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Review

Small regulatory RNAs as key modulators of antibiotic resistance in pathogenic bacteria: Yubin Yang, Hana Hyeon, Minju Joo, Kangseok Lee, Eunkyoung Shin; J. Microbiol. 2025;63(4):e2501027. Published online April 2, 2025; DOI: https://doi.org/10.71150/jm.2501027

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The escalating antibiotic resistance crisis poses a significant challenge to global public health, threatening the efficacy of current treatments and driving the emergence of multidrug-resistant pathogens. Among the various factors associated with bacterial antibiotic resistance, small regulatory RNAs (sRNAs) have emerged as pivotal post-transcriptional regulators which orchestrate bacterial adaptation to antibiotic pressure via diverse mechanisms. This review consolidates the current knowledge on sRNA-mediated mechanisms, focusing on drug uptake, drug efflux systems, lipopolysaccharides, cell wall modification, biofilm formation, and mutagenesis. Recent advances in transcriptomics and functional analyses have revealed novel sRNAs and their regulatory networks, expanding our understanding of resistance mechanisms. These findings highlight the potential of targeting sRNA-mediated pathways as an innovative therapeutic strategy to combat antibiotic resistance, and offer promising avenues for managing challenging bacterial infections.

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Biofilm, resistance, and quorum sensing: The triple threat in bacterial pathogenesis
Mohammad Nazrul Islam Bhuiyan
The Microbe.2025; 9: 100578. CrossRef
Biofilm maturation in carbapenem-resistant Pseudomonas aeruginosa is regulated by the sRNA PA213 and its corresponding encoded small protein
Yongli Song, Jie Li, Yating Zhang, Lingge Su, Shuang Qin, Chunyan Wu, Guibo Song
International Journal of Antimicrobial Agents.2025; 66(6): 107625. CrossRef

Journal Articles

CalR Inhibits the Swimming Motility and Polar Flagellar Gene Expression in Vibrio parahaemolyticus: Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Haisheng Wu, Renfei Lu, Yiquan Zhang; J. Microbiol. 2024;62(12):1125-1132. Published online December 6, 2024; DOI: https://doi.org/10.1007/s12275-024-00179-0

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Vibrio parahaemolyticus has two flagellar systems, the polar flagellum and lateral flagella, which are both intricately regulated by a multitude of factors. CalR, a LysR-type transcriptional regulator, is sensitive to calcium (Ca) and plays a crucial role in regulating the virulence and swarming motility of V. parahaemolyticus. In this study, we have demonstrated that the deletion of calR significantly enhances the swimming motility of V. parahaemolyticus under low Ca conditions but not under high Ca conditions or in the absence of Ca. CalR binds to the regulatory DNA regions of flgM, flgA, and flgB, which are located within the polar flagellar gene loci, with the purpose of repressing their transcription. Additionally, it exerts an indirect negative control over the transcription of flgK. The overexpression of CalR in Escherichia coli resulted in a reduction in the expression levels of flgM, flgA, and flgB, while having no impact on the expression of flgK. In summary, this research demonstrates that the negative regulation of V. parahaemolyticus swimming motility by CalR under low Ca conditions is achieved through its regulation on the transcription of polar flagellar genes.

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A DHH/DHHA1 family 3′-phosphoadenosine 5′-monophosphate (pAp) phosphoesterase Vp2835 is essential for regulating motility, biofilm formation and type III secretion system 1 in Vibrio parahaemolyticus
Chenzhi Zhuhuang, Chenxi Wang, Yu Sun, Min Chu, Menghua Yang, Guangzhi Xu
Food Bioscience.2025; 69: 106836. CrossRef
Chlorogenic Acid Targets Cell Integrity and Virulence to Combat Vibrio parahaemolyticus
Huan Liu, Jie Zhao, Yile Shi, Juanjuan Cao, Yanni Zhao
Foods.2025; 14(19): 3416. CrossRef
CalR is an activator of biofilm formation in Vibrio parahaemolyticus
Jingyang Chang, Yining Zhou, Miaomiao Zhang, Xue Li, Nan Zhang, Xi Luo, Bin Ni, Renfei Lu, Yiquan Zhang, Sophie Roussel
Applied and Environmental Microbiology.2025;[Epub] CrossRef
LtrA is critical for biofilm formation and colonization of Vibrio parahaemolyticus on food-related surfaces
Shuhui Xiong, Nan Zhang, Hui Sun, Miaomiao Zhang, Xue Li, Xi Luo, Yiquan Zhang, Renfei Lu
International Journal of Food Microbiology.2025; 441: 111327. CrossRef

H-NS is a Transcriptional Repressor of the CRISPR-Cas System in Acinetobacter baumannii ATCC 19606: Kyeongmin Kim, Md Maidul Islam, Seunghyeok Bang, Jeongah Kim, Chung-Young Lee, Je Chul Lee, Minsang Shin; J. Microbiol. 2024;62(11):999-1012. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00182-5

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Acinetobacter baumannii is a multidrug-resistant opportunistic pathogen primarily associated with hospital-acquired infections. The bacterium can gain multidrug resistance through several mechanisms, including horizontal gene transfer. A CRISPR-Cas system including several Cas genes could restrict the horizontal gene transfer. However, the molecular mechanism of CRISPR- Cas transcriptional regulation remains unclear. We identified a type I-F CRISPR-Cas system in A. baumannii ATCC 19606^T standard strain based on sequence analysis. We focused on the transcriptional regulation of Cas3, a key protein of the CRISPR-Cas system. We performed a DNA affinity chromatography-pulldown assay to identify transcriptional regulators of the Cas3 promoter. We identified several putative transcriptional factors, such as H-NS, integration host factor, and HU, that can bind to the promoter region of Cas3. We characterized AbH-NS using size exclusion chromatography and cross-linking experiments and demonstrated that the Cas3 promoter can be regulated by AbH-NS in a concentration-dependent manner via an in vitro transcription assay. CRISPR-Cas expression levels in wild-type and hns mutant strains in the early stationary phase were examined by qPCR and β-galactosidase assay. We found that H-NS can act as a repressor of Cas3. Our transformation efficiency results indicated that the hns mutation decreased the transformation efficiency, while the Cas3 mutation increased it. We report the existence and characterization of the CRISPR-Cas system in A. baumannii 19606^T and demonstrate that AbH-NS is a transcriptional repressor of CRISPR-Cas-related genes in A. baumannii.

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The H-NS homologues MvaT and MvaU repress CRISPR-Cas in Pseudomonas aeruginosa
Kira Céline Koonce, Jesper Juel Mauritzen, Ida Friberg Hitz, Emil Funk Vangsgaard, Elizabeth H. M. Putz, Anne Sofie Wajn, Frederik Hagelund Leth, Nina Molin Høyland-Kroghsbo
Philosophical Transactions of the Royal Society B: Biological Sciences.2025;[Epub] CrossRef
BaeR and H-NS control CRISPR-Cas-mediated immunity and virulence in Acinetobacter baumannii
Ting Yu, Jun Xie, Xinyue Huang, Jiayuan Huang, Guangyu Bao, Wenjie Yuan, Chengfeng Gao, Cuicui Liu, Jian Hu, Weixuan Yang, Guocai Li, Ryan McClure
mSystems.2025;[Epub] CrossRef

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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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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Synthesis, molecular docking and anti-biofilm activity of novel benzo[4,5]imidazo[2,1-a]quinazoline, 4H-chromene, and acridine derivatives as potent anti-candida agents
Farid M. Sroor, Ahmed Younis, Mohamed Abdelraof, Ismail A. Abdelhamid
Journal of Molecular Structure.2025; 1331: 141520. CrossRef
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

Enhancement of the solubility of recombinant proteins by fusion with a short-disordered peptide: Jun Ren , Suhee Hwang , Junhao Shen , Hyeongwoo Kim , Hyunjoo Kim , Jieun Kim , Soyoung Ahn , Min-gyun Kim , Seung Ho Lee , Dokyun Na; J. Microbiol. 2022;60(9):960-967. Published online July 14, 2022; DOI: https://doi.org/10.1007/s12275-022-2122-z

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In protein biotechnology, large soluble fusion partners are widely utilized for increased yield and solubility of recombinant proteins. However, the production of additional large fusion partners poses an additional burden to the host, leading to a decreased protein yield. In this study, we identified two highly disordered short peptides that were able to increase the solubility of an artificially engineered aggregationprone protein, GFP-GFIL4, from 0.6% to 61% (D3-DP00592) and 46% (D4-DP01038) selected from DisProt database. For further confirmation, the peptides were applied to two insoluble E. coli proteins (YagA and YdiU). The peptides also enhanced solubility from 52% to 90% (YagA) and from 27% to 93% (YdiU). Their ability to solubilize recombinant proteins was comparable with strong solubilizing tags, maltosebinding protein (40 kDa) and TrxA (12 kDa), but much smaller (< 7 kDa) in size. For practical application, the two peptides were fused with a restriction enzyme, I-SceI, and they increased I-SceI solubility from 24% up to 75%. The highly disordered peptides did not affect the activity of I-SceI while I-SceI fused with MBP or TrxA displayed no restriction activity. Despite the small size, the highly disordered peptides were able to solubilize recombinant proteins as efficiently as conventional fusion tags and did not interfere with the function of recombinant proteins. Consequently, the identified two highly disordered peptides would have practical utility in protein biotechnology and industry.

Citations

Citations to this article as recorded by

A review on computational models for predicting protein solubility
Teerapat Pimtawong, Jun Ren, Jingyu Lee, Hyang-Mi Lee, Dokyun Na
Journal of Microbiology.2025; 63(1): e:2408001. CrossRef
Synthetic intrinsically disordered protein fusion tags that enhance protein solubility
Nicholas C. Tang, Jonathan C. Su, Yulia Shmidov, Garrett Kelly, Sonal Deshpande, Parul Sirohi, Nikhil Peterson, Ashutosh Chilkoti
Nature Communications.2024;[Epub] CrossRef
Biosynthesis of Indigo Dyes and Their Application in Green Chemical and Visual Biosensing for Heavy Metals
Yan Guo, Shun-Yu Hu, Can Wu, Chao-Xian Gao, Chang-Ye Hui
ACS Omega.2024; 9(31): 33868. CrossRef
Functional small peptides for enhanced protein delivery, solubility, and secretion in microbial biotechnology
Hyang-Mi Lee, Thi Duc Thai, Wonseop Lim, Jun Ren, Dokyun Na
Journal of Biotechnology.2023; 375: 40. CrossRef
Directed Evolution of Soluble α-1,2-Fucosyltransferase Using Kanamycin Resistance Protein as a Phenotypic Reporter for Efficient Production of 2'-Fucosyllactose
Jonghyeok Shin, Seungjoo Kim, Wonbeom Park, Kyoung Chan Jin, Sun-Ki Kim, Dae-Hyuk Kweon
Journal of Microbiology and Biotechnology.2022; 32(11): 1471. CrossRef
Effects of spray drying, freeze drying, and vacuum drying on physicochemical and nutritional properties of protein peptide powder from salted duck egg white
Tianyin Du, Jicheng Xu, Shengnan Zhu, Xinjun Yao, Jun Guo, Weiqiao Lv
Frontiers in Nutrition.2022;[Epub] CrossRef

A mucin-responsive hybrid two-component system controls Bacteroides thetaiotaomicron colonization and gut homeostasis: Ju-Hyung Lee , Soo-Jeong Kwon , Ji-Yoon Han , Sang-Hyun Cho , Yong-Joon Cho , Joo-Hong Park; J. Microbiol. 2022;60(2):215-223. Published online February 1, 2022; DOI: https://doi.org/10.1007/s12275-022-1649-3

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The mammalian intestinal tract contains trillions of bacteria. However, the genetic factors that allow gut symbiotic bacteria to occupy intestinal niches remain poorly understood. Here, we identified genetic determinants required for Bacteroides thetaiotaomicron colonization in the gut using transposon sequencing analysis. Transposon insertion in BT2391, which encodes a hybrid two-component system, increased the competitive fitness of B. thetaiotaomicron. The BT2391 mutant showed a growth advantage in a mucin-dependent manner and had an increased ability to adhere to mucus-producing cell lines. The increased competitive advantage of the BT2391 mutant was dependent on the BT2392–2395 locus containing susCD homologs. Deletion of BT2391 led to changes in the expression levels of B. thetaiotaomicron genes during gut colonization. However, colonization of the BT2391 mutant promoted DSS colitis in low-fiber diet-fed mice. These results indicate that BT2391 contributes to a sustainable symbiotic relationship by maintaining a balance between mucosal colonization and gut homeostasis.

Citations

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The global RNA-binding protein RbpB is a regulator of polysaccharide utilization in Bacteroides thetaiotaomicron
Ann-Sophie Rüttiger, Daniel Ryan, Luisella Spiga, Vanessa Lamm-Schmidt, Gianluca Prezza, Sarah Reichardt, Madison Langford, Lars Barquist, Franziska Faber, Wenhan Zhu, Alexander J. Westermann
Nature Communications.2025;[Epub] CrossRef
Effect of Lactobacillus plantarum BFS1243 on a female frailty model induced by fecal microbiota transplantation in germ-free mice
Sashuang Dong, Qi Zeng, Weimin He, Wei Cheng, Ling Zhang, Ruimin Zhong, Wen He, Xiang Fang, Hong Wei
Food & Function.2024; 15(8): 3993. CrossRef
A conserved inhibitory interdomain interaction regulates DNA-binding activities of hybrid two-component systems in Bacteroides
Rong Gao, Ti Wu, Ann M. Stock, Michael T. Laub
mBio.2024;[Epub] CrossRef
Polysaccharides from Polygonatum cyrtonema Hua prevent depression-like behaviors in mice with chronic unpredictable mild stress through refining gut microbiota-lipopolysaccharide-paraventricular nucleus signal axis
Xinya Wang, Xueqing Wang, Feng Gao, Shaojie Yang, Yilan Zhen, Xuncui Wang, Guoqi Zhu
Heliyon.2024; 10(19): e38554. CrossRef
Metal Messengers: Communication in the Bacterial World through Transition-Metal-Sensing Two-Component Systems
Alexander Paredes, Chioma Iheacho, Aaron T. Smith
Biochemistry.2023; 62(16): 2339. CrossRef
Tang-Ping-San Decoction Remodel Intestinal Flora and Barrier to Ameliorate Type 2 Diabetes Mellitus in Rodent Model
Wen Yin, Si-Qi Zhang, Wen-Lin Pang, Xiao-Jiao Chen, Jing Wen, Jiong Hou, Cui Wang, Li-Yun Song, Zhen-Ming Qiu, Peng-Tao Liang, Jia-Li Yuan, Zhong-Shan Yang, Yao Bian
Diabetes, Metabolic Syndrome and Obesity: Targets and Therapy.2022; Volume 15: 2563. CrossRef

Characterization of a novel phage depolymerase specific to Escherichia coli O157:H7 and biofilm control on abiotic surfaces: Do-Won Park , Jong-Hyun Park; J. Microbiol. 2021;59(11):1002-1009. Published online October 6, 2021; DOI: https://doi.org/10.1007/s12275-021-1413-0

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The increasing prevalence of foodborne diseases caused by Escherichia coli O157:H7 as well as its ability to form biofilms poses major threats to public health worldwide. With increasing concerns about the limitations of current disinfectant treatments, phage-derived depolymerases may be used as promising biocontrol agents. Therefore, in this study, the characterization, purification, and application of a novel phage depolymerase, Dpo10, specifically targeting the lipopolysaccharides of E. coli O157, was performed. Dpo10, with a molecular mass of 98 kDa, was predicted to possess pectate lyase activity via genome analysis and considered to act as a receptor- binding protein of the phage. We confirmed that the purified Dpo10 showed O-polysaccharide degrading activity only for the E. coli O157 strains by observing its opaque halo. Dpo10 maintained stable enzymatic activities across a wide range of temperature conditions under 55°C and mild basic pH. Notably, Dpo10 did not inhibit bacterial growth but significantly increased the complement-mediated serum lysis of E. coli O157 by degrading its O-polysaccharides. Moreover, Dpo10 inhibited the biofilm formation against E. coli O157 on abiotic polystyrene by 8-fold and stainless steel by 2.56 log CFU/coupon. This inhibition was visually confirmed via fieldemission scanning electron microscopy. Therefore, the novel depolymerase from E. coli siphophage exhibits specific binding and lytic activities on the lipopolysaccharide of E. coli O157 and may be used as a promising anti-biofilm agent against the E. coli O157:H7 strain.

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Application of phage-derived enzymes for enhancing food safety
Junhwan Kim, Xinyu Liao, Song Zhang, Tian Ding, Juhee Ahn
Food Research International.2025; 209: 116318. CrossRef
Novel polygalacturonase PG-BG31 prevents biofilm formation and increases antibiotic efficacy against catheter-associated Escherichia coli
Marija Atanaskovic, Andjela Dilparic, Mario Zlatović, Lidija Senerovic
Journal of Biotechnology.2025; 406: 179. CrossRef
Isolation and identification of bacteriophage against Escherichia coli ATCC 25922 and their biofilm Inhibition studies
Lakshminarayanan Sivakumar, Jeya Vignesh John Durai Kumar, Subadarshini Madhavan, K U Mina Parvesh, Santhosh Kumar Arunagiri, Suriyaprakash Rajadesingu, Shobana Sugumar, Narenkumar Jayaraman, Kagithakara Vajravelu Leela, A. Karthik, Tabarak Malik, Parthip
Scientific Reports.2025;[Epub] CrossRef
Bacteriophage as Alternative Methods to Control Pathogens in Food
Nimisha Tehri, Dharun Vijay Puniya, Anil Kumar Puniya
Current Food Science and Technology Reports.2025;[Epub] CrossRef
Lytic bacteriophages as alternative to overcoming antibiotic-resistant biofilms formed by clinically significant bacteria
Abdul-Halim Osman, Samuel Darkwah, Fleischer C. N. Kotey, Adwoa Asante-Poku, Eric S. Donkor
Therapeutic Advances in Infectious Disease.2025;[Epub] CrossRef
Synergistic Disruption of Foodborne Pathogen Biofilms by Oregano Essential Oil and Bacteriophage phiLLS: Atomic Force Microscopy Insights
Ana Karina Kao Godínez, Carlos Regalado-González, Claudia Villicaña, José Basilio Heredia, José Benigno Valdez-Torres, María Muy-Rangel, Monserrat Escamilla-García, Josefina León-Félix
Molecules.2025; 30(17): 3552. CrossRef
Phage-encoded depolymerases and endolysins as prospective strategies to combat multidrug-resistant Klebsiella pneumoniae
Yunhan Zhang, Weiqing Lan, Xiaohong Sun
International Journal of Biological Macromolecules.2025; 321: 146159. CrossRef
Isolation and characterization of a novel K3-type capsule-targeting phage for the treatment of carbapenem-resistant Acinetobacter baumannii
Hewen Deng, Ziqiang Liu, Siyun Wang, Shitong Lu, Ruopeng Cai, Linwan Feng, Kun Shi, Xin Tan, Rui Du, Hui Wang
Microbiology Spectrum.2025;[Epub] CrossRef
Effect of Bacteriophages against Biofilms of Escherichia coli on Food Processing Surfaces
Ana Brás, Márcia Braz, Inês Martinho, João Duarte, Carla Pereira, Adelaide Almeida
Microorganisms.2024; 12(2): 366. CrossRef
Bacteriophage–Host Interactions and the Therapeutic Potential of Bacteriophages
Leon M. T. Dicks, Wian Vermeulen
Viruses.2024; 16(3): 478. CrossRef
Current Strategies for Combating Biofilm-Forming Pathogens in Clinical Healthcare-Associated Infections
Rashmita Biswas, Bhawana Jangra, Ganapathy Ashok, Velayutham Ravichandiran, Utpal Mohan
Indian Journal of Microbiology.2024; 64(3): 781. CrossRef
Phage Adsorption to Gram-Positive Bacteria
Audrey Leprince, Jacques Mahillon
Viruses.2023; 15(1): 196. CrossRef
Prevalence of Indigenous Antibiotic-Resistant Salmonella Isolates and Their Application to Explore a Lytic Phage vB_SalS_KFSSM with an Intra-Broad Specificity
Jaein Choe, Su-Hyeon Kim, Ji Min Han, Jong-Hoon Kim, Mi-Sun Kwak, Do-Won Jeong, Mi-Kyung Park
Journal of Microbiology.2023; 61(12): 1063. CrossRef
Phages against Pathogenic Bacterial Biofilms and Biofilm-Based Infections: A Review
Siyu Liu, Hongyun Lu, Shengliang Zhang, Ying Shi, Qihe Chen
Pharmaceutics.2022; 14(2): 427. CrossRef

Lentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food: Young Joon Oh , Joon Yong Kim , Hee Eun Jo , Hyo Kyeong Park , Seul Ki Lim , Min-Sung Kwon , Hak-Jong Choi; J. Microbiol. 2020;58(5):387-394. Published online April 11, 2020; DOI: https://doi.org/10.1007/s12275-020-9507-7

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Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5–9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3–99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3T (97.4–97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1- 9T (79.5–79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC- 220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains. The major cellular fatty acids of the strains were anteiso-C15:0 and anteiso- C17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2T (= KACC 21232T = JCM 33390T).

Citations

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Identification of Roseomonas xinghualingensis sp. nov. isolated from hospital air
Zhiming Kang, Wenjing Lei, Ji Pu, Lijun Zhao, Guowen Min, Yufeng Liu, Wenjuan Chang, Yuqian Gao, Kui Dong, Bin Sun
International Journal of Systematic and Evolutionary Microbiology .2025;[Epub] CrossRef
Lentibacillus songyuanensis sp. nov., A Drought- and Salt- Tolerant Bacterium with Ability to Degrade Aniline Blue Isolated from Saline-Alkali Soil
Enyi Wang, Leyao Chen, Leyun Dong, Jian He, Zongzhuan Shen, Jiandong Jiang, Qirong Shen
Current Microbiology.2025;[Epub] CrossRef
Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis
Cansu Çelik Doğan, Hafize Tuğba Yüksel Dolgun, Serkan İkiz, Şükrü Kırkan, Uğur Parın
Foods.2023; 12(19): 3538. CrossRef
Lentibacillus daqui sp. nov., isolated from high-temperature Daqu, a starter for production of Chinese Jiang-flavour Baijiu
Yuan Liang, Zhen-Ming Lu, Wei Shi, Lin-Huan Wu, Li-Juan Chai, Xiao-Juan Zhang, Su-Yi Zhang, Song-Tao Wang, Cai-Hong Shen, Zheng-Hong Xu
International Journal of Systematic and Evolutionary Microbiology .2023;[Epub] CrossRef
Occurrence of biogenic amines and their correlation with bacterial communities in the Ivorian traditional fermented fish adjuevan during the storage
Marina Ghislaine Abré, Clémentine Amenan Kouakou-Kouamé, Florent Kouadio N’guessan, Corinne Teyssier, Didier Montet
Folia Microbiologica.2023; 68(2): 257. CrossRef
Description of Corynebacterium poyangense sp. nov., isolated from the feces of the greater white-fronted geese (Anser albifrons)
Qian Liu, Guoying Fan, Kui Wu, Xiangning Bai, Xi Yang, Wentao Song, Shengen Chen, Yanwen Xiong, Haiying Chen
Journal of Microbiology.2022; 60(7): 668. CrossRef
Parasphingorhabdus cellanae sp. nov., isolated from the gut of a Korean limpet, Cellana toreuma
Ji-Ho Yoo, Jeong Eun Han, June-Young Lee, Su-Won Jeong, Yun-Seok Jeong, Jae-Yun Lee, So-Yeon Lee, Hojun Sung, Euon Jung Tak, Hyun Sik Kim, Pil Soo Kim, Jee-Won Choi, Do-Yeon Kim, In Chul Jeong, Do-Hun Gim, Seo Min Kang, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology .2022;[Epub] CrossRef
Isolation and characterization of tick-borne Roseomonas haemaphysalidis sp. nov. and rodent-borne Roseomonas marmotae sp. nov.
Wentao Zhu, Juan Zhou, Shan Lu, Jing Yang, Xin-He Lai, Dong Jin, Ji Pu, Yuyuan Huang, Liyun Liu, Zhenjun Li, Jianguo Xu
Journal of Microbiology.2022; 60(2): 137. CrossRef
The Methods of Digging for “Gold” within the Salt: Characterization of Halophilic Prokaryotes and Identification of Their Valuable Biological Products Using Sequencing and Genome Mining Tools
Jakub Lach, Paulina Jęcz, Dominik Strapagiel, Agnieszka Matera-Witkiewicz, Paweł Stączek
Genes.2021; 12(11): 1756. CrossRef
Lentibacillus saliphilus. sp. nov., a moderately halophilic bacterium isolated from a saltern in Korea
Yun Wang, Gang-Qiang Jiang, Hong-Ping Lin, Peng Sun, Hong-Yan Zhang, Dong-Mei Lu, Li-Yun Wang, Chang-Jin Kim, Shu-Kun Tang
Archives of Microbiology.2021; 203(2): 621. CrossRef
Salicibibacter cibarius sp. nov. and Salicibibacter cibi sp. nov., two novel species of the family Bacillaceae isolated from kimchi
Young Joon Oh, Joon Yong Kim, Seul Ki Lim, Min-Sung Kwon, Hak-Jong Choi
Journal of Microbiology.2021; 59(5): 460. CrossRef
Flaviflexus ciconiae sp. nov., isolated from the faeces of the oriental stork, Ciconia boyciana
Jae-Yun Lee, Woorim Kang, Pil Soo Kim, So-Yeon Lee, Na-Ri Shin, Hojun Sung, June-Young Lee, Ji-Hyun Yun, Yun-Seok Jeong, Jeong Eun Han, Mi-Ja Jung, Dong-Wook Hyun, Hyun Sik Kim, Euon Jung Tak, Jin-Woo Bae
International Journal of Systematic and Evolutionary Microbiology.2020; 70(10): 5439. CrossRef
List of new names and new combinations that have appeared in effective publications outside of the IJSEM and are submitted for valid publication
Aharon Oren, George M. Garrity
International Journal of Systematic and Evolutionary Microbiology .2019;[Epub] CrossRef

Differences in the gut microbiota between Cercopithecinae and Colobinae in captivity: Zongjin Huan , Yongfang Yao , Jianqiu Yu , Hongwei Chen , Meirong Li , Chaojun Yang , Bo Zhao , Qingyong Ni , Mingwang Zhang , Meng Xie , Huailiang Xu; J. Microbiol. 2020;58(5):367-376. Published online March 28, 2020; DOI: https://doi.org/10.1007/s12275-020-9493-9

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The gut microbiome of captive primates can provide a window into their health and disease status. The diversity and composition of gut microbiota are influenced by not only host phylogeny, but also host diet. Old World monkeys (Cercopithecidae) are divided into two subfamilies: Cercopithecinae and Colobinae. The diet and physiological digestive features differ between these two subfamilies. Accordingly, highthroughput sequencing was used to examine gut microbiota differences between these two subfamilies, using data from 29 Cercopithecinae individuals and 19 Colobinae individuals raised in captivity. Through a comparative analysis of operational taxonomic units (OTUs), significant differences in the diversity and composition of gut microbiota were observed between Cercopithecinae and Colobinae. In particular, the gut microbiota of captive Old World monkeys clustered strongly by the two subfamilies. The Colobinae microbial diversity was higher than that of Cercopithecinae. Additionally, Firmicutes, Lactobacillaceae, Veillonellaceae, and Prevotella abundance were higher in Cercopithecinae, while Bacteroidetes, Ruminococcaceae, Christensenellaceae, Bacteroidaceae, and Acidaminococcaceae abundance were higher in Colobinae. PICRUSt analysis revealed that the predicted metagenomes of metabolic pathways associated with proteins, carbohydrates, and amino acids were significantly higher in Colobinae. In the context of host phylogeny, these differences between Cercopithecinae and Colobinae could reflect adaptations associated with their respective diets. This well-organized dataset is a valuable resource for future related research on primates and gut microbiota. Moreover, this study may provide useful insight into animal management practices and primate conservation.

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Jejubacter calystegiae gen. nov., sp. nov., moderately halophilic, a new member of the family Enterobacteriaceae, isolated from beach morning glory: Lingmin Jiang , Dexin Wang , Jung-Sook Lee , Dae-Hyuk Kim , Jae Cheol Jeong , Cha Young Kim , Suk Weon Kim , Jiyoung Lee; J. Microbiol. 2020;58(5):357-366. Published online March 27, 2020; DOI: https://doi.org/10.1007/s12275-020-9294-1; Correction in: J. Microbiol 2025;63(8):e2508100

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Strain KSNA2T, a Gram-negative, moderately halophilic, facultatively anaerobic, motile, rod-shaped bacterium, was isolated from the surface-sterilized stem tissue of a beach morning glory (Calystegia soldanella) plant in Chuja Island, Jejudo, Republic of Korea. Phylogenetic analysis based on 16S rRNA gene and whole-genome sequences revealed that strain KSNA2T formed a distinct lineage within the family Enterobacteriaceae, with the highest 16S rRNA gene sequence similarity to Izhakiella australiensis KCTC 72143T (96.2%) and Izhakiella capsodis KCTC 72142T (96.0%), exhibited 95.5– 95.9% similarity to other genera in the family Enterobacteriaceae and Erwiniaceae. Conserved signature indels analysis elucidated that strain KSNA2T was delimited into family Enterobacteriaceae. KSNA2T genome comprises a circular chromosome of 5,182,800 bp with 56.1% G + C content. Digital DNA-DNA relatedness levels between strain KSNA2T and 18 closely related species were 19.3 to 21.1%. Average nucleotide identity values were between 72.0 and 76.7%. Growth of strain KSNA2T was observed at 4 to 45°C (optimum, 25°C) and pH 5.0 to 12.0 (optimum, pH 7.0) in the presence of 0 to 11% (w/v) NaCl (optimum, 0–7%). The major cellular fatty acids (> 10%) were C16:0 followed by summed feature 8 (C18:1 ω7c and/or C18:1 ω6c), summed feature 3 (C16:1 ω7c and/or C16:1 ω6c), C17:0 cyclo, and C14:0. The major isoprenoid quinone was ubiquinone-8 (Q-8). With combined phylogenetic, genomic, phenotypic, and chemotaxonomic features, strain KSNA2T represents a novel species of a new genus in the family Enterobacteriaceae, for which the name Jejubacter calystegiae gen. nov., sp. nov. is proposed. The type strain is KSNA2T (= KCTC 72234T = CCTCC AB 2019098T).

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Review

[MINIREVIEW] Alanine dehydrogenases in mycobacteria: Ji-A Jeong , Jeong-Il Oh; J. Microbiol. 2019;57(2):81-92. Published online January 31, 2019; DOI: https://doi.org/10.1007/s12275-019-8543-7

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Since NAD(H)-dependent L-alanine dehydrogenase (EC 1.1.4.1; Ald) was identified as one of the major antigens present in culture filtrates of Mycobacterium tuberculosis, many studies on the enzyme have been conducted. Ald catalyzes the reversible conversion of pyruvate to alanine with concomitant oxidation of NADH to NAD+ and has a homohexameric quaternary structure. Expression of the ald genes was observed to be strongly upregulated in M. tuberculosis and Mycobacterium smegmatis grown in the presence of alanine. Furthermore, expression of the ald genes in some mycobacteria was observed to increase under respiration-inhibitory conditions such as oxygen-limiting and nutrient-starvation conditions. Upregulation of ald expression by alanine or under respiration-inhibitory conditions is mediated by AldR, a member of the Lrp/AsnC family of transcriptional regulators. Mycobacterial Alds were demonstrated to be the enzymes required for utilization of alanine as a nitrogen source and to help mycobacteria survive under respiration-inhibitory conditions by maintaining cellular NADH/NAD+ homeostasis. Several inhibitors of Ald have been developed, and their application in combination with respiration-inhibitory antitubercular drugs such as Q203 and bedaquiline was recently suggested.

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Journal Article

A rule governing the FtsH-mediated proteolysis of the MgtC virulence protein from Salmonella enterica serovar Typhimurium: Jonghyun Baek , Eunna Choi , Eun-Jin Lee; J. Microbiol. 2018;56(8):565-570. Published online July 25, 2018; DOI: https://doi.org/10.1007/s12275-018-8245-6

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A tightly controlled turnover of membrane proteins is required for lipid bilayer stability, cell metabolism, and cell viability. Among the energy-dependent AAA+ proteases in Salmonella, FtsH is the only membrane-bound protease that contributes to the quality control of membrane proteins. FtsH preferentially degrades the C-terminus or N-terminus of misfolded, misassembled, or damaged proteins to maintain physiological functions. We found that FtsH hydrolyzes the Salmonella MgtC virulence protein when we substitute the MgtC 226th Trp, which is well conserved in other intracellular pathogens and normally protects MgtC from the FtsH-mediated proteolysis. Here we investigate a rule determining the FtsHmediated proteolysis of the MgtC protein at Trp226 residue. Substitution of MgtC tryptophan 226th residue to alanine, glycine, or tyrosine leads to MgtC proteolysis in a manner dependent on the FtsH protease whereas substitution to phenylalanine, methionine, isoleucine, leucine, or valine resists MgtC degradation by FtsH. These data indicate that a large and hydrophobic side chain at 226th residue is required for protection from the FtsH-mediated MgtC proteolysis.

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Reviews

Plasmodium falciparum apicoplast and its transcriptional regulation through calcium signaling: Praveen Rai , Drista Sharma , Rani Soni , Nazia Khatoon , Bhaskar Sharma , Tarun Kumar Bhatt; J. Microbiol. 2017;55(4):231-236. Published online March 1, 2017; DOI: https://doi.org/10.1007/s12275-017-6525-1

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Malaria has been present since ancient time and remains a major global health problem in developing countries. Plas-modium falciparum belongs to the phylum Apicomplexan, largely contain disease-causing parasites and characterized by the presence of apicoplast. It is a very essential organelle of P. falciparum responsible for the synthesis of key mole-cules required for the growth of the parasite. Indispensable nature of apicoplast makes it a potential drug target. Calcium signaling is important in the establishment of malaria para-site inside the host. It has been involved in invasion and egress of merozoites during the asexual life cycle of the parasite. Calcium signaling also regulates apicoplast metabolism. There-fore, in this review, we will focus on the role of apicoplast in malaria biology and its metabolic regulation through Ca++ signaling.

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REVIEW] Developmental regulators in Aspergillus fumigatus: Hee-Soo Park , Jae-Hyuk Yu; J. Microbiol. 2016;54(3):223-231. Published online February 27, 2016; DOI: https://doi.org/10.1007/s12275-016-5619-5

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The filamentous fungus Aspergillus fumigatus is the most prevalent airborne fungal pathogen causing severe and usually fatal invasive aspergillosis in immunocompromised patients. This fungus produces a large number of small hydrophobic asexual spores called conidia as the primary means of reproduction, cell survival, propagation, and infectivity. The initiation, progression, and completion of asexual development (conidiation) is controlled by various regulators that govern expression of thousands of genes associated with formation of the asexual developmental structure conidiophore, and biogenesis of conidia. In this review, we summarize key regulators that directly or indirectly govern conidiation in this important pathogenic fungus. Better understanding these developmental regulators may provide insights into the improvement in controlling both beneficial and detrimental aspects of various Aspergillus species.

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

Transcriptional profiles of laccase genes in the brown rot fungus Postia placenta MAD-R-698: Hongde An , Dongsheng Wei , Tingting Xiao; J. Microbiol. 2015;53(9):606-615. Published online August 1, 2015; DOI: https://doi.org/10.1007/s12275-015-4705-4

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One of the laccase isoforms in the brown rot fungus Postia placenta is thought to contribute to the production of hydroxyl radicals, which play an important role in lignocellulose degradation. However, the presence of at least two laccase isoforms in this fungus makes it difficult to understand the details of this mechanism. In this study, we systematically investigated the transcriptional patterns of two laccase genes, Pplcc1 and Pplcc2, by quantitative PCR (qPCR) to better understand the mechanism. The qPCR results showed that neither of the two genes was expressed constitutively throughout growth in liquid culture or during the degradation of a woody substrate. Transcription of Pplcc1 was upregulated under nitrogen depletion and in response to a high concentration of copper in liquid culture, and during the initial colonization of intact aspen wafer. However, it was subject to catabolite repression by a high concentration of glucose. Transcription of Pplcc2 was upregulated by stresses caused by ferulic acid, 2, 6-dimethylbenzoic acid, and ethanol, and under osmotic stress in liquid culture. However, the transcription of Pplcc2 was downregulated upon contact with the woody substrate in solid culture. These results indicate that Pplcc1 and Pplcc2 are differentially regulated in liquid and solid cultures. Pplcc1 seems to play the major role in producing hydroxyl radicals and Pplcc2 in the stress response during the degradation of a woody substrate.

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Laccase induction by synthetic dyes in Pycnoporus sanguineus and their possible use for sugar cane bagasse delignification
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Molecular characterization of a novel thermostable laccase PPLCC2 from the brown rot fungus Postia placenta MAD-698-R
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Oral administration of Lactobacillus plantarum lysates attenuates the development of atopic dermatitis lesions in mouse models: Hangeun Kim , Hye Rim Kim , Na-Ra Kim , Bong Jun Jeong , Jong Suk Lee , Soojin Jang , Dae Kyun Chung; J. Microbiol. 2015;53(1):47-52. Published online December 4, 2014; DOI: https://doi.org/10.1007/s12275-015-4483-z

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Lactobacillus plantarum is a well-documented probiotic that has been used in clinical trials for the regulation of the immune system and treatment of gastrointestinal diseases. In this study, we evaluated the effects of L. plantarum cell lysates on the immune regulation through the in vitro and in vivo studies. L. plantarum lysates were prepared by sonication
method
, and we observed that the repetition of disruption step increased indicator components within the bacterial lysates. Indicator components might affect TNF-α production. L. plantarum lysates did not induce TNF-α production, while LPS-induced TNF-α production was dramatically inhibited in a sonication-dependent manner in THP-1 cells. Oral administration of L. plantarum lysates effectively attenuated the horny layer formation and decreased epidermal thickening in NC/Nga mice skin. The damage to barrier function after the 8 weeks oral administration was reduced by L. plantarum lysates as compared to that in the atopic dermatitis (AD) mice. Further study revealed that L. plantarum lysates polarized Th1 response via induction of IL-12 and IFN-γ production and inhibition of IL-4 and IgE production in NC/Nga mice. Together, our results suggest that L. plantarum lysates are remarkable material for host homeostasis and it could be used for the treatment of inflammatory diseases.

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Note] Identification of High-Specificity H-NS Binding Site in LEE5 Promoter of Enteropathogenic Esherichia coli (EPEC): Abhay Prasad Bhat , Minsang Shin , Hyon E. Choy; J. Microbiol. 2014;52(7):626-629. Published online March 7, 2014; DOI: https://doi.org/10.1007/s12275-014-3562-x

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Histone-like nucleoid structuring protein (H-NS) is a small but abundant protein present in enteric bacteria and is involved in compaction of the DNA and regulation of the transcription. Recent reports have suggested that H-NS binds to a specific AT rich DNA sequence than to intrinsically curved DNA in sequence independent manner. We detected two high-specificity H-NS binding sites in LEE5 promoter of EPEC centered at -110 and -138, which were close to the proposed consensus H-NS binding motif. To identify H-NS binding sequence in LEE5 promoter, we took a random mutagenesis approach and found the mutations at around -138 were specifically defective in the regulation byH-NS. It was concluded that H-NS exertsmaximumrepression via the specific sequence at around -138 and ubsequently contacts α subunit of RNAP through oligomerization.

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

NOTE] The Helicobacter pylori Ferric Uptake Regulator (Fur) Is Essential for Growth Under Sodium Chloride Stress: Hanan Gancz , D. Scott Merrell; J. Microbiol. 2011;49(2):294-298. Published online May 3, 2011; DOI: https://doi.org/10.1007/s12275-011-0396-7

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Epidemiological data and animal models indicate that Helicobacter pylori and dietary NaCl have a synergistic ill effect on gastric maladies. Here we show that the Ferric Uptake Regulator (Fur), which is a crucial regulatory factor required for H. pylori colonization, is essential for growth in the presence of high NaCl concentrations. Moreover, we demonstrate that the transcriptional response induced by sodium chloride stress exhibits similarities to that seen under iron depletion.

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Cristina Sarasa-Buisan, Etienne Emonot, Marta Martínez-Júlvez, Emma Sevilla, Adrián Velázquez-Campoy, Serge Crouzy, M Teresa Bes, Isabelle Michaud-Soret, María F Fillat
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Interplay between Amoxicillin Resistance and Osmotic Stress in Helicobacter pylori
Ian H. Windham, D. Scott Merrell, George O’Toole
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Transcriptional response to metal starvation in the emerging pathogen Mycoplasma genitalium is mediated by Fur-dependent and –independent regulatory pathways
Carlos Martínez-Torró, Sergi Torres-Puig, Marta Monge, Lucía Sánchez-Alba, Miguel González-Martín, Marina Marcos-Silva, Alex Perálvarez-Marín, Francesc Canals, Enrique Querol, Jaume Piñol, Oscar Q. Pich
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High-Salt Conditions Alter Transcription of Helicobacter pylori Genes Encoding Outer Membrane Proteins
John T. Loh, Amber C. Beckett, Matthew B. Scholz, Timothy L. Cover, Vincent B. Young
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Bismuth-Induced Inactivation of Ferric Uptake Regulator from Helicobacter pylori
Xiaojun He, Xiangwen Liao, Hongyan Li, Wei Xia, Hongzhe Sun
Inorganic Chemistry.2017; 56(24): 15041. CrossRef
Characterization of Key Helicobacter pylori Regulators Identifies a Role for ArsRS in Biofilm Formation
Stephanie L. Servetas, Beth M. Carpenter, Kathryn P. Haley, Jeremy J. Gilbreath, Jennifer A. Gaddy, D. Scott Merrell, T. J. Silhavy
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Amira Suriaty Yaakop, Kok-Gan Chan, Robson Ee, Yan Lue Lim, Siew-Kim Lee, Fazilah Abd Manan, Kian Mau Goh
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Helicobacter pylori Adaptation In Vivo in Response to a High-Salt Diet
John T. Loh, Jennifer A. Gaddy, Holly M. Scott Algood, Silvana Gaudieri, Simon Mallal, Timothy L. Cover, S. R. Blanke
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Liang Yin, Yanfen Xue, Yanhe Ma, Marie-Joelle Virolle
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Metabolic Shift of Escherichia coli under Salt Stress in the Presence of Glycine Betaine
A. Metris, S. M. George, F. Mulholland, A. T. Carter, J. Baranyi, J. Björkroth
Applied and Environmental Microbiology.2014; 80(15): 4745. CrossRef
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Patrick M. Chong, Tarah Lynch, Stuart McCorrister, Pamela Kibsey, Mark Miller, Denise Gravel, Garrett R. Westmacott, Michael R. Mulvey, Axel Cloeckaert
PLoS ONE.2014; 9(1): e82622. CrossRef
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Aifen Zhou, Edward Baidoo, Zhili He, Aindrila Mukhopadhyay, Jason K Baumohl, Peter Benke, Marcin P Joachimiak, Ming Xie, Rong Song, Adam P Arkin, Terry C Hazen, Jay D Keasling, Judy D Wall, David A Stahl, Jizhong Zhou
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Marta Correia, Valérie Michel, Hugo Osório, Meriem El Ghachi, Mathilde Bonis, Ivo G. Boneca, Hilde De Reuse, António A. Matos, Pascal Lenormand, Raquel Seruca, Ceu Figueiredo, Jose Carlos Machado, Eliette Touati, Georgina L. Hold
PLoS ONE.2013; 8(4): e60657. CrossRef
The Ferric Uptake Regulator of Helicobacter Pylori : a Critical Player in the Battle for Iron and Colonization of the Stomach
Oscar Q Pich, D Scott Merrell
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Detailed analysis of Helicobacter pylori Fur‐regulated promoters reveals a Fur box core sequence and novel Fur‐regulated genes
Oscar Q. Pich, Beth M. Carpenter, Jeremy J. Gilbreath, D. Scott Merrell
Molecular Microbiology.2012; 84(5): 921. CrossRef
Analysis of Helicobacter pylori cagA Promoter Elements Required for Salt-Induced Upregulation of CagA Expression
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Infection and Immunity.2012; 80(9): 3094. CrossRef

Research Support, N.I.H., Extramural

Helicobacter pylori apo-Fur Regulation Appears Unconserved Across Species: Shana Miles , Beth M. Carpenter , Hanan Gancz , D. Scott Merrell; J. Microbiol. 2010;48(3):378-386. Published online June 23, 2010; DOI: https://doi.org/10.1007/s12275-010-0022-0

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Abstract PDF: The Ferric Uptake Regulator (Fur) is a transcriptional regulator that is conserved across a broad number of bacterial species and has been shown to regulate expression of iron uptake and storage genes. Additionally, Fur has been shown to be an important colonization factor of the gastric pathogen Helicobacter pylori. In H. pylori, Fur-dependent regulation appears to be unique in that Fur is able to act as a transcriptional repressor when bound to iron as well as in its iron free (apo) form. To date, apo-regulation has not been identified in any other bacterium. To determine whether Fur from other species has the capacity for aporegulation, we investigated the ability of Fur from Escherichia coli, Campylobacter jejuni, Desulfovibrio vulgaris Hildenborough, Pseudomonas aeruginosa, and Vibrio cholerae to complement both iron-bound and apo-Fur regulation within the context of a H. pylori fur mutant. We found that while some Fur species (E. coli, C. jejuni, and V. cholerae) complemented iron-bound regulation, apo-regulation was unable to be complemented by any of the examined species. These data suggest that despite the conservation among bacterial Fur proteins, H. pylori Fur contains unique structure/function features that make it novel in comparison to Fur from other species.

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

Transcriptional Regulation of hemO Encoding Heme Oxygenase in Clostridium perfringens: Sufi Hassan , Kaori Ohtani , Ruoyu Wang , Yonghui Yuan , Yun Wang , Yumi Yamaguchi , Tohru Shimizu; J. Microbiol. 2010;48(1):96-101. Published online March 11, 2010; DOI: https://doi.org/10.1007/s12275-009-0384-3

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Abstract PDF: A Gram-positive anaerobic pathogen, Clostridium perfringens, causes clostridial myonecrosis or gas gangrene in humans by producing numerous extracellular toxins and enzymes that act in concert to degrade host tissues. The ability of infectious bacteria to acquire sufficient iron during infection is essential for the pathogen to cause disease. In the C. perfringens strain 13 genome, a heme oxygenase gene homologue (CPE0214, hemO) was found and its role was examined. The purified recombinant HemO protein showed heme oxygenase activity that can convert heme to biliverdin. hemO transcription was induced in response to extracellular hemin in a dose-dependent manner. The global two-component VirR/VirS regulatory system and its secondary regulator VR-RNA had positive regulatory effects on the transcription of hemO. These data indicate that heme oxygenase may play important roles in iron acquisition and cellular metabolism, and that the VirR/VirS-VR-RNA system is also involved in the regulation of cellular iron homeostasis, which might be important for the survival of C. perfringens in a human host.

Expression and Regulation of Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Genes in Mycobacterium sp. Strain JC1 DSM 3803: Jae Ho Lee , Dong Oh Park , Sae Woong Park , Eun Ha Hwang , Jeong Il Oh , Young Min Kim; J. Microbiol. 2009;47(3):297-307. Published online June 26, 2009; DOI: https://doi.org/10.1007/s12275-008-0210-3

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Ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO) is the key enzyme of the Calvin reductive pentose phosphate cycle. Two sets of structural genes (cbbLS-1 and -2) for form I RubisCO have been previously identified in the Mycobacterium sp. strain JC1, which is able to grow on carbon monoxide (CO) or methanol as sole sources of carbon and energy. Northern blot and reverse transcriptase PCR showed that the cbbLS-1 and -2 genes are expressed in cells grown on either carbon monoxide (CO) or methanol, but not in cells grown in nutrient broth. A promoter assay revealed that the cbbLS-2 promoter has a higher activity than the cbbLS-1 promoter in both CO- and methanol-grown cells, and that the activities of both promoters were higher in CO-grown cells than in methanol-grown cells. A gel mobility shift assay and footprinting assays showed that CbbR expressed in Escherichia coli from a cbbR gene, which is located downstream of cbbLS-1 and transcribed in the same orientation as that of the cbbLS genes, specifically bound to the promoter regions of the cbbLS-1 and -2 genes containing inverted repeat sequence. A DNase I footprinting assay revealed that CbbR protected positions -59 to -3 and -119 to -78 of the cbbLS-1 and -2 promoters, respectively. Overexpression of CbbR induced the transcription of RubisCO genes in Mycobacterium sp. strain JC1 grown in nutrient broth. Our results suggest that the CbbR product from a single cbbR gene may positively regulate two cbbLS operons in the Mycobacterium sp. strain JC1 as is the case for Rhodobacter sphaeroides and Cupriavidus necator.

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Methylotrophy in Mycobacteria: Dissection of the Methanol Metabolism Pathway in Mycobacterium smegmatis
Abhishek Anil Dubey, Saloni Rajesh Wani, Vikas Jain, William W. Metcalf
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A thiotrophic microbial community in an acidic brine lake in Northern Chile
Lorena Escudero, Nia Oetiker, Karem Gallardo, Cinthya Tebes-Cayo, Mariela Guajardo, Claudia Nuñez, Carol Davis-Belmar, J. J. Pueyo, Guillermo Chong Díaz, Cecilia Demergasso
Antonie van Leeuwenhoek.2018; 111(8): 1403. CrossRef
Functional characterization of the cutI gene for the transcription of carbon monoxide dehydrogenase genes in Mycobacterium sp. strain JC1 DSM 3803
Jae Ho Lee, Sae Woong Park, Young Min Kim, Jeong-Il Oh
Journal of Microbiology.2017; 55(1): 31. CrossRef
Analysis of microbial communities in the oil reservoir subjected to CO2-flooding by using functional genes as molecular biomarkers for microbial CO2 sequestration
Jin-Feng Liu, Xiao-Bo Sun, Guang-Chao Yang, Serge M. Mbadinga, Ji-Dong Gu, Bo-Zhong Mu
Frontiers in Microbiology.2015;[Epub] CrossRef
CbbR, the Master Regulator for Microbial Carbon Dioxide Fixation
Andrew W. Dangel, F. Robert Tabita, W. Margolin
Journal of Bacteriology.2015; 197(22): 3488. CrossRef
Amino acid substitutions in the transcriptional regulator CbbR lead to constitutively active CbbR proteins that elevate expression of the cbb CO2 fixation operons in Ralstonia eutropha (Cupriavidus necator) and identify regions of CbbR necessary for gene
Andrew W. Dangel, F. Robert Tabita
Microbiology.2015; 161(9): 1816. CrossRef
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Antonie van Leeuwenhoek.2012; 101(4): 685. CrossRef
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Journal Article

DNA Adenine Methylation of sams1 Gene in Symbiont-Bearing Amoeba proteus: Taeck J. Jeon; J. Microbiol. 2008;46(5):564-570. Published online October 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0129-8

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The expression of amoeba sams genes is switched from sams1 to sams2 when amoebae are infected with Legionella jeonii. To elucidate the mechanism for the inactivation of host sams1 gene by endosymbiotic bacteria, methylation states of the sams1 gene of D and xD amoebae was compared in this study. The sams1 gene of amoebae was methylated at an internal adenine residue of GATC site in symbiont-bearing xD amoebae but not in symbiont-free D amoebae, suggesting that the modification might have caused the inactivation of sams1 in xD amoebae. The sams1 gene of xD amoebae was inactivated at the transcriptional level. Analysis of DNA showed that adenine residues in L. jeonii sams were also methylated, implying that L. jeonii bacteria belong to a Dam methylase-positive strain. In addition, both SAM and Met appeared to act as negative regulators for the expression of sams1 whereas the expression of sams2 was not affected in amoebae.

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Alternative migratory locust phenotypes are associated with differences in the expression of genes encoding the methylation machinery
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Research Support, Non-U.S. Gov'ts

Modulation of Secreted Virulence Factor Genes by Subinhibitory Concentrations of Antibiotics in Pseudomonas aeruginosa: Lixin Shen , Ying Shi , Dan Zhang , Jinhua Wei , Michael G. Surette , Kangmin Duan; J. Microbiol. 2008;46(4):441-447. Published online August 31, 2008; DOI: https://doi.org/10.1007/s12275-008-0054-x

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Abstract PDF: Recent studies have shown that subinhibitory antibiotics play important roles in regulating bacterial genes including virulence factor genes. In this study, the expression of 13 secreted virulence related gene clusters of Pseudomonas aeruginosa, an important opportunistic pathogen, was examined in the presence of subinhibitory concentrations of 4 antibiotics: vancomycin, tetracycline, ampicilin and azithromycin. Activation of gene expression was observed with phzA1, rhlAB, phzA2, lasB, exoY, and exoS. Subinhibitory concentrations of vancomycin resulted in more than 10-fold increase of rhlAB and phzA2 transcription. Both rhamnolipid production and pyocyanin production were significantly elevated, correlating phenotypes with the increased transcription. P. aeruginosa swarming and swimming motility also increased. Similar results were observed with subinhibitory tetracycline, azithromycin and ampicillin. These results indicate that the antibiotics at low concentrations can up-regulate virulence factors and therefore influence bacterial pathogenesis.

NOTE] Molecular Analysis of the fur (ferric uptake regulator) Gene of a Pathogenic Edwardsiella tarda Strain: Fang Wang , Shuang Cheng , Kun Sun , Li Sun; J. Microbiol. 2008;46(3):350-355. Published online July 5, 2008; DOI: https://doi.org/10.1007/s12275-008-0038-x

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The gene encoding the Edwardsiella tarda ferric uptake regulator (FurEt) was cloned from a pathogenic E. tarda strain isolated from diseased fish. FurEt shares 90% overall sequence identity with the Escherichia coli Fur (FurEc) and was able to complement the mutant phenotype of a furEc-defective E. coli strain. Mutational analysis indicated that C92S and C95S mutations inactivated FurEt whereas E112K mutation resulted in a superactive FurEt variant. FurEt negatively regulated its own expression; interruption of this regulation impaired bacterial growth, altered the production of certain outer membrane proteins, and attenuated bacterial virulence.

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Journal Article

Carbon Source-Dependent Regulation of the Schizosaccharomyces pombe pbh1 Gene: Su-Jung Kim , Nam-Chul Cho , In Wang Ryu , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2006;44(6):689-693.; DOI: https://doi.org/2454 [pii]

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Abstract PDF: Pbh1, from the fission yeast Schizosaccharomyces pombe, is a baculoviral inhibitor of apoptosis (IAP) repeat (BIR) domain-containing protein. Its unique encoding gene was previously found to be regulated by nitric oxide and nitrogen starvation. In the current work, the Pbh1-lacZ fusion gene was used to elucidate the transcriptional regulation of the pbh1 gene under various carbon sources. When fermentable carbon sources, such as glucose (at a low concentration of 0.2%), sucrose (2.0%) and lactose (2.0%), were the sole carbon source, the synthesis of β-galactosidase from the Pbh1-lacZ fusion gene was reasonably enhanced. However, the induction by these fermentable carbon sources was abolished in the Pap1-negative S. pombe cells, implying that this type of induction of the pbh1 gene is mediated by Pap1. Ethanol (2.0%), a nonfermentable carbon source, was also able to enhance the synthesis of β-galactosidase from the fusion gene in wild-type cells but not in Pap1-negative cells. The results indicate that the S. pombe pbh1 gene is up-regulated under metabolic oxidative stress in a Pap1-dependent manner.

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

Effect of Mutations of Five Conserved Histidine Residues in the Catalytic Subunit of the cbb3 Cytochrome c Oxidase on its Function: Jeong-Il Oh; J. Microbiol. 2006;44(3):284-292.; DOI: https://doi.org/2384 [pii]

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Abstract PDF: The cbb3 cytochrome c oxidase has the dual function as a terminal oxidase and oxygen sensor in the photosynthetic bacterium, Rhodobacter sphaeroides. The cbb3 oxidase forms a signal transduction pathway together with the PrrBA two-component system that controls photosynthesis gene expression in response to changes in oxygen tension in the environment. Under aerobic conditions the cbb3 oxidase generates an inhibitory signal, which shifts the equilibrium of PrrB kinase/phosphatase activities towards the phosphatase mode. Photosynthesis genes are thereby turned off under aerobic conditions. The catalytic subunit (CcoN) of the R. sphaeroides cbb3 oxidase contains five histidine residues (H214, H233, H303, H320, and H444) that are conserved in all CcoN subunits of the cbb3 oxidase, but not in the catalytic subunits of other members of copper-heme superfamily oxidases. H214A mutation of CcoN affected neither catalytic activity nor sensory (signaling) function of the cbb3 oxidase, whereas H320A mutation led to almost complete loss of both catalytic activity and sensory function of the cbb3 oxidase. H233V and H444A mutations brought about the partial loss of catalytic activity and sensory function of the cbb3 oxidase. Interestingly, the H303A mutant form of the cbb3 oxidase retains the catalytic function as a cytochrome c oxidase as compared to the wild-type oxidase, while it is defective in signaling function as an oxygen sensor. H303 appears to be implicated in either signal sensing or generation of the inhibitory signal to the PrrBA two-component system.

Transcriptional Analysis and Pap1-Dependence of the Unique Gene Encoding Thioredoxin Reductase from the Fission Yeast: Hyun-Jung Kang , Sung-Min Hong , Byung-Chul Kim , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2006;44(1):35-41.; DOI: https://doi.org/2339 [pii]

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Abstract PDF: The unique gene encoding thioredoxin reductase (TrxR) was previously cloned and characterized from the fission yeast Schizosaccharomyces pombe, and its expression was induced by oxidative stress. To elucidate the regulatory mechanism of the S. pombe TrxR gene, three fusion plasmids were generated using polymerase chain reaction: pYUTR20, pYUTR30, and pYUTR40. Plasmid pYUTR20 has an upstream region of 891 base pairs, pYUTR30 has 499 in this region, and pYUTR40 has an 186 bp upstream region. Negatively acting sequence is located between ‒1,526 ~ ‒891 bp upstream of the gene. The upstream sequence, responsible for the induction of TrxR by menadione (MD), is situated on the ‒499 ~ ‒186 bp region, which is also required for TrxR induction by mercuric chloride. The same region also appeared to be required for Pap1-mediated transcriptional regulation of the TrxR gene, which contains the two plausible Pap1 binding sites, TTACGAAT and TTACGCGA. Consistently, basal and inducible expression of the TrxR gene was markedly lower in the Pap1-negative TP108-3C cells than in wild-type yeast cells. In summary, up-regulation of the S. pombe TrxR gene is mediated by Pap1 via the transcriptional motif( s) located on the ‒499 ~ ‒186 bp region.

The Schizosaccharomyces pombe Gene Encoding [gamma]-Glutamyl Transpeptidase I Is Regulated by Non-fermentable Carbon Sources and Nitrogen Starvation: Hong-Gyum Kim , Hey-Jung Park , Hyun-Jung Kang , Hye-Won Lim , Kyunghoon Kim , Eun-Hee Park , Kisup Ahn , Chang-Jin Lim; J. Microbiol. 2005;43(1):44-48.; DOI: https://doi.org/2139 [pii]

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Abstract PDF: In our previous study, the first structural gene (GGTI) encoding g-glutamyl transpeptidase was cloned and characterized from the fission yeast Schizosaccharomyces pombe, and its transcription, using the GGTI-lacZ fusion gene, containing the 1,085 bp upstream region from the translational initiation point, was found to be enhanced by sodium nitroprusside and L-buthionine-(S,R)-sulfoximine (BSO). In the present work, regulation of the GGTI gene was further elucidated. Non-fermentable carbon sources, such as acetate and ethanol, markedly enhanced the synthesis of [beta]-galactosidase from the GGTI-lacZ fusion gene. However, its induction by non-fermentable carbon sources appeared to be independent of the presence of the Pap1 protein. Nitrogen starvation also gave rise to induction of GGTI gene expression in a Pap1-independent manner. The three additional fusion plasmids, carrying 754, 421 and 156 bp regions, were constructed. The sequence responsible for the induction by non-fermentable carbon sources and nitrogen starvation was identified to exist within a -421 bp region of the GGTI gene. Taken together, the S. pombe GGTI gene is regulated by non-fermentable carbon sources and nitrogen starvation.

Transcriptional Regulation of the Schizosaccharomyces pombe Gene Encoding Glutathione S-Transferase I by a Transcription Factor Pap1: Hong-Gyum Kim , Byung-Chul Kim , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2004;42(4):353-356.; DOI: https://doi.org/2099 [pii]

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Abstract PDF: In a previous study, a gst gene was isolated from the fission yeast Schizosaccharomyces pombe. This gene was dubbed gst I, and was characterized using the gstI-lacZ fusion plasmid pYSH2000. In this work, four additional fusion plasmids, pYSHSD1, pYSHSD2, pYSHSD3 and pYSHSD4, were constructed, in order to carry (respectively) 770, 551, 358 and 151 bp upstream regions from the translational initiation point. The sequence responsible for induction by aluminum, mercury and hydrogen peroxide was located in the range between -1,088 and -770 bp upstream of the S. pombe gst I gene. The same region was identified to contain the nucleotide sequence responsible for regulation by Pap1, and has one putative Pap1 binding site, TTACGTAT, located in the range between -954 ~ -947 bp upstream of the gst I gene. Negatively acting sequences are located between -1,088 and -151 bp. These findings imply that the Pap1 protein is involved in basal and inducible transcription of the gst I gene in the fission yeast S. pombe.

Journal Article

Growth and Physiological Properties of Wild Type and Mutants of Halomonas subglaciescola DH-1 in Saline Environment: Hye Jeong Ryu , Yoo Jung Jeong , Doo Hyun Park; J. Microbiol. 2004;42(3):174-180.; DOI: https://doi.org/2093 [pii]

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Abstract PDF: A halophilic bacterium was isolated from fermented seafood. The 16S rDNA sequence identity between the isolate and Halomonas subglaciescola AJ306801 was above 95%. The isolate that did not grow in the condition without NaCl or in the condition with other sodium (Na^+) or chloride ions (Cl^-) instead of NaCl was named H. subglaciescola DH-1. Two mutants capable of growing without NaCl were obtained by random mutagenesis, of which their total soluble protein profiles were compared with those of the wild type by two-dimensional electrophoresis. The external compatible solutes (betaine and choline) and cell extract of the wild type did not function as osmoprotectants, and these parameters within the mutants did not enhance their growth in the saline environment. In the proton translocation test, rapid acidification of the reactant was not detected for the wild type, but it was detected for the mutant in the condition without NaCl. From these results, we derived the hypothesis that NaCl may be absolutely required for the energy metabolism of H. subglaciescola DH-1 but not for its osmoregulation, and the mutants may have another modified proton translocation system that is independent of NaCl, except for those mutants with an NaCl-dependent system.

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

Transcriptional Regulation of the Gene Encoding g-Glutamylcysteine Synthetase from the Fission Yeast Schizosaccharomyces pombe: Su-Jung Kim , Hong-Gyum Kim , Byung-Chul Kim , Kyunghoon Kim , Eun-Hee Park , Chang-Jin Lim; J. Microbiol. 2004;42(3):233-238.; DOI: https://doi.org/2083 [pii]

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Abstract PDF: Transcriptional regulation of the Schizosaccharomyces pombe [gamma]-glutamylcysteine synthetase (GCS) gene was examined using the two GCS-lacZ fusion plasmids pUGCS101 and pUGCS102, which harbor 607 bp and 447 bp upstream regions, respectively. The negatively-acting sequence was located in the -607 ~ -447 bp upstream region of the GCS gene. The upstream sequence responsible for induction by menadione (MD) and L-buthionine-(S, R)-sulfoximine (BSO) resides in the -607 ~ -447 bp region, whereas the sequence which codes for nitric oxide induction is located within the -447 bp region, measured from the translational initiation point. Carbon source-dependent regulation of the GCS gene appeared to be dependent on the nucleotide sequence within -447 bp region. The transcription factor Pap1 is involved in the induction of the GCS gene by MD and BSO, but not by nitric oxide. Induction of the GCS gene occurring due to low glucose concentration does not depend on the presence of Pap1. These data imply that induction by MD and BSO may be mediated by the Pap1 binding site, probably located in the -607 ~ -447 region, and also that the nitric oxide-mediated regulation of the S. pombe GCS gene may share a similar mechanism with its carbon-dependent induction.

5’ Untranslated Region of the Pseudomonas putida WCS358 Stationary Phase Sigma Factor rpoS mRNA is Involved in RpoS Translational Regulation: Branko Jovcic , Iris Bertani , Vittorio Venturi , Ljubisa Topisirovic , Milan Kojic; J. Microbiol. 2008;46(1):56-61.; DOI: https://doi.org/10.1007/s12275-007-0127-2

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8 Crossref

Abstract PDF

The σS subunit of RNA polymerase is a central regulator which governs the expression of a host of stationary phase-induced and osmotically regulated genes in Gram-negative bacteria. The Pseudomonas putida rpoS gene is transcribed as a monocistronic rpoS mRNA with a 368 nucleotide-long 5’ untranslated region (5’ UTR). In this study, we investigate the posttranscriptional control of RpoS synthesis using rpoS-lacZ transcriptional and translational fusions consisting of the native promoter and deletions of 5’ UTR or insertion into UTR. The differing activity of constructed translational fusions strongly indicated that the 5’ UTR is involved in the translational regulation of RpoS expression in the stationary phase. The results obtained herein demonstrated that the structure of UTR performs an important function in the translational regulation of the rpoS gene.

Citations

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The potential of cold-shock promoters for the expression of recombinant proteins in microbes and mammalian cells
Yaneth Bartolo-Aguilar, Cipriano Chávez-Cabrera, Luis Bernardo Flores-Cotera, Jesús Agustín Badillo-Corona, Carmen Oliver-Salvador, Rodolfo Marsch
Journal of Genetic Engineering and Biotechnology.2022; 20(1): 173. CrossRef
RgsA, an RpoS-dependent sRNA, negatively regulates rpoS expression in Pseudomonas aeruginosa
Pei Lu, Yifei Wang, Yangbo Hu, Shiyun Chen
Microbiology .2018; 164(4): 716. CrossRef
The promoter region of lapA and its transcriptional regulation by Fis in Pseudomonas putida
Hanna Ainelo, Andrio Lahesaare, Annika Teppo, Maia Kivisaar, Riho Teras, Dongsheng Zhou
PLOS ONE.2017; 12(9): e0185482. CrossRef
Regulation of gene expression at low temperature: role of cold-inducible promoters
Ashish Kumar Singh, Kirti Sad, Shailendra Kumar Singh, Sisinthy Shivaji
Microbiology .2014; 160(7): 1291. CrossRef
Cyclic diguanylate turnover mediated by the sole GGDEF/EAL response regulator in Pseudomonas putida: its role in the rhizosphere and an analysis of its target processes
Miguel A. Matilla, María L. Travieso, Juan L. Ramos, María Isabel Ramos‐González
Environmental Microbiology.2011; 13(7): 1745. CrossRef
Regulation of the cyclopropane synthase cfaB gene in Pseudomonas putida KT2440
Cecilia Pini, Patricia Godoy, Patricia Bernal, Juan-Luis Ramos, Ana Segura
FEMS Microbiology Letters.2011; 321(2): 107. CrossRef
Aspartate aminotransferase is involved in cold adaptation in psychrophilic Pseudomonas syringae
V. R. Sundareswaran, Ashish Kumar Singh, Smita Dube, S. Shivaji
Archives of Microbiology.2010; 192(8): 663. CrossRef
Importance of trmE for Growth of the Psychrophile Pseudomonas syringae at Low Temperatures
Ashish K. Singh, Pavan Kumar Pindi, Smita Dube, V. R. Sundareswaran, S. Shivaji
Applied and Environmental Microbiology.2009; 75(13): 4419. CrossRef

Regulation of the Expression of nhaA Gene, Coding Na^+/H^+ Antiporter A of Escherichia coli.: Seo, Sung Yum , Lee, Seung Heon; J. Microbiol. 1995;33(2):120-125.

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Abstract PDF: β-galactosidase activity of Escherichia coli cells containing operon fusion nhaA'-'lacZ was monitored to study the regulation of expression of nhaA gene under various conditions. The expression of the fusion was enhanced only by chemicals containing Na^+ or Li^+. This Na^+ or Li^+. This Na^+(Li^+)-specific enhancement of β-galactosidase activity represented the increase in the rate of synthesis of β-galactosidase rather than the decrease in the breakdown rate. The induction pattern was influenced by copy numbers of the gene. Induction by Na^+ or Li^+ was concentration and time dependent, reaching maximum 5-6 fold induction after 2 hours at 0.4-0.5 M for Na^+ or at 0.25-0.35 M for Li^+, Although the expression was induced at much lower concentration of Na^+ at alkaline pH values than at neutral pH in the presence of Na^+, alkaline pH itself did not induced the expression of the fusion in the absence of Na^+. Temperature shift and growth phase of culture did not affect the level of induction.

Analysis of the Dual Promoters and the H 2 O 2 -responsive Element of the catA Gene Encoding Catalase A in Streptomyces coelicolor: You-Hee Cho , Ji-Sook Hahn , Jung-Hye Roe; J. Microbiol. 2000;38(4):239-244.

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Abstract PDF: The catA gene encodes the major catalase in Streptomyces coelicolor, whose production increases upon H_2O_2 treatment. Besides the previously identified primary promoter (catAp1), a minor promoter (catAp2) was newly assigned by S1 nuclease mapping. The catAp2 transcript was observed transiently upon entry into the stationary phase in liquid culture and upon differentiation on solid plates, whereas the level of catAp1 transcription did not change significantly during this growth transition. The catAp1 promoter was transcribed by the major vegetative RNA polymerase holoenzyme containing [sigma]^HrdB , whereas the catAp2 was transcribed in vitro by the holoenzyme containing [sigma]^R that is activated under oxidative conditions. The cis-element regulating the H_2 O_2 -inducibility of catAp1 was identified within the 23 bp inverted repeat sequence located between -65 and -43 of the catAp1 promoter. We named this sequence HRE (H_2O_2 -responsive element). The distal half of the inverted repeat was more crucial for H_2 O_2 ?pendent induction of the catAp1 transcript than the proximal half. HRE most likely serves as a binding site for the H_2 O_2 -responsive repressor CatR.

Regulation of Glycogen Concentration by the Histidine-Containing Phosphocarrier Protein HPr in Escherichia coli: Byoung-Mo Koo , Yeong-Jae Seok; J. Microbiol. 2001;39(1):24-30.

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Abstract PDF: In addition to effecting the catalysis of sugar uptake, the bacterial phosphoenolpyruvate:sugar phosphotransferase system regulates a variety of physiological processes. In a previous paper [Seok et al., (1997) J. Biol. Chem. 272, 26511-26521], we reported the interaction with and allosteric regulation of Escherichia coli glycogen phosphorylase activity by the histidine-containing phosphocarrier protein HPr in vitro. Here, we show that the specific interaction between HPr and glycogen phosphorylase occurs in vivo. To address the physiological role of the HPr-glycogen phosphorylase complex, intracellular glycogen levels were measured in E. coli strains transformed with various plasmids. While glycogen accumulated during the transition between exponential and stationary growth phases in wildtype cells, it did not accumulate in cells overproducing HPr or its inactive mutant regardless of the growth stage. From these results, we conclude that HPr mediates crosstalk between sugar uptake through the phosphoenolpyruvate:sugar phosphotransferase system and glycogen breakdown. The evolutionary significance of the HPr-glycogen phosphorylase complex is suggested.

Cloning and Regulation of Schizosaccharomyces pombe Gene Encoding Ribosomal Protein S20: Yoon-Jong Lee , Kyunghoon Kim , Eun-Hee Park , Ki-Sup Ahn , Daemyung Kim , Chang-Jin Lim; J. Microbiol. 2001;39(1):31-36.

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Abstract PDF: A cDNA clone encoding the ribosomal protein S20 has been isolated from the Schizosaccharomyces pombe cDNA library by colony hybridization. The insert contained in the original plasmid pYJ10 was transferred into shuttle vector pRS316 to generate plasmid pYJ11. The cDNA insert of plasmid pYJ11 contains 484 nucleotides and encodes a protein of 118 amino acids with a calculated mass of 13,544 daltons. The deduced amino acid sequence of S. pombe ribosomal protein S20 is very homologous with fruit fly, rat, and budding yeast counterparts. It is also homologous with Xenopus S22 ribosomal protein. S. pombe ribosomal protein S20 appears to be relatively hydrophobic except the C-terminal region. The 728 bp upstream region of the S20 gene was amplified from chromosomal DNA and transferred into the BamHI/EcoRI site of the promoterless b-galactosidase gene of the vector YEp357R, which resulted in fusion plasmid pYS20. The synthesis of b-galactosidase from the fusion plasmid appeared to be the highest in the mid-exponential phase. The S. pombe cells with the fusion plasmid grown at 35oC gave lower b-galactosidase activity than the cells grown at 30oC. Computer analysis showed the consensus sequence CAGTCACA in the upstream regions of various ribosomal protein genes in S. pombe, which would be involved in the coordinated expression of small ibosomal proteins.

Regulation of Actin Gene Expression During the Differentiation of Naegleria gruberi: Misook Kim , JooHun Lee; J. Microbiol. 2001;39(1):42-48.

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Abstract PDF: The regulation of actin gene expression during the differentiation of Naegleria gruberi was examined. Actin mRNA concentration was maximal in amoebae and decreased rapidly after the initiation of differentiation. At 20 min after initiation, the concentration of actin mRNA decreased to 55% of the maximal value. The actin mRNA concentration decreased to the minimum at 80 min (15% of the maximum), and then began to increase slightly at the end of differentiation. This decrease of actin mRNA concentration was regulated by the repression of actin gene transcription based on nuclear runon transcription experiments. The rates of transcription of actin gene in nuclei prepared at 40 and 80 min after the initiation of differentiation were 50 and 28% of that of nuclei prepared at the beginning of differentiation, respectively. The addition of cycloheximide at the initiation of differentiation inhibited both the rapid decrease in the concentration of actin mRNA and the repression of actin gene transcription. These results suggest that the rapid decrease in the concentration of actin mRNA during the differentiation of N. gruberi is accomplished by the repression of actin gene transcription and this transcriptional regulation requires continuous protein synthesis during the differentiation.

Polyamine Stimulation of arcA Expression in Escherichia coli: Mun Su Rhee , Young Sik Kim , Seon Young Park , Myung Hun Choi , Bo Min Kim , Seong Uk Kang , Kui Joo Lee , Jong Ho Lee; J. Microbiol. 2002;40(4):305-312.

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Abstract PDF: The effects of two natural polyamines (putrescine and spermidine) on the synthesis of ArcA, a response regulator of the Arc two-component signal transduction system, were studied using an E. coli mutant deficient in polyamine biosynthesis. Endogenous polyamine deficiency of the mutant resulted in marked reduction in the ArcA level determined by Western blot analysis. Putrescine supplement to the growth medium effectively increased the ArcA level of the mutant in a concentration-dependent manner. Spermidine also stimulated the ArcA level in the mutant to a greater degree than putrescine. Expression of arcA'::lacZ operon fusion in the mutant was stimulated 6-fold and 10-fold by putrescine and spermidine at a 1mM concentration, respectively, indicating that the stimulatory effect of the polyamines on ArcA synthesis is due to transcriptional induction, and that spermidine is a more potent arcA inducer than putrescine. The polyamine-dependent arcA'::lacZ induction was growth-phase-dependent and independent of either arcA or fnr which are two regulators involved in anaerobic stimulation of the ArcA level. These results suggested that putrescine and spermidine polyamines may be potential intracellular signal molecules in the control of arcA expression, and thereby may play an important role in cellular metabolism.

Regulation of nsdD Expression in Aspergillus nidulans: Kap Hoon Han , Kyu-Yong Han , Min-Su Kim , Dong-Beom Lee , Jong-Hak Kim , Suhn-Kee Chae , Keon-Sang Chae , Dong-Min Han; J. Microbiol. 2003;41(3):259-261.

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Abstract PDF: The nsdD gene has been predicted to encode a GATA type transcription factor with the type IVb zinc finger DNA binding domain functions in activating sexual development of A. nidulans. In several allelic mutants of nsdD producing truncated NsdD polypeptides lacking the C-terminal zinc finger, the transcription level of nsdD gene was greatly increased. Also in an over-expressed mutant, the transcription under its own promoter was reduced. These results suggest that the expression of nsdD is negatively autoregulated. When the nsdD gene was over-expressed, cleistothecia were formed in excess amounts even in the presence of 0.6M KCl that inhibited sexual development of the wild type. Northern blot analysis revealed that the expression of nsdD was repressed by 0.6M KCl. These results strongly suggest that the inhibition of sexual development by salts was carried out via the nsdD involved regulatory network.

Regulation of Class II Bacteriocin Production by Cell-Cell Signaling: Luis E. N. Quadri; J. Microbiol. 2003;41(3):175-182.

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Abstract PDF: Production of ribosomally synthesized antimicrobial peptides usually referred to as bacteriocins is an inducible trait in several gram positive bacteria, particularly in those belonging to the group of lactic acid bacteria. In many of these organisms, production of bacteriocins is inducible and induction requires secretion and extracellular accumulation of peptides that act as chemical messengers and trigger bacteriocin production. These inducer peptides are often referred to as autoinducers and are believed to permit a quorum sensing-based regulation of bacteriocin production. Notably, the peptides acting as autoinducers are dedicated peptides with or without antimicrobial activity or the bacteriocins themselves. The autoinducer-dependent induction of bacteriocin production requires histidine protein kinases and response regulator proteins of two-component signal transduction systems. The current working model for the regulation of class II bacteriocin production in lactic acid bacteria and the most relevant direct and indirect pieces of evidence supporting the model are discussed in this minireview.

Salmonella Invasion Gene Regulation: A Story of Environmental Awareness: Bradley D. Jones; J. Microbiol. 2005;43(1):110-117.

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Abstract PDF: Salmonella enterica serovar Typhimurium causes human gastroenteritis and a systemic typhoid-like infection in mice. A critical virulence determinant of Salmonella is the ability to invade mammalian cells. The expression of genes required for invasion is tightly regulated by environmental conditions and a variety of regulatory genes. The hilA regulator encodes an OmpR/ToxR family transcriptional regulator that activates the expression of invasion genes in response to both environmental and genetic regulatory factors. Work from several laboratories has highlighted that regulation of hilA expression is a key point for controlling expression of the invasive phenotype. A number of positive regulators of hilA expression have been identified including csrAB, sirA/barA, pstS, hilC/sirC/sprA, fis, and hilD. HilD, an AraC/XylS type transcriptional regulator, is of particular importance as a mutation in hilD results in a 14-fold decrease in chromosomal hilA::Tn5lacZY-080 expression and a 53-fold decrease in invasion of HEp-2 cells. It is believed that HilD directly regulates hilA expression as it has been shown to bind to hilA promoter sequences. In addition, our research group, and others, have identified genes (hilE, hha, pag, and lon) that negatively affect hilA transcription. HilE appears to be an important Salmonella-specific regulator that plays a critical role in inactivating hilA expression. Recent work in our lab has been directed at understanding how environmental signals that affect hilA expression may be processed through a hilE pathway to modulate expression of hilA and the invasive phenotype. The current understanding of this complex regulatory system is reviewed.

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