Journal of Microbiology

Review

Untranslated region engineering strategies for gene overexpression, fine-tuning, and dynamic regulation: Jun Ren, So Hee Oh, Dokyun Na; J. Microbiol. 2025;63(3):e2501033. Published online March 28, 2025; DOI: https://doi.org/10.71150/jm.2501033

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Precise and tunable gene expression is crucial for various biotechnological applications, including protein overexpression, fine-tuned metabolic pathway engineering, and dynamic gene regulation. Untranslated regions (UTRs) of mRNAs have emerged as key regulatory elements that modulate transcription and translation. In this review, we explore recent advances in UTR engineering strategies for bacterial gene expression optimization. We discuss approaches for enhancing protein expression through AU-rich elements, RG4 structures, and synthetic dual UTRs, as well as ProQC systems that improve translation fidelity. Additionally, we examine strategies for fine-tuning gene expression using UTR libraries and synthetic terminators that balance metabolic flux. Finally, we highlight riboswitches and toehold switches, which enable dynamic gene regulation in response to environmental or metabolic cues. The integration of these UTR-based regulatory tools provides a versatile and modular framework for optimizing bacterial gene expression, enhancing metabolic engineering, and advancing synthetic biology applications.

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Advancing microbial engineering through synthetic biology
Ki Jun Jeong
Journal of Microbiology.2025; 63(3): e2503100. CrossRef

Journal Articles

Upgrading Isoquercitrin Concentration via Submerge Fermentation of Mulberry Fruit Extract with Edible Probiotics to Suppress Gene Targets for Controlling Kidney Cancer and Inflammation: Md Rezaul Karim, Safia Iqbal, Shahnawaz Mohammad, Jong-Hoon Kim, Li Ling, Changbao Chen, Abdus Samad, Md Anwarul Haque, Deok-Chun Yang, Yeon Ju Kim, Dong Uk Yang; J. Microbiol. 2024;62(10):919-927. Published online October 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00163-8

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Abstract

In recent years, kidney cancer has become one of the most serious medical issues. Kidney cancer is treated with a variety of active compounds that trigger genes that cause cancer. We identified in our earlier research that isoquercitrin (IQ) can activate PIK3CA, IGF1R, and PTGS2. However, it has a very low bioavailability because of its lower solubility in water. So, we utilized sub-merge fermentation technology with two well-known probiotics, Lactobacillus acidophilus and Bacillus subtilis, as a microbial source and mulberry fruit extract as a substrate, which has a high IQ level to improve IQ yield. Furthermore, we compared the total phenolic, flavonoid, and antioxidant contents of fermented and non-fermented samples, and we found that the fermented samples had greater levels than non-fermented sample. In addition, the high-performance liquid chromatography (HPLC) results showed that the fermented mulberry fruit extract from B. subtilis and L. acidophilus showed higher IQ values (190.73 ± 0.004 μg/ml and 220.54 ± 0.007 μg/ml, respectively), compared to the non-fermented samples, which had IQ values (80.12 ± 0.002 μg/ml). Additionally, at 62.5 µg/ml doses of each sample, a normal kidney cell line (HEK 293) showed higher cell viability for fermented and non-fermented samples. Conversely, at the same doses, the fermented samples of L. acidophilus and B. subtilis in a kidney cancer cell line (A498) showed an inhibition of cell growth around 36% and 31%, respectively. Finally, we performed RT and qRT PCR assay, and we found a significant reduction in the expression of the PTGS2, PIK3CA, and IGF1R genes. We therefore can conclude that the fermented samples have a higher concentration of isoquercitrin, and also can inhibit the expression of the genes PTGS2, PIK3CA, and IGF1R, which in turn regulates kidney cancer and inflammation.

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Recent research on the bioactivity of polyphenols derived from edible fungi and their potential in chronic disease prevention
Wenbin Yu, Yufei Zhang, Yi Lu, Zhiwei Ouyang, Jiahua Peng, Yayi Tu, Bin He
Journal of Functional Foods.2025; 124: 106627. CrossRef

Hydroxychloroquine an Antimalarial Drug, Exhibits Potent Antifungal Efficacy Against Candida albicans Through Multitargeting: Sargun Tushar Basrani, Tanjila Chandsaheb Gavandi, Shivani Balasaheb Patil, Nandkumar Subhash Kadam, Dhairyasheel Vasantrao Yadav, Sayali Ashok Chougule, Sankunny Mohan Karuppayil, Ashwini Khanderao Jadhav; J. Microbiol. 2024;62(5):381-391. Published online April 8, 2024; DOI: https://doi.org/10.1007/s12275-024-00111-6

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Abstract: Candida albicans is the primary etiological agent associated with candidiasis in humans. Unrestricted growth of C. albicans can progress to systemic infections in the worst situation. This study investigates the antifungal activity of Hydroxychloroquine (HCQ) and mode of action against C. albicans. HCQ inhibited the planktonic growth and yeast to hyphal form morphogenesis of C. albicans significantly at 0.5 mg/ml concentration. The minimum inhibitory concentrations (MIC(50)) of HCQ for C. albicans adhesion and biofilm formation on the polystyrene surface was at 2 mg/ml and 4 mg/ml respectively. Various methods, such as scanning electron microscopy, exploration of the ergosterol biosynthesis pathway, cell cycle analysis, and assessment of S oxygen species (ROS) generation, were employed to investigate HCQ exerting its antifungal effects. HCQ was observed to reduce ergosterol levels in the cell membranes of C. albicans in a dose-dependent manner. Furthermore, HCQ treatment caused a substantial arrest of the C. albicans cell cycle at the G0/G1 phase, which impeded normal cell growth. Gene expression analysis revealed upregulation of SOD2, SOD1, and CAT1 genes after HCQ treatment, while genes like HWP1, RAS1, TEC1, and CDC 35 were downregulated. The study also assessed the in vivo efficacy of HCQ in a mice model, revealing a reduction in the pathogenicity of C. albicans after HCQ treatment. These results indicate that HCQ holds for the development of novel antifungal therapies.

Review

Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments: Felana Harilanto Andrianjakarivony , Yvan Bettarel , Christelle Desnues; J. Microbiol. 2023;61(6):589-602. Published online June 1, 2023; DOI: https://doi.org/10.1007/s12275-023-00052-6

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Abstract

The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one “ideal” viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.

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Review of carbon dot–hydrogel composite material as a future water-environmental regulator
Minghao Jiang, Yong Wang, Jichuan Li, Xing Gao
International Journal of Biological Macromolecules.2024; 269: 131850. CrossRef

Journal Articles

Coumarin-based combined computational study to design novel drugs against Candida albicans: Akhilesh Kumar Maurya , Nidhi Mishra; J. Microbiol. 2022;60(12):1201-1207. Published online November 10, 2022; DOI: https://doi.org/10.1007/s12275-022-2279-5

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Abstract

Candida species cause the most prevalent fungal illness, candidiasis. Candida albicans is known to cause bloodstream infections. This species is a commensal bacterium, but it can cause hospital–acquired diseases, particularly in COVID-19 patients with impaired immune systems. Candida infections have increased in patients with acute respiratory distress syndrome. Coumarins are both naturally occurring and synthetically produced. In this study, the biological activity of 40 coumarin derivatives was used to create a three-dimensional quantitative structure activity relationship (3D-QSAR) model. The training and test minimum inhibitory concentration values of C. albicans active compounds were split, and a regression model based on statistical data was established. This model served as a foundation for the creation of coumarin derivative QSARs. This is a unique way to create new therapeutic compounds for various ailments. We constructed novel structural coumarin derivatives using the derived QSAR model, and the models were confirmed using molecular docking and molecular dynamics simulation.

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Coumarin derivatives ameliorate the intestinal inflammation and pathogenic gut microbiome changes in the model of infectious colitis through antibacterial activity
Hui-su Jung, Yei Ju Park, Bon-Hee Gu, Goeun Han, Woonhak Ji, Su mi Hwang, Myunghoo Kim
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Therapeutic Effects of Coumarins with Different Substitution Patterns
Virginia Flores-Morales, Ana P. Villasana-Ruíz, Idalia Garza-Veloz, Samantha González-Delgado, Margarita L. Martinez-Fierro
Molecules.2023; 28(5): 2413. CrossRef
Cyclometalated iridium(III) complexes combined with fluconazole: antifungal activity against resistant C. albicans
Jun-Jian Lu, Zhi-Chang Xu, Hou Zhu, Lin-Yuan Zhu, Xiu-Rong Ma, Rui-Rui Wang, Rong-Tao Li, Rui-Rong Ye
Frontiers in Cellular and Infection Microbiology.2023;[Epub] CrossRef

Rasiella rasia gen. nov. sp. nov. within the family Flavobacteriaceae isolated from seawater recirculating aquaculture system: Seong-Jin Kim , Young-Sam Kim , Sang-Eon Kim , Hyun-Kyoung Jung , Jeeeun Park , Min-Ju Yu , Kyoung-Ho Kim; J. Microbiol. 2022;60(11):1070-1076. Published online October 17, 2022; DOI: https://doi.org/10.1007/s12275-022-2099-7

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Abstract

A novel bacterium designated RR4-40T was isolated from a biofilter of seawater recirculating aquaculture system in Busan, South Korea. Cells are strictly aerobic, Gram-negative, irregular short rod, non-motile, and oxidase- and catalase-negative. Growth was observed at 15–30°C, 0.5–6% NaCl (w/v), and pH 5.0–9.5. The strain grew optimally at 28°C, 3% salinity (w/v), and pH 8.5. The phylogenetic analysis based on 16S rRNA gene sequences showed that strain RR4-40T was most closely related to Marinirhabdus gelatinilytica NH83T (94.16% of 16S rRNA gene similarity) and formed a cluster with genera within the family Flavobacteriaceae. The values of the average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and average amino acid identity (AAI) between genomes of strain RR4-40T and M. gelatinilytica NH83T were 72.91, 18.2, and 76.84%, respectively, and the values against the strains in the other genera were lower than those. The major fatty acids were iso-C15:0 (31.34%), iso-C17:0 3-OH (13.65%), iso-C16:0 3-OH (10.61%), and iso-C15:1 G (10.38%). The polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, aminophospholipid, aminolipid, glycolipid, and sphingolipid. The major respiratory quinone was menaquinone-6 (MK-6) and the DNA G + C content of strain RR4-40T was 37.4 mol%. According to the polyphasic analysis, strain RR4-40T is considered to represent a novel genus within the family Flavobacteriaceae, for which the name Rasiella rasia gen. nov, sp. nov. is proposed. The type strain is RR4-40T (= KCTC 52650T = MCCC 1K04210T).

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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. 215. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef

Review

Overview of bioinformatic methods for analysis of antibiotic resistome from genome and metagenome data: Kihyun Lee , Dae-Wi Kim , Chang-Jun Cha; J. Microbiol. 2021;59(3):270-280. Published online February 23, 2021; DOI: https://doi.org/10.1007/s12275-021-0652-4

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Abstract

Whole genome and metagenome sequencing are powerful approaches that enable comprehensive cataloging and profiling of antibiotic resistance genes at scales ranging from a single clinical isolate to ecosystems. Recent studies deal with genomic and metagenomic data sets at larger scales; therefore, designing computational workflows that provide high efficiency and accuracy is becoming more important. In this review, we summarize the computational workflows used in the research field of antibiotic resistome based on genome or metagenome sequencing. We introduce workflows, software tools, and data resources that have been successfully employed in this rapidly developing field. The workflow described in this review can be used to list the known antibiotic resistance genes from genomes and metagenomes, quantitatively profile them, and investigate the epidemiological and evolutionary contexts behind their emergence and transmission. We also discuss how novel antibiotic resistance genes can be discovered and how the association between the resistome and mobilome can be explored.

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Unraveling resistance mechanisms in combination therapy: A comprehensive review of recent advances and future directions
Nami Morales-Durán, Angel León-Buitimea, José R. Morones-Ramírez
Heliyon.2024; 10(6): e27984. CrossRef
Resistome Mapping in Foodborne Pathogens: Understanding Role in the Transmission Dynamics of Resistance Genes
Muneer Oladipupo Yaqub, Chinedu Eucharia Joseph, Aashika Jain, Lekshmi K. Edison
Applied Microbiology.2024; 4(4): 1476. CrossRef
Metagenomic assemblies tend to break around antibiotic resistance genes
Anna Abramova, Antti Karkman, Johan Bengtsson-Palme
BMC Genomics.2024;[Epub] CrossRef
Comprehensive genomic landscape of antibiotic resistance in Staphylococcus epidermidis
Do-Hoon Lee, Kihyun Lee, Yong-Seok Kim, Chang-Jun Cha, Jack A. Gilbert
mSystems.2024;[Epub] CrossRef
Web-Based Tools Validation for Antimicrobial Resistance Prediction: An Empirical Comparative Analysis
Sweta Padma Routray, Swayamprabha Sahoo, Debasish Swapnesh Kumar Nayak, Sejal Shah, Tripti Swarnkar
SN Computer Science.2024;[Epub] CrossRef
Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater
Nafi’u Abdulkadir, Joao Pedro Saraiva, Junya Zhang, Stefan Stolte, Osnat Gillor, Hauke Harms, Ulisses Rocha, Adriana E. Rosato
Microbiology Spectrum.2024;[Epub] CrossRef
Identification of Antibiotic Resistance in ESKAPE Pathogens through Plasmonic Nanosensors and Machine Learning
Ting Yu, Ying Fu, Jintao He, Jun Zhang, Yunlei Xianyu
ACS Nano.2023; 17(5): 4551. CrossRef
The challenges of defining the human nasopharyngeal resistome
Lucy O’Connor, Robert Heyderman
Trends in Microbiology.2023; 31(8): 816. CrossRef
Resistome profiling reveals transmission dynamics of antimicrobial resistance genes from poultry litter to soil and plant
Animesh Tripathi, Dinesh Kumar, Priyank Chavda, Dalip Singh Rathore, Ramesh Pandit, Damer Blake, Fiona Tomley, Madhvi Joshi, Chaitanya G. Joshi, Suresh Kumar Dubey
Environmental Pollution.2023; 327: 121517. CrossRef
Prioritization of Critical Factors for Surveillance of the Dissemination of Antibiotic Resistance in Pseudomonas aeruginosa: A Systematic Review
Jung Hun Lee, Nam-Hoon Kim, Kyung-Min Jang, Hyeonku Jin, Kyoungmin Shin, Byeong Chul Jeong, Dae-Wi Kim, Sang Hee Lee
International Journal of Molecular Sciences.2023; 24(20): 15209. CrossRef
Flavobacterium psychrotrophum sp. nov. and Flavobacterium panacagri sp. nov., Isolated from Freshwater and Soil
Yong-Seok Kim, Eun-Mi Hwang, Chang-Myeong Jeong, Chang-Jun Cha
Journal of Microbiology.2023; 61(10): 891. CrossRef
Antimicrobial Resistance Genes (ARGs), the Gut Microbiome, and Infant Nutrition
Rufus J. Theophilus, Diana Hazard Taft
Nutrients.2023; 15(14): 3177. CrossRef
Metagenomic Insight into Sulfonamide-Induced Variation in Antibiotic Resistome of Soil Associated with Taxonomy, Mobile Genetic Elements (MGEs), and Function
Mi Li, Xiaoyu Xiao, Zhangsong Jiang, Haihui Tang, Lingling Rong, Tiao Zhang, Taijia Li, Cui Hu, Ligui Wu, Xiaoming Zou
ACS Agricultural Science & Technology.2022; 2(1): 123. CrossRef
Gold nanoparticle-DNA aptamer-assisted delivery of antimicrobial peptide effectively inhibits Acinetobacter baumannii infection in mice
Jaeyeong Park, Eunkyoung Shin, Ji-Hyun Yeom, Younkyung Choi, Minju Joo, Minho Lee, Je Hyeong Kim, Jeehyeon Bae, Kangseok Lee
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Rucha Datar, Sylvain Orenga, Romain Pogorelcnik, Olivier Rochas, Patricia J Simner, Alex van Belkum
Clinical Chemistry.2021; 68(1): 91. CrossRef
Chromosomal integration of Tn5253 occurs downstream of a conserved 11-bp sequence of the rbgA gene in Streptococcus pneumoniae and in all the other known hosts of this integrative conjugative element (ICE)
Francesco Santoro, Valeria Fox, Alessandra Romeo, Elisa Lazzeri, Gianni Pozzi, Francesco Iannelli
Mobile DNA.2021;[Epub] CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
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Journal Articles

Expression of sexual genes in Aspergillus fumigatus homogeneous culture produced by vegetative mass mating: Joo-Yeon Lim , Hee-Moon Park; J. Microbiol. 2019;57(8):688-693. Published online May 11, 2019; DOI: https://doi.org/10.1007/s12275-019-9094-7

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Abstract

There are presently no studies on the genes for sexual development of Aspergillus fumigatus in situ using mating culture, primarily because of challenging experimental conditions that require a significantly long period of induction and produce developmentally heterogenous culture, harboring very few sexual organs. In order to overcome these challenges, we developed an efficient and convenient procedure called ‘vegetative mass mating (VeM)’ for study at a molecular level. The VeM method enabled production of a developmentally homogenous A. fumigatus culture, harboring many sexual organs in a plate within a short period of two weeks. Feasibility of the use of VeM for functional study of genes during A. fumigatus sexual development was evaluated by analyzing the transcription pattern of genes involved in pheromone signal transduction and regulation of sexual development. Here, we present for the first time, an in situ expression pattern of sexual genes during the mating process, induced by the VeM
method
, which will enable and promote the sexual development study of A. fumigatus at the molecular level.

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The Gβ-like Protein AfCpcB Affects Sexual Development, Response to Oxidative Stress and Phagocytosis by Alveolar Macrophages in Aspergillus fumigatus
Joo-Yeon Lim, Yeon-Ju Kim, Hee-Moon Park
Journal of Fungi.2022; 8(1): 56. CrossRef
The LAMMER Kinase, LkhA, Affects Aspergillus fumigatus Pathogenicity by Modulating Reproduction and Biosynthesis of Cell Wall PAMPs
Joo-Yeon Lim, Yeon Ju Kim, Seul Ah Woo, Jae Wan Jeong, Yu-Ri Lee, Cheol-Hee Kim, Hee-Moon Park
Frontiers in Cellular and Infection Microbiology.2021;[Epub] CrossRef
Global Sexual Fertility in the Opportunistic Pathogen Aspergillus fumigatus and Identification of New Supermater Strains
Sameira S. Swilaiman, Céline M. O’Gorman, Wenyue Du, Janyce A. Sugui, Joanne Del Buono, Matthias Brock, Kyung J. Kwon-Chung, George Szakacs, Paul S. Dyer
Journal of Fungi.2020; 6(4): 258. CrossRef

Identification of a novel phospholipase D gene and effects of carbon sources on its expression in Bacillus cereus ZY12: Yu Zhao , Yinfeng Xu , Fang Yu , Chunzhi Zhang; J. Microbiol. 2018;56(4):264-271. Published online April 2, 2018; DOI: https://doi.org/10.1007/s12275-018-7529-1

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Abstract

In the present study, a new strain, Bacillus cereus ZY12, producing phospholipase D (PLD) was identified. The expression of PLD in this strain was found to be induced by its substrate, phosphatidylcholine (PC), and completely silenced by other carbon sources, such as glucose, fructose, and maltose, which are generally used in microbial growth cultures, thus presenting a unique expression pattern different from other PLD-producing microorganisms. This study is the first to report on the ability of B. cereus to produce PLD, and successfully clone its PLD-coding gene and identify its function, extending the knowledge on PLD distribution and evolution in microorganisms.

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Structural insights into PA3488-mediated inactivation of Pseudomonas aeruginosa PldA
Xiaoyun Yang, Zongqiang Li, Liang Zhao, Zhun She, Zengqiang Gao, Sen-Fang Sui, Yuhui Dong, Yanhua Li
Nature Communications.2022;[Epub] CrossRef
Construction of a Super-Folder Fluorescent Protein-Guided Secretory Expression System for the Production of Phospholipase D in Bacillus subtilis
Haiyang Zhang, Xuehan Li, Qi Liu, Jianan Sun, Francesco Secundo, Xiangzhao Mao
Journal of Agricultural and Food Chemistry.2021; 69(24): 6842. CrossRef
Microbial phospholipase D: Identification, modification and application
Zhenxia Zhang, Ming Chen, Wei Xu, Wenli Zhang, Tao Zhang, Cuie Guang, Wanmeng Mu
Trends in Food Science & Technology.2020; 96: 145. CrossRef

Alteration in the ultrastructural morphology of mycelial hyphae and the dynamics of transcriptional activity of lytic enzyme genes during basidiomycete morphogenesis: Elena Vetchinkina , Maria Kupryashina , Vladimir Gorshkov , Marina Ageeva , Yuri Gogolev , Valentina Nikitina; J. Microbiol. 2017;55(4):280-288. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6320-z

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Abstract

The morphogenesis of macromycetes is a complex multilevel process resulting in a set of molecular-genetic, physiological- biochemical, and morphological-ultrastructural changes in the cells. When the xylotrophic basidiomycetes Lentinus edodes, Grifola frondosa, and Ganoderma lucidum were grown on wood waste as the substrate, the ultrastructural morphology of the mycelial hyphal cell walls differed considerably between mycelium and morphostructures. As the macromycetes passed from vegetative to generative development, the expression of the tyr1, tyr2, chi1, chi2, exg1, exg2, and exg3 genes was acti-vated. These genes encode enzymes such as tyrosinase, chi-tinase, and glucanase, which play essential roles in cell wall growth and morphogenesis.

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Flow modeling and structural characterization in fungal pellets
J. Sánchez-Vargas, F.J. Valdés-Parada, L. Peraza-Reyes, D. Lasseux, M.A. Trujillo-Roldán
Journal of Theoretical Biology.2024; 590: 111853. CrossRef
Transcriptome analysis provides insight into gamma irradiation delaying quality deterioration of postharvest Lentinula edodes during cold storage
Hong Gao, Shuang Ye, Yani Liu, Xiuzhi Fan, Chaomin Yin, Ying Liu, Jingyu Liu, Yu Qiao, Xueling Chen, Fen Yao, Defang Shi
Food Chemistry: Molecular Sciences.2023; 6: 100172. CrossRef
Improvement of natamycin production by controlling the morphology of Streptomyces gilvosporeus Z8 with microparticle talc in seed preculture
Chaoping Yue, Haitao Xu, Yingying Yu, Xin Yu, Min Yu, Chen Zhang, Qian You, Shaofan Xia, Zixian Ding, Hao Fu, Xin Zeng, Feng Li
Journal of Chemical Technology & Biotechnology.2021; 96(6): 1533. CrossRef
The molecular mechanism of stipe cell wall extension for mushroom stipe elongation growth
Cuicui Liu, Jingjing Bi, Liqin Kang, Jiangsheng Zhou, Xiao Liu, Zhonghua Liu, Sheng Yuan
Fungal Biology Reviews.2021; 35: 14. CrossRef
UDP-glucose pyrophosphorylase gene affects mycelia growth and polysaccharide synthesis of Grifola frondosa
Xin-Yi Zan, Xi-Hong Wu, Feng-Jie Cui, Hong-An Zhu, Wen-Jing Sun, Li-Hua Jiang, Ting-Lei Tao, Xiu Zhao
International Journal of Biological Macromolecules.2020; 161: 1161. CrossRef
Chitinases Play a Key Role in Stipe Cell Wall Extension in the Mushroom Coprinopsis cinerea
Jiangsheng Zhou, Liqin Kang, Cuicui Liu, Xin Niu, Xiaojun Wang, Hailong Liu, Wenming Zhang, Zhonghua Liu, Jean-Paul Latgé, Sheng Yuan, Marie A. Elliot
Applied and Environmental Microbiology.2019;[Epub] CrossRef
Comparative Study of Pleurotus ostreatus Mushroom Grown on Modified PAN Nanofiber Mats
Lilia Sabantina, Franziska Kinzel, Thomas Hauser, Astrid Többer, Michaela Klöcker, Christoph Döpke, Robin Böttjer, Daria Wehlage, Anke Rattenholl, Andrea Ehrmann
Nanomaterials.2019; 9(3): 475. CrossRef
Algorithm for Physiological Interpretation of Transcriptome Profiling Data for Non-Model Organisms
R. F. Gubaev, V. Y. Gorshkov, L. M. Gapa, N. E. Gogoleva, E. P. Vetchinkina, Y. V. Gogolev
Molecular Biology.2018; 52(4): 497. CrossRef
Improved mycelia and polysaccharide production of Grifola frondosa by controlling morphology with microparticle Talc
Ting-Lei Tao, Feng-Jie Cui, Xiao-Xiao Chen, Wen-Jing Sun, Da-Ming Huang, Jinsong Zhang, Yan Yang, Di Wu, Wei-Min Liu
Microbial Cell Factories.2018;[Epub] CrossRef

Mycobacterium tuberculosis gene expression at different stages of hypoxia-induced dormancy and upon resuscitation: Elisabetta Iona , Manuela Pardini , Alessandro Mustazzolu , Giovanni Piccaro , Roberto Nisini , Lanfranco Fattorini , Federico Giannoni; J. Microbiol. 2016;54(8):565-572. Published online August 2, 2016; DOI: https://doi.org/10.1007/s12275-016-6150-4

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Abstract

The physiology of dormant Mycobacterium tuberculosis was studied in detail by examining the gene expression of 51 genes using quantitative Reverse-Transcription Polymerase Chain Reaction. A forty-day period of dormancy in the Wayne culture model depicted four major transcription patterns. Some sigma factors and many metabolic genes were constant, whereas genes belonging to the dormancy regulon were activated on day 9. In particular, alpha-crystallin mRNA showed more than a 1,000-fold increase compared to replicating bacilli. Genes belonging to the enduring hypoxic response were up-regulated at day 16, notably, transcription factors sigma B and E. Early genes typical of log-phase bacilli, esat-6 and fbpB, were uniformly down-regulated during dormancy. Late stages of dormancy showed a drop in gene expression likely due to a lack of substrates in anaerobic respiration as demonstrated by the transcriptional activation observed following nitrates addition. Among genes involved in nitrate metabolism, narG was strongly up-regulated by nitrates addition. Dormant bacilli responded very rapidly when exposed to oxygen and fresh medium, showing a transcriptional activation of many genes, including resuscitation-promoting factors, within one hour. Our observations extend the current knowledge on dormant M. tuberculosis gene expression and its response to nutrients and to aerobic and anaerobic respiration.

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Regulatory role of Mycobacterium tuberculosis MtrA on dormancy/resuscitation revealed by a novel target gene-mining strategy
Xiang Fu, Xiaoyu Wan, Aadil Ahmed Memon, Xiao-Yong Fan, Qiuhong Sun, Haifeng Chen, Yufeng Yao, Zixin Deng, Jian Ma, Wei Ma
Frontiers in Microbiology.2024;[Epub] CrossRef
Adaptation of the Mycobacterium tuberculosis transcriptome to biofilm growth
Madison A. Youngblom, Tracy M. Smith, Holly J. Murray, Caitlin S. Pepperell, Christopher M. Sassetti
PLOS Pathogens.2024; 20(4): e1012124. CrossRef
Identification of Rv1133c (MetE) as a marker of Mycobacterium tuberculosis replication and as a highly immunogenic antigen with potential immunodiagnostic power
Angelo Iacobino, Raffaela Teloni, Carmine Mancone, Francesco Facchiano, Alessandra Di Giamberardino, Cinzia Senatore, Antonio Di Virgilio, Alessio Lanni, Federico Giannoni, Roberto Nisini, Sabrina Mariotti
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Liangfei Niu, Hao Wang, Geyang Luo, Jing Zhou, Zhidong Hu, Bo Yan
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Youngeun Kim, Mary Beth Lewis, Jihyun Hwang, Zheyu Wang, Rohit Gupta, Yuxiong Liu, Tuhina Gupta, James P. Barber, Srikanth Singamaneni, Fred Quinn, Mark R. Prausnitz
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Review

MINIREVIEW] Overview: Replication of Porcine Reproductive and Respiratory Syndrome Virus: Sang-Im Yun , Young-Min Lee; J. Microbiol. 2013;51(6):711-723. Published online December 19, 2013; DOI: https://doi.org/10.1007/s12275-013-3431-z

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Abstract

Porcine reproductive and respiratory syndrome virus (PRRSV), an arterivirus that causes significant losses in the pig industry, is one of the most important animal pathogens of global significance. Since the discovery of the virus, significant progress has been made in understanding its epidemiology and transmission, but no adequate control measures are yet available to eliminate infection with this pathogen. The genome replication of PRRSV is required to reproduce, within a few hours of infection, the millions of progeny virions that establish, disseminate, and maintain infection. Replication of the viral RNA genome is a multistep process involving a replication complex that is formed not only from components of viral and cellular origin but also from the viral genomic RNA template; this replication complex is embedded within particular virus-induced membrane vesicles. PRRSV RNA replication is directed by at least 14 replicase proteins that have both common enzymatic activities, including viral RNA polymerase, and also unusual and poorly understood RNAprocessing functions. In this review, we summarize our current understanding of PRRSV replication, which is important for developing a successful strategy for the prevention and control of this pathogen.

Citations

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

Detailed Modes of Action and Biochemical Characterization of endo-Arabinanase from Bacillus licheniformis DSM13: Jung-Mi Park , Myoung-Uoon Jang , Jung-Hyun Kang , Min-Jeong Kim , So-Won Lee , Yeong Bok Song , Chul-Soo Shin , Nam Soo Han , Tae-Jip Kim; J. Microbiol. 2012;50(6):1041-1046. Published online December 30, 2012; DOI: https://doi.org/10.1007/s12275-012-2489-3

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Abstract: An endo-arabinanase (BLABNase) gene from Bacillus licheniformis DSM13 was cloned and expressed in Escherichia coli, and the biochemical properties of its encoded enzyme were characterized. The BLABNase gene consists of a single open reading frame of 987 nucleotides that encodes 328 amino acids with a predicted molecular mass of about 36 kDa. BLABNase exhibited the highest activity against debranched α-(1,5)-arabinan in 50 mM sodium acetate buffer (pH 6.0) at 55°C. Enzymatic characterization revealed that BLABNase hydrolyzes debranched or linear arabinans with a much higher activity than branched arabinan from sugar beet. Enzymatic hydrolysis pattern analyses demonstrated BLABNase to be a typical endo-(1,5)-α-L-arabinanase (EC 3.2.1.99) that randomly cleaves the internal α-(1,5)-linked L-arabinofuranosyl residues of a branchless arabinan backbone to release arabinotriose mainly, although a small amount of arabino-oligosaccharide intermediates is also liberated. Our results indicated that BLABNase acts preferentially along with the oligosaccharides longer than arabinopentaose, thus enabling the enzymatic production of various arabinooligosaccharides.

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

Transcriptional Control of Genes Involved in Yeast Phospholipid Biosynthesis: Roshini Wimalarathna , Chen-Han Tsai , Chang-Hui Shen; J. Microbiol. 2011;49(2):265-273. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-1130-1

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Abstract: Phospholipid biosynthetic genes encode enzymes responsible for phospholipid biosynthesis. They are coordinately regulated by the availability of phospholipid precursors through the inositol-sensitive upstream activating sequence (UASINO). However, not all phospholipid genes are UASINO-containing genes and not all UASINO-containing genes have the same response to the phospholipid precursors. Therefore, the transcriptional regulation of phospholipid genes in response to the availability of phospholipid precursors is still unclear. Here, 22 out of 47 phospholipid biosynthetic genes were identified as UASINO-containing genes, including EKI1, EPT1, INM1, IPK2, KCS1, PAH1, and PIK1 which have never been reported before. We also showed, using qRTPCR technique, that 12 UASINO-containing genes are down-regulated by 100 μM inositol in the wild type cells and up-regulated by 100 μM inositol in the ino2Δ cells. Therefore, it is possible that these genes are transcriptionally regulated by the UASINO through the negative response of Ino2p to inositol. One other UASINO-containing gene might be regulated by the positive response of Ino2p to 100 μM inositol. Surprisingly, we found 9 UASINO-containing genes are not dependent on the response of Ino2p to 100 μM inositol, indicating that they may be regulated by other pathway. Furthermore, we identified 9 and 3 non-UASINO-containing genes that are possibly regulated by the negative and positive response of Ino2p to 100 μM inositol, respectively. Therefore, these observations provide insight into the understanding of the co-regulated phospholipid biosynthetic genes expression.

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

Characterization, Gene Cloning, and Heterologous Expression of β-Mannanase from a Thermophilic Bacillus subtilis: Pijug Summpunn , Suttidarak Chaijan , Duangnate Isarangkul , Suthep Wiyakrutta , Vithaya Meevootisom; J. Microbiol. 2011;49(1):86-93. Published online March 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0357-1

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Abstract: Bacillus subtilis BCC41051 producing a thermostable β-mannanase was isolated from soybean meal-enriched soil and was unexpectedly found to be thermophilic in nature. The extracellular β-mannanase (ManA) produced was hydrophilic, as it was not precipitated even with ammonium sulfate at 80% saturation. The estimated molecular weight of ManA was 38.0 kDa by SDS-PAGE with a pI value of 5.3. Optimal pH and temperature for mannan-hydrolyzing activity was 7.0 and 60°C, respectively. The enzyme was stable over a pH range of 5.0-11.5, and at temperatures of up to 60°C for 30 min, with more than 80% of its activity retained. ManA was strongly inhibited by Hg2+ (1 mM), but was sensitive to other divalent ions to a lesser degree. The gene of ManA encoded a protein of 362 amino acid residues, with the first 26 residues identified as a signal peptide. High expression of recombinant ManA was achieved in both Escherichia coli BL21 (DE3) (415.18 U/ml) and B. megaterium UNcat (359 U/ml).

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