Location of the Bases Modified by M.BcoKIA and M.BcoKIB Methylases in the Sequence 5′-CTCTTC-3′/5′-GAAGAG-3′

Svad’bina, I. V.; Zheleznaya, L. A.; Matvienko, N. I.

doi:10.1007/s10541-005-0234-9

Cited by 3 publications

(1 citation statement)

References 12 publications

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“…Our SMRT sequencing analysis has indicated that M.TdeII carries out an m4C modification in one strand (5′- m4 CTCTTCNG-3′) and another m6A modification in the opposite strand (5′-G m6 AAGAG-3′). A single Type II R-M system in Bacillus coagulans has been shown to recognize the sequence 5′-CTCTTC-3′/5′-GAAGAG-3′ and converts the first cytosine to N4-methylcytosine in one strand and the second adenine to N6-methyladenine in the opposite strand ( 68 ). However, in that case, the two strands are separately methylated by two MTases (M1.BcoKI and M2.BcoKI) encoded by different hsdM genes.…”

Section: Discussionmentioning

confidence: 99%

Prevalence of phase variable epigenetic invertons among host-associated bacteria

Huang

Wang

et al. 2020

Nucleic Acids Research

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Type I restriction-modification (R-M) systems consist of a DNA endonuclease (HsdR, HsdM and HsdS subunits) and methyltransferase (HsdM and HsdS subunits). The hsdS sequences flanked by inverted repeats (referred to as epigenetic invertons) in certain Type I R-M systems undergo invertase-catalyzed inversions. Previous studies in Streptococcus pneumoniae have shown that hsdS inversions within clonal populations produce subpopulations with profound differences in the methylome, cellular physiology and virulence. In this study, we bioinformatically identified six major clades of the tyrosine and serine family invertases homologs from 16 bacterial phyla, which potentially catalyze hsdS inversions in the epigenetic invertons. In particular, the epigenetic invertons are highly enriched in host-associated bacteria. We further verified hsdS inversions in the Type I R-M systems of four representative host-associated bacteria and found that each of the resultant hsdS allelic variants specifies methylation of a unique DNA sequence. In addition, transcriptome analysis revealed that hsdS allelic variations in Enterococcus faecalis exert significant impact on gene expression. These findings indicate that epigenetic switches driven by invertases in the epigenetic invertons broadly operate in the host-associated bacteria, which may broadly contribute to bacterial host adaptation and virulence beyond the role of the Type I R-M systems against phage infection.

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Section: Discussionmentioning

confidence: 99%

Prevalence of phase variable epigenetic invertons among host-associated bacteria

Huang

Wang

et al. 2020

Nucleic Acids Research

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Diversity of DNA methyltransferases that recognize asymmetric target sequences

Madhusoodanan

Rao

2010

Critical Reviews in Biochemistry and Molecular Biology

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DNA methyltransferases (MTases) are a group of enzymes that catalyze the methyl group transfer from S-adenosyl-L-methionine in a sequence-specific manner. Orthodox Type II DNA MTases usually recognize palindromic DNA sequences and add a methyl group to the target base (either adenine or cytosine) on both strands. However, there are a number of MTases that recognize asymmetric target sequences and differ in their subunit organization. In a bacterial cell, after each round of replication, the substrate for any MTase is hemimethylated DNA, and it therefore needs only a single methylation event to restore the fully methylated state. This is in consistent with the fact that most of the DNA MTases studied exist as monomers in solution. Multiple lines of evidence suggest that some DNA MTases function as dimers. Further, functional analysis of many restriction-modification systems showed the presence of more than one or fused MTase genes. It was proposed that presence of two MTases responsible for the recognition and methylation of asymmetric sequences would protect the nascent strands generated during DNA replication from cognate restriction endonuclease. In this review, MTases recognizing asymmetric sequences have been grouped into different subgroups based on their unique properties. Detailed characterization of these unusual MTases would help in better understanding of their specific biological roles and mechanisms of action. The rapid progress made by the genome sequencing of bacteria and archaea may accelerate the identification and study of species- and strain-specific MTases of host-adapted bacteria and their roles in pathogenic mechanisms.

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Types and Applications of Nicking Enzyme-Combined Isothermal Amplification

Cao

Tang

Chen

et al. 2022

IJMS

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Due to the sudden outbreak of COVID-19 at the end of 2019, rapid detection has become an urgent need for community clinics and hospitals. The rapid development of isothermal amplification detection technology for nucleic acids in the field of molecular diagnostic point-of-care testing (POCT) has gained a great deal of attention in recent years. Thanks to intensive research on nicking enzymes, nicking enzyme-combined isothermal amplification has become a promising platform for rapid detection. This is a novel technique that uses nicking enzymes to improve ordinary isothermal amplification. It has garnered significant interest as it overcomes the complexity of traditional molecular diagnostics and is not subject to temperature limitations, relying on cleavage enzymes to efficiently amplify targets in a very short time to provide a high level of amplification efficiency. In recent years, several types of nicking enzyme-combined isothermal amplification have been developed and they have shown great potential in molecular diagnosis, immunodiagnosis, biochemical identification, and other fields. However, this kind of amplification has some disadvantages. In this review, the principles, advantages and disadvantages, and applications of several nicking enzyme-combined isothermal amplification techniques are reviewed and the prospects for the development of these techniques are also considered.

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Location of the Bases Modified by M.BcoKIA and M.BcoKIB Methylases in the Sequence 5′-CTCTTC-3′/5′-GAAGAG-3′

Cited by 3 publications

References 12 publications

Prevalence of phase variable epigenetic invertons among host-associated bacteria

Prevalence of phase variable epigenetic invertons among host-associated bacteria

Diversity of DNA methyltransferases that recognize asymmetric target sequences

Types and Applications of Nicking Enzyme-Combined Isothermal Amplification

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