects of biofuel recovery from contaminated regions
Kriti Sengupta, Siddhartha Pal
Environmental Science and Pollution Research.2021; 28(30): 40288. CrossRef
Iron and total organic carbon shape the spatial distribution pattern of sediment Fe(III) reducing bacteria in a volcanic lake, NE China
Yue Zhan, Mengran Yang, Yu Zhang, Jian Yang, Weidong Wang, Lei Yan, Shuang Zhang
World Journal of Microbiology and Biotechnology.2021;[Epub] CrossRef
Maize straw biochar addition inhibited pentachlorophenol dechlorination by strengthening the predominant soil reduction processes in flooded soil
Min Zhu, Xiaofei Lv, Ashley E. Franks, Philip C. Brookes, Jianming Xu, Yan He
Journal of Hazardous Materials.2020; 386: 122002. CrossRef
New Frontiers of Anaerobic Hydrocarbon Biodegradation in the Multi-Omics Era
Krisztián Laczi, Ágnes Erdeiné Kis, Árpád Szilágyi, Naila Bounedjoum, Attila Bodor, György Erik Vincze, Tamás Kovács, Gábor Rákhely, Katalin Perei
Frontiers in Microbiology.2020;[Epub] CrossRef
Enrichment of Marinobacter sp. and Halophilic Homoacetogens at the Biocathode of Microbial Electrosynthesis System Inoculated With Red Sea Brine Pool
Manal F. Alqahtani, Suman Bajracharya, Krishna P. Katuri, Muhammad Ali, Ala’a Ragab, Grégoire Michoud, Daniele Daffonchio, Pascal E. Saikaly
Frontiers in Microbiology.2019;[Epub] CrossRef

Mutational analysis of the RNA helicase Dhh1 in Ste12 expression and yeast mating: Daehee Jung , Jihye Ahn , Boram Rhee , Jinmi Kim; J. Microbiol. 2017;55(5):373-378. Published online April 29, 2017; DOI: https://doi.org/10.1007/s12275-017-7020-4

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Abstract

Dhh1 and Dhh1 homologues (RCK/p54/DDX6) are mem-bers of the DEAD-box protein family of RNA helicases. These proteins display conserved sequence motifs for ATPase and RNA binding activities. Dhh1 is a component of the P-bodies (processing bodies) of mRNA granules and functions as an mRNA decapping activator in Saccharomyces cerevisiae. Dhh1 also contributes to gene-specific regulation during yeast mating. The dhh1 deletion mutation results in a significant decrease in the expression of Ste12, a mating-specific trans-cription factor, showing severe mating defects. Here, we in-troduced amino-acid substitution mutations in the ATPase and RNA binding domains of Dhh1 and also constructed a deletion of 79 amino acids at the Q/P-rich C-terminal region. The mutations in ATPase A and B motif (K96R, D195A) and C-terminus deletion showed reduced levels of mating effi-ciency as well as Ste12 protein expression. The Q/P-rich C- terminal region of Dhh1 was dispensable for growth at non- permissive temperature 37°C but appeared to play an im-portant role in regulating the Ste12 protein expression and mating processes. The P-body accumulation induced by treatment with α-mating factor required ATPase, RNA-bind-ing and the Q/P-rich C-terminal domains of Dhh1.

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Fus3 and Tpk2 protein kinases regulate the phosphorylation-dependent functions of RNA helicase Dhh1 in yeast mating and Ste12 protein expression
Jaehee Hwang, Daehee Jung, Jinmi Kim
Journal of Microbiology.2022; 60(8): 843. CrossRef
The Role of DEAD-Box ATPases in Gene Expression and the Regulation of RNA–Protein Condensates
Karsten Weis, Maria Hondele
Annual Review of Biochemistry.2022; 91(1): 197. CrossRef
Roles of Dhh1 RNA helicase in yeast filamentous growth: Analysis of N-terminal phosphorylation residues and ATPase domains
Eunji Lee, Daehee Jung, Jinmi Kim
Journal of Microbiology.2020; 58(10): 853. CrossRef
Functional association of Loc1 and Puf6 with RNA helicase Dhh1 in translational regulation of Saccharomyces cerevisiae Ste12
Daehee Jung, Jong Seok Seo, Jayoung Nam, Jinmi Kim, Enrico Baruffini
PLOS ONE.2019; 14(7): e0220137. CrossRef
Roles of eIF4E-binding protein Caf20 in Ste12 translation and P-body formation in yeast
Kiyoung Park, Yu-Seon Lee, Daehee Jung, Jinmi Kim
Journal of Microbiology.2018; 56(10): 744. CrossRef

Kinetic characterization of a novel acid ectophosphatase from Enterobacter asburiae: Vanessa Sayuri Sato , Renato F. Galdiano Júnior , Gisele Regina Rodrigues , Eliana G. M. Lemos , João Martins Pizauro Junior; J. Microbiol. 2016;54(2):106-113. Published online February 2, 2016; DOI: https://doi.org/10.1007/s12275-015-5354-3

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Abstract

Expression of acid ectophosphatase by Enterobacter asburiae, isolated from Cattleya walkeriana (Orchidaceae) roots and identified by the 16S rRNA gene sequencing analysis, was strictly regulated by phosphorus ions, with its optimal activity being observed at an inorganic phosphate concentration of 7 mM. At the optimum pH 3.5, intact cells released p-nitrophenol at a rate of 350.76 ± 13.53 nmol of p-nitrophenolate (pNP)/min/108 cells. The membrane-bound enzyme was obtained by centrifugation at 100,000 × g for 1 h at 4°C. p-Nitrophenylphosphate (pNPP) hydrolysis by the enzyme follows “Michaelis-Menten” kinetics with V = 61.2 U/mg and K0.5 = 60 μM, while ATP hydrolysis showed V = 19.7 U/mg, K0.5 = 110 μM, and nH = 1.6 and pyrophosphate hydrolysis showed V = 29.7 U/mg, K0.5 = 84 μM, and nH = 2.3. Arsenate and phosphate were competitive inhibitors with Ki = 0.6 mM and Ki = 1.8 mM, respectively. p-Nitrophenyl phosphatase (pNPPase) activity was inhibited by vanadate, while p-hydroxymercuribenzoate, EDTA, calcium, copper, and cobalt had no inhibitory effects. Magnesium ions were stimulatory (K0.5 = 2.2 mM and nH = 0.5). Production of an acid ectophosphatase can be a mechanism for the solubilization of mineral phosphates by microorganisms such as Enterobacter asburiae that are versatile in the solubilization of insoluble minerals, which, in turn, increases the availability of nutrients for plants, particularly in soils that are poor in phosphorus.

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Potential inhibition of entomopathogenic nematodes and plant growth-promoting bacteria with exposure to selected herbicides and insecticides
Oluwatoyin Adenike Fabiyi, Olusoji Olusegun Adebisi, Sunday Olubusuyi Falore, Abiodun Olufunmilayo Claudius-Cole
Vegetos.2023; 37(4): 1503. CrossRef
Biofilm Formation, Production of Matrix Compounds and Biosorption of Copper, Nickel and Lead by Different Bacterial Strains
Md. Manjurul Haque, Md Khaled Mosharaf, Md. Amdadul Haque, Md. Zahid Hasan Tanvir, Md. Khairul Alam
Frontiers in Microbiology.2021;[Epub] CrossRef
Immunoglobulin Y in the diagnosis of Aeromonas hydrophila infection in Nile tilapia (Oreochromis niloticus)
Dayanne C. Fernandes, Silas F. Eto, Michelli I.G. Funnicelli, Camila C. Fernandes, Ives Charlie-Silva, Marco A.A. Belo, João M. Pizauro
Aquaculture.2019; 500: 576. CrossRef
Validation of IgY for the diagnosis of Streptococcus agalactiae-caused endocarditis and bacterial meningitis in Nile tilapia (Oreochromis niloticus)
Silas F. Eto, Dayanne C. Fernandes, Alessandra C. Moraes, Ed Johnny R. Prado, Amanda C. Baldassi, Wilson G. Manrique, Ives C. Silva, Andrea S.R. Medeiros, Marco A.A. Belo, Tiago S. Balbuena, Samir I. Samara, João M. Pizauro
Fish & Shellfish Immunology.2018; 76: 153. CrossRef
An endophytic microbe from an unusual volcanic swamp corn seeks and inhabits root hair cells to extract rock phosphate
Hanan R. Shehata, Christopher Dumigan, Sophia Watts, Manish N. Raizada
Scientific Reports.2017;[Epub] CrossRef

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

The ATPase Activity of The G2alt Gene Encoding an Aluminium Tolerance Protein from Anoxybacillus gonensis G2: Fatih Saban Beris , Lina De Smet , Hakan Karaoglu , Sabriye Canakci , Jozef Van Beeumen , Ali Osman Belduz; J. Microbiol. 2011;49(4):641-650. Published online September 2, 2011; DOI: https://doi.org/10.1007/s12275-011-0522-6

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Abstract: The G2ALT gene was cloned and sequenced from the thermophilic bacterium Anoxybacillus gonensis G2. The gene is 666 bp long and encodes a protein 221 amino acids in length. The gene was overexpressed in E. coli and purified to homogeneity and biochemically characterized. The enzyme has a molecular mass of 24.5 kDa and it could be classified as a member of the family of bacterial aluminium resistance proteins based on homology searches. When this fragment was expressed in E. coli, it endowed E. coli with Al tolerance to 500 μM. The purified G2ALT protein is active at a broad pH range (pH 4.0-10.0) and temperature range (25°C-80°C) with optima of 6.0 and the apparent optimal temperature of 73°C respectively. Under optimal conditions, G2ALT exhibited a low ATPase activity with Km- and Vmax- values of 10±0.55 μM and 26.81±0.13 mg Pi released/min/mg enzyme, respectively. The ATPase activity of G2ALT requires Mg2+ and Na+ ions, while Zn2+ and Al3+ stimulate the activity. Cd2+ and Ag+ reduced the activity and Li+, Cu2+, and Co2+ inhibited the activity. Known inhibitors of most ATPases, like such as β-mercaptoethanol and ouabain, also inhibited the activity of the G2ALT. These biochemical characterizations suggested that G2ALT belongs to the PP-loop ATPase superfamily and it can be responsible for aluminium tolerance in A. gonensis G2.

Rapid Propagational Interactions of Slow Binding Inhibitor with RecA Protein Occur on the Longer Nucleoprotein Filaments: Jong-Il Kim; J. Microbiol. 2010;48(1):71-76. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0306-4

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Abstract: RecA protein is a DNA-dependent ATPase. RecA protein-mediated ATP hydrolysis occurs throughout the filamentous nucleoprotein complexes of RecA and DNA. Nucleotide analog ATP[γS] may not act simply as a competitive inhibitor, leading to inhibition kinetic patterns that are informative. When a mixture of ATP and ATP[γS] is present at the beginning of reaction, a transient phase lasting several minutes is observed in which the system approaches the state characteristic of the new ATP/ATP[γS] ratio. This phase consists of a burst or lag in ATP hydrolysis, depending on whether ATP or ATP[γS] respectively, is added first. The transition phase reflects a slow conformational change in a RecA monomer or a general adjustment in the structure of RecA filaments. The RecA filaments formed on longer DNA cofactor were more sensitive, and respond more rapidly to ATP[γS] than on shorter DNA cofactors.

Functional Characterization of the Copper-Transporting P-Type ATPase Gene of Penicillium janthinellum Strain GXCR: Hongmin Lai , Changbin Sun , Huaying Tang , Xianwei Fan , Yili Ma; J. Microbiol. 2009;47(6):736-745. Published online February 4, 2010; DOI: https://doi.org/10.1007/s12275-009-0074-1

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Abstract: Copper (Cu)-transporting P-type ATPase (CTPA) genes have been documented to play an important role in resistance to heavy metals. However, our understanding of roles of CTPA genes of the filamentous fungi was based only on sequence similarity prediction before. In a previous study, we isolated a Penicillum janthinellum strain GXCR of higher tolerance to Cu (200 mM). In this study, we cloned the partial cDNA of CTPA gene, named PcpA, from the strain GXCR. Sequence alignment indicated that the cloned cDNA sequence has the highest identity (94.4%) with a predictive CTPA gene of Aspergillus clavatus. The PcpA- encoded protein, termed PcpA, has classical functional domains of CTPAs, and shows differences from reported CTPAs in some specific sequence motifs and transmembrane regions. Expression of the PcpA was induced by extracellular Cu, cadmium (Cd), and silver (Ag). PcpA RNA interference (RNAi) mutants with a reduced level of PcpA mRNA were more sensitive to Cu, iron, Cd, and Ag than the wild-type (WT) strain GXCR. When grown in the presence of Cu, iron, and Cd, intracellular Cu and iron contents in the PcpA RNAi mutant were significantly (P<0.05) lower than those in the WT; However, intracellular Cd content in the mutant was significantly (P<0.05) higher than that in the WT. Taken together, it can be concluded that the PcpA functions in Cu uptake and homeostasis, iron uptake, and Cd export from the cytosol to the extracytosol.

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