Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp.
            <i>acnes</i>
            Strains DSM 16379 and DSM 1897
            <sup>T</sup>

Deptula, Paulina; Laine, Pia; Paulín, Lars; Auvinen, Petri; Roberts, Richard J.; Johnston, Christopher A.; Varmanen, Pekka

doi:10.1128/mra.00705-20

Cited by 5 publications

(5 citation statements)

References 13 publications

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“…acnes or in our laboratory strains. We have shown the IIIB system in SLST H2 (KPA171202) to be the only functional one and detected its specific AGCAGY recognition motif in genomic, plasmid and phage DNA through ONT sequencing, being consistent with previous findings [ 20 ].…”

Section: Discussionsupporting

confidence: 90%

“…acnes clade II strains contain full CRISPR/Cas type I-E systems with spacers matching phages while clade I has lost big parts over time, indicating that they represent a more recent evolutionary lineage compared to clade II strains [ 13 ]. Putative R-M systems have been described in REBASE but only one active system has been identified up to date: a type IIIB system recognizing the motif 5`-AGCAGY-3`[ 20 ]. In addition, the described linear plasmid contains a toxin-antitoxin system which was previously proposed to be synonymous in their function to R-M systems by regulating and limiting the genetic flux between lineages [ 21 ].…”

Section: Introductionmentioning

confidence: 99%

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Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

et al. 2022

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Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris. The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes strains. To investigate the activity of these putative R-M and their relevance in host protective mechanisms, we analyzed the methylome of six representative C. acnes strains by Oxford Nanopore Technologies (ONT) sequencing. We detected the presence of a 6-methyladenine modification at a defined DNA consensus sequence in strain KPA171202 and recombinant expression of this R-M system confirmed its methylation activity. Additionally, a R-M knockout mutant verified the loss of methylation properties of the strain. We studied the potential of one C. acnes bacteriophage (PAD20) in killing various C. acnes strains and linked an increase in its specificity to phage DNA methylation acquired upon infection of a methylation competent strain. We demonstrate a therapeutic application of this mechanism where phages propagated in R-M deficient strains selectively kill R-M deficient acne-prone clades while probiotic ones remain resistant to phage infection.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

et al. 2022

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“…In particular, we studied three putative systems corresponding to R-M IIB, IIG and IIIB, all shown to be present either in the available genome assemblies of C. acnes or in our laboratory strains. We have shown the IIIB system in SLST H2 (KPA171202) to be the only functional one and detected its specific AGCAGY recognition motif in genomic, plasmid and phage DNA through ONT sequencing, being consistent with previous findings 20 .…”

Section: Discussionsupporting

confidence: 90%

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Knoedlseder

Nevot

Fábrega

et al. 2021

Preprint

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Cutibacterium acnes (C. acnes) is a gram-positive bacterium and a member of the human skin microbiome. Despite being the most abundant skin commensal, certain members have been associated with common inflammatory disorders such as acne vulgaris. The availability of the complete genome sequences from various C. acnes clades have enabled the identification of putative methyltransferases, some of them potentially belonging to restriction-modification (R-M) systems which protect the host of invading DNA. However, little is known on whether these systems are functional in the different C. acnes strains. To investigate the activity of these putative R-M and their relevance in host protective mechanisms, we analyzed the methylome of seven representative C. acnes strains by Oxford Nanopore Technologies (ONT) sequencing. We detected the presence of a 6-methyladenine modification at a defined DNA consensus sequence in strain KPA171202 and recombinant expression of this R-M system confirmed its methylation activity. Additionally, a R-M knockout mutant verified the loss of methylation properties of the strain. We studied the potential of one C. acnes bacteriophage (PAD20) in killing various C. acnes strains and linked an increase in its specificity to phage DNA methylation acquired upon infection of a methylation competent strain. We demonstrate a therapeutic application of this mechanism where phages propagated in R-M deficient strains selectively kill R-M deficient acne-prone clades while probiotic ones remain resistant to phage infection.

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“…The resulting two scaffolds with read depths of 499× for the chromosome and 309× for the plasmid were annotated at NCBI using the Prokaryotic Genome Annotation Pipeline PGAP-6.5 ( 17 – 19 ). Prophage sequences were predicted using the PHASTER server ( 20 ), and SEQWARE methylome analysis at REBASE ( 21 ) was conducted as previously described ( 22 , 23 ). Due to the high sequence identity (99.63%) of the plasmid to the previously published plasmid sequence of ATCC 927 T ( 24 ), the plasmid was named pMMRN.…”

Section: Announcementmentioning

confidence: 99%

Revised whole genome and DNA methylome of Mycobacterium marinum type strain ATCC 927 ^T

Savijoki,

Deptula,

Roberts

et al. 2024

Microbiol Resour Announc

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Mycobacterium marinum , a slow-growing Actinobacterium, typically induces tuberculosis-like disease in fish. Here, we report a new reference sequence for M. marinum ATCC 927 T , along with its DNA methylome. This aims to maximize the research potential of this type strain and facilitates investigations into the pathomechanisms of human tuberculosis.

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Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897 ^T

Cited by 5 publications

References 13 publications

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Revised whole genome and DNA methylome of Mycobacterium marinum type strain ATCC 927 ^T

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Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897 T

Cited by 5 publications

References 13 publications

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Engineering selectivity of Cutibacterium acnes phages by epigenetic imprinting

Revised whole genome and DNA methylome of Mycobacterium marinum type strain ATCC 927 T

Contact Info

Product

Resources

About

Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897 ^T

Revised whole genome and DNA methylome of Mycobacterium marinum type strain ATCC 927 ^T