Restriction enzymes and their isoschizomers

Specific cleavage of DNA molecules at RecA-mediated triple-strand structure

A novel procedure to cleave DNA molecules at any desired base sequence is presented. This procedure is based upon our finding that double-stranded DNA molecules at a site where RecA-mediated triple-stranded DNA structure with a complimentary deoxyoligonucleotide is located can be cleaved by a single-strand specific nuclease, such as nuclease S1 or BAL31, between the first base at the 5' termini of the deoxyoligonucleotides and the nearest base proximal to the 5' termini. Accordingly, the sequence as well as the number of the cleavage sites to be cleaved can be custom designed by selecting deoxyoligonucleotides with specific base sequences for triple-stranded DNA formation. The basic characteristics of the cleavage reaction and typical applications of the procedure are presented with actual results, including those which involve cleavage of complex genomic DNA at the very sites one desires.

Isolation of SagI, a new HaeIII isoschizomer from Streptococcus agalactiae

A new HaeIII isoschizomer from Streptococcus agalactiae was isolated by a single-step purification method. The highly active restriction endonuclease, SagI, was free of nonspecific nuclease activity and was suitable for use in molecular biology procedures. The rapid isolation procedure may be applicable for the recovery of other restriction endonucleases from bacteria.

Effect of site-specific modification on restriction endonucleases and DNA modification methyltransferases

Restriction endonucleases have site-specific interactions with DNA that can often be inhibited by site-specific DNA methylation and other site-specific DNA modifications. However, such inhibition cannot generally be predicted. The empirically acquired data on these effects are tabulated for over 320 restriction endonucleases. In addition, a table of known site-specific DNA modification methyltransferases and their specificities is presented along with EMBL database accession numbers for cloned genes.

Bacterial genomics

During the last decade, great advances have been made in the study of bacterial genomes which is perhaps better described by the term bacterial genomics. The application of powerful techniques, such as pulsed-field gel electrophoresis of macro-restriction fragments of genomic DNA, has freed the characterisation of the chromosomes of many bacteria from the constraints imposed by classical genetic analysis. It is now possible to analyse the genome of virtually every microorganism by direct molecular methods and to construct detailed physical and gene maps. In this review, the various practical approaches are compared and contrasted, and some of the emerging themes of bacterial genomics, such as the size, shape, number and organisation of chromosomes are discussed.

The cleavage sites and localization of genes encoding the restriction endonucleases Eco1831I and EcoHI

The restriction endonucleases Eco1831I and EcoHI cleave before the first 5'-cytosine in the recognition sequence 5'-decreases CCSGG--3'/3'--GGSCC increases-5' (where S = G or C), generate 5-base 5' cohesive ends, and are encoded by homologous plasmids that are restricted in McrA+ hosts. Thus, they differ in their cleavage specificity from that of the BcnI isoschizomer, which cleaves after the second 5' cytosine.

Construction of a Neisseria gonorrhoeae MS11 derivative deficient in NgoMI restriction and modification

We have cloned from Neisseria gonorrhoeae MS11 the gene encoding a methylase that modifies the sequence GCCGGC. The corresponding restriction enzyme was also encoded by this clone. Sequence analysis demonstrated that the methylase shares sequence similarities with other cytosine methylases, but the sequence organization of M.NgoMI is different from that seen for other cytosine methylases. A deletion was introduced into the chromosome of N. gonorrhoeae MS11 to produce strain MUG701, a strain that is inactivated in both the methylase and the restriction genes. Although this strain no longer methylated its DNA at the NgoMI recognition sequence, cells were viable and had no other significant phenotypic changes. Transformation data indicated that MS11 does not produce enough restriction activity to block plasmid transformation in the gonococcus, even though restriction activity could be demonstrated in E. coli containing the cloned gene.

Endonuclease (R) subunits of type-I and type-III restriction-modification enzymes contain a helicase-like domain

A statistically significant amino acid sequence similarity is demonstrated between the endonuclease (R) subunit of EcoK restriction-modification (R-M) enzyme, and RNA and DNA helicases of the so-called 'DEAD' family. It is further shown that all three known sequences of R subunits of type-I and type-III R-M enzymes contain the conserved amino acid sequence motifs typical of the previously described helicase superfamily II [(1989) Nucleic Acids Res. 17, 4713-4730]. A hypothesis is proposed that these enzymes may exert helicase activity possibly required for local unwinding of DNA in the cleavage sites.

Plasmodium falciparum: evidence for a DNA methylation pattern

The methylation status of the adenine and cytosine residues in the genome of Plasmodium falciparum was studied using restriction enzymes exhibiting differential activity dependent on the methylation state of these residues in their recognition site. The gene coding for the enzyme dihydrofolate reductase-thymidylate synthase was studied for that purpose. No methylated adenine residues were observed in this gene in four strains tested. However, partial methylation of cytosine residues was observed in all strains. This methylation occurred at a specific site of the gene and was of the eukaryotic type, namely at a CpG sequence.

Specificity of restriction endonucleases and DNA modification methyltransferases a review (Edition 3)

The properties and sources of all known class-I, class-II and class-III restriction endonucleases (ENases) and DNA modification methyltransferases (MTases) are listed and newly subclassified according to their sequence specificity. In addition, the enzymes are distinguished in a novel manner according to sequence specificity, cleavage position and methylation sensitivity. Furthermore, new nomenclature rules are proposed for unambiguously defined enzyme names. In the various Tables, the enzymes are cross-indexed alphabetically according to their names (Table I), classified according to their recognition sequence homologies (Table II), and characterized within Table II by the cleavage and methylation positions, the number of recognition sites on the DNA of the bacteriophages lambda, phi X174, and M13mp7, the viruses Ad2 and SV40, the plasmids pBR322 and pBR328, and the microorganisms from which they originate. Other tabulated properties of the ENases include relaxed specificities (integrated within Table II), the structure of the generated fragment ends (Table III), interconversion of restriction sites (Table IV) and the sensitivity to different kinds of DNA methylation (Table V). Table VI shows the influence of class-II MTases on the activity of class-II ENases with at least partially overlapping recognition sequences. Table VII lists all class-II restriction endonucleases and MTases which are commercially available. The information given in Table V focuses on the influence of methylation of the recognition sequences on the activity of ENases. This information might be useful for the design of cloning experiments especially in Escherichia coli containing M.EcodamI and M.EcodcmI [H16, M21, U3] or for studying the level and distribution of site-specific methylation in cellular DNA, e.g., 5'- (M)CpG-3' in mammals, 5'-(M)CpNpG-3' in plants or 5'-GpA(M)pTpC-3' in enterobacteria [B29, E4, M30, V4, V13, W24]. In Table IV a cross index for the interconversion of two- and four-nt 5'-protruding ends into new recognition sequences is complied. This was obtained by the fill-in reaction with the Klenow (large) fragment of the E. coli DNA polymerase I (PolIk), or additional nuclease S1 treatment followed by ligation of the modified fragment termini [P3]. Interconversion of restriction sites generates novel cloning sites without the need of linkers. This should improve the flexibility of genetic engineering experiments [K56, P3].(ABSTRACT TRUNCATED AT 400 WORDS)

Expression of cloned restriction and modification genes, hjaIRM from Hyphomonas jannaschiana in Escherichia coli

A type-II RM system, HjaI, was identified in the marine bacterium, Hyphomonas jannaschiana. The ENase recognizes GATATC, and DNA fragments generated after cleavage with this enzyme contain blunt ends. A DNA fragment encoding these enzymes was cloned and expressed in Escherichia coli, although the level of expression of the cloned genes was low. DNA methylated by M.HjaI was not restricted by the Mcr or Mrr restriction systems of E. coli. Although H. jannaschiana is a marine bacterium isolated near the thermal vents on the floor of the Pacific Ocean, the biochemical properties of the ENase were similar to those of EcoRV, an isoschizomer isolated from E. coli.

Nucleotide sequence of the FokI restriction-modification system: separate strand-specificity domains in the methyltransferase

The genes for FokI, a type-IIS restriction-modification system from Flavobacterium okeanokoites (asymmetric recognition sequence: 5'-GGATG/3'-CCTAC), were cloned into Escherichia coli. Recombinants carrying the fokIR and fokIM genes were found to modify their DNA completely, and to restrict lambdoid phages weakly. The nt sequences of the genes were determined, and the probable start codons were confirmed by aa sequencing. The FokI endonuclease (R.FokI) and methyltransferase (M.FokI) are encoded by single, adjacent genes, aligned in the same orientation, in the order M then R. The genes are large by the standards of type-II systems, 1.9 kb for the M gene, and 1.7 kb for the R gene. Preceding each gene is a pair of FokI recognition sites; it is conceivable that interactions between the sites and the FokI proteins could regulate expression of the genes. The aa sequences of the N- and C-terminal halves of M.FokI are similar to one another, and to certain other DNA-adenine methyltransferases, suggesting that the enzyme has a 'tandem' structure, such as could have arisen by the fusion of a pair of adjacent, ancestral M genes. Truncated derivatives of M. FokI were constructed by deleting the 5'- or 3'-ends of the fokIM gene. Deleting most of the C-terminus of M.FokI produced derivatives that methylated only the top (GGATG) strand of the recognition sequence. Conversely, deleting most of the N-terminus produced derivatives that methylated only the bottom (CATCC) strand of the recognition sequence. These results indicate that the domains in M.FokI for methylating the two strands of the recognition sequence are largely separate.

Identification of a novel site specific endonuclease produced by Mycoplasma fermentans: discovery while characterizing DNA binding proteins in T lymphocyte cell lines

We have discovered a new restriction endonuclease, MfeI, in nuclear extracts from T cells contaminated with Mycoplasma fermentans. This endonuclease was identified while studying proteins binding to the interleukin-2 receptor alpha chain gene promoter. MfeI cuts at the recognition sequence C'AATTG generating EcoRI compatible cohesive ends. Potential applications are discussed.

M.FokI methylates adenine in both strands of its asymmetric recognition sequence

M.FokI, a type-IIS modification enzyme from Flavobacterium okeanokoites, was purified, and its activity was characterized in vitro. The enzyme was found to be a DNA-adenine methyltransferase and to methylate both strands of the asymmetric FokI recognition sequence: (formula; see text) M.FokI does not methylate single-stranded DNA, nor does it methylate double-stranded DNA at sequences other than FokI sites.

Characterization and cloning of MwoI (GCN7GC), a new type-II restriction-modification system from Methanobacterium wolfei

R.MwoI, a type-II restriction enzyme with the new specificity 5'-GCN7GC-3', was found in extracts of the thermophilic archaebacterium, Methanobacterium wolfei. R.MwoI cleaves duplex DNA producing fragments with 3-nt, 3'-terminal extensions, thus: GCN5/N2GC. The genes coding for the MwoI restriction and modification enzymes were cloned into Escherichia coli on the plasmid vector pBR322. The clones synthesize a low level of R.MwoI endonuclease. The plasmids display incomplete MwoI-specific modification, suggesting that the clones synthesize a low level of the M.MwoI methyltransferase, too.

Enzymatic cleavage of a bacterial genome at a 10-base-pair recognition site

The circular genome of Staphylococcus aureus was cut into two fragments by a simple enzymatic method that cleaves a 10-base-pair site. The recognition sequence, A-T-C-G-mA decreases T-C-G-mA-T, was created by the combined use of the methylase M.Cla I (A-T-C-G-mA-T) and the restriction endonuclease Dpn I (G-mA decreases T-C). This technique is insensitive to CpG methylation and in human DNA is predicted to produce fragments that, on average, are greater than five million base pairs. The ability to create such long pieces of DNA should facilitate mapping of large, complex chromosomes.

The 5'-GGATCC-3' cleavage specificity of BamHI is increased to 5'-CCGGATCCGG-3' by sequential double methylation with M.HpaII and M.BamHI

Site-specific DNA methylation is known to block cleavage by a number of restriction endonucleases. We show that methylation at 'non-canonical' DNA modification sites can also block methylation by five of 13 DNA methyltransferases (MTases) tested. Furthermore, MTases and endonucleases that recognize the same nucleotide sequence can differ in their sensitivity to non-canonical methylation. In particular, BamHI endonuclease can cut 5'-GGATCm5C efficiently, whereas M.BamHI cannot methylate this modified sequence. Methyltransferase/endonuclease pairs which differ in their sensitivity to non-canonical methylation can be exploited to generate rare DNA cleavage sites. For example, we show that M.HpaII, M.BamHI, and BamHI can be used sequentially in a three-step procedure to specifically cleave DNA at the 10-bp sequence 5'-CCGGATCCGG. Several highly selective DNA cutting strategies are made possible by these sequential double methylation-blocking reactions.

Cloned restriction-modification systems--a review

The genes for numerous restriction endonucleases and modification methylases have been cloned into Escherichia coli. A summary is given for the clones isolated so far (115 entries) and of the procedures used to obtain them.

Cloning of the BamHI methyl transferase gene from Bacillus amyloliquefaciens

We wish to report the initial characterization of a recombinant clone containing the BamHI methylase gene. Genomic chromosomal DNA purified from Bacillus amyloliquefaciens was partially cleaved with HindIII, fractionated by size, and cloned into pSP64. Plasmid DNA from this library was challenged with BamHI endonuclease and transformed into Escherichia coli HB101. A recombinant plasmid pBamM6.5 and a subclone pBamM2.5 were shown to contain the BamHI methylase gene based on three independent observations. Both plasmids were found to be resistant to BamHI endonuclease cleavage, and chromosomal DNA isolated from E.coli HB101 cells harboring either of the plasmids pBamM6.5 or pBamM2.5 was resistant to cleavage by BamHI endonuclease. In addition, DNA isolated from lambda phage passaged through E.coli HB101 containing either plasmid was also resistant to BamHI cleavage. Expression of the BamHI methylase gene is dependent on orientation in pSP64. In these clones preliminary evidence indicates that methylase gene expression may be under the direction of the plasmid encoded LacZ promoter.

Identification of a new restriction endonuclease, R.NgoBI, from Neisseria gonorrhoeae

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