Journal of Microbiology

Journal Articles

Characterization of Marinilongibacter aquaticus gen. nov., sp. nov., a unique marine bacterium harboring four CRISPR-Cas systems in the phylum Bacteroidota: Dao-Feng Zhang , Yu-Fang Yao , Hua-Peng Xue , Zi-Yue Fu , Xiao-Mei Zhang , Zongze Shao; J. Microbiol. 2022;60(9):905-915. Published online August 1, 2022; DOI: https://doi.org/10.1007/s12275-022-2102-3

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A novel bacterium, designated YYF0007T, was isolated from an agar-degrading co-culture. The strain was found harboring four CRISPR-Cas systems of two classes in the chromosome and subsequently subjected to a study on polyphasic taxonomy. Pairwise analyses of the 16S rRNA gene sequences indicated that strain YYF0007T had highest 16S rRNA gene sequence similarity (92.2%) to Jiulongibacter sediminis JN- 14-9T. The phylogenomic trees based on the 16S rRNA gene and 269 single-copy orthologous gene clusters (OCs) indicated that strain YYF0007T should be recognized as a novel genus of the family Spirosomaceae. The cells were Gramstain- negative, nonmotile, strictly aerobic, and straight long rods with no flagellum. Optimum growth occurred at 28°C and pH 7.0 with the presence of NaCl concentration 1.0–3.0% (w/v). The strain showed oxidase and catalase activities. The major fatty acids were C16:1ω5c, iso-C15:0 and summed feature 3 (C16:1 ω7c and/or C16:1 ω6c). The predominant isoprenoid quinone was MK-7. The complete genome size was 4.64 Mb with a DNA G + C content of 44.4%. Further typing of CRISPR-Cas systems in the family Spirosomaceae and the phylum Bacteroidota indicated that it was remarkable for strain YYF0007T featured by such a set of CRISPR-Cas systems. This trait highlights the applications of strain YYF- 0007T in studies on the evolutionary dynamics and bacterial autoimmunity of CRISPR-Cas system as a potential model. The name Marinilongibacter aquaticus gen. nov., sp. nov. is proposed, and the type strain is YYF0007T (= MCCC 1K06017T = GDMCC 1.2428T = JCM 34683T).

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Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects
Jiashun Li, Shuaishuai Wu, Kaidian Zhang, Xueqiong Sun, Wenwen Lin, Cong Wang, Senjie Lin
Microorganisms.2024; 12(1): 118. CrossRef
Unraveling the mechanisms behind sodium persulphate-induced changes in petroleum-contaminated aquifers’ biogeochemical parameters and microbial communities
Yuqi Qi, Jun Zeng, Junshi Tao, Rentao Liu, Renchuan Fu, Chao Yan, Xiao Liu, Na Liu, Yanru Hao
Chemosphere.2024; 351: 141174. CrossRef
Arcicella gelida sp. nov. and Arcicella lustrica sp. nov., isolated from streams in China and re-examining the taxonomic status of all the genera within the families Spirosomataceae and Cytophagaceae
Huibin Lu, Li Chen, Linpei Huang
International Journal of Systematic and Evolutionary Microbiology .2024;[Epub] CrossRef
Thalassospira aquimaris sp. nov. and Winogradskyella marincola sp. nov. two marine bacteria isolated from an agar-degrading co-culture
Zi-Yue Fu, Dao-Feng Zhang, Meng-Han Huang, Hong-Chuan Wang, Xiao-Ye Chen, Yu-Fang Yao, Yang Yuan, Wen-Jun Li
Antonie van Leeuwenhoek.2024;[Epub] CrossRef
Validation List no. 209. Valid publication of new names and new combinations effectively published outside the IJSEM
Aharon Oren, Markus Göker
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Telluribacter roseus sp. nov., Isolated from the Kumtag Desert Soil
Chu-Ying Feng, Jia-Rui Han, Chun-Yan Lu, Li Gu, Shuai Li, Wen-Hui Lian, Lei Dong, Wen-Jun Li
Current Microbiology.2023;[Epub] CrossRef

Gut microbiota metabolic characteristics in coronary artery disease patients with hyperhomocysteine: Ran Tian , Hong-Hong Liu , Si-Qin Feng , Yi-Fei Wang , Yi-Yang Wang , Yu-Xiong Chen , Hui Wang , Shu-Yang Zhang; J. Microbiol. 2022;60(4):419-428. Published online March 4, 2022; DOI: https://doi.org/10.1007/s12275-022-1451-2

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Abstract

Hyperhomocysteine (HHcy) is known as a risk factor for coronary artery disease (CAD). Despite the knowledge that gut microbiota related metabolism pathway shares metabolites with that of Hcy, little has been shown concerning the association between HHcy and gut microbiota. To explore their relationship in the context of CAD, 105 patients and 14 healthy controls were recruited from one single medical center located in Beijing, China. Their serum and fecal samples were collected, with multi-omics analyses performed via LC/MS/ MS and 16S rRNA gene V3-V4 region sequencing, respectively. Participants from the prospective cohort were divided into CAD, CAD & HHcy and healthy controls (HC) groups based on the diagnosis and serum Hcy concentration. The
results
revealed significant different metabolic signatures between CAD and CAD & HHcy groups. CAD patients with HHcy suffered a heavier atherosclerotic burden compared to CAD patients, and the difference was closely associated to betaine-homocysteine S-methyltransferase (BHMT)-related metabolites and trimethylamine N-oxide (TMAO)-related metabolites. Dimethylglycine (DMG) exhibited a strong positive correlation with serum total Hcy (tHcy), and TMAO and trimethylysine (TML) were associated with heavier atherosclerotic burden. Multiple other metabolites were also identified to be related to distinct cardiovascular risk factors. Additionally, Clostridium cluster IV and Butyricimonas were enriched in CAD patients with elevated tHcy. Our study suggested that CAD patients with elevated tHcy were correlated with higher atherosclerotic burden, and the impaired Hcy metabolism and cardiovascular risk were closely associated with BHMT-related metabolites, TMAO-related metabolites and impaired gut microbiota homeostasis.

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Homocysteine, Nutrition, and Gut Microbiota: A Comprehensive Review of Current Evidence and Insights
Deborah Agostini, Alessia Bartolacci, Rossella Rotondo, Maria Francesca De Pandis, Michela Battistelli, Matteo Micucci, Lucia Potenza, Emanuela Polidori, Fabio Ferrini, Davide Sisti, Francesco Pegreffi, Valerio Pazienza, Edy Virgili, Vilberto Stocchi, Sab
Nutrients.2025; 17(8): 1325. CrossRef
Serum homocysteine showed potential association with cognition and abnormal gut microbiome in major depressive disorder
Chen-Chen Xu, Wen-Xuan Zhao, Yu Sheng, Ya-Jun Yun, Ting Ma, Ning Fan, Jia-Qi Song, Jun Wang, Qi Zhang
World Journal of Psychiatry.2025;[Epub] CrossRef
Unravelling the Gut Microbiome Role in Cardiovascular Disease: A Systematic Review and a Meta-Analysis
Diana Martins, Cláudia Silva, António Carlos Ferreira, Sara Dourado, Ana Albuquerque, Francisca Saraiva, Ana Beatriz Batista, Pedro Castro, Adelino Leite-Moreira, António S. Barros, Isabel M. Miranda
Biomolecules.2024; 14(6): 731. CrossRef
Gut Commensal Bacteroides thetaiotaomicron Promote Atherothrombosis via Regulating L-Tryptophan Metabolism
Honghong Liu, Siqin Feng, Muyun Tang, Ran Tian, Shuyang Zhang
Reviews in Cardiovascular Medicine.2024;[Epub] CrossRef
Relation between homocysteine-to-adropin ratio and severity of coronary artery disease
Ola Hassan Abd Elaziz, Bassem Mohamed Abdel Hady, Ghada Mohamed S Ahmad, Safaa Abo Alfadl Mohamed, Abeer Ahmed Elmalah, Inass Hassan Ahmad, Entesar O Elsaghier, Marwa FM Elsayed, Hala Naguib Mohamed, Marwa Khairy Abd Elwahab, Ahmed Salah
Electronic Journal of General Medicine.2024; 21(1): em556. CrossRef
Association of serum homocysteine levels with intestinal flora and cognitive function in schizophrenia
Hehua Li, Hanqiu Li, Zhimin Zhu, Xiang Xiong, Yuanyuan Huang, Yangdong Feng, Zezhi Li, Kai Wu, Fengchun Wu
Journal of Psychiatric Research.2023; 159: 258. CrossRef
Association analysis of gut microbiota-metabolites-neuroendocrine changes in male rats acute exposure to simulated altitude of 5500 m
Jianan Wang, Shiying Liu, Yalei Xie, Chengli Xu
Scientific Reports.2023;[Epub] CrossRef

Molecular characterization of the Saccharomycopsis fibuligera ATF genes, encoding alcohol acetyltransferase for volatile acetate ester formation: Hye Yun Moon , Hyeon Jin Kim , Ki Seung Kim , Su Jin Yoo , Dong Wook Lee , Hee Je Shin , Jeong Ah Seo , Hyun Ah Kang; J. Microbiol. 2021;59(6):598-608. Published online May 29, 2021; DOI: https://doi.org/10.1007/s12275-021-1159-8

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Abstract

Aroma ester components produced by fermenting yeast cells via alcohol acetyltransferase (AATase)-catalyzed intracellular reactions are responsible for the fruity character of fermented alcoholic beverages, such as beer and wine. Acetate esters are reportedly produced at relatively high concentrations by non-Saccharomyces species. Here, we identified 12 ATF orthologues (SfATFs) encoding putative AATases, in the diploid genome of Saccharomycopsis fibuligera KJJ81, an isolate from wheat-based Nuruk in Korea. The identified SfATF proteins (SfAtfp) display low sequence identities with S. cerevisiae Atf1p (between 13.3 and 27.0%). All SfAtfp identified, except SfAtf(A)4p and SfAtf(B)4p, contained the activation domain (HXXXD) conserved in other Atf proteins. Culture supernatant analysis using headspace gas chromatography mass spectrometry confirmed that the recombinant S. cerevisiae strains expressing SfAtf(A)2p, SfAtf(B)2p, and SfAtf(B)6p produced high levels of isoamyl and phenethyl acetates. The volatile aroma profiles generated by the SfAtf proteins were distinctive from that of S. cerevisiae Atf1p, implying difference in the substrate preference. Cellular localization analysis using GFP fusion revealed the localization of SfAtf proteins proximal to the lipid particles, consistent with the presence of amphipathic helices at their N- and C-termini. This is the first report that systematically characterizes the S. fibuligera ATF genes encoding functional AATases responsible for acetate ester formation using higher alcohols as substrate, demonstrating their biotechnological potential for volatile ester production.

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Investigating the role of primary fungi in Huangjiu fermentation: Insights from flavor orientation and synthetic microbiomes
Qi Peng, Huihui Zhou, Huajun Zheng, Guangfa Xie
Food Microbiology.2025; 129: 104765. CrossRef
Genome-Wide Identification and Biochemical Characterization of Alcohol Acyltransferases for Aroma Generation in Wickerhamomyces subpelliculosus Isolates from Fermented Food
Su Jin Yoo, Hyeon Jin Kim, Hye Yun Moon, Min-Seung Jeon, Yong Uk Cho, Che Ok Jeon, Seong-Il Eyun, Hyun Ah Kang
Journal of Agricultural and Food Chemistry.2024; 72(50): 28194. CrossRef
Characterization and phylogenetic analysis of the complete mitochondrial genome of Saccharomycopsis fibuligera (lindner) Klocker 1907 (saccharomycetales: saccharomycopsidaceae)
Yue Deng, Guangjiu Chen, Xuedong Bao, Jie He
Mitochondrial DNA Part B.2024; 9(6): 743. CrossRef
Optimization of High-Density Fermentation Conditions for Saccharomycopsis fibuligera Y1402 through Response Surface Analysis
Hongyang Yuan, Qi Sun, Lanshuang Wang, Zhilei Fu, Tianze Zhou, Jinghao Ma, Xiaoyan Liu, Guangsen Fan, Chao Teng
Foods.2024; 13(10): 1546. CrossRef
Genomic and functional features of yeast species in Korean traditional fermented alcoholic beverage and soybean products
Da Min Jeong, Hyeon Jin Kim, Min-Seung Jeon, Su Jin Yoo, Hye Yun Moon, Eun-joo Jeon, Che Ok Jeon, Seong-il Eyun, Hyun Ah Kang
FEMS Yeast Research.2023;[Epub] CrossRef
Beer fermentation performance and sugar uptake of Saccharomycopsis fibuligera–A novel option for low-alcohol beer
Yvonne Methner, Frederico Magalhães, Luis Raihofer, Martin Zarnkow, Fritz Jacob, Mathias Hutzler
Frontiers in Microbiology.2022;[Epub] CrossRef
Comparative analysis of aroma components and quality of Geotrichum candidum after space mutation breeding
Junjie Chen, Qianying Li, Jie Wang, Weizhe Chen, Qikai Zheng, Qingping Zhong, Xiang Fang, Zhenlin Liao
Frontiers in Microbiology.2022;[Epub] CrossRef

Mst1/2-ALK promotes NLRP3 inflammasome activation and cell apoptosis during Listeria monocytogenes infection: Aijiao Gao , Huixin Tang , Qian Zhang , Ruiqing Liu , Lin Wang , Yashan Liu , Zhi Qi , Yanna Shen; J. Microbiol. 2021;59(7):681-692. Published online April 20, 2021; DOI: https://doi.org/10.1007/s12275-021-0638-2

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Abstract

Listeria monocytogenes (L. monocytogenes) is a Gram-positive intracellular foodborne pathogen that causes severe diseases, such as meningitis and sepsis. The NLR family pyrin domain-containing 3 (NLRP3) inflammasome has been reported to participate in host defense against pathogen infection. However, the exact molecular mechanisms underlying NLRP3 inflammasome activation remain to be fully elucidated. In the present study, the roles of mammalian Ste20- like kinases 1/2 (Mst1/2) and Anaplastic Lymphoma Kinase (ALK) in the activation of the NLRP3 inflammasome induced by L. monocytogenes infection were investigated. The expression levels of Mst1/2, phospho (p)-ALK, p-JNK, Nek7, and NLRP3 downstream molecules including activated caspase- 1 (p20) and mature interleukin (IL)-1β (p17), were upregulated in L. monocytogenes-infected macrophages. The ALK inhibitor significantly decreased the expression of p-JNK, Nek7, and NLRP3 downstream molecules in macrophages infected with L. monocytogenes. Furthermore, the Mst1/2 inhibitor markedly inhibited the L. monocytogenes-induced activation of ALK, subsequently downregulating the expression of p-JNK, Nek7, and NLRP3 downstream molecules. Therefore, our study demonstrated that Mst1/2-ALK mediated the activation of the NLRP3 inflammasome by promoting the interaction between Nek7 and NLRP3 via JNK during L. monocytogenes infection, which subsequently increased the maturation and release of proinflammatory cytokine to resist pathogen infection. Moreover, Listeriolysin O played a key role in the process. In addition, we also found that the L. monocytogenes-induced apoptosis of J774A.1 cells was reduced by the Mst1/2 or ALK inhibitor. The present study reported, for the first time, that the Mst1/2-ALK-JNK-NLRP3 signaling pathway plays a vital proinflammatory role during L. monocytogenes infection.

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PDE4B promotes JNK/NLRP3 activation in the nucleus pulposus and mediates intervertebral disc degeneration
Weixing Xu, Rana Dhar, Kaiyue Li, Danyang Zheng, Minxin He, Weiguo Ding, Long Xin, Bin Xu, Yuqing He, Qi Peng, Huifang Tang
Scientific Reports.2025;[Epub] CrossRef
IL-18 biology in severe asthma
Sarita Thawanaphong, Aswathi Nair, Emily Volfson, Parameswaran Nair, Manali Mukherjee
Frontiers in Medicine.2024;[Epub] CrossRef
TRAF6-TAK1-IKKβ pathway mediates TLR2 agonists activating “one-step” NLRP3 inflammasome in human monocytes
Mengdan Chen, Shi Yu, Yuhui Gao, Jiaxun Li, Xun Wang, Bin Wei, Guangxun Meng
Cytokine.2023; 169: 156302. CrossRef
ALK-JNK signaling promotes NLRP3 inflammasome activation and pyroptosis via NEK7 during Streptococcus pneumoniae infection
Xia Wang, Yan Zhao, Dan Wang, Chang Liu, Zhi Qi, Huixin Tang, Yashan Liu, Shiqi Zhang, Yali Cui, Yingying Li, Ruiqing Liu, Yanna Shen
Molecular Immunology.2023; 157: 78. CrossRef
Inflammasome activation by Gram-positive bacteria: Mechanisms of activation and regulation
A. Marijke Keestra-Gounder, Prescilla Emy Nagao
Frontiers in Immunology.2023;[Epub] CrossRef
Toxoplasma gondii profilin induces NLRP3 activation and IL-1β production/secretion in THP-1 cells
Hossein Pazoki, Hamed Mirjalali, Maryam Niyyati, Seyed Javad Seyed Tabaei, Nariman Mosaffa, Shabnam Shahrokh, Hamid Asadzadeh Ahdaei, Andreas Kupz, Mohammad Reza Zali
Microbial Pathogenesis.2023; 180: 106120. CrossRef
The Critical Role of Potassium Efflux and Nek7 in Pasteurella multocida-Induced NLRP3 Inflammasome Activation
Yu Wang, Zheng Zeng, Jinrong Ran, Lianci Peng, Xingping Wu, Chao Ye, Chunxia Dong, Yuanyi Peng, Rendong Fang
Frontiers in Microbiology.2022;[Epub] CrossRef
Coral and it's symbionts responses to the typical global marine pollutant BaP by 4D-Proteomics approach
Yuebin Pei, Shuai Chen, Yuting Zhang, Volovych Olga, Yuanchao Li, Xiaoping Diao, Hailong Zhou
Environmental Pollution.2022; 307: 119440. CrossRef
NEK7-Mediated Activation of NLRP3 Inflammasome Is Coordinated by Potassium Efflux/Syk/JNK Signaling During Staphylococcus aureus Infection
Ruiqing Liu, Yashan Liu, Chang Liu, Aijiao Gao, Lin Wang, Huixin Tang, Qiang Wu, Xia Wang, Derun Tian, Zhi Qi, Yanna Shen
Frontiers in Immunology.2021;[Epub] CrossRef

Review

[MINIREVIEW]Regulation of gene expression by protein lysine acetylation in Salmonella: Hyojeong Koo , Shinae Park , Min-Kyu Kwak , Jung-Shin Lee; J. Microbiol. 2020;58(12):979-987. Published online November 17, 2020; DOI: https://doi.org/10.1007/s12275-020-0483-8

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Abstract

Protein lysine acetylation influences many physiological functions, such as gene regulation, metabolism, and disease in eukaryotes. Although little is known about the role of lysine acetylation in bacteria, several reports have proposed its importance in various cellular processes. Here, we discussed the function of the protein lysine acetylation and the post-translational modifications (PTMs) of histone-like proteins in bacteria focusing on Salmonella pathogenicity. The protein lysine residue in Salmonella is acetylated by the Pat-mediated enzymatic pathway or by the acetyl phosphate-mediated non-enzymatic pathway. In Salmonella, the acetylation of lysine 102 and lysine 201 on PhoP inhibits its protein activity and DNAbinding, respectively. Lysine acetylation of the transcriptional regulator, HilD, also inhibits pathogenic gene expression. Moreover, it has been reported that the protein acetylation patterns significantly differ in the drug-resistant and -sensitive Salmonella strains. In addition, nucleoid-associated proteins such as histone-like nucleoid structuring protein (H-NS) are critical for the gene silencing in bacteria, and PTMs in H-NS also affect the gene expression. In this review, we suggest that protein lysine acetylation and the post-translational modifications of H-NS are important factors in understanding the regulation of gene expression responsible for pathogenicity in Salmonella.

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Global Insights into the Lysine Acetylome Reveal the Role of Lysine Acetylation in the Adaptation of Bacillus altitudinis to Salt Stress
Xujian Li, Shanshan Dai, Shanshan Sun, Dongying Zhao, Hui Li, Junyi Zhang, Jie Ma, Binghai Du, Yanqin Ding
Journal of Proteome Research.2025; 24(1): 210. CrossRef
The concentration of medium-chain fatty acids in breast milk is influenced by maternal diet and associated with gut microbiota in infants
Menglu Xi, Ignatius Man-Yau Szeto, Sufang Duan, Ting Li, Yalu Yan, Xia Ma, Ting Sun, Weilian Hung, Celi Yang, Yonghua Zhang, Ai Zhao
Journal of Functional Foods.2025; 128: 106782. CrossRef
Reversible acetylation of ribosomal protein S1 serves as a smart switch for Salmonella to rapidly adapt to host stress
Yi-Lin Shen, Tian-Xian Liu, Lei Xu, Bang-Ce Ye, Ying Zhou
Nucleic Acids Research.2025;[Epub] CrossRef
Bacterial protein acetylation: mechanisms, functions, and methods for study
Jocelin Rizo, Sergio Encarnación-Guevara
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
Acetyl-proteome profiling revealed the role of lysine acetylation in erythromycin resistance of Staphylococcus aureus
Miao Feng, Xiaoyu Yi, Yanling Feng, Feng He, Zonghui Xiao, Hailan Yao
Heliyon.2024; 10(15): e35326. CrossRef
Short-chain fatty acids in breast milk and their relationship with the infant gut microbiota
Menglu Xi, Yalu Yan, Sufang Duan, Ting Li, Ignatius Man-Yau Szeto, Ai Zhao
Frontiers in Microbiology.2024;[Epub] CrossRef
Acetylomics reveals an extensive acetylation diversity within Pseudomonas aeruginosa
Nand Broeckaert, Hannelore Longin, Hanne Hendrix, Jeroen De Smet, Mirita Franz-Wachtel, Boris Maček, Vera van Noort, Rob Lavigne
microLife.2024;[Epub] CrossRef
Lysine acetylation regulates the AT-rich DNA possession ability of H-NS
Yabo Liu, Mengqing Zhou, Yifan Bu, Liang Qin, Yuanxing Zhang, Shuai Shao, Qiyao Wang
Nucleic Acids Research.2024; 52(4): 1645. CrossRef
Acetylation of K188 and K192 inhibits the DNA-binding ability of NarL to regulate Salmonella virulence
Liu-Qing Zhang, Yi-Lin Shen, Bang-Ce Ye, Ying Zhou, Christopher A. Elkins
Applied and Environmental Microbiology.2023;[Epub] CrossRef
Acetylome and Succinylome Profiling of Edwardsiella tarda Reveals Key Roles of Both Lysine Acylations in Bacterial Antibiotic Resistance
Yuying Fu, Lishan Zhang, Huanhuan Song, Junyan Liao, Li Lin, Wenjia Jiang, Xiaoyun Wu, Guibin Wang
Antibiotics.2022; 11(7): 841. CrossRef
Pat- and Pta-mediated protein acetylation is required for horizontally-acquired virulence gene expression in Salmonella Typhimurium
Hyojeong Koo, Eunna Choi, Shinae Park, Eun-Jin Lee, Jung-Shin Lee
Journal of Microbiology.2022; 60(8): 823. CrossRef
Acetylation of CspC Controls the Las Quorum-Sensing System through Translational Regulation of rsaL in Pseudomonas aeruginosa
Shouyi Li, Xuetao Gong, Liwen Yin, Xiaolei Pan, Yongxin Jin, Fang Bai, Zhihui Cheng, Un-Hwan Ha, Weihui Wu, Pierre Cornelis, Gerald B. Pier
mBio.2022;[Epub] CrossRef
Trans-acting regulators of ribonuclease activity
Jaejin Lee, Minho Lee, Kangseok Lee
Journal of Microbiology.2021; 59(4): 341. CrossRef
Acetylation of the CspA family protein CspC controls the type III secretion system through translational regulation ofexsAinPseudomonas aeruginosa
Shouyi Li, Yuding Weng, Xiaoxiao Li, Zhuo Yue, Zhouyi Chai, Xinxin Zhang, Xuetao Gong, Xiaolei Pan, Yongxin Jin, Fang Bai, Zhihui Cheng, Weihui Wu
Nucleic Acids Research.2021; 49(12): 6756. CrossRef
Transcriptional Regulation of the Multiple Resistance Mechanisms in Salmonella—A Review
Michał Wójcicki, Olga Świder, Kamila J. Daniluk, Paulina Średnicka, Monika Akimowicz, Marek Ł. Roszko, Barbara Sokołowska, Edyta Juszczuk-Kubiak
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Journal Articles

Omp16, a conserved peptidoglycan-associated lipoprotein, is involved in Brucella virulence in vitro: Feijie Zhi , Dong Zhou , Junmei Li , Lulu Tian , Guangdong Zhang , Yaping Jin , Aihua Wang; J. Microbiol. 2020;58(9):793-804. Published online September 1, 2020; DOI: https://doi.org/10.1007/s12275-020-0144-y

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Abstract

Brucella, the bacterial agent of common zoonotic brucellosis, primarily infects specific animal species. The Brucella outer membrane proteins (Omps) are particularly attractive for developing vaccine and improving diagnostic tests and are associated with the virulence of smooth Brucella strains. Omp16 is a homologue to peptidoglycan-associated lipoproteins (Pals), and an omp16 mutant has not been generated in any Brucella strain until now. Very little is known about the functions and pathogenic mechanisms of Omp16 in Brucella. Here, we confirmed that Omp16 has a conserved Pal domain and is highly conserved in Brucella. We attempted to delete omp16 in Brucella suis vaccine strain 2 (B. suis S2) without success, which shows that Omp16 is vital for Brucella survival. We acquired a B. suis S2 Omp16 mutant via conditional complementation. Omp16 deficiency impaired Brucella outer membrane integrity and activity in vitro. Moreover, inactivation of Omp16 decreased bacterial intracellular survival in macrophage RAW 264.7 cells. B. suis S2 and its derivatives induced marked expression of IL-1β, IL-6, and TNF-α mRNA in Raw 264.7 cells. Whereas inactivation of Omp16 in Brucella enhanced IL-1β and IL-6 expression in Raw 264.7 cells. Altogether, these findings show that the Brucella Omp16 mutant was obtained via conditional complementation and confirmed that Omp16 can maintain outer membrane integrity and be involved in bacterial virulence in Brucella in vitro and in vivo. These results will be important in uncovering the pathogenic mechanisms of Brucella.

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Neurobrucellosis (Brucella ceti) in striped dolphins (Stenella coeruleoalba): Immunohistochemical studies on immune response and neuroinflammation
Agustín Rebollada-Merino, Federica Giorda, Martí Pumarola, Laura Martino, Alberto Gomez-Buendia, Umberto Romani-Cremaschi, Cristina Casalone, Virginia Mattioda, Fabio Di Nocera, Giuseppe Lucifora, Antonio Petrella, Lucas Domínguez, Mariano Domingo, Carla
Veterinary Pathology.2025; 62(2): 226. CrossRef
Enhancing host defense against Brucella: The immune effect exerted by anti-OMP16 monoclonal antibody
Yunyi Zhai, Hui Wang, Kaihui Sun, Ye Yuan, Shurong Yin, Jiaoyang Fang, Weifang Zheng, Gaowa Wudong, Xiaofang Liu, Yuanhao Yang, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
International Immunopharmacology.2025; 148: 114142. CrossRef
Brucella mediates autophagy, inflammation, and apoptosis to escape host killing
Yaqiong Qin, Gengxu Zhou, Fengyuan Jiao, Chuan Cheng, Chi Meng, Lingjie Wang, Shengping Wu, Cailiang Fan, Jixiang Li, Bo Zhou, Yuefeng Chu, Hanwei Jiao
Frontiers in Cellular and Infection Microbiology.2024;[Epub] CrossRef
A Thermosensitive and Degradable Chitin-Based Hydrogel as a Brucellosis Vaccine Adjuvant
Ruibao Ju, Yanjing Lu, Zhiwen Jiang, Jinhua Chi, Shuo Wang, Wanshun Liu, Yanbo Yin, Baoqin Han
Polymers.2024; 16(19): 2815. CrossRef
The (p)ppGpp synthetase Rsh promotes rifampicin tolerant persister cell formation in Brucella abortus by regulating the type II toxin-antitoxin module mbcTA
Xiaofang Liu, Pingping Wang, Ningqiu Yuan, Yunyi Zhai, Yuanhao Yang, Mingyue Hao, Mingxing Zhang, Dong Zhou, Wei Liu, Yaping Jin, Aihua Wang
Frontiers in Microbiology.2024;[Epub] CrossRef
Pal Affects the Proliferation in Macrophages and Virulence of Brucella, and as Mucosal Adjuvants, Provides an Effective Protection to Mice Against Salmonella Enteritidis
Yubin Chen, Yanfang Fu, Lingcong Kong, Fengjie Wang, Xiaowei Peng, Zhiqiang Zhang, Qiumei Shi, Qingmin Wu, Tonglei Wu
Current Microbiology.2023;[Epub] CrossRef
Clearance of bacteria from lymph nodes in sheep immunized with Brucella suis S2 vaccine is associated with M1 macrophage activation
Si Chen, Yuanyuan Chen, Zizhuo Jiao, Chengqiang Wang, Dantong Zhao, Yongbin Liu, Wenguang Zhang, Shihua Zhao, Bin Yang, Qinan Zhao, Shaoyin Fu, Xiaolong He, Qiaoling Chen, Churiga Man, Guoying Liu, Xuefeng Wei, Li Du, Fengyang Wang
Veterinary Research.2023;[Epub] CrossRef
A Brucella Omp16 Conditional Deletion Strain Is Attenuated in BALB/c Mice
Feijie Zhi, Jiaoyang Fang, Weifang Zheng, Junmei Li, Guangdong Zhang, Dong Zhou, Yaping Jin, Aihua Wang
Journal of Microbiology and Biotechnology.2022; 32(1): 6. CrossRef
A designed peptide-based vaccine to combat Brucella melitensis, B. suis and B. abortus: Harnessing an epitope mapping and immunoinformatics approach
Hossein Tarrahimofrad, Javad Zamani, Michael R. Hamblin, Maryam Darvish, Hamed Mirzaei
Biomedicine & Pharmacotherapy.2022; 155: 113557. CrossRef
A LysR Transcriptional Regulator Manipulates Macrophage Autophagy Flux During Brucella Infection
Lu Zhang, Siyuan Yu, Xinnuan Ning, Hui Fang, Jie Li, Feijie Zhi, Junmei Li, Dong Zhou, Aihua Wang, Yaping Jin
Frontiers in Cellular and Infection Microbiology.2022;[Epub] CrossRef
Uncovering the Hidden Credentials ofBrucellaVirulence
R. Martin Roop, Ian S. Barton, Dariel Hopersberger, Daniel W. Martin
Microbiology and Molecular Biology Reviews.2021;[Epub] CrossRef
RNA-Seq Analysis Reveals the Role of Omp16 in Brucella-Infected RAW264.7 Cells
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Frontiers in Veterinary Science.2021;[Epub] CrossRef

The NADP+-dependent glutamate dehydrogenase Gdh1 is subjected to glucose starvation-induced reversible aggregation that affects stress resistance in yeast: Woo Hyun Lee , Ju Yeong Oh , Pil Jae Maeng; J. Microbiol. 2019;57(10):884-892. Published online August 3, 2019; DOI: https://doi.org/10.1007/s12275-019-9065-z

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Abstract

The yeast Saccharomyces cerevisiae has two isoforms of NADP+-dependent glutamate dehydrogenase (Gdh1 and Gdh3) that catalyze the synthesis of glutamate from α-ketoglutarate and NH4 +. In the present study, we confirmed that Gdh3, but not Gdh1, mainly contributes to the oxidative stress resistance of stationary-phase cells and found evidence suggesting that the insignificance of Gdh1 to stress resistance is possibly resulted from conditional and reversible aggregation of Gdh1 into punctuate foci initiated in parallel with postdiauxic growth. Altered localization to the mitochondria or peroxisomes prevented Gdh1, which was originally localized in the cytoplasm, from stationary phase-specific aggregation, suggesting that some cytosolic factors are involved in the process of Gdh1 aggregation. Glucose starvation triggered the transition of the soluble form of Gdh1 into the insoluble aggregate form, which could be redissolved by replenishing glucose, without any requirement for protein synthesis. Mutational analysis showed that the N-terminal proximal region of Gdh1 (NTP1, aa 21-26, TLFEQH) is essential for glucose starvation-induced aggregation. We also found that the substitution of NTP1 with the corresponding region of Gdh3 (NTP3) significantly increased the contribution of the mutant Gdh1 to the stress resistance of stationary-phase cells. Thus, this suggests that NTP1 is responsible for the negligible role of Gdh1 in maintaining the oxidative stress resistance of stationary- phase cells and the stationary phase-specific stresssensitive phenotype of the mutants lacking Gdh3.

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Genomic characterization of denitrifying methylotrophic Pseudomonas aeruginosa strain AAK/M5 isolated from municipal solid waste landfill soil
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Evaluation and application of constitutive promoters for cutinase production by Saccharomyces cerevisiae: Juan Zhang , Yanqiu Cai , Guocheng Du , Jian Chen , Miao Wang , Zhen Kang; J. Microbiol. 2017;55(7):538-544. Published online June 30, 2017; DOI: https://doi.org/10.1007/s12275-017-6514-4

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died and applied in processes targeted for industrial scale. In this work, the cutinase gene tfu from Thermobifida fusca was artificially synthesized according to codon usage bias of Saccharomyces cerevisiae and investigated in Saccharomyces cerevisiae. Using the α-factor signal peptide, the T. fusca cutinase was successfully overexpressed and secreted with the GAL1 expression system. To increase the cutinase level and overcome some of the drawbacks of induction, four different strong promoters (ADH1, HXT1, TEF1, and TDH3) were comparatively evaluated for cutinase production. By comparison, promoter TEF1 exhibited an outstanding property and significantly increased the expression level. By fed-batch fermentation with a constant feeding approach, the activity of cutinase was increased to 29.7 U/ml. The result will contribute to apply constitutive promoter TEF1 as a tool for targeted cutinase production in S. cerevisiae cell factory.

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[Minireview] Unraveling new functions of superoxide dismutase using yeast model system: Beyond its conventional role in superoxide radical scavenging: Woo-Hyun Chung ,; J. Microbiol. 2017;55(6):409-416. Published online March 9, 2017; DOI: https://doi.org/10.1007/s12275-017-6647-5

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Abstract

To deal with chemically reactive oxygen molecules constantly threatening aerobic life, cells are readily equipped with elabo-rate biological antioxidant systems. Superoxide dismutase is a metalloenzyme catalytically eliminating superoxide radi-cal as a first-line defense mechanism against oxidative stress. Multiple different SOD isoforms have been developed through-out evolution to play distinct roles in separate subcellular com-partments. SOD is not essential for viability of most aerobic organisms and intriguingly found even in strictly anaerobic bacteria. Sod1 has recently been known to play important roles as a nuclear transcription factor, an RNA binding pro-tein, a synthetic lethal interactor, and a signal modulator in glucose metabolism, most of which are independent of its canonical function as an antioxidant enzyme. In this review, recent advances in understanding the unconventional role of Sod1 are highlighted and discussed with an emphasis on its genetic crosstalk with DNA damage repair/checkpoint path-ways. The budding yeast Saccharomyces cerevisiae has been successfully used as an efficient tool and a model organism to investigate a number of novel functions of Sod1.

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Journal Article

HST1 increases replicative lifespan of a sir2Δ mutant in the absence of PDE2 in Saccharomyces cerevisiae: Woo Kyu Kang , Mayur Devare , Jeong-Yoon Kim; J. Microbiol. 2017;55(2):123-129. Published online January 26, 2017; DOI: https://doi.org/10.1007/s12275-017-6535-z

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Abstract

Silent information regulator 2 (Sir2), which is the founding member of the sirtuin family of proteins, is a pro-longevity factor for replicative lifespan (RLS) in Saccharomyces cerevisiae. Sir2 is required for transcriptional silencing at mating type loci, telomeres, and rDNA loci. Sir2 also represses transcription of highly expressed growth-related genes, such as PMA1 and some ribosomal protein genes. Although the Sir2 paralogues Hst1, Hst2, Hst3, and Hst4 occur in S. cerevisiae, none of them could replace the transcriptional regulation of PMA1 by Sir2 in the wild type. In this study, we demonstrate that Hst1, the closest Sir2 paralogue, deacetylates the acetylated lysine 16 of histone H4 (H4K16Ac) and represses PMA1 transcription in the sir2Δ pde2Δ mutant. We further show that Hst1 plays a role in extending the RLS of the sir2Δ pde2Δ mutant. Collectively, our results suggest that Hst1 can substitute for Sir2 by deacetylating H4K16Ac only in the sir2Δ pde2Δ.

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Selective production, relationship and controversy between Monascus pigments and citrinin
Xueling Qin, Bin Xie, Xuanli Zong, Xiang Yu, Yanli Feng
Food Bioscience.2023; 56: 103233. CrossRef
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Safia Mahabub Sauty, Kholoud Shaban, Krassimir Yankulov
Current Genetics.2021; 67(1): 3. CrossRef
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Research Support, Non-U.S. Gov't

Identification of Psk2, Skp1, and Tub4 as trans-acting factors for uORF-containing ROK1 mRNA in Saccharomyces cerevisiae: Soonmee Jeon , Suran Lim , Jeemin Ha , Jinmi Kim; J. Microbiol. 2015;53(9):616-622. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-5389-5

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Abstract

Rok1, a DEAD-box RNA helicase, is involved in rRNA processing and the control of cell cycle progression in Saccharomyces cerevisiae. Rok1 protein expression is cell cycle-regulated, declining at G1/S and increasing at G2. The downregulation of Rok1 expression in G1/S phase is mediated by the inhibitory action of two upstream open reading frames (uORFs) in the ROK1 5􍿁-untranslated region (5􍿁UTR). We identified Psk2 (PAS kinase), Skp1 (kinetochore protein) and Tub4 (γ-tubulin protein) as ROK1 5􍿁UTR-interacting proteins using yeast three-hybrid system. A deletion analysis of PSK2 or inactivation of temperature-sensitive alleles of SKP1 and TUB4 revealed that Rok1 protein synthesis is repressed by Psk2 and Skp1. This repression appeared to be mediated through the ROK1 uORF1. In contrast, Tub4 plays a positive role in regulating Rok1 protein synthesis and likely after the uORF1-mediated inhibitory regulation. These results suggest that 5􍿁UTR-interacting proteins, identified using three hybrid screening, are important for uORF-mediated regulation of Rok1 protein expression.

Citations

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Identification of short open reading frames in plant genomes
Yong Feng, Mengyun Jiang, Weichang Yu, Jiannan Zhou
Frontiers in Plant Science.2023;[Epub] CrossRef
HST1 increases replicative lifespan of a sir2Δ mutant in the absence of PDE2 in Saccharomyces cerevisiae
Woo Kyu Kang, Mayur Devare, Jeong-Yoon Kim
Journal of Microbiology.2017; 55(2): 123. CrossRef

Review

MINIREVIEW] The Potential Hazards of Aspergillus sp. in Foods and Feeds, and the Role of Biological Treatment: A Review: Sheikh Imranudin Sheikh-Ali , Akil Ahmad , Siti-Hamidah Mohd-Setapar , Zainul Akmal Zakaria , Norfahana Abdul-Talib , Aidee Kamal Khamis , Md Enamul Hoque; J. Microbiol. 2014;52(10):807-818. Published online October 1, 2014; DOI: https://doi.org/10.1007/s12275-014-4294-7

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Abstract

The contamination of food and feed by Aspergillus has become a global issue with a significant worldwide economic impact. The growth of Aspergillus is unfavourable to the development of food and feed industries, where the problems happen mostly due to the presence of mycotoxins, which is a toxic metabolite secreted by most Aspergillus groups. Moreover, fungi can produce spores that cause diseases, such as allergies and asthma, especially to human beings. High temperature, high moisture, retarded crops, and poor food storage conditions encourage the growth of mold, as well as the development of mycotoxins. A variety of chemical, biological, and physical strategies have been developed to control the production of mycotoxins. A biological approach, using a mixed culture comprised of Saccharomyces cerevisiae and Lactobacillus rhamnosus resulted in the inhibition of the growth of fungi when inoculated into fermented food. The
results
reveal that the mixed culture has a higher potential (37.08%) to inhibit the growth of Aspergillus flavus (producer of Aflatoxin) compared to either single culture, L. rhamnosus NRRL B-442 and S. cerevisiae, which inhibit the growth by 63.07% and 64.24%, respectively.

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

Growth Phase-dependent Roles of Sir2 in Oxidative Stress Resistance and Chronological Lifespan in Yeast: Woo Kyu Kang , Yeong Hyeock Kim , Byoung-Soo Kim , Jeong-Yoon Kim; J. Microbiol. 2014;52(8):652-658. Published online July 5, 2014; DOI: https://doi.org/10.1007/s12275-014-4173-2

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Abstract

Silent Information Regulator 2 (Sir2), a conserved NAD+- dependent histone deacetylase, has been implicated as one of the key factors in regulating stress response and longevity. Here, we report that the role of Sir2 in oxidative stress resistance and chronological lifespan is dependent on growth phase in yeast. In exponential phase, sir2Δ cells were more resistant to H2O2 stress and had a longer chronological lifespan than wild type. By contrast, in post-diauxic phase, sir2Δ cells were less resistant to H2O2 stress and had a shorter chronological lifespan than wild type cells. Similarly, the expression of antioxidant genes, which are essential to cope with oxidative stress, was regulated by Sir2 in a growth phasedependent manner. Collectively, our findings highlight the importance of the metabolic state of the cell in determining whether Sir2 can protect against or accelerate cellular aging of yeast.

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NOTE] A Protective Role of Methionine-R-Sulfoxide Reductase against Cadmium in Schizosaccharomyces pombe: Chang-Jin Lim , Hannah Jo , Kyunghoon Kim; J. Microbiol. 2014;52(11):976-981. Published online May 30, 2014; DOI: https://doi.org/10.1007/s12275-014-3512-7

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Abstract

The Schizosaccharomyces pombe cells harboring the methionine- R-sulfoxide reductase (MsrB)-overexpressing recombinant plasmid pFMetSO exhibited better growth than vector control cells, when shifted into fresh medium containing cadmium chloride (abbreviated as Cd). Although both groups of cells contained enhanced reactive oxygen species (ROS) and nitric oxide (NO) levels in the presence of Cd, ROS and NO levels were significantly lower in the S. pombe cells harboring pFMetSO than in vector control cells. Conversely, the S. pombe cells harboring pFMetSO possessed higher total glutathione (GSH) levels and a greater reduced/oxidized GSH ratio than vector control cells under the same conditions.

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Review

MINIREVIEW] To Peep into Pif1 Helicase: Multifaceted All the Way from Genome Stability to Repair-Associated DNA Synthesis: Woo-Hyun Chung; J. Microbiol. 2014;52(2):89-98. Published online February 1, 2014; DOI: https://doi.org/10.1007/s12275-014-3524-3

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Abstract

Pif1 DNA helicase is the prototypical member of a 5' to 3' helicase superfamily conserved from bacteria to humans. In Saccharomyces cerevisiae, Pif1 and its homologue Rrm3, localize in both mitochondria and nucleus playing multiple roles in the maintenance of genomic homeostasis. They display relatively weak processivities in vitro, but have largely non-overlapping functions on common genomic loci such as mitochondrial DNA, telomeric ends, and many replication forks especially at hard-to-replicate regions including ribosomal DNA and G-quadruplex structures. Recently, emerging evidence shows that Pif1, but not Rrm3, has a significant new role in repair-associated DNA synthesis with Polδ during homologous recombination stimulating D-loop migration for conservative DNA replication. Comparative genetic and biochemical studies on the structure and function of Pif1 family helicases across different biological systems are further needed to elucidate both diversity and specificity of their mechanisms of action that contribute to genome stability.

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