Restriction enzymes and their isoschizomers

Direct molecular analysis of Malassezia species from the clinical samples of patients with pityriasis versicolor

Background and Purpose

Species identification of Malassezia using culture-dependent methods is time-consuming due to their fastidious growth requirements. This study aimed to evaluate a rapid and accurate molecular method in order to diagnose the pityriasis versicolor (PV) and identify Malassezia species from direct clinical samples.

Materials and Methods

Skin scraping or tape samples from patients with PV and healthy volunteers as the control group were collected. Diagnosis of PV was confirmed by direct microscopic examination. The DNA extraction was performed according to the steel-bullet beating method. Polymerase chain reaction-restriction fragment length polymorphism assay using HhaI restriction enzyme was applied for the identification and differentiation of Malassezia species.

Results

The PCR method was able to detect Malassezia in 92.1% of specimens which were also confirmed with microscopic examination. Statistically, a significant association was observed between the results of the two assays (P < 0.001). Moderate agreement was identified between the two methods to diagnose the PV in both populations (Kappa: 0.55). Considering microscopic examination as the gold standard method for confirmation of PV, the sensitivity, specificity, positive predictive value, and negative predictive value values of the PCR assay for recognition of PV were 85%, 75%, 92%, and 60%, respectively. M. globosa and M. restricta were the most prevalent species isolated from patients.

Conclusion

In this study, the two-step molecular method based on the amplification of the D1/D2 domain and digestion of the PCR product by one restriction enzyme was able to diagnose and identify Malassezia directly from clinical samples. Consequently, it can be said that the molecular-based method provides more facilities to identify fastidious species, such as M. restricta.

Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum

Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.

Closed Genome Sequence of Clostridium pasteurianum ATCC 6013

We report here the closed genome of Clostridium pasteurianum ATCC 6013, a saccharolytic, nitrogen-fixing, and spore-forming Gram-positive obligate anaerobe. The organism is of biotechnological interest due to the production of solvents (butanol and 1,3-propanediol) but can be associated with food spoilage. The genome comprises a total of 4,351,223 bp.

Rapid and reliable method for identification of associated endonuclease cleavage and recognition sites

One barrier to cross during genetic engineering is the restriction-modification system found in many bacteria. In this study, we developed a fast and reliable method for mapping the recognition and cleavage site of the restriction endonucleases. Clostridium pasteurianum, a model organism for the study of nitrogen fixation, has been found to harbour at least two restriction-modification systems including the restriction endonucleases CpaPI, which is an isoschizomer of MboI and CpaAI. Dam-methylated DNA was used to isolate the activity of CpaAI. Exposing freshly prepared cell lysate to known nucleotide fragments and directly sequencing the pool of digested nucleotide fragments enabled identification of the cleavage sites in the fragments. By aligning the sequences adjacent to the cleavage site, it was possible to identify the recognition sequence. Using this method, we successfully located all CpaAI recognition and cleavage sites within the template sequence. By modifying DNA with both Dam and CpG methylases (M.SssI) and thereby preventing digestion by CpaPI and CpaAI, no further endonuclease activity was detected.

SIGNIFICANCE AND IMPACT OF THE STUDY

Restriction-modification systems are important barriers to successful genetic modification in many bacterial species. In this study, we demonstrate an efficient and general applicable method for identifying endonuclease recognition and cleavage sites. For the study and the trails, the model organism for nitrogen fixation Clostridium pasteurianum was used. The method was proven to be reliable, and by modifying DNA at the identified sites, it is possible to prevent digestion.

Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: chromosomal gene disruption of the endogenous CpaAI restriction enzyme

BACKGROUND

Clostridium pasteurianum is one of the most promising biofuel producers within the genus Clostridium owing to its unique metabolic ability to ferment glycerol into butanol. Although an efficient means is available for introducing foreign DNA to C. pasteurianum, major genetic tools, such as gene knockout, knockdown, or genome editing, are lacking, preventing metabolic engineering of C. pasteurianum.

RESULTS

Here we present a methodology for performing chromosomal gene disruption in C. pasteurianum using the programmable lactococcus Ll.ltrB group II intron. Gene disruption was initially found to be impeded by inefficient electrotransformation of Escherichia coli-C. pasteurianum shuttle vectors, presumably due to host restriction. By assessing the ability of various vector deletion derivatives to electrotransform C. pasteurianum and probing the microorganism's methylome using next-generation sequence data, we identified a new C. pasteurianum Type I restriction-methylation system, CpaAII, with a predicted recognition sequence of 5'-AAGNNNNNCTCC-3' (N = A, C, G, or T). Following rescue of high-level electrotransformation via mutation of the sole CpaAII site within the shuttle vectors, we retargeted the intron to the cpaAIR gene encoding the CpaAI Type II restriction endonuclease (recognition site of 5'-CGCG-3'). Intron insertion was potentially hindered by low retrohoming efficiency, yet this limitation could be overcome by a procedure for enrichment of the intron insertion. The resulting ΔcpaAIR mutant strain was efficiently electrotransformed with M.FnuDII-unmethylated plasmid DNA.

CONCLUSIONS

The markerless and plasmidless ΔcpaAIR mutant strain of C. pasteurianum developed in this study can serve as a general host strain for future genetic and metabolic manipulation. Further, the associated gene disruption protocol should not only serve as a guide for chromosomal gene inactivation studies involving mobile group II introns, but also prove invaluable for applying metabolic engineering strategies to C. pasteurianum.

Immunochemical analysis of protein expression in breast epithelial cells transformed by estrogens and high linear energy transfer (LET) radiation

Breast cancer is a complex disease involving numerous genetic aberrations. Immunochemical analysis of protein expression is presented in a human breast epithelial cell line neoplastically transformed by high linear energy transfer (LET) alpha particle radiation in the presence of 17beta estradiol (E) and in the parental human breast epithelial cell line (MCF-10F) which served as a non-tumorigenic control. The aim of this work was to determine the levels of mRNA and protein expression in control and transformed cells at various stages of the neoplastic process. The levels of mRNA and protein expression of PCNA, c-fos, JNK2 and Fra-1 were increased in the transformed cell line compared to the levels in non-tumorigenic control cells. The transforming factor Rho A was significantly increased only in the tumor cell line. Furthermore, the levels of mRNA and protein expression of ErbB2 were significantly increased in the transformed cell line and in tumor cells derived from the transformed cells after injecting them into nude mice. A decrease in RbA/p48 protein expression and mRNA levels was observed in cells treated with double doses of alpha particle radiation in the presence of estrogen, regardless of tumorigenicity. Such expression was lower than that in the control untreated MCF-10F cells. In summary, these studies show that estrogen and high LET-radiation induce changes in oncoprotein expression and mRNA levels of human breast cell lines. These changes are indicative of a cascade of events that characterize the process of cell transformation in breast cancer. These results provide evidence that multiple steps with consecutive changes are involved when normal cells become tumorigenic cells as a result of alpha particle irradiation and estrogen treatments.

Isolation and characterization of two types of actinophage infecting Streptomyces scabies

Two types of actinophages, phi S and phi L, were isolated from soil samples by using Streptomyces scabies, a potato scab pathogen, as indicator strain. The phages were partially characterized according to their physicochemical properties, plaques and particles morphology, and their host range; this varied from narrow (for phi S) to wide (for phi L). The adsorption rate constants of the phi S and phi L were 3.44 and 3.18 pL/min, and their burst sizes were 1.61 and 3.75 virions per mL, respectively. One-step growth indicated that phi S and phi L have a latent period of 1/2 h followed by a rise period of 1/2 h. The temperate character of these phages was tested in other isolates of Streptomyces. Four of the phages (phi SS3, phi SS12, phi SS13 and phi SS17) were identified as temperate phages, since they were able to lysogenize SS3, SS12, SS13 and SS17. phi SS3, phi SS12 and phi SS13 were homoimmune, and they were heteroimmune with respect to phi SS17. The restriction barriers of lysogenic isolates (SS12, SS13 and SS17) interfered with the blockage of plaque formation by phages (phi SS12, phi SS13 or phi SS17) propagated on them, about 75% of lysogenic isolates had restriction systems. The exposure of the lysogenic isolates (SS12, SS13 and SS17) to UV-irradiation prevented the possible restriction barriers of these isolates so that these barriers could be overcome.

Step-wise DNA relaxation and decatenation by NaeI-43K

Nae I protein was originally isolated for its restriction endonuclease properties. Nae I was later discovered to either relax or cleave supercoiled DNA, depending upon whether Nae I position 43 contains a lysine (43K) or leucine (43L) respectively. Nae I-43K DNA relaxation activity appears to be the product of coupling separate endonuclease and ligase domains within the same polypeptide. Whereas Nae I relaxes supercoiled DNA like a topoisomerase, even forming a transient covalent intermediate with the substrate DNA, Nae I shows no obvious sequence similarity to the topoisomerases. To further characterize the topoisomerase activity of Nae I, we report here that Nae I-43K changes the linking number of a single negatively supercoiled topoisomer of pBR322 by units of one and therefore is a type I topoisomerase. Positively supercoiled pBR322 was resistant to Nae I-43K. At low salt concentration Nae I-43K was processive; non-saturating amounts of enzyme relaxed a fraction of the DNA. At high salt concentration the same non-saturating amounts of Nae I-43K partially relaxed all the DNA in a step-wise fashion to give a Gaussian distribution of topoisomers, demonstrating a switch from a processive to a distributive mode of action. Nae I-43K decatenated kinetoplast DNA containing nicked circles, implying that Nae I-43K can cleave opposite a nick. The products of the reaction are decatenated nicked circles under both processive and distributive conditions. The behavior of Nae I-43K is consistent with that of a prokaryotic type I topoisomerase.

Factors involved in the transformation of previously non-transformable Clostridium perfringens type B

The pre-shock incubation of cells plus DNA and the methylation state of plasmid DNA were found to play a role in the electroporation-based transformation of Clostridium perfringens 3626B. Following pre-shock incubation, the highest number of C. perfringens 3626B transformants was obtained when plasmid pGK201 was both dam+ dcm+ modified, while no transformants were obtained when pGK201 was not methylated or only dcm methylated. This is consistent with the observation that plasmid pGK201 was protected against digestion by C. perfringens 3626B cell-associated nucleases for up to 3 min when methylated by both methylases. C. perfringens 3626B was successfully transformed only within a narrow cell recovery rate window. The ermAM gene associated with pGK201 and pAK102 was found to integrate into the chromosome of C. perfringens strain 13A and 3626B.

Cloning and expression of the NaeI restriction endonuclease-encoding gene and sequence analysis of the NaeI restriction-modification system

NaeI, a type-II restriction-modification (R-M) system from the bacterium Nocardia aerocolonigenes, recognizes the sequence 5'-GCCGGC. The NaeI DNA methyltransferase (MTase)-encoding gene, naeIM, had been cloned previously in Escherichia coli [Van Cott and Wilson, Gene 74 (1988) 55-59]. However, none of these clones expressed detectable levels of the restriction endonuclease (ENase). The absence of the intact ENase-encoding gene (naeIR) within the isolated MTase clones was confirmed by recloning the MTase clones into Streptomyces lividans. The complete NaeI system was finally cloned using E. coli AP1-200 [Piekarowicz et al., Nucleic Acids Res. 19 (1991) 1831-1835] and less stringent MTase-selection conditions. The naeIR gene was expressed first by cloning into S. lividans, and later by cloning under control of a regulated promoter in an E. coli strain preprotected by the heterologous MspI MTase (M.MspI). The DNA sequence of the NaeI R-M system has been determined, analyzed and compared to previously sequenced R-M systems.

A differential cloning procedure for rearranged or altered genomic DNA based on in-gel competitive reassociation

We have developed a substantially improved differential cloning procedure designed for cloning anonymous altered restriction DNA fragments from higher organisms. The improvements include (i) in-gel dissociation and reassociation of biotinylated restriction digests of target DNA fragments, (ii) replacement of agarose gel by a synthetic gel material for electrophoresis, (iii) use of a reassociation enhancing reagent (CTAB) for in-gel reassociation, and (iv) introduction of PCR. After several cycles of IGCR, we attained considerable enrichment of altered or rearranged DNA fragments which were originally present at one copy or less per complex eukaryotic genome. Examples of enrichment include those of an exogenously added DNA fragment, a chromosomal DNA sequence that has undergone a deletion, and DNA fragments containing a recombination junction.

Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824

We have previously cloned the acetone-formation pathway gene, encoding acetoacetate decarboxylase (adc), and butyrate-formation pathway gene, encoding phosphotransbutyrylase (ptb), of Clostridium acetobutylicum ATCC 824 in Escherichia coli. Here we report their subcloning in Bacillus subtilis and transfer to strain ATCC 824 via electrotransformation, where the corresponding enzyme activities were expressed at elevated levels, using pFNK1, a new B. subtilis/C. acetobutylicum shuttle vector. Plasmid pFNK1 was used because shuttle vectors that function in E. coli were unable to electrotransform ATCC 824 unless they became deleted in the E. coli-plasmid regions. The difficulties with shuttle vectors that function in E. coli are probably due to the presence of a restriction endonuclease in ATCC 824. This endonuclease recognizes the sequence 5'-GCNGC-3', which is prevalent in E. coli plasmids but occurs infrequently in pFNK1 and C. acetobutylicum genes. Cloning of genes in C. acetobutylicum is critical for redirecting the cellular metabolism (metabolic engineering) as well as for genetic studies of this industrial organism.

Conformation of DNA packaged in bacteriophage T7. Analysis by use of ultraviolet light-induced DNA-capsid cross-linking

The conformation of the linear, double-stranded, 39,936 kilobase-pair DNA packaged in the protein capsid of bacteriophage T7 is investigated here by use of short wavelength ultraviolet light-induced DNA-capsid cross-linking. To detect both DNA-capsid and DNA-DNA cross-links, DNA is expelled from the T7 capsid and the products of expulsion are analyzed by use of Nycodenz buoyant density centrifugation, followed by either pulsed field gel electrophoresis or invariant field gel electrophoresis. Short wavelength ultraviolet light is found to progressively induce both DNA-DNA and DNA-protein cross-links in intact bacteriophage T7, but not in T7 from which DNA had been expelled before exposure to ultraviolet light. Protein-protein cross-links are not induced. When DNA expelled from previously cross-linked T7 is cleaved with restriction endonuclease (1 to 3 sites cleaved), analysis of the resulting fragments reveals no regions on T7 DNA that are excluded from cross-linking to the capsid. However, the efficiency of cross-linking decreases as the distance from the left end (last end packaged) of the packaged DNA increases. Electron microscopy of negatively stained capsid-DNA complexes reveals no DNA-retaining structure other than the outer shell of the capsid. Together with previously reported data that indicate lack of protein-based specificity for ultraviolet light-induced cross-linking, these observations are interpreted by the assumptions that, within the limits of resolution of these experiments: (1) no region of packaged T7 DNA is excluded from contact with the outer shell of the T7 capsid; (2) the probability of contacting the outer shell decreases as the distance from the left end of packaged T7 DNA increases. Thus, T7 DNA packaging concentrates the last end packaged near the inner surface of the outer shell of the T7 capsid.

Isolation of temperature-sensitive McrA and McrB mutations and complementation analysis of the McrBC region of Escherichia coli K-12

We isolated temperature-sensitive mcrA and mcrBC mutants of Escherichia coli. At 42 degrees C, they were unable to restrict the T-even bacteriophages T6gt and T4gt or plasmids encoding cloned DNA methylase genes whose specificities confer sensitivity to the McrA and McrBC nucleases. Complementation analysis of the McrBC region (mcrB251) with the complete cloned McrBC system or a derivative with mcrB alone indicated that the mutation shows an absolute defect for the restriction of DNA containing hydroxymethylcytosine and a thermosensitive defect for the restriction of DNA containing methylcytosine. The properties of the McrA temperature-sensitive mutants suggest that some of these mutations can also influence the restriction of DNA containing hydroxymethylcytosine or methylcytosine residues.

Effects of fractionated x-irradiation on the Ly-6--Ril-1--Pol-5 region

Our laboratory has focused on defining, localizing, and understanding the mode of action of genes involved in fractionated x-irradiation (FXI) leukemia in susceptible and restraint mouse strains. We have described the genetic and molecular evidence suggesting the existence of multiple independent loci involved in FXI-induced leukemogenesis. These studies indicated that one of these, Ril-1, a locus on the distal portion of chromosome 15, is the major locus influencing susceptibility to the disease. Our data unequivocally place Ril-1 in the gene complex Ly-6--Ril-1--Sis--H-30--Pol-5. Ril-1 appears to be closest to Ly-6 and Sis. We report that in FXI-induced leukemias there are hypomethylation changes in the Ly-6 region as compared to normal thymocytes. In contrast, Sis was found to be hypermethylated and not expressed. In addition, we have noted DNA rearrangements in the Ly-6--Pol-5 region in the majority of tumors examined using the Ly-6 and spleen focus-forming virus (SFFLV) molecular probes. Increased expression of Ly-6 and other surface markers encoded in this region has been noted in FXI-induced thymomas.

Role of gene 6 exonuclease in the replication and packaging of bacteriophage T7 DNA

When bacteriophage T7 gene 6 exonuclease is genetically removed from T7-infected cells, degradation of intracellular T7 DNA is observed. By use of rate zonal centrifugation, followed by either pulsed-field agarose gel electrophoresis or restriction endonuclease analysis, in the present study, the following observations were made. (1) Most degradation of intracellular DNA requires the presence of T7 gene 3 endonuclease and is independent of DNA packaging; rapidly sedimenting, branched DNA accumulates when both the gene 3 and gene 6 products are absent. (2) A comparatively small amount of degradation requires packaging and occurs at both the joint between genomes in a concatemer and near the left end of intracellular DNA; DNA packaging is only partially blocked and end-to-end joining of genomes is not blocked in the absence of gene 6 exonuclease. (3) Fragments produced in the absence of gene 6 exonuclease are linear and do not further degrade; precursors of the fragments are non-linear. (4) Some, but not most, of the cleavages that produce these fragments occur selectively near two known origins of DNA replication. On the basis of these observations, the conclusion is drawn that most degradation that occurs in the absence of T7 gene 6 exonuclease is caused by cleavage at branches. The following hypothesis is presented: most, possibly all, of the extra branching induced by removal of gene 6 exonuclease is caused by strand displacement DNA synthesis at the site of RNA primers of DNA synthesis; the RNA primers, produced by multiple initiations of DNA replication, are removed by the RNase H activity of gene 6 exonuclease during a wild-type T7 infection. Observation of joining of genomes in the absence of gene 6 exonuclease and additional observations indicate that single-stranded terminal repeats required for concatamerization are produced by DNA replication. The observed selective shortening of the left end indicates that gene 6 exonuclease is required for formation of most, possibly all, mature left ends.

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)

Factors involved in the electroporation-induced transformation of Clostridium perfringens

The following factors were found to improve the efficiency of transformation of Clostridium perfringens 3624A Rifr Strr: (1) a reduction in cuvette sample volume (DNA and cell suspension) to 0.8 ml, (2) use of a 1 microgram/ml concentration of transforming DNA, (3) use of late-logarithmic phase cells, (4) 3-fold concentration of cell density (3.0 x 10(8) CFU/ml), and (5) a reduction in the pH of the expression and selective plating medium to 6.4. Application of the improved conditions resulted in transformation efficiencies for C. perfringens 3624A Rifr Strr ranging from 7.1 transformants/microgram DNA for plasmic pIP401 to 9.2 x 10(4) transformants per microgram DNA for plasmid pAK201. The greatest transformation efficiency obtained using pAK201 was 9.8 x 10(6) transformants/micrograms DNA for C. perfringens strain 13. Using the improved protocol, pAM beta 1 was transformed at a 42-fold greater level when compared with the values reported earlier [1]. In addition to C. perfringens 3624A Rifr Strr, strains 13, 10543A, 3628C, NTG-4, and 3624A were successfully transformed. Nuclease does not appear to be a factor in the C. perfringens strain-specific electro-transformation protocol.

Methylation of ribosomal RNA genes inPetunia hybrida plants, callus cultures and regenerated shoots

The extent of methylation of the 18S-25S ribosomal RNA genes ofPetunia hybrida has been investigated using methylation-sensitive restriction endonucleases and Southern hybridisation. The genes in leaves, ovaries, petals, stigmas, anthers, and seed are methylated to a similar extent, but those in roots are hypomethylated. Genes in adventitious roots formed from stem cuttings are also hypomethylated. Genes in callus cultures initiated from leaf discs vary widely in the extent of methylation, but the pattern obtained is stable during culture. Callus cells containing hypomethylated genes can give rise to shoots in which the extent of methylation has reverted to that of the original leaf explant. These results demonstrate the striking plasticity of ribosomal RNA gene methylation inPetunia.

Recent advances in the genetics of the clostridia

Several laboratories around the world have started work on genetic analysis of clostridia. Interest in this diverse group of anaerobic organisms has grown with increasing awareness of the benefits that may accrue from their biotechnological exploitation. Research to date has focussed on construction of shuttle vectors containing replicons from clostridial and streptococcal plasmids, development of methods for transferring genes, and molecular cloning of genes--especially those involved in toxigenicity, fermentative metabolism and polysaccharide utilization. In selected species gene transfer by protoplast transformation, electroporation and conjugation has been accomplished and transposable elements have been introduced. It can be anticipated that our understanding of the molecular biology of these interesting organisms will grow rapidly in the future, bringing with it improved prospects for rational biotechnological exploitation.

DNA and spermidine provide a switch mechanism to regulate the activity of restriction enzyme Nae I

Sequence-specific DNA-protein interactions are basic to DNA function. To better understand these interactions, we studied the effect of position on cleavage of DNA by the type II restriction enzyme (EC 3.1.21.4) Nae I. We discovered two classes of Nae I restriction sites: sites susceptible and sites resistant to cleavage. Kinetic analysis showed that Nae I was activated by DNA containing cleavable Nae I sites to rapidly cleave resistant Nae I sites by a noncompetitive mechanism with a Km for substrate DNA of about 2 nM and a KA for activating DNA of about 6 nM; activation increased catalysis but not substrate binding. Deletion mutagenesis in vitro showed that sequences flanking the Nae I recognition site were responsible for the differences between activating and nonactivating Nae I sites. The polyamine spermidine had a dramatic effect on the interaction of Nae I with DNA; in the presence of 1 mM spermidine, resistant sites were cleaved rapidly and cleavable DNA inhibited cleavage. The direct regulation of enzymatic activity by DNA sequences in trans, and the modulation of this regulation by a polyamine that is sensitive to the cell cycle, provides a regulatory switch mechanism. The implications of this switch for biological control functions are discussed.

Purification and characterization of the FokI restriction endonuclease

The restriction endonuclease FokI from Flavobacterium okeanokoites was purified to homogeneity. Based on gel filtration, sedimentation and sodium dodecyl sulfate-polyacrylamide-gel electrophoresis, the following properties of the enzyme were determined: FokI exists in one active monomeric form, and has an Mr of 64-65.4 x 10(3).FokI is a strongly basic protein with an isoelectric point of 9.4. The enzyme exhibits restriction activity in the pH range 5.0 to 10.5 (maximum level at pH 7.0-8.5) and its divalent cation requirement is satisfied not only by Mg2+, but also by Co2+, Mn2+, Ni2+, Cd2+, Zn2+ and Fe2+.

Human telomeres contain at least three types of G-rich repeat distributed non-randomly

Using a combination of different oligonucleotides and restriction enzymes we have examined the gross organisation of repeats within the most distal region of human chromosomes. We demonstrate here that human telomeres do not contain a pure uniform 6 base pair repeat unit but that there are at least three types of repeat. These three types of repeat are present at the ends of most or all human chromosomes. The distribution of each type of repeat appears to be non-random. Each human telomere has a similar arrangement of these repeats relative to the ends of the chromosome. This could reflect differences in the functions that they perform, or might result from the mutation and correction processes occurring at human telomeres. The number of repeat units, the repeat types and arrangement differs at mouse telomeres. Analysing the change in length of the telomeric repeat region between an individuals blood and germline DNA reveals that this is due to variable amounts of the TTAGGG repeat and not the other repeat types. This organization of repeat units at human telomeres will only be confirmed upon the isolation and sequencing of full length (10-15 kb), intact human telomeres.

Genetic analysis of the lytic replicon of bacteriophage P1. II. Organization of replicon elements

The region of bacteriophage P1 DNA containing a lytic (vegetative) replicon has been identified by cloning P1 fragments into a phage lambda vector. We present the sequence of that replicon. Using a novel fusion vector containing two P1 loxP recombination sites, we have developed a transformation assay for replicon function and have used that assay to identify some of the components of the P1 lytic replicon. Among those components is a transcription promoter, P53, whose activity is essential for replicon function. When that promoter is inactivated by the binding of P1 repressor to an operator site, Op53, whose sequence overlaps the promoter, replicon function is blocked. The P53 promoter can be replaced for replicon function by other promoters and, when the lacZ promoter was used, the extent of replication was shown to be proportional to promoter activity. Two open reading frames are located downstream from P53. The promoter-proximal reading frame is 266 amino acid residues long and is not essential for replicon function. In fact, expression of that open reading frame either interferes with plasmid establishment after transformation or is lethal to cells. The promoter-distal reading frame, designated the repL open reading frame, is either 269 or 281 amino acid residues long and is essential for replicon function. Insertion of a Tn5 transposon into the 266 amino acid residue open reading frame inactivates the cloned lytic replicon probably by interfering with the transcription of the repL open reading frame from P53. In P1, this Tn5 insertion mutation completely blocks lytic replication, indicating that the replicon identified here is either the only P1 lytic replicon or, if not, is at least necessary for the function of any other lytic replicon. A four base insertion in the repL open reading frame has largely the same inhibitory effect on phage lytic replication as the Tn5 insertion.

Specificity of mismatch repair following transformation of Saccharomyces cerevisiae with heteroduplex plasmid DNA

A method is described for genetic detection of mismatch repair products following transformation of Saccharomyces cerevisiae. The method is based on the detection of beta-galactosidase activity in clonal derivatives of cells transformed with heteroduplex plasmid DNA. Heteroduplex plasmid substrates were constructed by insertion of an oligonucleotide heteroduplex into the coding sequence of the Escherichia coli lacZ gene. The plasmid and oligonucleotides were designed so that one strand of the construct would code for a functional beta-galactosidase and the other strand would contain an in-frame nonsense codon. The frequencies of transformed clones containing only Lac+ cells, only Lac- cells, or a mixture of the two Lac phenotypes provided information on the efficiency of the repair reaction. With this method, plasmids carrying single-base substitution mismatches, a single-base frameshift mismatch (T/delta), or a 3-base-pair substitution mismatch (TGA/GAA) were tested. A/C, G/T, G/A, G/G, and T/delta mismatches were repaired with significantly greater efficiencies than C/C, A/A, T/T, and TGA/GAA. T/C was repaired with an intermediate efficiency. The frequencies of products obtained with G/G, G/A, and T/delta mismatches suggested modest inequality of repair in the two possible directions. Strains carrying the repair-deficient pms1-1 mutation were also tested. The efficiencies of repair of A/C, G/T, G/G, and A/A mismatches were reduced in pms1-1 cells compared with wild-type cells. In addition, a change in repair inequality was detected when transformation of the two strains with an A/C mismatch was compared.

Enhancement of assays of activities of endonucleases on defined substrates by Poisson and non-Poisson combinatoric analysis

Assay of endonuclease activity, as performed in most laboratories, depends upon change in form of small, defined substrate molecules, with a secondary computation required to obtain a determination of enzyme activity. We now explore the assumptions inherent in these computations and provide a series of equations that permit more accurate determinations of enzyme activity from assays of this type. These equations allow information to be obtained not only from substrate fractions left uncleaved by the endonuclease, upon which conventional systems rely, but also from products cleaved by the enzyme. Some information yielded by these equations is unobtainable using conventional methods of analysis.

Cloning of the HhaI and HinPI restriction-modification systems

The genes for the HhaI (Roberts et al., 1976) and HinPI (Roberts, 1987) restriction-modification (R-M) systems have been cloned in pBR322. The HhaI system was isolated on a 9-kb PstI fragment, and the HinPI system was isolated on two PstI fragments of 1.5 and 4.6 kb in length. The clones were isolated by selecting for recombinant molecules that had protectively modified themselves. The HhaI and HinPI R-M systems recognize the same sequence, GCGC, but hybridization between the DNA fragments encoding them does not take place.

Cloning type-II restriction and modification genes

We have cloned into Escherichia coli the genes for 38 type-II bacterial modification methyltransferases. The clones were isolated by selecting in vitro for protectively modified recombinants. Most of the clones modify their DNA fully but a substantial number modify only partially. In approximately one-half of the clones, the genes for the corresponding endonucleases are also present. Some of these clones restrict infecting phages and others do not. Clones carrying endonuclease genes but lacking methyltransferase genes have been found, in several instances, to be viable.

Investigation of sequence homology in a group of type-II restriction/modification isoschizomers

We have dissected the cloned PstI M and R genes to make DNA hybridization probes spanning most of the sequence. These subclones, and also the intact sequence, were used to search for nucleic acid homology by Southern blot in the DNA from twelve organisms which produce PstI isoschizomers. One of these probes, a 206-bp fragment from the N-terminal domain of the endonuclease, showed significant hybridisation in four strains (Escherichia coli strains RFL48, RFL49 and RFL83, and Streptomyces albus P). No significant hybridisation was detected with other parts of the PstI sequences. We have used computer similarity searches to look for homology between the PstI proteins and the known sequences of other type-II systems that recognise different sites. We postulate a possible recognition domain within the M.PstI methyltransferase based on similarity to the M.PaeR7 and M.TaqI methyltransferases.

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.

Cloning the FnuDI, NaeI, NcoI and XbaI restriction-modification systems

Methyltransferase genes from the FnuDI, NaeI, NcoI, and XbaI restriction-modification systems have been isolated in Escherichia coli by 'shot-gun' cloning bacterial DNA fragments into plasmid vectors and selecting for protectively modified molecules that resist digestion by the corresponding restriction endonuclease.

Repetitive sequence element cloned from Leptospira interrogans serovar hardjo type hardjo-bovis provides a sensitive diagnostic probe for bovine leptospirosis

A repetitive sequence element was cloned from the primary etiological agent causing bovine leptospirosis in North America, Leptospira interrogans serovar hardjo type hardjo-bovis. This element was used to design a sensitive diagnostic probe which distinguishes hardjo-bovis from other pathogenic leptospires which commonly infect domestic animals in North America and discriminates between hardjo-bovis and the reference strain for serovar hardjo, hardjoprajitno. By using this probe, it was possible to identify infected cattle shedding hardjo-bovis in their urine. This is the first practical demonstration of a cloned DNA probe for leptospirosis, and it provides a sensitive method for studying the transmission and pathogenesis of L. interrogans infections. Control measures for L. interrogans infections may now be improved by rapidly and efficiently identifying infected animals.

Use of restriction endonucleases to study relationships between DNA double-strand breaks, chromosomal aberrations and other end-points in mammalian cells

Some of the cellular effects of radiation, such as mutations, chromosomal aberrations and cell killing, can be mimicked by inducing 'pure' double-strand breaks (dsb) in DNA of cells with restriction endonucleases (RE), although the chemical structure of the ends of dsb induced by RE are likely to differ from those induced by X-rays. Chromosomal aberrations are induced by treatment of cells with a variety of RE at all stages of the cell cycle. The frequency with which RE induce dsb in the DNA may be one factor determining the number of aberrations induced. However, the structure of the dsb generated may also determine the frequencies of aberrations induced. RE which generate 'cohesive-ended' dsb in the DNA have been shown to induce lower frequencies of aberrations than those causing 'blunt-ended' dsb, when inactivated Sendai virus is used to permeabilize cells. Other methods, involving a hypertonic shock to the treated cells, have led to results in which there is little or no difference in the effectiveness between the two types of dsb. It is argued here that the use of treatments which cause a hypertonic shock may influence the frequencies of aberrations induced.

Purification and characterization of the restriction endonuclease RsrI, an isoschizomer of EcoRI

Rhodobacter sphaeroides strain 630 produces restriction enzyme RsrI which is an isoschizomer of EcoRI. We have purified this enzyme and initiated a comparison with the EcoRI endonuclease. The properties of RsrI are consistent with a reaction mechanism similar to that of EcoRI: the position of cleavage within the -GAATTC-site is identical, the MgCl2 optimum for the cleavage is identical, and the pH profile is similar. Methylation of the substrate sequence by the EcoRI methylase protects the site from cleavage by the RsrI endonuclease. RsrI cross-reacts strongly with anti-EcoRI serum indicating three-dimensional structural similarities. We have determined the sequence of 34 N terminal amino acids for RsrI and this sequence possesses significant similarity to the EcoRI N terminus.

Recognition and cleavage site of the intron-encoded omega transposase

The optional group I intron of the mitochondrial 21S rRNA gene of Saccharomyces cerevisiae contains a 235-codon-long open reading frame the translation product of which (the omega transposase) catalyzes the formation of a double-strand break within the intron-minus (omega-) copies of the same gene. Purified omega transposase generates in vitro a 4-base-pair staggered cut with 3' hydroxyl overhangs at the exact position where the intron eventually inserts in the gene. Using randomly mutagenized synthetic oligonucleotides, single-base mutants were produced at 21 positions around the cleavage site. Experiments with these oligonucleotides show that the recognition site extends over an 18-base pair-long sequence within which minimal sequence degeneracy is tolerated. The intron-encoded omega transposase is, therefore, one of the most specific restriction endonucleases known to date.

AsnI: a novel class II restriction endonuclease from Arthrobacter sp., strain N-CM, recognizing 5'-AT/TAAT-3'

A new class II restriction endonuclease, AsnI, with a novel sequence specificity was isolated from the Gram-positive eubacterium Arthrobacter species, strain N-CM. AsnI recognizes the unambiguously defined palindromic hexanucleotide (Formula: see text) consisting of A- and T-residues. The novel enzyme in the presence of Mg2+ cleaves specifically both strands as indicated by the arrows. The staggered cuts generate 5'-protruding ends with single-stranded 5'-TA-3' dinucleotide extensions. The novel enzyme may be a useful tool for cloning experiments by complementation of the few enzymes such as PstI and PvuI cutting only once in the Ampr-gene of plasmids pBR322 and pBR328.

Genetic analysis of the tomato golden mosaic virus. II. The product of the AL1 coding sequence is required for replication

Tomato golden mosaic virus (TGMV) belongs to the geminivirus subgroup that is characterized by a split genome consisting of two single-stranded circular DNAs. The TGMV A genome component encodes the virus coat protein as well as all of the functions necessary for viral DNA replication. Analysis of the nucleotide sequence indicates that the TGMV A component has, in addition to the coat protein encoding ORF, four overlapping open reading frames (ORFs) with the potential to encode proteins of greater than 10 kD. We have investigated the functions of these putative proteins in both symptom formation and DNA replication by creating mutations in each of the ORFs. Our results show that the AL4 ORF, which is encoded within the N-terminal region of ORF AL1, is not essential for normal virus infection. In contrast, we find that disruption of the AL3 ORF results in delay and attenuation of symptom formation. We also report that the products of the AL1 and AL2 ORFs are absolutely required for symptom formation. Studies of DNA replication show that only the AL1 open reading frame is essential for viral DNA synthesis. The significance of these results for the development of vectors from the geminiviruses is discussed.

Ksp632I, a novel class-IIS restriction endonuclease from Kluyvera sp. strain 632 with the asymmetric hexanucleotide recognition sequence: 5'-CTCTTC(N)1-3' 3'-GAGAAG(N)4-5'

A new class-IIS restriction endonuclease, Ksp632I, with novel sequence specificity has been discovered in a non-pathogenic species of Kluyvera. The presence of only a single site-specific activity in this Kluyvera sp. strain 632 enables Ksp632I to be isolated in highly purified form free of contaminating nucleases. Ksp632I recognition sites and cleavage positions were deduced using experimental and computer-assisted mapping and sequencing. The cleavage specificity corresponds to the sequence 5'-CTCTTCN decreases NNN-N-3' 3'-GAGAAGN-NNN increases N-5'. The enzyme recognizes an asymmetric hexanucleotide sequence and cleaves in the presence of Mg2+ ions specific phosphodiester bonds in both DNA strands, 1 and 4 nucleotides distal to the recognition sequence. The staggered cuts generate 5'-protruding ends with single-stranded 5'-phosphorylated trinucleotides. Several slow cleavage sites for Ksp632I were observed on lambda cI857Sam7 DNA. Ksp632I may complement other class-IIS enzymes in the universal restriction approach and may serve as a tool for generating defined unidirectional deletions or insertions.

BcefI, a new type IIS restriction endonuclease

A new Type IIS restriction endonuclease was identified, partially purified and characterized from a Bacillus cereus subsp. fluorescens strain. The enzyme recognizes the nonpalindromic sequence ACGGC and cleaves at a distance from it. The cleavage appears to occur with a +/- 1 basepair uncertainty. Thus the cleavage and recognition site is as shown below: ACGGC(N)11-13 TGCCG(N)12-14.

McrA and McrB restriction phenotypes of some E. coli strains and implications for gene cloning

The McrA and McrB (modified cytosine restriction) systems of E. coli interfere with incoming DNA containing methylcytosine. DNA from many organisms, including all mammalian and plant DNA, is expected to be sensitive, and this could interfere with cloning experiments. The McrA and B phenotypes of a few strains have been reported previously (1-4). The Mcr phenotypes of 94 strains, primarily derived from E. coli K12, are tabulated here. We briefly review some evidence suggesting that McrB restriction of mouse-modified DNA does occur in vivo and does in fact interfere with cloning of specific mouse sequences.