The HaeIV restriction modification system of Haemophilus aegyptius is encoded by a single polypeptide

The HaeIV restriction endonuclease (ENase) belongs to a distinct class of ENases, characterized by its ability to cleave double-stranded DNA on both sides of its recognition sequence, excising a short DNA fragment that includes the recognition sequence. The gene encoding the HaeIV ENase was cloned from Haemophilus aegyptius into pUC19 using a previously described system that does not need the knowledge that a particular ENase is produced by a bacterial strain. DNA sequence analysis of the insert contained on this plasmid identified a single open reading frame (ORF), with the predicted protein having an apparent molecular mass of approximately 110 kDa. The protein encoded by this ORF was purified to homogeneity from Escherichia coli strain ER1944 carrying the haeIVRM gene on a recombinant plasmid under the control of the inducible ara promoter. The protein possessed both ENase and methyltransferase (MTase) activities. Amino acid sequence analysis was able to identify several conserved motifs found in DNA MTases, located in the middle of the protein. The enzyme recognizes the interrupted palindromic sequence 5' GAPyNNNNNPuTC 3', cleaving double-stranded DNA on both strands upstream and downstream of the recognition sequence, releasing an approximately 33 bp fragment. The ENase possessed an absolute requirement only for Mg(+2). ATP had no influence on ENase or MTase activities. The ENase made the first strand cleavage randomly on either side of the recognition sequence, but the second cleavage occurred more slowly. The MTase activity modified symmetrically located adenine residues on both strands within the recognition sequence yielding N6-methyl adenine. Furthermore, the MTase was active as a dimer.

Sensitivity of the restriction endonucleases HaeIII, BsrI, EaeI and CfrI to cytosine N4-methylation

HaeIII, BsrI and NgoII are isochizomers that recognize the sequence GGCC while EaeI and CfrI recognize the overlapping sequence YGGCCR. It has previously been shown that all these enzymes are inhibited by cytosine C5-methylation within the recognition sequence. The methylation sensitivities of these enzymes to cytosine N4-methylation have not been previously reported. In this paper we present data demonstrating that all these enzymes, except NgoII, are inhibited by cytosine N4-methylation of the second 5' cytosine residue within the recognition sequence.

Cloning and characterization of the gene encoding a new DNA methyltransferase from Neisseria gonorrhoeae

A HindIII fragment of N. gonorrhoeae MS11 DNA coding for DNA methyltransferase (MTase) activity was cloned and expressed in E. coli AP1-200-9 cells. The sequence of 4681 bp was determined, and its analysis revealed two open reading frames (ORFs) sharing some similarity with known DNA MTases. ORF1 encodes an active N4mC MTase (M.NgoMV). The enzyme modifies only one strand of double stranded DNA and preferentially recognises the sequence GCCHR although it is able to methylate other sites. The exact recognition sequence cannot be precisely defined due to a relaxed specificity. The second ORF shows high homology to 5mC Mtases, but we were unable to demonstrate DNA methylating activity of its product either in vivo or in vitro.

Sequence similarities between the genes encoding the S.NgoI and HaeII restriction/modification systems

The DNA sequence encoding the S.NgoI restriction/modification (R/M) system was identified from a gene bank made from Neisseria gonorrhoeae strain WR302 by identifying recombinant plasmids that induced the reporter system in a methylase detection strain AP1-200-9 (Piekarowicz et al., 1991) and were resistant to digestion with NgoI. The DNA sequence was determined from one of these (pUCP30). M.NgoI is a protein of 315 aa with a predicted MW of 35296 Da and R.NgoI is a protein of 350 aa with a predicted MW of 40650 Da. The termination codon of M.NgoI overlapped the start codon of R.NgoI. The same strategy was used to clone the R/M system encoding HaeII from Haemophilus aegyptius strain ATCC 11116. The DNA sequence from one clone representing this class (pAP704) was determined. HaeII methylase is a protein of 318 aa with a predicted MW of 35669 Da and R.HaeII contains 352 aa with a predicted MW of 40800 Da. aa alignments between the two methylases indicated that they were 74.3% identical and 79% similar. DNA sequence alignments revealed 68% identity. An aa alignment between the two restriction enzymes indicated that they were 60% identical and 68% similar. DNA sequence alignments revealed 61% identity. The DNA sequences flanking these two systems were identified and used to determine the genomic organization of the two systems. The S.NgoI genes were found between two genes, one with high homology to GTP binding proteins of unknown function and one with homology to genes involved in tRNA synthetase synthesis. The HaeII R/M genes were located between two genes, mucF and mucE. The DNA sequence of the HaeII R/M system was compared to the genomic DNA sequence of H. influenzae Rd. Although the DNA sequences flanking the HaeII system were > 99% identical to contiguous DNA fragments found in the genome of H. influenzae Rd, no homology was seen with the DNA sequences encoding the HaeII R/M system, indicating that it is not found in this strain. Given the vast difference in the GC content of S.NgoI and HaeII, their apparent insertion into polycistronic operons, and their difference in codon usage when compared to the species from which they were isolated, the data suggest that these R/M systems originated in an organism other than Neisseria or Haemophilus.

Determination of the cos sequence of the mature genome of S2/HP1 type B bacteriophage of Haemophilus influenzae

The cos region of Haemophilus influenzae phage HP1/S2 type B has been cloned and its nucleotide (nt) sequence determined. The nt sequence of the cohesive ends (cos) and whole cos site of type-B phage have been compared to corresponding sequences of the HP1c1 phage. The results of a search for symmetry elements and IHF-binding sites in this region are presented.

Restriction and modification systems of Neisseria gonorrhoeae

An individual strain of Neisseria gonorrhoeae may produce up to 16 different DNA methytransferases (MTases). We have used a novel cloning system that is able to detect MTase clones in the absence of direct selection [Piekarowicz et al., Nucleic Acids Res. 19 (1991) 1831-1835] to identify 14 different MTase clones. Initial characterization of these clones indicates that at least seven of these MTases are linked to restriction endonuclease (ENase) systems. Six of these systems have been characterized by DNA sequence analysis, and the open reading frames encoding each of these systems have been identified. The recognition sequences for the cloned systems have the following specificities: S.NgoI, RGCGCY; S.NgoII, GGCC; S.NgoIV, GCCGCC; S.NgoV, GGNNCC; S.NgoVII, GCSGC; S.NgoVIIIA, GGTGA; and S.NgoVIIIC, TCACC. Of those systems that have been cloned, NgoI-NgoVII are typical type II R-M systems, with each encoding a DNA MTase that methylates cytosine in position 5. NgoVIII is a type IIS system, containing an ENase and two different MTases. One of these is a cytosine MTase (NgoVIIIC) and the other is an adenine MTase (NgoVIIIA). Although most of our clones encodes both the ENase and the MTase, none of the six R-M systems are genetically linked on the chromosome.

Purification and characterization of a new DNA methyltransferase from Neisseria gonorrhoeae

A new DNA methyltransferase, M.NgoBVII, was isolated from Neisseria gonorrhoeae strain WR302. M.NgoBVII recognizes the sequence 5'-GCNGC-3'.

Improvement of the strain for the rapid identification of genes encoding restriction and modification enzymes

The E. coli AP1-200-9 strain for rapid identification of genes encoding restriction and modification enzymes carries a temperature sensitive lacZ gene fused to the damage-inducible dinD locus. A derivative of this strain was constructed that has a wild-type form of this locus which allows for a more efficient identification of recombinant plasmids encoding restriction and modifications enzymes.

Macroevolution by transposition: drastic modification of DNA recognition by a type I restriction enzyme following Tn5 transposition

We have characterized a novel mutant of EcoDXXI, a type IC DNA restriction and modification (R-M) system, in which the specificity has been altered due to a Tn5 insertion into the middle of hsdS, the gene which encodes the polypeptide that confers DNA sequence specificity to both the restriction and the modification reactions. Like other type I enzymes, the wild type EcoDXXI recognizes a sequence composed of two asymmetrical half sites separated by a spacer region: TCA(N7)RTTC. Purification of the EcoDXXI mutant methylase and subsequent in vitro DNA methylation assays identified the mutant recognition sequence as an interrupted palindrome, TCA(N8)TGA, in which the 5' half site of the wild type site is repeated in inverse orientation. The additional base pair in the non-specific spacer of the mutant recognition sequence maintains the proper spacing between the two methylatable adenine groups. Sequencing of both the wild type and mutant EcoDXXI hsdS genes showed that the Tn5 insertion occurred at nucleotide 673 of the 1221 bp gene. This effectively deletes the entire carboxyl-terminal DNA binding domain which recognizes the 3' half of the EcoDXXI binding site. The truncated hsdS gene still encodes both the amino-terminal DNA binding domain and the conserved repeated sequence that defines the length of the recognition site spacer region. We propose that the EcoDXXI mutant methylase utilizes two truncated hsdS subunits to recognize its binding site. The implications of this finding in terms of subunit interactions and the malleability of the type I R-M systems will be discussed.

Cloning and linkage analysis of Neisseria gonorrhoeae DNA methyltransferases

We have cloned DNA methyltransferases (MTases) from various strains of Neisseria gonorrhoeae. Each of these clones represents a single specificity, indicating that the multiple gonococcal MTase specificities are encoded by monospecific MTases. The DNAs of five strains (FA5100, F62, MS11, Pgh3-2, and WR302) were digested with NheI, SpeI, or NheI plus SpeI and subjected to pulsed-field gel electrophoresis. The DNA MTase clones were used to probe Southern blots of these pulsed-field gels to determine whether the MTase genes are linked and whether there are strain-to-strain differences. The results indicate that none of these genes are closely linked, but variable hybridization patterns indicate that there exist restriction fragment length polymorphisms between the strains tested. Most of the chromosomal regions containing these restriction fragment length polymorphisms are clustered in regions containing gonococcal genes known or suspected to antigenically vary via genetic recombination.

Recombination of constant and variable modules alters DNA sequence recognition by type IC restriction-modification enzymes

EcoR124 and EcoDXXI are allelic type I restriction-modification (R-M) systems whose specificity genes consist of common structural elements: two variable regions are separated by a constant, homologous region containing a number of repetitive sequence elements. In vitro recombination of variable and constant elements has led to fully active, hybrid R-M systems exhibiting new and predictable target site specificities. Methylation of synthetic DNA sequences with purified, hybrid modification methylases was used to confirm the proposed recognition sequences. The results clearly demonstrate the correlation between protein domains and target site specificity. Our data suggest that a bacterial population may switch the recognition sequences of its type I R-M system by single recombination events and thus is able to maintain a prokaryotic analogue of the immune system of variable specificity.

A new method for the rapid identification of genes encoding restriction and modification enzymes

We have constructed derivatives of Escherichia coli that can be used for the rapid identification of recombinant plasmids encoding DNA restriction enzymes and methyltransferases. The induction of the DNA-damage inducible SOS response by the Mcr and Mrr systems, in the presence of methylated DNA, is used to select plasmids encoding DNA methyltransferases. The strains of E. coli that we have constructed are temperature-sensitive for the Mcr and Mrr systems and have been further modified to include a lacZ gene fused to the damage-inducible dinD locus of E. coli. The detection of recombinant plasmids encoding DNA methyltransferases and restriction enzymes is a simple, one step procedure that is based on the induction at the restrictive temperature of the lacZ gene. Transformants encoding DNA methyltransferase genes are detected on LB agar plates supplemented with X-gal as blue colonies. Using this method, we have cloned a variety of DNA methyltransferase genes from diverse species such as Neisseria, Haemophilus, Treponema, Pseudomonas, Xanthomonas and Saccharopolyspora.

Nomenclature relating to restriction of modified DNA in Escherichia coli

At least three restriction systems that attack DNA containing naturally modified bases have been found in common Escherichia coli K-12 strains. These systems are McrA, McrBC, and Mrr. A brief summary of the genetic and phenotypic properties so far observed in laboratory strains is set forth, together with a proposed nomenclature for describing these properties.

Cleavage of DNA by HaeII is inhibited by the presence of 5-methylcytosine at the second cytosine within the recognition sequence

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The EcoDXX1 restriction and modification system: cloning the genes and homology to type I restriction and modification systems

The Escherichia coli plasmid pDXX1 codes for a type I restriction and modification system, EcoDXX1. A 15.5-kb BamHI fragment from pDXX1 has been cloned and contains the hsdR, hsdM, and hsdS genes that encode the EcoDXX1 system. The EcoDXX1 hsd genes can complement the gene products of the EcoR124 and EcoR124/3 hsd systems, but not those of EcoK and EcoB. Hybridization experiments using EcoDXX1 hsd genes as a probe demonstrate homology between EcoDXX1 and EcoR124 and EcoR124/3 restriction-modification systems, but weak or no homology between EcoDXX1 and EcoK or EcoB systems.

Transfer of plasmid Hly in vivo in pigs intestine

The results of our study suggest the in vivo transfer of Hly plasmid from native pathogenic and enterotoxigenic Escherichia coli strain to autochtonous Escherichia coli, using ileal loop test. To confirm this hypothesis pHly::Tn5 and PHly::Tn3 were obtained using an in vitro recombination method, and introduced to Escherichia coli laboratory strain. For experiments the laboratory strain, carrying pHly::Tn5 and pHly::Tn3 and pHly::Tn5 strain which acquired K88(F4) by means of conjugation, were used. In the study in which the donor Escherichia coli pHly::Tn5 strain, carrying antigen K88(F4), was injected into the ileum, pHly conjugants were isolated from faeces after 48 h in 2 out of 5 pigs, which was a low frequency. After the oral introduction of 10(9) cells of pHly::Tn5 and pHly::Tn3 Escherichia coli strains without the colonizing factor K88(F4), conjugants were not isolated from faeces of experimental animals. However when the pigs received donor CSH55 pHly::Tn5 Escherichia coli strain orally, which were also carrying plasmid K88(F4), transconjugants were obtained in a low frequency of 3 out of 9 pigs. Our experiments confirmed the suggestion of Smith that in vivo transfer of plasmid in the intestine of animals is only possible when the donor transfers the plasmid with high frequency and readily colonizes the intestine. The pHly::Tn5 plasmid acquired by in vitro recombination does not spread with time throughout the autochtonic population of Escherichia coli present in the intestine of swine. The results of our study showed the in vivo transfer in pigs intestine of Hly pathogenicity marker from both native pathogenic strains carrying antigen K88(F4) and constructed donor laboratory strain of Escherichia coli pHly::Tn5 also carrying antigen K88(F4) to autochtonous intestinal strains.

Neisseria gonorrhoeae M.Ngo AI DNA methyltransferase: physical and catalytic properties of the homogeneous enzyme

A DNA methyltransferase, M.NgoAI, was purified to homogeneity from Neisseria gonorrhoeae strain WR220 by successive column chromatography. Its Mr is 25,000, as determined by both gel filtration and denaturing polyacrylamide gel electrophoresis. Maximal enzymatic activity was obtained in 50 mM Tris.HCl (pH 7.4), 10 mM EDTA, with incubation at 37 degrees C. An apparent Km value for S-adenosylmethionine and 5' -GGCC sites was determined to be 1.25 microM and 89.6 nM, respectively.

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

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Purification and characterization of DNA methyltransferases from Neisseria gonorrhoeae

Three DNA methyltransferases, M.NgoAI, and M.NgoBI and M.NgoBII, free of any nuclease activities were isolated from Neisseria gonorrhoeae strains WR220 and MUG116 respectively. M.NgoAI recognizes the sequence 5' GGCC 3' and methylates the first 5' cytosine on both strands. M.NgoBI and M.NgoBII recognize 5' TCACC 3' and 5' GTAN5CTC 3' respectively. M.NgoBII methylates cytosine on only one strand to produce 5' GTAN5mCTC 3'.

Restriction of plasmid DNA during transformation but not conjugation in Neisseria gonorrhoeae

Neisseria gonorrhoeae strains WR302 and PGH3-2 were characterized with respect to their restriction-modification phenotype. WR302 DNA was cleaved by HaeIII, indicating the lack of methylation at the GGCC sequence. PGH3-2 produced NgoSI (an isoschizomer of NgoII). WR302 produced a restriction enzyme with a recognition sequence different from that of NgoI, NgoII, or NgoIII. Plasmid pFT180 isolated from WR302 was unable to transform PGH3-2, whereas plasmid pFT180 isolated from PGH3-2 was able to transform PGH3-2 at a very high frequency. When plasmid pFT180 isolated from WR302 was methylated in vitro with meth M. HaeIII, this plasmid was able to transform PGH3-2. NgoSI was able to restrict WR302 DNA in vitro, whereas it was incapable of restricting PGH3-2 DNA in vitro. When the self-transmissible R factor pFT6 was mobilized from WR302 to PGH3-2 by conjugation, a 1-order-of-magnitude difference in transfer frequencies was observed, as compared with an isogenic cross. The data indicate that host-mediated restriction can prevent the gonococcus from acquiring DNA via transformation but not via conjugation.

Restriction mapping and close relationship of the DNA of Streptomyces erythraeus phages 121 and SE-5

The biological properties and genome structure of two actinophages, 121 and SE-5, infecting Streptomyces erythraeus were characterized. They had the same host range (limited to S. erythraeus) and similar DNA G + C contents (around 60 mol %). Restriction maps of their genomes also showed many similarities. The close relationship between the two phages was confirmed by DNA hybridization experiments: large parts of their genomes were homologous, except for a segment in the middle of the map, where no hybridization was detected.

The DNA sequence recognized by the EcoDXX1 restriction endonuclease

EcoDXX1 is a type-I restriction enzyme coded for by the plasmid pDXX1. Like other type-I restriction endonucleases, the enzyme catalyses the modification of susceptible DNA. We have determined the DNA sequence recognised by EcoDXX1 to be: 5'TCANNNNNNNATTC-3' 3'-AGTNNNNNNNTAAG-5' where N can be any nucleotide. This sequence has an overall structure very similar to previously determined type-I sequences.

Major spontaneous genomic rearrangements in Haemophilus influenzae S2 and HP1c1 bacteriophages

Physical maps constructed by the localization of the cleavage site of several restriction endonucleases have shown that the genomes of the Haemophilus bacteriophages S2 and HP1c1 exist in variant forms which differ in the molecular organization of the genomes. At least three regions of different organization of the bacteriophage chromosomes have been identified. The different types of molecular organization can be detected both in the DNA isolated from the mature phage particles and after integration of the phage DNA into the bacterial chromosome.

The EcoDXX1 restriction and modification system of Escherichia coli ET7. Purification, subunit structure and properties of the restriction endonuclease

The Escherichia coli plasmid pDXX1 codes for a new restriction-modification system. The specific restriction endonuclease coded by this system has been purified by a procedure that includes phosphocellulose and heparin-agarose chromatography. Sedimentation on glycerol gradients showed one peak of activity with a value of about 12 S. The highly purified enzyme require ATP and Mg2+ for activity as well as S-adenosylmethionine, although some S-adenosylmethionine molecules are probably bound to the enzyme. The enzyme does not cleave lambda DNA at well-defined sites and has a strong non-modified DNA-dependent ATPase activity. The enzyme has also methylase activity acting against non-modified DNA.