DNA Methylation in Prokaryotes

Casadesús, Josep; Sánchez-Romero, María Antonia

doi:10.1007/978-3-031-11454-0_2

Cited by 6 publications

(5 citation statements)

References 169 publications

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“…Enzymatic methylation of nucleosides in genomic DNA is the most well‐known type of epigenetic modification, common to all domains of living organisms, from bacteria and archaea to higher eukaryotes, including humans. DNA methylation is catalysed by S‐adenosylmethionine (SAM)‐dependent methyltransferases (MTases), a vast, highly diverse superfamily of enzymes widespread in cellular organisms (Casadesús & Sánchez‐Romero, 2022 ). These enzymes likely appeared in prokaryotes at the root of the tree of life (Harris & Goldman, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Interplay of intracellular and trans‐cellular DNA methylation in natural archaeal consortia

Reva,

La Cono,

Crisafi

et al. 2024

Environ Microbiol Rep

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DNA methylation serves a variety of functions across all life domains. In this study, we investigated archaeal methylomics within a tripartite xylanolytic halophilic consortium. This consortium includes Haloferax lucertense SVX82, Halorhabdus sp. SVX81, and an ectosymbiotic Candidatus Nanohalococcus occultus SVXNc, a nano‐sized archaeon from the DPANN superphylum. We utilized PacBio SMRT and Illumina cDNA sequencing to analyse samples from consortia of different compositions for methylomics and transcriptomics. Endogenous cTAG methylation, typical of Haloferax, was accompanied in this strain by methylation at four other motifs, including GDGcHC methylation, which is specific to the ectosymbiont. Our analysis of the distribution of methylated and unmethylated motifs suggests that autochthonous cTAG methylation may influence gene regulation. The frequency of GRAGAaG methylation increased in highly expressed genes, while CcTTG and GTCGaGG methylation could be linked to restriction‐modification (RM) activity. Generally, the RM activity might have been reduced during the evolution of this archaeon to balance the protection of cells from intruders, the reduction of DNA damage due to self‐restriction in stressful environments, and the benefits of DNA exchange under extreme conditions. Our methylomics, transcriptomics and complementary electron cryotomography (cryo‐ET) data suggest that the nanohaloarchaeon exports its methyltransferase to methylate the Haloferax genome, unveiling a new aspect of the interaction between the symbiont and its host.

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Section: Introductionmentioning

confidence: 99%

Interplay of intracellular and trans‐cellular DNA methylation in natural archaeal consortia

Reva,

La Cono,

Crisafi

et al. 2024

Environ Microbiol Rep

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“…DNA methylases are enzymes responsible for introducing methyl groups into DNA and have high potential in the development of tools for molecular and synthetic biology, genetic engineering, and epigenetics (Galbraith and Snuderl 2022;Lin and O'Callaghan 2018;Matsumura 2022). Bacteria produce methylases as solitary (orphan) enzymes, or as part of restriction-modification (R-M) systems in which they are associated with a restriction enzyme (Adhikari and Curtis 2016;Casadesús and Sánchez-Romero 2022). The function of a methylase in an R-M system is to protect the bacterial genomes from self-digestion by the associated restriction enzyme.…”

Section: Introductionmentioning

confidence: 99%

“…Necessarily, each one of these two enzymes has a specificity function. Type II are the most common and studied R-M systems (Casadesús and Sánchez-Romero 2022;Chen et al 2021;Ge and Qiu 2022;Gulati et al 2023;Loenen et al 2014;Tock and Dryden 2005).…”

Section: Introductionmentioning

confidence: 99%

DNA methylases for site-selective inhibition of type IIS restriction enzyme activity

Flores-Fernández,

Lin,

Robins

et al. 2024

Appl Microbiol Biotechnol

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DNA methylases of the restriction-modifications (R-M) systems are promising enzymes for the development of novel molecular and synthetic biology tools. Their use in vitro enables the deployment of independent and controlled catalytic reactions. This work aimed to produce recombinant DNA methylases belonging to the R-M systems, capable of in vitro inhibition of the type IIS restriction enzymes BsaI, BpiI, or LguI. Non-switchable methylases are those whose recognition sequences fully overlap the recognition sequences of their associated endonuclease. In switch methylases, the methylase and endonuclease recognition sequences only partially overlap, allowing sequence engineering to alter methylation without altering restriction. In this work, ten methylases from type I and II R-M systems were selected for cloning and expression in E. coli strains tolerant to methylation. Isopropyl β-D-1-thiogalactopyranoside (IPTG) concentrations and post-induction temperatures were tested to optimize the soluble methylases expression, which was achieved with 0.5 mM IPTG at 20 °C. The C-terminal His6-Tag versions showed better expression than the N-terminal tagged versions. DNA methylation was analyzed using purified methylases and custom test plasmids which, after the methylation reactions, were digested using the corresponding associated type IIS endonuclease. The non-switchable methylases M2.Eco31I, M2.BsaI, M2.HpyAII, and M1.MboII along with the switch methylases M.Osp807II and M2.NmeMC58II showed the best activity for site-selective inhibition of type IIS restriction enzyme activity. This work demonstrates that our recombinant methylases were able to block the activity of type IIS endonucleases in vitro, allowing them to be developed as valuable tools in synthetic biology and DNA assembly techniques. Key points • Non-switchable methylases always inhibit the relevant type IIS endonuclease activity • Switch methylases inhibit the relevant type IIS endonuclease activity depending on the sequence engineering of their recognition site • Recombinant non-switchable and switch methylases were active in vitro and can be deployed as tools in synthetic biology and DNA assembly Graphical Abstract

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“…[4] These modifications are crucial components of restriction-modification (R-M) systems, participating in bacterial innate immunity. [5] In eukaryotic genomes, 5mC and its derivatives, including 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), are the most common modifications, playing important roles as epigenetic signals in development and disease. [6,7] By contrast, the presence of 6 mA in most eukaryotic genomes is extremely sparse, with its location and abundance need to be carefully assessed.…”

Section: Introductionmentioning

confidence: 99%

“…Methylation modifications of DNA are prevalent in bacteria, where N6‐methyladenine (6 mA), N4‐methylcytosine (4 mC), and 5‐methylcytosine (5mC) together constitute the major methylome [4] . These modifications are crucial components of restriction‐modification (R–M) systems, participating in bacterial innate immunity [5] . In eukaryotic genomes, 5mC and its derivatives, including 5‐hydroxymethylcytosine (5hmC), 5‐formylcytosine (5fC), and 5‐carboxylcytosine (5caC), are the most common modifications, playing important roles as epigenetic signals in development and disease [6,7] .…”

Section: Introductionmentioning

confidence: 99%

Discovery and Accurate Detection of Rare Nucleic Acid Modifications

Luo,

Chen,

Kong

et al. 2024

Israel Journal of Chemistry

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Nucleic acid modifications play essential roles in diverse biological processes, ranging from gene expression regulation to stress response. While traditional research focused on common modifications like methylation, recent discoveries are unveiling a wide range of rare modifications with potentially crucial functions. However, accurately detecting and mapping these modifications pose significant challenges due to their low abundance and diverse chemical properties. This article summarizes the recent discoveries of rare DNA and RNA modifications across various organisms, highlighting their potential biological significance. Furthermore, it critically evaluates the limitations of current mapping techniques, including potential sources of false positives and negatives. Finally, the article discusses emerging strategies for overcoming these challenges and future opportunities in the field of rare nucleic acid modification detection.

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DNA Methylation in Prokaryotes

Cited by 6 publications

References 169 publications

Interplay of intracellular and trans‐cellular DNA methylation in natural archaeal consortia

Interplay of intracellular and trans‐cellular DNA methylation in natural archaeal consortia

DNA methylases for site-selective inhibition of type IIS restriction enzyme activity

Discovery and Accurate Detection of Rare Nucleic Acid Modifications

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