Cloning type-II restriction and modification genes

Lunnen, Keith D.; Barsomian, Janet M.; Camp, Russell R.; Card, Charles O.; Chen, Shu-Zi; Croft, Rebecca; Looney, Mary C.; Meda, Marta M.; Moran, Laurie S.; Nwankwo, Donald O.; Slatko, Barton E.; Cott, Elizabeth M. Van; Wilson, Geoffrey G.

doi:10.1016/0378-1119(88)90242-9

Cited by 75 publications

(29 citation statements)

References 32 publications

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“…The BsaI R-M system was cloned into E. coli by MTase selection 16,17 and inverse PCR to characterize the open reading frames (ORFs) adjacent to the M gene. The Bsa I R-M system consisted of three genes: bsaIM1 (1710 bp), bsaIM2 (1188 bp), and bsaIR (1635 bp) coding for M1.BsaI, M2.BsaI, and BsaI REase, respectively.…”

Section: Resultsmentioning

confidence: 99%

“…16,29 B. stearothermophilus 6-55 (BsaI-producing strain) genomic DNA was partially digested with ApoI, NlaIII, and Sau3AI, respectively. The partially digested DNA was ligated to a modified pUC19 vector carrying two BsaI sites with compatible ends (ApoI ligated to EcoRI ends, NlaIII ligated to SphI ends, Sau3AI ligated to BamHI ends).…”

Section: Genomic Dna Library Constructionmentioning

confidence: 99%

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Engineering Strand-specific DNA Nicking Enzymes from the Type IIS Restriction Endonucleases BsaI, BsmBI, and BsmAI

Zhu

Samuelson

Zhou

et al. 2004

Journal of Molecular Biology

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Section: Resultsmentioning

confidence: 99%

Section: Genomic Dna Library Constructionmentioning

confidence: 99%

Engineering Strand-specific DNA Nicking Enzymes from the Type IIS Restriction Endonucleases BsaI, BsmBI, and BsmAI

Zhu

Samuelson

Zhou

et al. 2004

Journal of Molecular Biology

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“…In principal, however, it is typical that several cycles of digestion and transformation are needed to accomplish successful cloning. More than a hundred R-M systems have been cloned using this approach (21,38,55). In our procedure, to enhance the efficiency of the cloning of the R-M genes, the selection is made in vivo with the use of a lethal plasmid, pKILLER, which contains a functional ENase gene along with an inactive gene (deletion derivative) coding for the cognate MTase.…”

Section: Discussionmentioning

confidence: 99%

A Rapid and Efficient Method for Cloning Genes of Type II Restriction-Modification Systems by Use of a Killer Plasmid

Mruk

Kaczorowski

2007

Appl Environ Microbiol

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We present a method for cloning restriction-modification (R-M) systems that is based on the use of a lethal plasmid (pKILLER). The plasmid carries a functional gene for a restriction endonuclease having the same DNA specificity as the R-M system of interest. The first step is the standard preparation of a representative, plasmid-borne genomic library. Then this library is transformed with the killer plasmid. The only surviving bacteria are those which carry the gene specifying a protective DNA methyltransferase. Conceptually, this in vivo selection approach resembles earlier methods in which a plasmid library was selected in vitro by digestion with a suitable restriction endonuclease, but it is much more efficient than those methods. The new method was successfully used to clone two R-M systems, BstZ1II from Bacillus stearothermophilus 14P and Csp231I from Citrobacter sp. strain RFL231, both isospecific to the prototype HindIII R-M system.In the biology of microorganisms, the restriction-modification (R-M) systems play the important role of "molecular wardens" by protecting bacteria against phage infections. On the other hand, the enzymatic constituents of these systems have also made great contributions to the field of recombinant DNA technology and have served as attractive models for the study of DNA-protein interactions due to the exact mode of target recognition (33,34,37). However, practical applications are limited almost solely to the enzymes belonging to type II R-M systems. Each of these systems is composed of two entities that act independently: a restriction endonuclease (ENase) that recognizes and cleaves a specific short nucleotide sequence (4 to 8 bp) in DNA and a methyltransferase (MTase) that modifies the same sequence in order to protect the host genomic DNA against the action of the cognate restriction enzyme. As both genes coding for R-M systems are usually localized in close proximity (55), cloning an MTase gene often results in the cloning of a matching ENase gene.Until now, more than 400 type II R-M systems have been cloned (38) by the use of either (i) the "Hungarian trick" (45), which selects clones carrying the gene coding for a specific DNA MTase that confers resistance to digestion by the cognate restriction enzyme; (ii) methods based on the detection of SOS response induction in Escherichia coli (10, 32); or (iii) a direct search through genomic databases to identify open reading frames coding for conserved amino acid sequence motifs characteristic of DNA MTases, followed by PCR-based cloning (27).Our research is focused on the nature of the isospecificity phenomenon among type II R-M systems. We would like to know (i) how similar the genes coding for isospecific enzymes are, (ii) whether is it possible to map their functional domains, (iii) whether the systems recognize a cognate sequence in the same way, (iv) what their mode of action is, and (v) how those systems spread among bacteria.For the model in our study, we decided to use a group of systems isospecific to HindIII, an R-M s...

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“…Many RM systems have been well characterized (4), and the genes encoding these have been cloned from numerous bacteria (16). The enzymes responsible for restriction and modification are usually site-specific endo-DNases (ENases) and DNA methyltransferases (MTases), respectively.…”

mentioning

confidence: 99%

“…Another application of cloned methylase genes is to allow the cloning of restriction enzyme genes. Attempts have been made to clone the genes encoding the XmaI and XmaIII restriction enzymes, but these were not successful (16). The approach used was to seek closely linked methylase and restriction enzyme genes, and one possible reason for the failure is that these genes may be unlinked.…”

mentioning

confidence: 99%

Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum

Feyter

Gabriel

1991

J Bacteriol

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In vitro-packaged cosmid libraries of DNA from the bacterium Xanthomonas campestris pv. malvacearum were restricted 200- to 1,000-fold when introduced into Mcr+ strains of Escherichia coli compared with restriction in the Mcr- strain HB101. Restriction was predominantly associated with the mcrBC+ gene in E. coli. A plasmid (pUFR052) encoding the XmaI and XmaIII DNA methylases was isolated from an X. campestris pv. malvacearum library by a screening procedure utilizing Mcr+ and Mcr- E. coli strains. Transfer of plasmids from E. coli strains to X. campestris pv. malvacearum by conjugation was enhanced by up to five orders of magnitude when the donor cells contained pUFR052 as well as the plasmid to be transferred. Subcloning of pUFR052 revealed that at least two regions of the plasmid were required for full modification activity. Use of such modifier plasmids is a simple, novel method that may allow the efficient introduction of genes into any organism in which restriction systems provide a potent barrier to such gene transfer.

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Cloning type-II restriction and modification genes

Cited by 75 publications

References 32 publications

Engineering Strand-specific DNA Nicking Enzymes from the Type IIS Restriction Endonucleases BsaI, BsmBI, and BsmAI

Engineering Strand-specific DNA Nicking Enzymes from the Type IIS Restriction Endonucleases BsaI, BsmBI, and BsmAI

A Rapid and Efficient Method for Cloning Genes of Type II Restriction-Modification Systems by Use of a Killer Plasmid

Use of cloned DNA methylase genes to increase the frequency of transfer of foreign genes into Xanthomonas campestris pv. malvacearum

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