EcoRI Restriction Research Articles

Two Subunits of EcoRII Restriction Endonuclease Interact with Two DNA Recognition Sites

The cleavage of a 14 base pair DNA duplex containing one EcoRII recognition site by EcoRII restriction endonuclease (R. EcoRII) was studied in single turnover experiments with varying enzyme concentrations in the micromolar range. The reaction rate increased with enzyme concentration until a ratio of one dimeric R. EcoRII enzyme to two double stranded oligonucleotide molecules. Excess of R. EcoRII lead to inhibition of cleavage. Maximum cleavage was also found with pBR322 DNA containing six EcoRII recognition sites at a ratio of one dimeric enzyme to two EcoRII recognition sites of the plasmid DNA. At higher ratios inhibition was observed. These observations indicate that the active enzyme complex is formed when two subunits of the enzyme interact with two R. EcoRII recognition sites.

Plasmid diversity in Escherichia coli isolated from processed poultry and poultry processors

Plasmids of bacteria selected from different bacterial populations because they shared a distinctive antimicrobial resistance phenotype have sometimes had identical restriction fragments. Such identical plasmids are thought to belong to small and thus epidemic clones because the plasmid content of unselected resistant isolates has seemed diverse. To survey this presumed diversity and its implications for the lineage of resistance plasmids we examined the transferability, sizes and EcoR1 restriction fragment sizes of plasmids in both Escherichia coli isolated randomly from poultry raised by 16 growers as they were being processed through two plants and in isolates from the urine of women processing poultry in those plants. Forty two (24%) of 175 resistant isolates from poultry of 16 growers and 9 (26%) of 34 resistant isolates from the poultry processors transferred resistance conjugatively to varied combinations of antimicrobials. No poultry isolate had both the same expressed and the same transferred combination as any processor's isolate. The DNA bands which could be discerned in electrophoresis gels of restricted or unrestricted plasmid extracts of isolates or their transconjugants from 156 of the poultry and 24 of the poultry processors appeared diverse. Pairs of related-appearing plasmids were seen in consecutive isolates of poultry from each of two growers and in one pair from different growers. One set of identical-appearing plasmids was seen in 3 consecutive isolates from poultry of one grower, others in 2 consecutive isolates from a second grower's poultry, in 2 non-consecutive isolates of a third grower's, and in single isolates from poultry of 2 different growers. None of the plasmids from any of the human isolates appeared related to those from any other human isolate or to those of any poultry isolate. These results indicate that resistance plasmids are highly diverse and that all but two of the exceptions to complete diversity in the isolates surveyed here could be ascribed to cross colonization within flocks of individual poultry growers. Also, while none of the plasmids in the poultry isolates appeared ancestral to any of plasmids in the poultry processors' isolates, their diversity indicates that those sampled plasmids would be only a very small fraction of the total number of different plasmids in bacteria colonizing poultry processed at that time or earlier.

Selective digestion of mouse chromosomes with restriction endonucleases. Oligonucleotide priming of single-stranded DNA produced with exonuclease III

L-929 mouse chromosomes prepared for electron microscopy have been treated with MspI, EcoRI, and HaeIII restriction endonucleases (REs). RE-induced nicks were amplified with exonuclease III to obtain single-stranded DNA (ss-DNA) motifs. The ss-DNA produced was enough to permit hybridization of a series of random oligonucleotides. These can be used as primers, which are extended by the Klenow fragment using non-isotopic labelled dUTP. The incorporation of biotinylated dUTP is detected with a gold-tagged streptoavidin as the reporter molecule. This allows, in mouse chromosomes, the detection of different rates of sensitivity to the digestion with specific REs in distinct intraheterochromatic DNA subsets. In addition, these results show that enzymatic production of ss-DNA seems to be adequate for electron microscopy work since the chromatin fiber is preserved better than in denatured DNA produced with heat, NaOH, or formamide.

Sequence motifs common to the Eco RII restriction endonuclease and the proposed sequence specificity domain of three DNA-[cytosine-C5] methyltransferases

We have compared the deduced amino acid (aa) sequences of the Eco RII restriction endonuclease (R. Eco RII) and the proposed specificity (target recognition) domains of three DNA-[cytosine-C5] methyltransferases (MTases), M · Eco RII, M · Dcm, and M · SPR, each of which recognizes the same nucleotide sequence, CCWGG (where W is A or T). We have identified a region containing sequence motifs that are partially conserved in the MTases and R · Eco RII. This may be the first example of aa sequence homology between a MTase specificity (target recognition) domain and its cognate restriction endonuclease (ENase). It suggests that this region is important for DNA recognition by R · Eco RII and that the Eco RII ENase and MTase genes may have evolved from a common progenitor.

Diversity of ribosomal DNA fingerprints of Leptospira serovars provides a database for subtyping and species assignation

Ribosomal DNA fingerprints from 103 pathogenic Leptospira strains were examined using EcoRI restriction and fragment length polymorphisms of rRNA genes. Sixty-nine new leptospiral ribotypes were described, in addition to 49 previously observed. Except for 5 strains, a good correlation between DNA homology data and ribotyping was observed. The genospecies of 31 reference strains could be presumed, since they shared 13 ribotypes with strain(s) previously studied by DNA homology. Furthermore, the definition of common rRNA hybridization fragments in each recognized DNA hybridization group provides information about the status of Leptospira reference strains yet to be classified. With 118 ribotypes now defined among the validated serovar reference strains, rRNA fingerprints constitute a database for subtyping Leptospira species.

A METHOD FOR the DETERMINATION of STRANDEDNESS of DNA FRAGMENTS CLONED IN PHAGE M13

Recombinant M13Hol phage containing Eco R1 restriction endonuclease fragments B, E, and F of adenovirus type 2 (Ad2) DNA were constructed by cloning into the unique Eco R1 site of the replicative form of the phage M13Hol176 DNA. Polarity of the adenovirus inserts in recombinant molecules was deduced by the following procedures: Viral DNA fragments obtained from Ad2 DNA molecules were purified, denatured, and subjected to electrophoresis. the separated DNA strands were transferred from agarose to nitrocellulose by the Southern procedure and hybridized with radioactive 3′‐end labeled Hae III fragments of the recombinant phage DNAs. This procedure provided a rapid test for assaying strandedness of the cloned fragments.

Mechanism of the interaction of EcoRII restriction endonuclease with two recognition sites. Probing of modified DNA duplexes as activators of the enzyme.

The efficiency of cleavage of DNA duplexes with single EcoRII recognition sites by the EcoRII restriction endonuclease decreases with increasing substrate length. DNA duplexes of more than 215 bp are not effectively cleaved by this enzyme. Acceleration of the hydrolysis of long single-site substrates by EcoRII is observed in the presence of 11-14-bp substrates. The stimulation of hydrolysis depends on the length and concentration of the second substrate. To study the mechanism of EcoRII endonuclease stimulation, DNA duplexes with base analogs and modified internucleotide phosphate groups in the EcoRII site have been investigated as activators. These modified duplexes are cleaved by EcoRII enzyme with different efficiencies or are not cleaved at all. It has been discovered that the resistance of some of them can be overcome by incubation with a susceptible canonical substrate. The acceleration of cleavage of long single-site substrates depends on the type of modification of the activator. The modified DNA duplexes can activate EcoRII catalyzed hydrolysis if they can be cleaved by EcoRII themselves or in the presence of the second canonical substrate. It has been demonstrated that EcoRII endonuclease interacts in a cooperative way with two recognition sites in DNA. The cleavage of one of the recognition sites depends on the cleavage of the other. We suggest that the activator is not an allosteric effector but acts as a second substrate.

Sensitivity of a ribosomal RNA gene probe for identification of life stages of Anopheles arabiensis and An. gambiae (Diptera: Culicidae) using three storage methods.

Individual larvae, pupae, female adults, and adult body parts of Anopheles arabiensis Patton and An. gambiae Giles were stored for 1 mo either in isopropanol at room temperature, over a desiccant at room temperature, or at -70 degrees C. DNA was extracted, digested with EcoR1 restriction enzyme, subjected to electrophoresis in agarose gel, transferred to filters, then hybridized to a 32P-labeled rDNA probe. There was no difference among storage treatments in the proportion of correctly identified samples. First instars were not identifiable. Pupae and female adults were more likely to be identified than earlier life history stages. Nonetheless, the probe identified greater than 75% of second instars, 94% of third instars, and 74% of fourth instars. There were no differences between the species in the proportion of identifiable samples for any life history stage.

A new affinity reagent for the site-specific, covalent attachment of DNA to active-site nucleophiles: application to the EcoRI and RsrI restriction and modification enzymes.

A modified oligodeoxyribonucleotide duplex containing an unnatural internucleotide trisubstituted 3' to 5' pyrophosphate bond in one strand [5'(oligo1)3'-P(OCH3)P-5'(oligo2) 3'] reacts with nucleophiles in aqueous media by acting as a phosphorylating affinity reagent. When interacted with a protein, a portion of the oligonucleotide [--P-5'(oligo2)3'] becomes attached to an amino acid nucleophilic group through a phosphate of the O-methyl-modified pyrophosphate linkage. We demonstrate the affinity labeling of nucleophilic groups at the active sites of the EcoRI and RsrI restriction and modification enzymes with an oligodeoxyribonucleotide duplex containing a modified scissile bond in the EcoRI recognition site. With the EcoRI and RsrI endonucleases in molar excess approximately 1% of the oligonucleotide becomes attached to the protein, and with the companion methyltransferases the yield approaches 40% for the EcoRI enzyme and 30% for the RsrI methyltransferase. Crosslinking proceeds only upon formation of a sequence-specific enzyme-DNA complex, and generates a covalent bond between the 3'-phosphate of the modified pyrophosphate in the substrate and a nucleophilic group at the active site of the enzyme. The reaction results in the elimination of an oligodeoxyribonucleotide remnant that contains the 3'-O-methylphosphate [5'(oligo1)3'-P(OCH3)] derived from the modified phosphate of the pyrophosphate linkage. Hydrolysis properties of the covalent protein-DNA adducts indicate that phosphoamide (P-N) bonds are formed with the EcoRI endonuclease and methyltransferase.

Assignment of the lens intrinsic membrane protein MP19 structural gene to human chromosome 19

We have isolated and characterized a bovine cDNA clone encoding the bovine lens intrinsic membrane protein, MP19. This cDNA was used as a probe to analyze a panel of Southern blots of human-Chinese hamster somatic cell hybrid DNAs to assign the gene coding for MP19 to its human chromosome. Control human and Chinese hamster DNAs displayed a distinct EcoR1 restriction fragment pattern when hybridized with the bovine MP19 cDNA. When somatic cell hybrid DNAs were restricted with Eco R1 and Southern blots hybridized with the bovine MP19 cDNA, the characteristic human restriction pattern was observed only when human chromosome 19 was present in the hybrid panel. This assignment was confirmed using a human chromosome 19-specific genomic library. A clone from this human chromosome 19-specific library was identified and further characterized. This clone contained a 7.9 kilobase fragment that contained identical DNA sequences with that of the authentic bovine MP19 cDNA, and with a separate human genomic clone containing the MP19 gene.

Simultaneous amplification of epidermal growth factor-receptor and multidrug-resistance genes in a newly. Established human lung cancer cell line : Shin HJ, Shin DM, Grant G, Hong WK, Pathak S. Cellular Genetics Laboratory, University of Texas M.D. Anderson Cancer Center, Box 181, 1515 Holcombe Blvd., Houston, TX 77030. Anticancer Res 1991;11:241-8

We have investigated amplification and expression of the epidermal growth factor (EGF)-receptor gene and the multidrug-resistance (MDRI) gene in a newly established lung adenocarcinoma cell line and its subcell lines. Of these cell lines, the EGF-receptor was amplified (64-fold) and rearranged (6.5 and 5.4 Kb with EcoRI restriction) in an early passage cell line, DMS-4CS. MDRI gene amplification (10.5-fold), accompanied by rearrangement (4.6 and 3.7 Kb with Hind III restriction), was found in the same cell line. All other subcell lines derived from DMS-4C5 failed to demonstrate any amplification of these genes. Moreover, mRNA expression of these two genes was not overproduced. Our findings seem to indicate that highly selected cells at an early stage have undergone spontaneous amplification of these genes. However, cells containing such amplified DNA sequences may exhibit growth disadvantage, and, therefore, the amplified DNA sequences were not present in the sublines. The cytogenetic study demonstrated that early passage cells, DMS-4C6, only showed one unique marker chromosome, M10, which may represent amplification of these genes in question.

Ultraviolet light induction of lambda from dcm host strains alleviates Eco RII restriction of phage

A new form of restriction alleviation is demonstrated for phage induced by ultraviolet light from dcm strains of Escherichia coli K-12. EcoRII restriction of the induced phage is alleviated, which is the first report of Type II restriction alleviation. Unlike previously reported restriction alleviation, the increase in phage-plating efficiency is not dependent upon irradiation of the plating host for its induction.

Ultraviolet light induction of lambda fromdcmhost strains alleviatesEcoRII restriction of phage

A new form of restriction alleviation is demonstrated for phage induced by ultraviolet light from dcm strains of Escherichia coli K-12. EcoRII restriction of the induced phage is alleviated, which is the first report of Type II restriction alleviation. Unlike previously reported restriction alleviation, the increase in phage-plating efficiency is not dependent upon irradiation of the plating host for its induction.

Specific DNA Fragments Coding for ST1 and LT1 Toxins, and K88 (F4) Adhesin in Enterotoxigenic Escherichia coli

Ten porcine strains of enterotoxigenic Escherichia coli possessing the K88 (F4) adhesion fimbriae, were selected for study of enterotoxin- and fimbriae-encoding plasmids. Plasmid DNA, separated according to size by gel electrophoresis was transferred to nylon membranes by Southern blotting, and hybridized with enzyme-labelled oligonucleotide probes for ST1 and LT1 enterotoxins, and a 32P-labelled probe for the F4 fimbriae. Plasmids possessing the enterotoxin genes ranged from 50 MDa to 78 MDa in size. The ST1 genes were located on a common 8-MDa EcoR1 restriction endonuclease fragment, while the LT1 genes were located on a 4.5-MDa EcoR1 fragment from the different plasmids. Plasmids with the F4 genes ranged from 50 MDa to 118 MDa in size, but the F4 encoding genes were located on a common 3-MDa HindIII restriction endonuclease fragment. ST1 and LT1 genes were found on the same plasmid in only one strain, LT1 and F4 genes on the same plasmids in 5 strains, while no plasmid contained genes for both ST1 and F4.

Possible in-vivo transfer of β-lactamase TEM-3 from Klebsiella pneumoniae to Salmonella kedougou

Salmonella kedougou BM2659 was isolated from the stools and a blood culture of a patient and Klebsiella pneumoniae BM2657 and S. kedougou BM2658 were isolated later from the stools of the same patient. Strains BM2657 and BM2658 had identical resistance phenotypes, to beta-lactams, aminoglycosides and tetracycline, due to the presence of the same genes, blaT, aacA4 and tetC, respectively. Oligotyping indicating that beta-lactam resistance in these strains was encoded by blaT-3 and synthesis of TEM-3 was confirmed by isoelectric focusing. In BM2657 and BM2658, the resistance characters were located on Inc7 or M self-transferable plasmids with indistinguishable EcoRI and HindIII restriction patterns. Southern hybridization of plasmid DNA of these strains with probes pCFFO4, the prototype plasmid encoding TEM-3, genes blaT, aacA4 and tetC gave identical patterns. S. kedougou BM2658 and BM2659 had identical biotypes and serotypes but BM2659 was susceptible to all the study antibiotics. These observations suggest possible transfer, in the digestive tract, of a plasmid encoding TEM-3 beta-lactamase from K. pneumoniae BM2657 to S. kedougou BM2659.

Use of a ribosomal RNA gene probe for the epidemiological study of methicillin and ciprofloxacin resistantStaphylococcus aureus

Conventional bacteriophage typing was combined with ribotyping in the analysis of methicillin and ciprofloxacin resistant Staphylococcus aureus strains isolated in increasing frequency since the introduction of the new 4-quinolones as therapeutic agents in the Tel-Aviv Medical Center. Whole-cell DNA was digested with EcoRI and HindIII restriction endonucleases. Agarose gel electrophoresis, Southern blotting, and hybridization by biotinylated probe DNA coding for ribosomal RNA revealed 7 to 14 bands. Analysis of the patterns established a single DNA type in EcoRI as well as in HindIII digests for all strains except one. Control strains from other sources differed in their band patterns. Bacteriophage typing confirmed the results of DNA typing. Thus, the frequent occurrence of staphylococcal isolates resistant to 4-quinolones in the hospital was not due to mutational development of resistance in many strains, but to the spread of a resistant strain.

Human aminoacylase-1: Cloning, regional assignment to distal chromosome 3p21.1, and identification of a cross-hybridizing sequence on chromosome 18

Aminoacylase-1 (ACY1, EC 3.5.1.14) is a cytosolic enzyme with a wide range of tissue expression and has been postulated to function in the catabolism and salvage of acylated amino acids. ACY1 has been assigned to chromosome 3p21, a region reduced to homozygosity in small-cell lung cancer and renal cell carcinoma, and has been reported to exhibit reduced or absent expression in small-cell lung cancer cell lines and tumors. Using monoclonal antibodies to human ACY1, we have isolated cDNA clones from a liver λgt11 cDNA library. As proof of identity, the fusion protein encoded by a putative ACY1 cDNA displayed ACY1 enzymatic activity. Additionally, it was determined that the putative ACY1 cDNA clones hybridize to an EcoR1 restriction fragment that has been mapped to chromosome 3p. Both ACY1 activity and this restriction fragment have been further demonstrated to be syntenic to distal 3p21.1 through the use of a panel of human-rodent somatic cell hybrids containing fragments of chromosome 3. An additional EcoR1 restriction fragment to which the probe hybridizes has been assigned to chromosome 18. The major mRNA species to which the ACY1 cDNA hybridizes is 0.9 kb; faint hybridization to a 4.2-kb mRNA species is also detected. These studies further refine a region of interest in the investigation of gene inactivation in small-cell lung cancer and provide a new marker on chromosome 18.

The kalilo senescence plasmid of Neurospora intermedia has covalently-linked 5? terminal proteins

Kalilo is a linear plasmid associated with senescence in Neurospora. The terminal Eco R1 restriction fragments of this element are linked to a protein component which remains bound despite denaturation with high concentrations of SDS. Following digestion with proteinase K, the 5′ termini of the plasmid remain resistant to lambda exonuclease whereas the 3′ termini are sensitive to exonuclease III, suggesting that the terminal protein is covalently linked. From an analysis of iodinated proteins released by nuclease digestion, the size of the terminal protein was estimated to be 120 kDa. The covalent linkage between DNA and protein was shown to be alkali-labile suggesting that it is a phosphodiester bond. Electron micrographs of the intact plasmid demonstrate that the associated proteins are terminal, and may be involved in replication.

Ribosomal RNA genes inQuercus spp. (Fagaceae)

The taxonomy of the genusQuercus is still unclear. In order to elucidate the taxonomy of Mediterranean oaks we have analyzed ribosomal RNA genes ofQuercus cerris, Q. coccifera, Q. trojana, Q. ilex, Q. suber, andQ. macrolepis by means of Southern blot hybridization. Oak nuclear DNA was extracted from root tips of 300 acorns and from catkins of single plants. EcoRI and BamHI restriction endonucleases were used. DNA electrophoresis and rRNA/DNA hybridization were performed usingVicia faba rRNA 18 S and 25 S as probes. The rRNA genes of all the species studied have an identical restriction mapping in the 18 S and 25 S regions, while differences in length are present in the intergenic regions.Q. cerris possesses at least four types of genes of 12.1, 11.5, 8.5, and 8.3 kb;Q. coccifera at least three types of 12.4, 10.4, and 10.1 kb;Q. trojana possesses the same rRNA genes asQ. cerris plus another gene type 12.0 kb long, with EcoRI and BamHI restriction sites in the intergenic spacer;Q. ilex at least three types of 12.4, 10.85, and 9.5 kb;Q. suber at least five types of 11.5, 11.0, 8.6, 8.5, and 8.3 kb;Q. macrolepis, finally, at least seven types of 11.5, 11.0, 10.2, 8.6, 8.5, 8.3, and 8.15 kb.Q. coccifera andQ. ilex rDNA appears quite different respect to other species examined, while high similarity seems to exist betweenQ. cerris, Q. trojana, Q. suber, andQ. macrolepis. These results are in agreement with the taxonomic model proposed bySchwarz for the genusQuercus.

Nucleotide sequence of the EcoRII restriction endonuclease gene

The nucleotide sequence of a 1394 basepair (bp) DNA fragment containing the EcoRII restriction endonuclease (R.EcoRII) gene was determined. The endonuclease gene is 1206 bp in length (predicted 402 amino acids (aa) and M r = 45 178) and is separated by 33 bp from the EcoRII modification methylase (M.EcoRII) gene. The EcoRII restriction-modification system has a tail-to-tail organization of the two genes.