Journal of Microbiology

Journal Article

An Optimized Method for Reconstruction of Transcriptional Regulatory Networks in Bacteria Using ChIP-exo and RNA-seq Datasets: Minchang Jang, Joon Young Park, Gayeon Lee, Donghyuk Kim; J. Microbiol. 2024;62(12):1075-1088. Published online November 11, 2024; DOI: https://doi.org/10.1007/s12275-024-00181-6

59 View
0 Download
1 Web of Science
1 Crossref

Transcriptional regulatory networks (TRNs) in bacteria are crucial for elucidating the mechanisms that regulate gene expression and cellular responses to environmental stimuli. These networks delineate the interactions between transcription factors (TFs) and their target genes, thereby uncovering the regulatory processes that modulate gene expression under varying environmental conditions. Analyzing TRNs offers valuable insights into bacterial adaptation, stress responses, and metabolic optimization from an evolutionary standpoint. Additionally, understanding TRNs can drive the development of novel antimicrobial therapies and the engineering of microbial strains for biofuel and bioproduct production. This protocol integrates advanced data analysis pipelines, including ChEAP, DEOCSU, and DESeq2, to analyze omics datasets that encompass genome-wide TF binding sites and transcriptome profiles derived from ChIP-exo and RNA-seq experiments. This approach minimizes both the time required and the risk of bias, making it accessible to non-expert users. Key steps in the protocol include preprocessing and peak calling from ChIP-exo data, differential expression analysis of RNA-seq data, and motif and regulon analysis. This method offers a comprehensive and efficient framework for TRN reconstruction across various bacterial strains, enhancing both the accuracy and reliability of the analysis while providing valuable insights for basic and applied research.

Citations

Citations to this article as recorded by

ChIP-mini: a low-input ChIP-exo protocol for elucidating DNA-binding protein dynamics in intracellular pathogens
Joon Young Park, Minchang Jang, Eunna Choi, Sang-Mok Lee, Ina Bang, Jihoon Woo, Seonggyu Kim, Eun-Jin Lee, Donghyuk Kim
Nucleic Acids Research.2025;[Epub] CrossRef

Review

Application of computational approaches to analyze metagenomic data: Ho-Jin Gwak , Seung Jae Lee , Mina Rho; J. Microbiol. 2021;59(3):233-241. Published online February 10, 2021; DOI: https://doi.org/10.1007/s12275-021-0632-8

49 View
0 Download
12 Web of Science
12 Crossref

Abstract

Microorganisms play a vital role in living systems in numerous ways. In the soil or ocean environment, microbes are involved in diverse processes, such as carbon and nitrogen cycle, nutrient recycling, and energy acquisition. The relation between microbial dysbiosis and disease developments has been extensively studied. In particular, microbial communities in the human gut are associated with the pathophysiology of several chronic diseases such as inflammatory bowel disease and diabetes. Therefore, analyzing the distribution of microorganisms and their associations with the environment is a key step in understanding nature. With the advent of nextgeneration sequencing technology, a vast amount of metagenomic data on unculturable microbes in addition to culturable microbes has been produced. To reconstruct microbial genomes, several assembly algorithms have been developed by incorporating metagenomic features, such as uneven depth. Since it is difficult to reconstruct complete microbial genomes from metagenomic reads, contig binning approaches were suggested to collect contigs that originate from the same genome. To estimate the microbial composition in the environment, various methods have been developed to classify individual reads or contigs and profile bacterial proportions. Since microbial communities affect their hosts and environments through metabolites, metabolic profiles from metagenomic or metatranscriptomic data have been estimated. Here, we provide a comprehensive review of computational
methods
that can be applied to investigate microbiomes using metagenomic and metatranscriptomic sequencing data. The limitations of metagenomic studies and the key approaches to overcome such problems are discussed.

Citations

Citations to this article as recorded by

A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data
Arunmozhi Bharathi Achudhan, Priya Kannan, Annapurna Gupta, Lilly M. Saleena
Biochemical Genetics.2024; 62(2): 621. CrossRef
Benchmarking bacterial taxonomic classification using nanopore metagenomics data of several mock communities
Alexander Van Uffelen, Andrés Posadas, Nancy H. C. Roosens, Kathleen Marchal, Sigrid C. J. De Keersmaecker, Kevin Vanneste
Scientific Data.2024;[Epub] CrossRef
Metagenomic approaches and opportunities in arid soil research
Muhammad Riaz Ejaz, Kareem Badr, Zahoor Ul Hassan, Roda Al-Thani, Samir Jaoua
Science of The Total Environment.2024; 953: 176173. CrossRef
DeepCheck: multitask learning aids in assessing microbial genome quality
Guo Wei, Nannan Wu, Kunyang Zhao, Sihai Yang, Long Wang, Yan Liu
Briefings in Bioinformatics.2024;[Epub] CrossRef
Integrated multi-omics analyses of microbial communities: a review of the current state and future directions
Muzaffer Arıkan, Thilo Muth
Molecular Omics.2023; 19(8): 607. CrossRef
Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective
Yan Zhang, Jiao Jin, Biyan Huang, Huimin Ying, Jie He, Liang Jiang
Biomolecules.2022; 12(7): 917. CrossRef
Advances in experimental and computational methodologies for the study of microbial-surface interactions at different omics levels
Juan José González-Plaza, Cristina Furlan, Tomaž Rijavec, Aleš Lapanje, Rocío Barros, Juan Antonio Tamayo-Ramos, Maria Suarez-Diez
Frontiers in Microbiology.2022;[Epub] CrossRef
Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests
Sylvie Buffet-Bataillon, Guillaume Rizk, Vincent Cattoir, Mohamed Sassi, Vincent Thibault, Jennifer Del Giudice, Jean-Pierre Gangneux
Microorganisms.2022; 10(4): 711. CrossRef
Establishment and Validation of a New Analysis Strategy for the Study of Plant Endophytic Microorganisms
Feng Chen, Xianjin Wang, Guiping Qiu, Haida Liu, Yingquan Tan, Beijiu Cheng, Guomin Han
International Journal of Molecular Sciences.2022; 23(22): 14223. CrossRef
Novel technologies to characterize and engineer the microbiome in inflammatory bowel disease
Alba Boix-Amorós, Hilary Monaco, Elisa Sambataro, Jose C. Clemente
Gut Microbes.2022;[Epub] CrossRef
Current Understanding on the Genetic Basis of Key Metabolic Disorders: A Review
Kenneth Francis Rodrigues, Wilson Thau Lym Yong, Md. Safiul Alam Bhuiyan, Shafiquzzaman Siddiquee, Muhammad Dawood Shah, Balu Alagar Venmathi Maran
Biology.2022; 11(9): 1308. CrossRef
Omics-based microbiome analysis in microbial ecology: from sequences to information
Jang-Cheon Cho
Journal of Microbiology.2021; 59(3): 229. CrossRef

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

Roles of RpoS in Yersinia pseudotuberculosis stress survival, motility, biofilm formation and type VI secretion system expression: Jingyuan Guan , Xiao Xiao , Shengjuan Xu , Fen Gao , Jianbo Wang , Tietao Wang , Yunhong Song , Junfeng Pan , Xihui Shen , Yao Wang; J. Microbiol. 2015;53(9):633-642. Published online August 27, 2015; DOI: https://doi.org/10.1007/s12275-015-0099-6

46 View
0 Download
44 Crossref

Abstract

RpoS (σS), the stationary phase/stress σ factor, controls the expression of a large number of genes involved in cellular responses to a variety of stresses. However, the role of RpoS appears to differ in different bacteria. While RpoS is an important regulator of flagellum biosynthesis, it is associated with biofilm development in Edwardsiella tarda. Biofilms are dense communities formed by bacteria and are important for microbe survival under unfavorable conditions. The type VI secretion system (T6SS) discovered recently is reportedly associated with several phenotypes, ranging from biofilm formation to stress sensing. For example, Vibrio anguillarum T6SS was proposed to serve as a sensor for extracytoplasmic signals and modulates RpoS expression and stress response. In this study, we investigated the physiological roles of RpoS in Yersinia pseudotuberculosis, including bacterial survival under stress conditions, flagella formation, biofilm development and T6SS expression. We found that RpoS is important in resistance to multiple stressors–including H2O2, acid, osmotic and heat shock–in Y. pseudotuberculosis. In addition, our study showed that RpoS not only modulates the expression of T6SS but also regulates flagellum formation by positively controlling the flagellar master regulatory gene flhDC, and affects the formation of biofilm on Caenorhabditis elegans by regulating the synthesis of exopolysaccharides. Taken together, these results show that RpoS plays a central role in cell fitness under several adverse conditions in Y. pseudotuberculosis.

Citations

Citations to this article as recorded by

Biofilm-mediated infections by multidrug-resistant microbes: a comprehensive exploration and forward perspectives
Mai M. Zafer, Gamal A. Mohamed, Sabrin R. M. Ibrahim, Soumya Ghosh, Charné Bornman, Mahmoud A. Elfaky
Archives of Microbiology.2024;[Epub] CrossRef
The role of the type VI secretion system in the stress resistance of plant-associated bacteria
Rui Yin, Juanli Cheng, Jinshui Lin
Stress Biology.2024;[Epub] CrossRef
OxyR-regulated T6SS functions in coordination with siderophore to resist oxidative stress
Changfu Li, Zhiyan Wei, Xinquan He, Haiyang He, Yuqi Liu, Yuxin Zuo, He Xiao, Yao Wang, Xihui Shen, Lingfang Zhu, Olaya Rendueles
Microbiology Spectrum.2024;[Epub] CrossRef
Genome sequence of Leclercia adecarboxylata QDSM01 with multiple plant growth promoting properties
Wenjing Chen, Zhigang Wang, Weihui Xu, Yunlong Hu
Plant Growth Regulation.2024; 102(2): 445. CrossRef
Function and Global Regulation of Type III Secretion System and Flagella in Entomopathogenic Nematode Symbiotic Bacteria
Xiyin Huang, Chen Li, Ke Zhang, Kunyan Li, Jiajie Xie, Yuyuan Peng, Meifang Quan, Yunjun Sun, Yibo Hu, Liqiu Xia, Shengbiao Hu
International Journal of Molecular Sciences.2024; 25(14): 7579. CrossRef
RpoS sigma factor mediates adaptation and virulence in Vibrio mimicus
Ziyan Jiang, Anting Chen, Zhen Chen, Jingwen Xu, Xiaojian Gao, Qun Jiang, Xiaojun Zhang
International Journal of Biological Macromolecules.2024; 279: 135307. CrossRef
The Missing Pieces: The Role of Secretion Systems in Campylobacter jejuni Virulence
Amber D. Gabbert, Jennifer L. Mydosh, Prabhat K. Talukdar, Lisa M. Gloss, Jason E. McDermott, Kerry K. Cooper, Geremy C. Clair, Michael E. Konkel
Biomolecules.2023; 13(1): 135. CrossRef
Transcriptional organization and regulation of the Pseudomonas putida K1 type VI secretion system gene cluster
Patricia Bernal, Cristina Civantos, Daniel Pacheco-Sánchez, José M. Quesada, Alain Filloux, María A. Llamas
Microbiology .2023;[Epub] CrossRef
Regulation of type VI secretion systems at the transcriptional, posttranscriptional and posttranslational level
Julia Takuno Hespanhol, Luize Nóbrega-Silva, Ethel Bayer-Santos
Microbiology .2023;[Epub] CrossRef
RpoS-Regulated Genes and Phenotypes in the Phytopathogenic Bacterium Pectobacterium atrosepticum
Olga Petrova, Elizaveta Semenova, Olga Parfirova, Ivan Tsers, Natalia Gogoleva, Yuri Gogolev, Yevgeny Nikolaichik, Vladimir Gorshkov
International Journal of Molecular Sciences.2023; 24(24): 17348. CrossRef
DegS protease regulates the motility, chemotaxis, and colonization of Vibrio cholerae
Mei Zou, Kaiying Wang, Jiajun Zhao, Huifang Lu, Hui Yang, Meirong Huang, Lu Wang, Guangli Wang, Jian Huang, Xun Min
Frontiers in Microbiology.2023;[Epub] CrossRef
Roles of Hcp2, a Hallmark of T6SS2 in Motility, Adhesive Capacity, and Pathogenicity of Vibrio alginolyticus
Shuilong Wu, Jufen Tang, Bei Wang, Jia Cai, Jichang Jian
Microorganisms.2023; 11(12): 2893. CrossRef
The GacS/A-Rsm Pathway Positively Regulates Motility and Flagella Synthesis in Azotobacter vinelandii
Liliana López-Pliego, Norarizbeth Lara-Flores, Dalia Molina-Romero, Gabriela May-Compañ, Ricardo Carreño-López, Cinthia E. Núñez, Miguel Castañeda
Current Microbiology.2022;[Epub] CrossRef
Sigma factor RpoS positively affects the spoilage activity of Shewanella baltica and negatively regulates its adhesion effect
Caili Zhang, Jiaqi Chen, Xiaoming Pan, Haimei Liu, Yanlong Liu
Frontiers in Microbiology.2022;[Epub] CrossRef
Exploring the Function of Quorum Sensing Regulated Biofilms in Biological Wastewater Treatment: A Review
Sania Sahreen, Hamid Mukhtar, Kálmán Imre, Adriana Morar, Viorel Herman, Sundas Sharif
International Journal of Molecular Sciences.2022; 23(17): 9751. CrossRef
A c-di-GMP Signaling Cascade Controls Motility, Biofilm Formation, and Virulence in Burkholderia thailandensis
Zhuo Wang, Xiaorong Xie, Daohan Shang, Laigong Xie, Yueyue Hua, Li Song, Yantao Yang, Yao Wang, Xihui Shen, Lei Zhang, Gladys Alexandre
Applied and Environmental Microbiology.2022;[Epub] CrossRef
Transcriptomic and phenotype analysis revealed the role of rpoS in stress resistance and virulence of pathogenic Enterobacter cloacae from Macrobrachium rosenbergii
Xiaojian Gao, Qieqi Qian, Yujie Zhu, Zhen Chen, Jingwen Xu, Wenjing Xu, Qun Jiang, Jun Wang, Xiaojun Zhang
Frontiers in Microbiology.2022;[Epub] CrossRef
Cpx-signalling facilitates Hms-dependent biofilm formation by Yersinia pseudotuberculosis
Dharmender K. Gahlot, Sun N. Wai, David L. Erickson, Matthew S. Francis
npj Biofilms and Microbiomes.2022;[Epub] CrossRef
MomL inhibits bacterial antibiotic resistance through the starvation stringent response pathway
Qin Dou, Jin Yuan, Rilei Yu, Jiahui Yang, Jiayi Wang, Yuxiang Zhu, Jing Zhong, Hongan Long, Zhiqing Liu, Xianghong Wang, Yuying Li, Yichen Xiao, Jiazhen Liang, Xiao‐Hua Zhang, Yan Wang
mLife.2022; 1(4): 428. CrossRef
Bacterial Stress Responses as Potential Targets in Overcoming Antibiotic Resistance
Jirapat Dawan, Juhee Ahn
Microorganisms.2022; 10(7): 1385. CrossRef
The GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus
Yangyang Li, Weidong Sun, Quan Wang, Ying Yu, Ying Wan, Kai Zhou, Rong Guo, Xiangan Han, Zhaoguo Chen, Weihuan Fang, Wei Jiang
Microbial Pathogenesis.2022; 167: 105546. CrossRef
The transcriptional regulator Zur regulates the expression of ZnuABC and T6SS4 in response to stresses in Yersinia pseudotuberculosis
Ran Cai, Fen Gao, Junfeng Pan, Xinwei Hao, Zonglan Yu, Yichen Qu, Jialin Li, Dandan Wang, Yao Wang, Xihui Shen, Xingyu Liu, Yantao Yang
Microbiological Research.2021; 249: 126787. CrossRef
RpoS Activates the Prodigionsin Production by Activating the Transcription of the RpoS-Dependent Pig Gene Cluster in Serratia marcescens FS14
Baoling Yang, Fenglian Chu, Haixia Li, Weiwu Wang, Tingting Ran, Dongqing Xu
Indian Journal of Microbiology.2021; 61(3): 355. CrossRef
Beyond dueling: roles of the type VI secretion system in microbiome modulation, pathogenesis and stress resistance
Jinshui Lin, Lei Xu, Jianshe Yang, Zhuo Wang, Xihui Shen
Stress Biology.2021;[Epub] CrossRef
Role of RpoS in stress resistance, biofilm formation and quorum sensing of Shewanella baltica
C. Zhang, C. Wang, A.‐N. Jatt, H. Liu, Y. Liu
Letters in Applied Microbiology.2021; 72(3): 307. CrossRef
Roles of Type VI Secretion System in Transport of Metal Ions
Xiaobing Yang, Hai Liu, Yanxiong Zhang, Xihui Shen
Frontiers in Microbiology.2021;[Epub] CrossRef
Microbial biofilm ecology, in silico study of quorum sensing receptor-ligand interactions and biofilm mediated bioremediation
Biji Balan, Amit S. Dhaulaniya, Diksha A. Varma, Kushneet K. Sodhi, Mohit Kumar, Manisha Tiwari, Dileep Kumar Singh
Archives of Microbiology.2021; 203(1): 13. CrossRef
Baicalin, a natural antimicrobial and anti-biofilm agent
Mahdi Asghari Ozma, Ehsaneh Khodadadi, Farzaneh Pakdel, Fadhil S. Kamounah, Mehdi Yousefi, Bahman Yousefi, Mohammad Asgharzadeh, Khudaverdi Ganbarov, Hossein Samadi Kafil
Journal of Herbal Medicine.2021; 27: 100432. CrossRef
RovC - a novel type of hexameric transcriptional activator promoting type VI secretion gene expression
Vanessa Knittel, Pooja Sadana, Stephanie Seekircher, Anne-Sophie Stolle, Britta Körner, Marcel Volk, Cy M. Jeffries, Dmitri I. Svergun, Ann Kathrin Heroven, Andrea Scrima, Petra Dersch, Joan Mecsas
PLOS Pathogens.2020; 16(9): e1008552. CrossRef
Roles of the Hcp family proteins in the pathogenicity of Salmonella typhimurium 14028s
Ping Wang, Jun-Fang Dong, Ren-Qing Li, Lei Li, Qing-Hua Zou
Virulence.2020; 11(1): 1716. CrossRef
Differential Gene Expression Patterns of Yersinia pestis and Yersinia pseudotuberculosis during Infection and Biofilm Formation in the Flea Digestive Tract
Iman Chouikha, Daniel E. Sturdevant, Clayton Jarrett, Yi-Cheng Sun, B. Joseph Hinnebusch, Seth Bordenstein
mSystems.2019;[Epub] CrossRef
Confirmed and Potential Roles of Bacterial T6SSs in the Intestinal Ecosystem
Can Chen, Xiaobing Yang, Xihui Shen
Frontiers in Microbiology.2019;[Epub] CrossRef
Combined Transcriptome and Proteome Analysis of RpoS Regulon Reveals Its Role in Spoilage Potential of Pseudomonas fluorescens
Xiaoxiang Liu, Jun Xu, Junli Zhu, Peng Du, Aihua Sun
Frontiers in Microbiology.2019;[Epub] CrossRef
The type VI secretion system protein AsaA in Acinetobacter baumannii is a periplasmic protein physically interacting with TssM and required for T6SS assembly
Lei Li, Yi-Nuo Wang, Hong-Bing Jia, Ping Wang, Jun-Fang Dong, Juan Deng, Feng-Min Lu, Qing-Hua Zou
Scientific Reports.2019;[Epub] CrossRef
Anti-bacterial activity of baicalin against APEC through inhibition of quorum sensing and inflammatory responses
Lu-Yuan Peng, Meng Yuan, Zong-Mei Wu, Ke Song, Chun-Lei Zhang, Qiang An, Fang Xia, Jia-Lin Yu, Peng-Fei Yi, Ben-Dong Fu, Hai-Qing Shen
Scientific Reports.2019;[Epub] CrossRef
The stringent response factor, RelA, positively regulates T6SS4 expression through the RovM/RovA pathway in Yersinia pseudotuberculosis
Xiaobing Yang, Yunhong Song, Qingyun Dai, Hongyun Zhang, Li Song, Zhuo Wang, Junfeng Pan, Yao Wang
Microbiological Research.2019; 220: 32. CrossRef
Xanthomonas citri T6SS mediates resistance to Dictyostelium predation and is regulated by an ECF σ factor and cognate Ser/Thr kinase
Ethel Bayer‐Santos, Lídia dos Passos Lima, Lucas de Moraes Ceseti, Camila Yuri Ratagami, Eliane Silva de Santana, Aline Maria da Silva, Chuck Shaker Farah, Cristina Elisa Alvarez‐Martinez
Environmental Microbiology.2018; 20(4): 1562. CrossRef
Role of RpoS in stress resistance, quorum sensing and spoilage potential of Pseudomonas fluorescens
Xiaoxiang Liu, Lei Ji, Xu Wang, Jianrong Li, Junli Zhu, Aihua Sun
International Journal of Food Microbiology.2018; 270: 31. CrossRef
Type VI Secretion Systems Present New Insights on Pathogenic Yersinia
Xiaobing Yang, Junfeng Pan, Yao Wang, Xihui Shen
Frontiers in Cellular and Infection Microbiology.2018;[Epub] CrossRef
The alternative sigma factor RpoQ regulates colony morphology, biofilm formation and motility in the fish pathogen Aliivibrio salmonicida
Miriam Khider, Nils Peder Willassen, Hilde Hansen
BMC Microbiology.2018;[Epub] CrossRef
RsmA and AmrZ orchestrate the assembly of all three type VI secretion systems in Pseudomonas aeruginosa
Luke P. Allsopp, Thomas E. Wood, Sophie A. Howard, Federica Maggiorelli, Laura M. Nolan, Sarah Wettstadt, Alain Filloux
Proceedings of the National Academy of Sciences.2017; 114(29): 7707. CrossRef
A starvation-induced regulator, RovM, acts as a switch for planktonic/biofilm state transition in Yersinia pseudotuberculosis
Ruoxi Zhao, Yunhong Song, Qingyun Dai, Yiwen Kang, Junfeng Pan, Lingfang Zhu, Lei Zhang, Yao Wang, Xihui Shen
Scientific Reports.2017;[Epub] CrossRef
ZntR positively regulates T6SS4 expression in Yersinia pseudotuberculosis
Tietao Wang, Keqi Chen, Fen Gao, Yiwen Kang, Muhammad Tausif Chaudhry, Zhuo Wang, Yao Wang, Xihui Shen
Journal of Microbiology.2017; 55(6): 448. CrossRef
Transcriptomic and Phenotypic Analysis Reveals New Functions for the Tat Pathway in Yersinia pseudotuberculosis
Ummehan Avican, Michael Beckstette, Ann Kathrin Heroven, Moa Lavander, Petra Dersch, Åke Forsberg, P. J. Christie
Journal of Bacteriology.2016; 198(20): 2876. CrossRef

Effect of promoter-upstream sequence on σ38-dependent stationary phase gene transcription: Hyung-Ju Lim , Kwangsoo Kim , Minsang Shin , Jae-Ho Jeong , Phil Youl Ryu , Hyon E. Choy; J. Microbiol. 2015;53(4):250-255. Published online April 8, 2015; DOI: https://doi.org/10.1007/s12275-015-4681-8

46 View
0 Download
3 Crossref

Abstract

σ38 in Escherichia coli is required for expression of a subset of stationary phase genes. However, the promoter elements for σ38-dependent genes are virtually indistinguishable from that for σ70-dependent house-keeping genes. hdeABp is a σ38-dependent promoter and LEE5p is a σ70-dependent promoter, but both are repressed by H-NS, a bacterial histone- like protein, which acts at promoter upstream sequence. We swapped the promoter upstream sequences of the two promoters and found that the σ dependency was switched. This was further verified using lacUV5 core promoter. The
results
suggested that the determinant for σ38-dependent promoter lies in the promoter upstream sequence.

Citations

Citations to this article as recorded by

Sequence-dependent model of genes with dual σ factor preference
Ines S.C. Baptista, Vinodh Kandavalli, Vatsala Chauhan, Mohamed N.M. Bahrudeen, Bilena L.B. Almeida, Cristina S.D. Palma, Suchintak Dash, Andre S. Ribeiro
Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms.2022; 1865(3): 194812. CrossRef
Function Enhancement of a Metabolic Module via Endogenous Promoter Replacement for Pseudomonas sp. JY-Q to Degrade Nicotine in Tobacco Waste Treatment
Jun Li, Fengmei Yi, Guoqing Chen, Fanda Pan, Yang Yang, Ming Shu, Zeyu Chen, Zeling Zhang, Xiaotong Mei, Weihong Zhong
Applied Biochemistry and Biotechnology.2021; 193(9): 2793. CrossRef
Recent advances in genetic engineering tools based on synthetic biology
Jun Ren, Jingyu Lee, Dokyun Na
Journal of Microbiology.2020; 58(1): 1. CrossRef

Production of and Applications for a Polyclonal IgY Diagnostic Reagent Specific for Mycobacterium avium subsp. paratuberculosis: Sung Jae Shin , Seung-Sub Lee , Elizabeth J. B. Manning , Michael T. Collins; J. Microbiol. 2009;47(5):600-609. Published online October 24, 2009; DOI: https://doi.org/10.1007/s12275-009-0052-7

33 View
0 Download
13 Scopus

Abstract: Antibodies specific to the cell surface antigens of Mycobacterium avium subsp. paratuberculosis (MAP) have multiple useful applications, e.g. organism detection, immunoconcentration, and cell visualization. The aim of this study was to produce and compare polyclonal antibodies for such research and diagnostic purposes. Three polyclonal antibodies to MAP were produced using sera from immunized rabbits and chickens plus naturally infected cows. Cross-reactive antibodies in each MAP antibody preparation were removed by absorption with heterologous mycobacterial and non-mycobacterial cells. The specificity of each resulting polyclonal antibody preparation was evaluated by ELISA to multiple bacterial cell wall extract antigens. After absorption, chicken anti-MAP IgY had the highest specificity of the three antibody preparations. FITC-labeled anti-MAP IgY was used to effectively locate MAP in macrophages 12 h post-infection. Also, immuno- magnetic beads coated with anti-MAP IgY enhanced recovery of MAP from bacterial suspensions in comparison with non-antibody coated beads. Anti-MAP IgY provides a novel new reagent with broad diagnostic and research applications requiring specific concentration, detection, and quantification of MAP.

Effect of gacS and gacA Mutations on Colony Architecture, Surface Motility, Biofilm Formation and Chemical Toxicity in Pseudomonas sp. KL28: Kyung Soon Choi , Yaligara Veeraragouda , Kyoung Mi Cho , Soo O Lee , Geuk Rae Jo , Kyungyun Cho , Kyoung Lee; J. Microbiol. 2007;45(6):492-498.; DOI: https://doi.org/2646 [pii]

35 View
0 Download

Abstract: GacS and GacA proteins form a two component signal transduction system in bacteria. Here, Tn5 transposon gacS and gacA (Gac) mutants of Pseudomonas sp. KL28, an alkylphenol degrader, were isolated by selecting for smooth colonies of strain KL28. The mutants exhibited reduced ability to migrate on a solid surface. This surface motility does not require the action of flagella unlike the well-studied swarming motility of other Pseudomonas sp. The Gac mutants also showed reduced levels of biofilm and pellicle formation in liquid culture. In addition, compared to the wild type KL28 strain, these mutants were more resistant to high concentrations of m-cresol but were more sensitive to H2O2, which are characteristics that they share with an rpoS mutant. These results indicate that the Gac regulatory cascade in strain KL28 positively controls wrinkling morphology, biofilm formation, surface translocation and H2O2 resistance, which are important traits for its capacity to survive in particular niches.

Initial Characterization of yliH in Salmonella typhimurium: Kyung-Hwa Park , Miryung Song , Hyon E. Choy; J. Microbiol. 2007;45(6):558-565.; DOI: https://doi.org/2608 [pii]

36 View
0 Download

Abstract: Using microarray analysis, we determined those Salmonella genes induced at the entry of stationary phase, and subsequently discovered that uncharacterized yliH was induced most dramatically. We set out to establish the molecular mechanism underlying the stationary phase induction of yliH under the standard culture condition, LB with vigorous aeration, by analyzing its promoter activity in various mutant backgrounds, lacking stationary phase σ, RpoS-, or stringent signal molecules ppGpp, ΔrelA ΔspoT. It was found that the stationary phase induction of yliHp was partially dependent on rpoS but entirely dependent on ppGpp. DNA sequence analysis revealed that the Salmonella yliH gene is composed of 381 base-pair nucleotides, with overall amino acid sequence revealing 76.38% amino acid identity and 88.98% similarity with Escherichia coli yliH, although no motif from data base was noted for its possible role. Recently however, it has been reported that yliH in E. coli was implicated in biofilm formation and motility by repressing these activities (Domka et al., 2006). We have constructed a mutant Salmonella deleting yliH gene by allele replacement and examined its phenotype, and found that the yliH in Salmonella more or less affects motility and adherence by enhancing these activities. The effect on biofilm formation in Salmonella was uncertain. Moreover, addition of cloned yliH of E. coli into Salmonella did not reduce motility or adherence. Taken together, it appears that the pathways implicating yliH for biofilm formation and motility in E. coli and in Salmonella are somewhat different.

Development of a Bottle-Free Multipurpose Incubator for Generating Various Bacterial Culture Conditions: Nam Woong Yang , Yong Lim; J. Microbiol. 2005;43(1):28-33.; DOI: https://doi.org/2142 [pii]

38 View
0 Download

Abstract: The purpose of this study was to develop a multipurpose incubator, without the gas cylinders (bottles) which are required for H_2 and CO_2 supplementation. In our bottle-free multipurpose incubator, the H_2 and CO_2 were generated by chemical reactions induced within the chamber. The reaction between sodium borohydride and acetic acid at a molar ratio of 1:1 was used to generate H_2, according to the following formula: 4NaBH_4 + 2CH_3COOH + 7H_2O → 2CH_3COONa + Na_2B_4O_7 + 16H_2, whereas the other reaction, citric acid and sodium bicarbonate at a 1:1 molar ratio, was used to generate CO_2, according to the following formula: C_6H_8O_7 + 3NaHCO_3 → Na_3(C_6H_5O_7) + 3H_2O + 3CO_2. Five species of obligate anaerobic bacteria, one strain of capnophilic bacterium, and one strain of microaerophilic bacterium were successfully cultured in the presence of their respective suitable conditions, all of which were successfully generated by our bottle-free multipurpose incubator. We conclude that, due to its greater safety, versatility, and significantly lower operating costs, this bottle-free multipurpose incubator can be used for the production of fastidious bacterial cultures, and constitutes a favorable step above existing anaerobic incubators. <br>

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

36 View
0 Download
9 Scopus

Abstract: 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.

Identification of the Genes Involved in Stationary-Phase Specific Acid Resistance of Salmonella typhimurium: Bang, Iel Soo , Lee, In Soo , Lee, Yung Nok , Park, Yong keun; J. Microbiol. 1995;33(1):21-27.

40 View
0 Download

Abstract: Salmonella encounters variables pH fluctuation during its life cycle and has been developed adaptative systems such as acid tolerance response (ATR) to survive at severe acidic environment. As part of on going investigation of stationary-phase specific acid resistance, we have searched for acid sensitive mutations in virulent Salmonella typhimurim UK-1 usin the MudJ fusion technique and two lethal selection procedures including DNP(dinitrophenol) selection media and microtiterplate selection method. Two acid sensitive mutations have been identified and designated, spatrK2, spatrK5. These mutations removed both stationary-phase acid tolerant effect and stationary-phase specific acid resistance. Non-specific histone like protein, H-NS and stationary-phase specific sigma factor, RpoS made little contribution to that system at respective single mutation(5-10 fold decrease). But, when both mutations were combined together, no acid resistance was achieved while acid tolerance response was still effective. Two dimensional SDS polyacrylamide gel electrophoresis showed new stationary-phase specific acid shock proteins as well as proteins already known. Not expectedly, the gels from acid adapted samples of both rpoS and hns mutation showed that double mutation of those regulators does not make change of the standard acid shock proteins. Only four acid shock proteins were regulated by these regulators, while fifteen proteins were newly identified as the members of acid shock response system by these regulators. These results implicate that stationary-phase acid resistance of that organism has RpoS/H-NS soubly dependent acid protective system and independent acid tolerance response system.

Osmotic Tolerance Response of Salmonella typhimurium with Respect ro Growth-Phase and Identification of otr201, a rpoS-Related Gene: Lim, Si Keun , Bang, Soo Iel , Bang, Seong Ho , Lee, Yung Nok , Park, Yong Keun; J. Microbiol. 1995;33(1):66-73.

39 View
0 Download

Abstract: Salmonella typhimurium can stand against and survive under lethal osmotic exposure. Two systems of osmotic tolerance response(OTR) were found to be utilized by that organism, which were possibly overlapping with each other. The first system is an induction in response to non-lethal high osmoshock(0.3~0.7 M NaCl) at log-phase. The second system is induced during famine condition of stationary-phase. The viability of wild types(UK1, LT2) under these unfavorable conditions was increased by both systems. The viability of stationary-phase cells was approximately 5-fold that of the cells adapted at log-phase. In addition, a few regulatory fenes(rpoS, fur, crp, atp), one carbonstarvation-inducible(cstA104), and an osmotic-inducible gene(proU) were found to play an important role in osmotic tolerance at both growth phases. RpoS, a putative alternative sigma factor (σ^38), was found to participate in OTR systems regardless of growth-phase, but rpoS-defective mutant could still develope the adaptive tolerance. Thus, we concluded that there is rpoS-defective and rpoS-independent systems for osmotic tolerance at both growth-phase. Of the possible otr mutants newly isolated using MudJ(Km, lac) operon fusion techniques, YK3092 (otr201::MudJ) was most sensitive to osmotic challenge regardless of growth phase. It was mapped nearby at 57 min on chromosome and showed rpoS-negative phenotypes such as no catalase activity and inability to accumulate glycogen : but was not linked to rpoS. Therefore, this result strongly suggest that otr201 might be a rpoS-related regulatory gene not gound before.

rpoS mutation relieves biosynthesis of flagella in hns mutants of salmonella typhimurium UK1: Cho, Mi Ook , Bang, Ile Soo , Hong, Seong Karp , Bang, Seong Ho , Park, Yong Keun; J. Microbiol. 1998;36(3):184-188.

38 View
0 Download

Abstract: The biosynthesis and function of flagella is positively regulated by the cyclic AMP-catabolite activator protein (cAMP-CAP) complex and the nucleoid protein H-NS. In this report, we show that nonmotile Salmonella typhimurium hns mutants could recover its motility by introducing the rpoSmutation. In a swarm plate assay, rpoS/hns double mutants could woim while hns mutants could not. This regeneration of motility resulted from the flagella synthesis. Transmission electron microscopy analysis showed the capability of rpoS/hns double mutants for flagella synthesis. And rpoS mutation derepressed the transcription of flhD, the flagella master gene, in hns mutants.

Regulation of the sufABCDSE Operon by Fur: Joon-Hee Lee , Won-Sik Yeo , Jung-Hye Roe; J. Microbiol. 2003;41(2):109-114.

35 View
0 Download

Abstract: A promoter that is inducible by paraquat and menadione, the superoxide generators, independently of soxRS has been found in front of the sufABCDSE operon in Escherichia coli. Based on the observation that SufA is a holomog of IscA that functions in the assembly of iron sulfur cluster and the sufA promoter (sufAp) contains a putative Fur-binding consensus, we investigated whether this gene is regulated by Fur, a ferric uptake regulator. When examined in several sufAp-lacZ chromosomal fusion strains, sufAp was induced by EDTA, an iron chelator and a well-known Fur-inducer. The basal level of sufA expression increased dramatically in fur mutant, suggesting repression of sufAp by Fur. The derepression in fur mutant and EDTA-induction of sufA expression required nucleotides up to -61, where a putative Fur box is located. Purified Fur protein bound to the DNA fragment containing the putative Fur box between -35 and -10 promoter elements. The regulation by Fur and menadione induction of sufAp acted independently. The rpoS mutation increased sufA induction by menadione, suggesting that the stationary sigma factor RpoS acts negatively on sufA induction.

First
Prev
Page of 1
Next
Last

Search