Nomenclature relating to restriction of modified DNA in Escherichia coli

Raleigh, Elisabeth A.; Benner, Jack S.; Bloom, Fredric R.; Braymer, Hugh D.; Decruz, Exmond E.; Dharmalingam, Kuppamuthu; Heitman, Joseph; Weidner, M Noyer; Piekarowicz, Andrzej; Kretz, Patricia L.

doi:10.1128/jb.173.8.2707-2709.1991

Cited by 27 publications

(11 citation statements)

References 23 publications

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“…Type IV, although it contains some methylation-based systems, chiefly contains MDS's that target foreign DNA based upon its unusual base modifications8, 9. In addition to a Type I enzyme, E. coli K12 contains three MDS systems (McrA,Mrr,and McrBC10,11) that specifically recognize modified DNA. Among these, McrBC, which targets Teven HMC DNAs, is the best characterized (see Discussion).…”

Section: Introductionmentioning

confidence: 99%

A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs

Bair

Black

2007

Journal of Molecular Biology

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The E. coli CT596 prophage exclusion genes gmrS and gmrD were found to encode a novel Type IV modification dependent restriction nuclease that targets and digests glucosylated (glc)-hydroxymethylcytosine (HMC) DNAs. The protein products GmrS (36 kDa) and GmrD (27 KDa) were purified and found to be inactive separately, but together degraded several different glc-HMC modified DNAs (T4, T2, T6). The GMR enzyme is able to degrade both α-glucosy-HMC T4 DNA and β-glucosyl-HMC T4 DNA, whereas no activity was observed against non-modified DNAs including unmodified T4 cytosine (C) DNA or non-glucosylated T4 HMC DNA. Enzyme activity requires NTP, favors UTP, is stimulated by calcium, and initially produces 4 kb DNA fragments that are further degraded to low molecular weight products. The enzyme is inhibited by the T4 phage Internal Protein I* (IPI*) to which it was found to bind. Overall activities of the purified GmrSD enzyme are in good agreement with the properties of the cloned gmr genes in vivo and suggest a restriction enzyme specific for sugar modified HMC DNAs. IPI* thus represents a third generation bacteriophage defense against restriction nucleases of the Gmr type.

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Section: Introductionmentioning

confidence: 99%

A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs

Bair

Black

2007

Journal of Molecular Biology

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“…Mrr does not. The restriction of T-even phage is designated Rgl (for restricts glucoseless phage [56,57,61]) restriction. Each system also restricts DNA with methylated bases in different specific sequence contexts (24,36,58,77).…”

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confidence: 99%

Response to UV damage by four Escherichia coli K-12 restriction systems

Kelleher

Raleigh

1994

J Bacteriol

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To understand the role of restriction in regulating gene flow in bacterial populations, we would like to understand the regulation of restriction enzyme activity. Several antirestriction (restriction alleviation) systems are known that reduce the activity of type I restriction enzymes like EcoKI in vivo. Most of these do not act on type II or type Ill enzymes, but little information is available for the unclassified modificationdependent systems, of which there are three in E. coli K-12. Of particular interest are two physiological controls on type I enzymes: EcoKI restriction is reduced 2 to 3 orders of magnitude following DNA damage, and a similar effect is seen constitutively in Dam-cells. We used the behavior of EcoKI as a control for testing the response to UV treatment of the three endogenous modification-dependent restriction systems of K-12, McrA, McrBC, and Mrr. Two of these were also tested for response to Dam status. We find that all four resident restriction systems show reduced activity following UV treatment, but not in a unified fashion; each response was genetically and physiologically distinct. Possible mechanisms are discussed.

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“…Since only cytosine methylation has been identified in murine cells, it is likely that this mrr region contains a gene responsible for restriction of methylated cytosines with specificity differing from that of mcrA and mcrBC. This activity may be identical to the proposed McrF activity of mrr (31).…”

Section: Resultsmentioning

confidence: 54%

Identification and characterization of a gene responsible for inhibiting propagation of methylated DNA sequences in mcrA mcrB1 Escherichia coli strains

Kretz¹,

Kohler²,

Short³

1991

J Bacteriol

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Identifying and eliminating endogenous bacterial enzyme systems can significantly increase the efficiency of propagation of eukaryotic DNA in Escherichia coli. We have recently examined one such system which inhibits the propagation of lambda DNA rescued from transgenic mouse tissues. This rescue procedure utilizes lambda packaging extracts for excision of the lambda DNA from the transgenic mouse genome, as well as E. coli cells for subsequent infection and propagation. This assay, in combination with conjugal mating, P1 transduction, and gene cloning, was used to identify and characterize the E. coli locus responsible for this difference in efficiency. It was determined that the E. coli K-12 mcrB gene when expressed on a high-copy-number plasmid can cause a decrease in rescue efficiency despite the presence of the mcrBl mutation, which inactivates the classic McrB restriction activity. (This mutation was verified by sequence analysis.) However, this McrBl activity is not observed when the cloned mcrBl gene is inserted into the E. coil genome at one copy per chromosome. A second locus was identified which causes a decrease in rescue efficiency both when expressed on a high-copy-number plasmid and when inserted into the genome. The data presented here suggest that this locus is mrr and that the mrr gene product can recognize and restrict cytosine-methylated sequences. Removal of this DNA region including the mrr gene from E. coli K-12 strains allows high rescue efficiencies equal to those of E. coli C strains. These modified E. coli K-12 plating strains and lambda packaging extract strains should also allow a significant improvement in the efficiency and representation of eukaryotic genomic and cDNA libraries.

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Nomenclature relating to restriction of modified DNA in Escherichia coli

Cited by 27 publications

References 23 publications

A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs

A Type IV Modification Dependent Restriction Nuclease that Targets Glucosylated Hydroxymethyl Cytosine Modified DNAs

Response to UV damage by four Escherichia coli K-12 restriction systems

Identification and characterization of a gene responsible for inhibiting propagation of methylated DNA sequences in mcrA mcrB1 Escherichia coli strains

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