Skip Navigation
Skip to contents

Journal of Microbiology : Journal of Microbiology

OPEN ACCESS
SEARCH
Search

Articles

Page Path
HOME > J. Microbiol > Volume 59(3); 2021 > Review
Review
Prokaryotic DNA methylation and its functional roles
Hoon Je Seong 1, Sang-Wook Han 2, Woo Jun Sul 1
Journal of Microbiology 2021;59(3):242-248.
DOI: https://doi.org/10.1007/s12275-021-0674-y
Published online: February 23, 2021
1Department of Systems Biotechnology, Chung-Ang University, Anseong 17546, Republic of Korea, 2Department of Plant Science and Technology, Chung-Ang University, Anseong 17546, Republic of Korea
Corresponding author:  Sang-Wook Han , Tel: +82-31-670-4707;, 
Woo Jun Sul , Tel: +82-31-670-4707;, 
Received: 21 December 2020   • Revised: 29 January 2021   • Accepted: 1 February 2021
prev next
  • 577 Views
  • 3 Download
  • 58 Web of Science
  • 56 Crossref
  • 61 Scopus

Citations

Citations to this article as recorded by  Crossref logo
  • Structure of defense against restriction proteins DarA and Hdf in phage P1 reveals a new molecular mechanism during phage assembly, infection and DNA ejection
    Jing Zheng, Yuan Chen, Siting Chen, Junquan Zhou, Hao Xiao, Fan Yang, Hongrong Liu, Ekaterina E. Heldwein
    PLOS Pathogens.2026; 22(1): e1013869.     CrossRef
  • Advancing Plant Microbiome Research Through Host DNA Depletion Techniques
    Yao Wang, Junbo Yang, Huiyu Hou, Luyang Song, Xu Cheng, Yong‐Xin Liu
    Plant Biotechnology Journal.2026; 24(3): 1189.     CrossRef
  • Comparative view of DNA methylation in stramenopiles and other eukaryotes: Focus on 5-methylcytosine
    Ananya Khatei, Leïla Tirichine, M. Junaid Sidiq, J. Mark Cock, Alexander Juterbock
    Algal Research.2026; 94: 104551.     CrossRef
  • memod-s: a standardised workflow to explore and analyse prokaryotic methylation patterns for Nanopore sequencing data
    Alessia Marotta, Lapo Doni, Alessia Avesani, Iacopo Passeri, Camilla Fagorzi, Alessio Mengoni, Jaime Martinez-Urtaza, Frederico M Batista, Luigi Vezzulli, Emanuele Bosi, Jorge Duitama
    Bioinformatics Advances.2026;[Epub]     CrossRef
  • How to Unmask an Unknown: The Restriction-Modification System MhoVII of Mycoplasma hominis Expresses Two Complementary Methylation Activities in One Enzyme
    Lars Vogelgsang, Dana Bäcker, Sebastian Alexander Scharf, Azlan Nisar, Alexander T. Dilthey, Birgit Henrich
    International Journal of Molecular Sciences.2026; 27(3): 1591.     CrossRef
  • Epigenetic regulation in prokaryotes: transcriptional and phenotypic outcomes of DNA methyltransferase activity
    Sara Sharaf, Martina Cappelletti, Marco R Oggioni, Karolin Hijazi, Grzegorz Wegrzyn
    FEMS Microbiology Reviews.2026;[Epub]     CrossRef
  • Elucidation of caffeine degradation in kombucha by Komagataeibacter saccharivorans KS1 and low-caffeine kombucha production
    Da-Eun Jang, Seong-Jin Hong, Ki-Nam Yoon, Hye-Jin Kang, Ok Cheol Kim, Young-Min Kim
    Food Bioscience.2026; 80: 108786.     CrossRef
  • Sulfonamide resistance gene sul4 is hosted by common wastewater sludge bacteria and found in various newly described contexts and hosts
    Melina Markkanen, Denise Pezzutto, Marko Virta, Antti Karkman, Michael Owusu
    Microbiology Spectrum.2026;[Epub]     CrossRef
  • Epigenetic enzyme inhibitors targeting DNA, histone, and RNA methylation: Mechanisms and therapeutic applications in cancer
    Yiman Wang, Chen Ma, Xinya Liu, Junkai Cheng, Dan Zhu, Peng Liu, Peng Qi, Xiankai Li, Jian Gu, Qin Wang
    European Journal of Medicinal Chemistry.2026; 306: 118590.     CrossRef
  • Gene regulation during bacterial dormancy: coordinated control of chromosome architecture, transcription machinery, and RNA turnover
    Zhenyu Qi, Hai Zhou, Bing Zhou
    Current Opinion in Microbiology.2026; 91: 102758.     CrossRef
  • Erasing Methylation Marks on DNA by Plant-Specific DEMETER Family DNA Glycosylases
    Praveen Rai, Poonam Kumari, Vineet Gaur
    Journal of Plant Growth Regulation.2025; 44(5): 1810.     CrossRef
  • DNA methylome regulates virulence and metabolism in Pseudomonas syringae
    Jiadai Huang, Fang Chen, Beifang Lu, Yue Sun, Youyue Li, Canfeng Hua, Xin Deng
    eLife.2025;[Epub]     CrossRef
  • DNA methylation confers epigenetic changes in cold-adapted microorganisms in response to cold stress
    Xuying Bu, Xufeng Dou, Zhe Chen, Lan Liu, Yuxia Mei, Min Ren
    Extremophiles.2025;[Epub]     CrossRef
  • The soil microbial methylome: A tool to explore the role of epigenetic memory in driving soil abiotic legacy effects
    Tom Sizmur, Alexey Larionov
    Soil Biology and Biochemistry.2025; 202: 109712.     CrossRef
  • Decoding the genome and epigenome of avian Escherichia coli strains by R10.4.1 nanopore sequencing
    Jingyao Wang, Xudong Liu, Yanwen Shao, Runsheng Li, Surya Paudel
    Frontiers in Veterinary Science.2025;[Epub]     CrossRef
  • Lactococcal mobile genetic elements harbour a diverse phage defensome rich in restriction-modification systems
    Brian McDonnell, Philip Kelleher, Alexey Fomenkov, Guillermo Ortiz Charneco, Keith Coughlan, Pascal Quénée, Saulius Kulakauskas, Christian Cambillau, Brian P Anton, Paul P de Waal, Noël N M E van Peij, Francesca Bottacini, Jennifer Mahony, Richard John Ro
    Nucleic Acids Research.2025;[Epub]     CrossRef
  • The restriction impacts of the Type III restriction-modification system on the transmission dynamics of antimicrobial resistance genes in Campylobacter jejuni
    Yu Qiu, Pengbo Guo, Hui Tian, Ye Zhou, Hongling Wen, Hao Liang
    Frontiers in Microbiology.2025;[Epub]     CrossRef
  • Long-read methylome analysis of Oleidesulfovibrio alaskensis G20 biofilm under copper stress
    Payal Thakur, Ram Nageena Singh, Rajesh Kumar Sani
    Scientific Reports.2025;[Epub]     CrossRef
  • A case for aneural cognition: E. coli and its cognitive repertoire
    Breno B. Just, Sávio Torres de Farias
    BioSystems.2025; 258: 105645.     CrossRef
  • Engineering and laboratory evolution of lactose-utilizing Pseudomonas putida strains
    Signe Saumaa, Tanel Ilmjärv, Ingrem Popazova, Lea Ets, Age Brauer, Maia Kivisaar
    Journal of Biotechnology.2025; 406: 225.     CrossRef
  • From sequence to activity: the HgaI-homologous restriction modification system RM.MhoVI of Mycoplasma hominis
    Lars Vogelgsang, Manuel Dolgopolow-Schmidt, Azlan Nisar, Dana Bäcker, Alexander T. Dilthey, Birgit Henrich
    BMC Microbiology.2025;[Epub]     CrossRef
  • Multiple roles of DNA methylation in sea-ice bacterial communities and associated viruses
    Georges Kanaan, Jody W Deming
    The ISME Journal.2025;[Epub]     CrossRef
  • Targeted Deletion of the Cytopathogenic Toxin A Gene in Sneathia vaginalis
    Rishi M. Ray, Phoebe V. Bridy, Aubree G. Musicant, Shiny Chandravel, Youstina Y. Aziz, Jasmine C. Cruz, Kimberly K. Jefferson
    Molecular Microbiology.2025; 124(6): 481.     CrossRef
  • Transcriptomic profiles reveal DNA-dependent ATPase MbovRecD modulates Mycoplasma bovis survival through methyltransferase activity and carbohydrate metabolism regulation
    Xifang Zhu, Yajiao Li, Doukun Lu, Gang Zhao, Yankai Liu, Aiping Wang, Aizhen Guo
    International Journal of Biological Macromolecules.2025; 318: 145256.     CrossRef
  • Irreversible Inhibition of DNMT3A by an N‐Mustard Analog of S‐Adenosyl‐L–Methionine
    Nichanun Sirasunthorn, Isabelle Roseto, Lindsay Pecor, Lindsay R. Comstock
    ChemBioChem.2024;[Epub]     CrossRef
  • Restriction modification systems in archaea: A panoramic outlook
    Pallavi Gulati, Ashish Singh, Sandeep Patra, Shreyas Bhat, Anil Verma
    Heliyon.2024; 10(8): e27382.     CrossRef
  • BsuMI regulates DNA transformation in Bacillus subtilis besides the defense system and the constructed strain with BsuMI-absence is applicable as a universal transformation platform for wild-type Bacillus
    Zhao Xingya, Fu Xiaoping, Zhen Jie, Yang Jun, Zheng Hongchen, Bai Wenqin, Song Hui
    Microbial Cell Factories.2024;[Epub]     CrossRef
  • Toward DNA-Based Recording of Biological Processes
    Hyeri Jang, Sung Sun Yim
    International Journal of Molecular Sciences.2024; 25(17): 9233.     CrossRef
  • The complete genome sequence of unculturable Mycoplasma faucium obtained through clinical metagenomic next-generation sequencing
    Artur J. Sabat, Tim Durfee, Schuyler Baldwin, Viktoria Akkerboom, Andreas Voss, Alexander W. Friedrich, Erik Bathoorn
    Frontiers in Cellular and Infection Microbiology.2024;[Epub]     CrossRef
  • Approaches for Benchmarking Single-Cell Gene Regulatory Network Methods
    Karamveer, Yasin Uzun
    Bioinformatics and Biology Insights.2024;[Epub]     CrossRef
  • Widespread prevalence of a methylation-dependent switch to activate an essential DNA damage response in bacteria
    Aditya Kamat, Ngat T. Tran, Mohak Sharda, Neha Sontakke, Tung B. K. Le, Anjana Badrinarayanan, Lotte Søgaard-Andersen
    PLOS Biology.2024; 22(3): e3002540.     CrossRef
  • Evaluation of the enzymatic properties of DNA (cytosine-5)-methyltransferase M.ApeKI from archaea in the presence of metal ions
    Mao Hayashi, Yoshinari Wada, Akira Yamamura, Hideki Inoue, Naoya Yamashita, Shigetoshi Ichimura, Yasuhiro Iida
    Bioscience, Biotechnology, and Biochemistry.2024; 88(10): 1155.     CrossRef
  • Moving toward the Inclusion of Epigenomics in Bacterial Genome Evolution: Perspectives and Challenges
    Iacopo Passeri, Francesca Vaccaro, Alessio Mengoni, Camilla Fagorzi
    International Journal of Molecular Sciences.2024; 25(8): 4425.     CrossRef
  • Bacmethy: A novel and convenient tool for investigating bacterial DNA methylation pattern and their transcriptional regulation effects
    Ji‐Hong Liu, Yizhou Zhang, Ning Zhou, Jiale He, Jing Xu, Zhao Cai, Liang Yang, Yang Liu
    iMeta.2024;[Epub]     CrossRef
  • Unraveling host regulation of gut microbiota through the epigenome–microbiome axis
    Michael L. Pepke, Søren B. Hansen, Morten T. Limborg
    Trends in Microbiology.2024; 32(12): 1229.     CrossRef
  • Combined analysis of genome-wide DNA methylome and transcriptome reveals the first epigenetic-based antibiotic-resistance mechanism in Acinetobacter baumannii
    Rosario Nicola Brancaccio, Veronica Folliero, Domenico Di Rosa, Federica Dell’Annunziata, Elena Alexandrova, Marharyta Smal, Giorgio Giurato, Giovanni Boccia, Vittorio Panetta, Rita Greco, Alessandro Weisz, Francesca Rizzo, Gianluigi Franci
    Discover Bacteria.2024;[Epub]     CrossRef
  • The evolutionary consequences of interactions between the epigenome, the genome and the environment
    Pierre Baduel, Iris Sammarco, Rowan Barrett, Marta Coronado‐Zamora, Amélie Crespel, Bárbara Díez‐Rodríguez, Janay Fox, Dario Galanti, Josefa González, Alexander Jueterbock, Eric Wootton, Ewan Harney
    Evolutionary Applications.2024;[Epub]     CrossRef
  • KinMethyl: robust methylation detection in prokaryotic SMRT sequencing via kinetic signal modeling and deep feature integration
    Jichen Zhang, Yutaka Saito, Alex Bateman
    Bioinformatics Advances.2024;[Epub]     CrossRef
  • Comparative Genomics of Pesticide-Degrading Enterococcus Symbionts of Spodoptera frugiperda (Lepidoptera: Noctuidae) Leads to the Identification of Two New Species and the Reappraisal of Insect-Associated Enterococcus Species
    Ana Flávia Freitas Gomes, Luís Gustavo de Almeida, Fernando Luis Cônsoli
    Microbial Ecology.2023; 86(4): 2583.     CrossRef
  • Recent advances in phage defense systems and potential overcoming strategies
    Xiaoming Yuan, Zhichao Huang, Zhenjun Zhu, Jumei Zhang, Qingping Wu, Liang Xue, Juan Wang, Yu Ding
    Biotechnology Advances.2023; 65: 108152.     CrossRef
  • Comprehensive insights into the metabolism characteristics of small RNA Qrr4 in Vibrio alginolyticus
    Yanni Zhao, Ningning Zhou, Jiamin Ren, Wang Liu, Chuang Zhou, Xuefeng Chen, Jieyu Zhao, Juanjuan Cao, Jinfang Yang, Jie Han, Huan Liu
    Applied Microbiology and Biotechnology.2023; 107(5-6): 1887.     CrossRef
  • Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli
    Georgia L Breckell, Olin K Silander, B. Andrews
    G3.2023;[Epub]     CrossRef
  • The DNA cytosine methylome revealed two methylation motifs in the upstream regions of genes related to morphological and physiological differentiation in Streptomyces coelicolor A(3)2 M145
    Annalisa Pisciotta, Alessia Maria Sampino, Alessandro Presentato, Marco Galardini, Angel Manteca, Rosa Alduina
    Scientific Reports.2023;[Epub]     CrossRef
  • Characterisation of Type II DNA Methyltransferases of Metamycoplasma hominis
    Lars Vogelgsang, Azlan Nisar, Sebastian Alexander Scharf, Anna Rommerskirchen, Dana Belick, Alexander Dilthey, Birgit Henrich
    Microorganisms.2023; 11(6): 1591.     CrossRef
  • The Restriction–Modification Systems of Clostridium carboxidivorans P7
    Patrick Kottenhahn, Gabriele Philipps, Boyke Bunk, Cathrin Spröer, Stefan Jennewein
    Microorganisms.2023; 11(12): 2962.     CrossRef
  • Dual thermal ecotypes coexist within a nearly genetically identical population of the unicellular marine cyanobacteriumSynechococcus
    Joshua D. Kling, Michael D. Lee, Nathan G. Walworth, Eric A. Webb, Jordan T. Coelho, Paul Wilburn, Stephanie I. Anderson, Qianqian Zhou, Chunguang Wang, Megan D. Phan, Feixue Fu, Colin T. Kremer, Elena Litchman, Tatiana A. Rynearson, David A. Hutchins
    Proceedings of the National Academy of Sciences.2023;[Epub]     CrossRef
  • Comparison of Yersinia enterocolitica DNA Methylation at Ambient and Host Temperatures
    Dustin J. Van Hofwegen, Carolyn J. Hovde, Scott A. Minnich
    Epigenomes.2023; 7(4): 30.     CrossRef
  • Genome-wide lone strand adenine methylation in Deinococcus radiodurans R1: Regulation of gene expression through DR0643-dependent adenine methylation
    Suraj Joshi, Payel Ghosh, Sagar Barage, Bhakti Basu, Deepti D. Deobagkar
    Microbiological Research.2022; 257: 126964.     CrossRef
  • MuLan-Methyl—multiple transformer-based language models for accurate DNA methylation prediction
    Wenhuan Zeng, Anupam Gautam, Daniel H Huson
    GigaScience.2022;[Epub]     CrossRef
  • Evolution of Complex Regulation for Cell-Cycle Control
    Samuel H. A. von der Dunk, Berend Snel, Paulien Hogeweg, Laurence Hurst
    Genome Biology and Evolution.2022;[Epub]     CrossRef
  • Advanced biotechnology using methyltransferase and its applications in bacteria: a mini review
    Jun Ren, Hyang-Mi Lee, JunHao Shen, Dokyun Na
    Biotechnology Letters.2022; 44(1): 33.     CrossRef
  • Phase-variable Type I methyltransferase M.NgoAV from Neisseria gonorrhoeae FA1090 regulates phasevarion expression and gonococcal phenotype
    Monika Adamczyk-Poplawska, Pawel Bacal, Agnieszka Mrozek, Natalia Matczynska, Andrzej Piekarowicz, Agnieszka Kwiatek
    Frontiers in Microbiology.2022;[Epub]     CrossRef
  • DNA Methyltransferases: From Evolution to Clinical Applications
    Victor M. Del Castillo Falconi, Karla Torres-Arciga, Genaro Matus-Ortega, José Díaz-Chávez, Luis A. Herrera
    International Journal of Molecular Sciences.2022; 23(16): 8994.     CrossRef
  • Analyzing Modern Biomolecules: The Revolution of Nucleic-Acid Sequencing – Review
    Gabriel Dorado, Sergio Gálvez, Teresa E. Rosales, Víctor F. Vásquez, Pilar Hernández
    Biomolecules.2021; 11(8): 1111.     CrossRef
  • Omics-based microbiome analysis in microbial ecology: from sequences to information
    Jang-Cheon Cho
    Journal of Microbiology.2021; 59(3): 229.     CrossRef
  • RecA gene genetic diversity and its regulatory element analysis: The case of Vibrio cholerae
    Birhanu Zeleke, Hunduma Dinka
    Gene Reports.2021; 25: 101333.     CrossRef
  • Cite this Article
    Cite this Article
    export Copy Download
    Close
    Download Citation
    Download a citation file in RIS format that can be imported by all major citation management software, including EndNote, ProCite, RefWorks, and Reference Manager.

    Format:
    • RIS — For EndNote, ProCite, RefWorks, and most other reference management software
    • BibTeX — For JabRef, BibDesk, and other BibTeX-specific software
    Include:
    • Citation for the content below
    Prokaryotic DNA methylation and its functional roles
    J. Microbiol. 2021;59(3):242-248.   Published online February 23, 2021
    Close
Related articles

Journal of Microbiology : Journal of Microbiology
TOP