Journal of Microbiology

Journal Articles

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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Abstract: 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.

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.

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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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Abstract

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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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

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

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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Abstract

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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Isolation, characterization and optimizations of laccase producer from soil: A comprehensive study of application of statistical approach to enhance laccase productivity in Myrothecium verrucaria NFCCI 4363
J.P. Jawale, V.S. Nandre, R.V. Latpate, M.V. Kulkarni, P.J. Doshi
Bioresource Technology Reports.2021; 15: 100751. CrossRef
Multicopper oxidase of Acinetobacter baumannii: Assessing its role in metal homeostasis, stress management and virulence
Kavleen Kaur, Harsimran Sidhu, Neena Capalash, Prince Sharma
Microbial Pathogenesis.2020; 143: 104124. CrossRef
Reference genes for accurate normalization of gene expression in wood-decomposing fungi
Jiwei Zhang, Hugh D. Mitchell, Lye Meng Markillie, Matthew J. Gaffrey, Galya Orr, Jonathan Schilling
Fungal Genetics and Biology.2019; 123: 33. CrossRef
Multicopper oxidases: Biocatalysts in microbial pathogenesis and stress management
Kavleen Kaur, Aarjoo Sharma, Neena Capalash, Prince Sharma
Microbiological Research.2019; 222: 1. CrossRef
Expression Profile of Laccase Gene Family in White-Rot Basidiomycete Lentinula edodes under Different Environmental Stresses
Lianlian Yan, Ruiping Xu, Yinbing Bian, Hongxian Li, Yan Zhou
Genes.2019; 10(12): 1045. CrossRef
Laccase induction by synthetic dyes in Pycnoporus sanguineus and their possible use for sugar cane bagasse delignification
Christian Hernández, Anne-Marie Farnet Da Silva, Fabio Ziarelli, Isabelle Perraud-Gaime, Beatriz Gutiérrez-Rivera, José Antonio García-Pérez, Enrique Alarcón
Applied Microbiology and Biotechnology.2017; 101(3): 1189. CrossRef
Transcriptome Sequencing and Comparative Analysis of Piptoporus betulinus in Response to Birch Sawdust Induction
Lixia Yang, Mu Peng, Syed Shah, Qiuyu Wang
Forests.2017; 8(10): 374. CrossRef
Molecular characterization of a novel thermostable laccase PPLCC2 from the brown rot fungus Postia placenta MAD-698-R
Hongde An, Tingting Xiao, Huan Fan, Dongsheng Wei
Electronic Journal of Biotechnology.2015; 18(6): 451. CrossRef

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: 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

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: 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.

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: 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.

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: 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.

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