Restriction of nonglucosylated T-even bacteriophage: Properties of permissive mutants of Escherichia coli B and K12

Revel, Helen R.

doi:10.1016/0042-6822(67)90197-3

Cited by 125 publications

(68 citation statements)

References 31 publications

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“…Another example is the well-studied T4 phage, in which 5-hydroxymethylcytosine (5hmC) is incorporated into the DNA during replication and additional glucosyltransferases further modify all 5hmC to glucosylated-hydroxymethylcytosine (5ghmC). T4 genomic DNA containing 5ghmC is resistant to cleavage by most restriction endonucleases, with the exception of Type IV modification-dependent endonucleases (4,5).…”

Section: -Methylcytosine | Methylomementioning

confidence: 99%

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

Cohen-Karni

Xu²,

Apone³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

121

140

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MspJI is a novel modification-dependent restriction endonuclease that cleaves at a fixed distance away from the modification site. Here, we present the biochemical characterization of several MspJI homologs, including FspEI, LpnPI, AspBHI, RlaI, and SgrTI. All of the enzymes specifically recognize cytosine C5 modification (methylation or hydroxymethylation) in DNA and cleave at a constant distance (N 12 ∕N 16 ) away from the modified cytosine. Each displays its own sequence context preference, favoring different nucleotides flanking the modified cytosine. By cleaving on both sides of fully modified CpG sites, they allow the extraction of 32-base long fragments around the modified sites from the genomic DNA. These enzymes provide powerful tools for direct interrogation of the epigenome. For example, we show that RlaI, an enzyme that prefers m CWG but not m CpG sites, generates digestion patterns that differ between plant and mammalian genomic DNA, highlighting the difference between their epigenomic patterns. In addition, we demonstrate that deep sequencing of the digested DNA fragments generated from these enzymes provides a feasible method to map the modified sites in the genome. Altogether, the MspJI family of enzymes represent appealing tools of choice for method development in DNA epigenetic studies. 5-methylcytosine | methylomeM odified DNA bases appear in genomic DNAs in all domains of life, spanning the evolutionary distance from viruses to eukaryotic species. DNA base modifications vary in form and genomic location enriching the information content encoded by genomes. The biological role of base modifications varies, ranging from protection against restriction endonucleases in bacteria and bacteriophages to transcriptional regulation in mammals. In prokaryotes, DNA methyltransferases in restriction-modification systems modify the host genomic DNA, so that restriction endonucleases can target foreign DNA and protect the host cell from invaders (1). However, a few bacteriophages respond by incorporating modified bases into their genomes as a way to block restriction endonuclease cleavage (2). For example, in Xanthomonas oryzae phage XP12, all cytosines exist in the form of 5-methylcytosine (5mC) (3). Another example is the well-studied T4 phage, in which 5-hydroxymethylcytosine (5hmC) is incorporated into the DNA during replication and additional glucosyltransferases further modify all 5hmC to glucosylated-hydroxymethylcytosine (5ghmC). T4 genomic DNA containing 5ghmC is resistant to cleavage by most restriction endonucleases, with the exception of Type IV modification-dependent endonucleases (4, 5).Several different types of modification-dependent endonucleases are found in prokaryotes. For example, N6-adenosine methylation is recognized by a few known enzymes, e.g., DpnI (G m ATC). A group of sequence-specific cytosine methylationdependent restriction endonucleases including GlaI (G m CG m C), BisI (G m CNGC), etc., have been reported recently, which cleave within the recognition site in a Type IIP-like ...

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Section: -Methylcytosine | Methylomementioning

confidence: 99%

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

Cohen-Karni

Xu²,

Apone³

et al. 2011

Proc. Natl. Acad. Sci. U.S.A.

121

140

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“…Two independent genes control the restricting functions in E. coli K12 (10,11). The r6 function restricts all T* phages, while the r2,4 function restricts T*2 and T*4 phages, but not T*6 phage.…”

Section: Resultsmentioning

confidence: 99%

Analysis of Host Range Restriction in Escherichia coli Treated with Toluene

Fleischman

Richardson

1971

Proc. Natl. Acad. Sci. U.S.A.

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“…RR1 carries merB information from E. coli B. This mcrB function is of different specificity than the K12 activity (20,37) and may have a weaker effect. Therefore we worked in an merB::TnlO host ER1467.…”

Section: Discussionmentioning

confidence: 99%

“…It has been recently shown that certain E. coli strains have systems that block introduction of DNA containing cytosine methylation (20); the locus responsible for this activity has been designated 'mcrB' (modified gytosine restriction, 20). In RR1, this locus is derived from E. coli B and is of different specificity and apparently weaker activity (20,37). A new series of cloning strains has been constructed by inactivating this locus with TnlO insertions.…”

Section: Only Insertions Betweenmentioning

confidence: 99%

Cloning theDdeI restriction-modification system using a two-step method

Howard¹,

Card²,

Benner³

et al. 1986

Nucl Acids Res

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DdeI, a Type II restriction-modification system from the gram-negative anaerobic bacterium Desulfovibrio desulfuricans, recognizes the sequence CTNAG. The system has been cloned into E. coli in two steps. First the methylase gene was cloned into pBR322 and a derivative expressing higher levels was constructed. Then the endonuclease gene was located by Southern blot analyses; BamHI fragments large enough to contain the gene were cloned into pACYC184, introduced into a host containing the methylase gene, and screened for endonuclease activity. Both genes are stably maintained in E. coli on separate but compatible plasmids.The DdeI methylase is shown to be a cytosine methylase. DdeI methylase clones decrease in viability as methylation activity increases in E. coli RR1 (our original cloning strain). Therefore the DdeI system has been cloned and maintained in ER1467, a new

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Restriction of nonglucosylated T-even bacteriophage: Properties of permissive mutants of Escherichia coli B and K12

Cited by 125 publications

References 31 publications

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

The MspJI family of modification-dependent restriction endonucleases for epigenetic studies

Analysis of Host Range Restriction in Escherichia coli Treated with Toluene

Cloning theDdeI restriction-modification system using a two-step method

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