Recognition sequences of restriction endonucleases and methylases--a review

Hydrogel bead-based isothermal detection (BEAD-ID) for assessing the activity of DNA-modifying enzymes

DNA-modifying enzymes are crucial in biological processes and have significant clinical implications. Traditional quantification methods often overlook enzymatic activity, the true determinants of enzymes' functions. We present hydrogel Bead-based Isothermal Detection (BEAD-ID), utilizing uniform hydrogel bead-based microreactors to evaluate DNA-modifying enzyme activity on-bead. We fabricated homogeneous oligo-conjugated polyacrylamide (oligo-PAA) beads via droplet microfluidics, optimized for capturing and amplifying enzyme-modified nanosensors. By incorporating DNA oligos within the hydrogel network, BEAD-ID retains isothermally amplified products, facilitating in situ detection of enzyme activities on-bead. We validate BEAD-ID by quantifying human topoisomerase I (TOP1) and restriction endonuclease EcoRI, showing a direct correlation between enzyme concentration and fluorescence intensity, demonstrating the platform's sensitivity (6.25 nM TOP1, 6.25 U/μL EcoRI) and reliability in food matrix (25 U/μL EcoRI). Additionally, a customized flow cytometry-mimicking setup allows high-throughput detection at 352 Hz with objective assessment. BEAD-ID, offering flexibility and scalability, is a promising tool for studying DNA-modifying enzymes.

Rolling Circle Enhanced Detection of Specific Restriction Endonuclease Activities in Crude Cell Extracts

Restriction endonucleases are expressed in all bacteria investigated so far and play an essential role for the bacterial defense against viral infections. Besides their important biological role, restriction endonucleases are of great use for different biotechnological purposes and are indispensable for many cloning and sequencing procedures. Methods for specific detection of restriction endonuclease activities can therefore find broad use for many purposes. In the current study, we demonstrate proof-of-concept for a new principle for the detection of restriction endonuclease activities. The method is based on rolling circle amplification of circular DNA products that can only be formed upon restriction digestion of specially designed DNA substrates. By combining the activity of the target restriction endonuclease with the highly specific Cre recombinase to generate DNA circles, we demonstrate specific detection of selected restriction endonuclease activities even in crude cell extracts. This is, to our knowledge, the first example of a sensor system that allows activity measurements of restriction endonucleases in crude samples. The presented sensor system may prove valuable for future characterization of bacteria species or strains based on their expression of restriction endonucleases as well as for quantification of restriction endonuclease activities directly in extracts from recombinant cells.

Recombinant Enterovirus 71 Viral Protein 1 Fused to a Truncated Newcastle Disease Virus NP (NPt) Carrier Protein

Enterovirus 71 (EV71) is the major causative agent in hand, foot, and mouth disease (HFMD), and it mainly infects children worldwide. Despite the risk, there is no effective vaccine available for this disease. Hence, a recombinant protein construct of truncated nucleocapsid protein viral protein 1 (NPt-VP1_198–297), which is capable of inducing neutralizing antibody against EV71, was evaluated in a mouse model. Truncated nucleocapsid protein Newcastle disease virus that was used as immunological carrier fused to VP1 of EV71 as antigen. The recombinant plasmid carrying corresponding genes was constructed by recombinant DNA technology and the corresponding protein was produced in Escherichia coli expression system. The recombinant NPt-VP1_198–297 protein had elicited neutralizing antibodies against EV71 with the titer of 1:16, and this result is higher than the titer that is elicited by VP1 protein alone (1:8). It was shown that NPt containing immunogenic epitope(s) of VP1 was capable of inducing a greater functional immune response when compared to full-length VP1 protein alone. It was capable to carry larger polypeptide compared to full-length NP protein. The current study also proved that NPt-VP1_198–297 protein can be abundantly produced in recombinant protein form by E. coli expression system. The findings from this study support the importance of neutralizing antibodies in EV71 infection and highlight the potential of the recombinant NPt-VP1_198–297 protein as EV71 vaccine.

Detailed characterization and comparison of four lactic streptococcal bacteriophages based on morphology, restriction mapping, DNA homology, and structural protein analysis

Bacteriophages uc1001 and uc1002, which are lytic for Streptococcus cremoris UC501 and UC502, respectively, were characterized in detail. Comparisons were made with a previously characterized phage, P008, which is lytic for Streptococcus lactis subsp. diacetylactis F7/2, and uc3001, which is a lytic phage for S. cremoris UC503. Phages uc1001 and uc1002 had small isometric heads (diameters, 52 and 50 nm, respectively) and noncontractile tails (lengths, 152 and 136 nm, respectively), and uc1002 also had a collar. Both had 30.1 +/- 0.6 kilobase pairs (kbp) of DNA with cross-complementary cohesive ends. Restriction endonuclease maps made with seven endonucleases showed no common fragments. Despite this there was a very high level of homology between uc1001 and uc1002, and results of cross-hybridization experiments showed that the organization of both phage genomes was similar. Heteroduplex analysis confirmed this and quantified the level of homology at 83%. The regions of nonhomology comprised 2.1-, 1.1-, and 1.0-kbp deletion loops and 13 smaller loops and bubbles. The sodium dodecyl sulfate-polyacrylamide gel electrophoretic structural protein profiles were related, with a major band of about 40,000 molecular weight and minor bands of 35,000 and 34,000 molecular weight in common. There were also differences, however, in that uc1001 had a second major band of 68,000 molecular weight and two extra minor bands. Except for the restriction maps, which were strain specific, phages uc1001, uc1002, and P008 were closely related by all the criteria listed above. Their DNAs also showed a very significant bias against the cleavage sites of 9 of 11 restriction endonucleases. Phage uc3001 was unrelated to uc1001, uc1002, or P008 in that it had a prolate head (53 by 39 nm) and a shorter tail (105 nm), contained approximately 22 kbp of DNA, had unrelated cohesive ends, showed no DNA homology with the isometric-headed phages, and displayed a very different structural protein profile.

Resistance to In Vitro Restriction of DNA from Lactic Streptococcal Bacteriophage c6A

DNA isolated from streptococcal bacteriophage c6A was cut only infrequently by many restriction endonucleases. Fragments of c6A DNA cloned in Escherichia coli plasmids were similarly resistant to cleavage. We conclude that the low frequency of cleavage is due to an unusually low number of restriction enzyme recognition sequences in c6A DNA.

Epigenetic gene regulation in the bacterial world

Like many eukaryotes, bacteria make widespread use of postreplicative DNA methylation for the epigenetic control of DNA-protein interactions. Unlike eukaryotes, however, bacteria use DNA adenine methylation (rather than DNA cytosine methylation) as an epigenetic signal. DNA adenine methylation plays roles in the virulence of diverse pathogens of humans and livestock animals, including pathogenic Escherichia coli, Salmonella, Vibrio, Yersinia, Haemophilus, and Brucella. In Alphaproteobacteria, methylation of adenine at GANTC sites by the CcrM methylase regulates the cell cycle and couples gene transcription to DNA replication. In Gammaproteobacteria, adenine methylation at GATC sites by the Dam methylase provides signals for DNA replication, chromosome segregation, mismatch repair, packaging of bacteriophage genomes, transposase activity, and regulation of gene expression. Transcriptional repression by Dam methylation appears to be more common than transcriptional activation. Certain promoters are active only during the hemimethylation interval that follows DNA replication; repression is restored when the newly synthesized DNA strand is methylated. In the E. coli genome, however, methylation of specific GATC sites can be blocked by cognate DNA binding proteins. Blockage of GATC methylation beyond cell division permits transmission of DNA methylation patterns to daughter cells and can give rise to distinct epigenetic states, each propagated by a positive feedback loop. Switching between alternative DNA methylation patterns can split clonal bacterial populations into epigenetic lineages in a manner reminiscent of eukaryotic cell differentiation. Inheritance of self-propagating DNA methylation patterns governs phase variation in the E. coli pap operon, the agn43 gene, and other loci encoding virulence-related cell surface functions.

Alteration of DNA methylation in gastrointestinal carcinogenesis

DNA methylation is the main epigenetic modification in humans. The methylation of promoter inhibits the transcription in most genes. In normal tissues, isolated CpG dinucleotides in bulk chromatin are often methylated, whereas cytosines in CpG islands are unmethylated. In neoplasms including gastrointestinal cancer, this pattern of methylation is commonly reversed. The alteration of DNA methylation plays a key role in the process of carcinogenesis. The gastrointestinal carcinogenesis is suggested to be associated with the decrease of total genomic DNA methylation; hypomethylation of certain specific oncogenes such as c-myc, c-Ha-ras, c-fos and alpha-fetoprotein; and hypermethylation of the promoter of some tumor suppressor genes containing p16(INK4A), E-cadherin and hMLH1 genes. This review focuses on the analysis methods for methylation, studies for aberrant DNA methylation in gastrointestinal carcinogenesis, and the intervention changing methylation, including the treatment of 5-azacytidine, supplement of folate and gene therapy.

DNA hypermethylation at the D17S5 locus and reduced HIC-1 mRNA expression are associated with hepatocarcinogenesis

To examine the significance of aberrant DNA methylation in hepatocarcinogenesis, the DNA methylation status at the D17S5 locus and mRNA expression of a candidate tumor suppressor gene, HIC-1 (hypermethylated-in-cancer), which was identified at the D17S5 locus, in primary hepatocellular carcinomas (HCCs) and their corresponding noncancerous liver tissues were assessed. DNA hypermethylation at the D17S5 locus was detected in 44% of the noncancerous liver tissues showing chronic hepatitis or cirrhosis, which are widely considered to be precancerous conditions, but was not observed in noncancerous liver tissues showing no remarkable histological findings. The incidence of DNA hypermethylation at this locus was significantly higher in HCCs (90%) than noncancerous liver tissues (P <.001). Loss of heterozygosity at the D17S5 locus, which was preceded by DNA hypermethylation at the same locus, was detected in 54% of HCCs. The HIC-1 mRNA expression level of noncancerous liver tissues showing chronic hepatitis or cirrhosis was significantly lower than that of noncancerous liver tissues showing no remarkable histological findings (P <.01), and that of HCCs was even lower than that of noncancerous liver tissues (P <.05). Poorly differentiated HCCs showed lower expression levels than well- to moderately differentiated HCCs. Mutation of the p53 gene may be involved in HIC-1 inactivation. Moreover, wild-type p53 did not overcome DNA hypermethylation at the D17S5 locus to activate HIC-1 in HCCs. These data suggest that aberrant DNA methylation at this locus and reduced HIC-1 mRNA expression participate in hepatocarcinogenesis during both early developmental stages and malignant progression of HCCs.

Reduced DNA methylation in Arabidopsis thaliana results in abnormal plant development

Arabidopsis plants transformed with an antisense construct of an Arabidopsis methyltransferase cDNA (METI) have reduced cytosine methylation in CG dinucleotides. Methylation levels in progeny of five independent transformants ranged from 10% to 100% of the wild type. Removal of the antisense construct by segregation in sexual crosses did not fully restore methylation patterns in the progeny, indicating that methylation patterns are subject to meiotic inheritance in Arabidopsis. Plants with decreased methylation displayed a number of phenotypic and developmental abnormalities, including reduced apical dominance, smaller plant size, altered leaf size and shape, decreased fertility, and altered flowering time. Floral organs showed homeotic transformations that were associated with ectopic expression of the floral homeotic genes AGAMOUS and APETALA3 in leaf tissue. These observations suggest that DNA methylation plays an important role in regulating many developmental pathways in plants and that the developmental abnormalities seen in the methyltransferase antisense plants may be due to dysregulation of gene expression.

Role of the propilin leader peptide in the maturation of F pilin

F-pilin maturation and translocation result in the cleavage of a 51-amino-acid leader sequence from propilin and require LepB and TraQ but not the SecA-SecY secretion pathway. The unusual propilin leader peptide and the dependence of its cleavage on TraQ suggested that TraQ recognition may be specific for the leader peptide. An in vitro propilin cleavage assay yielded propilin (13 kDa), the pilin polypeptide (7 kDa), and a 5.5-kDa protein as the traA products. The 5.5-kDa protein comigrates with the full-length 51-amino-acid leader peptide, and [14C]proline labeling confirmed its identity since the only proline residues of propilin are found within the leader peptide. The in vitro and in vivo propilin-processing reactions proceed similarly in a single polypeptide cleavage step. Furthermore, TraQ dependence is a property of F-pilin maturation specifically rather than a property of the leader peptide. A propilin derivative with an amino-terminal signal sequence generated by deleting codons 2 to 28 required TraQ for processing in vivo. On the other hand, a chimeric protein with the propilin wild-type leader peptide fused to the mature portion of beta-lactamase was processed in a TraQ-independent manner. Thus, despite its unusual length, the propilin leader peptide seems to perform a function similar to that of the typical amino-terminal signal sequence. This work suggests that TraQ is not necessary for the proteolysis of propilin and therefore is likely to act as a chaperone-like protein that promotes the translocation of propilin.

Membrane insertion of the F-pilin subunit is Sec independent but requires leader peptidase B and the proton motive force

F pilin is the subunit required for the assembly of conjugative pili on the cell surface of Escherichia coli carrying the F plasmid. Maturation of the F-pilin precursor, propilin, involves three F plasmid transfer products: TraA, the propilin precursor; TraQ, which promotes efficient propilin processing; and TraX, which is required for acetylation of the amino terminus of the 7-kDa pilin polypeptide. The mature pilin begins at amino acid 52 of the TraA propilin sequence. We performed experiments to determine the involvement of host cell factors in propilin maturation. At the nonpermissive temperature in a LepBts (leader peptidase B) host, propilin processing was inhibited. Furthermore, under these conditions, only full-length precursor was observed, suggesting that LepB is responsible for the removal of the entire propilin leader peptide. Using propilin processing as a measure of propilin insertion into the plasma membrane, we found that inhibition or depletion of SecA and SecY does not affect propilin maturation. Addition of a general membrane perturbant such as ethanol also had no effect. However, dissipation of the proton motive force did cause a marked inhibition of propilin processing, indicating that membrane insertion requires this energy source. We propose that propilin insertion in the plasma membrane proceeds independently of the SecA-SecY secretion machinery but requires the proton motive force. These results present a model whereby propilin insertion leads to processing by leader peptidase B to generate the 7-kDa peptide, which is then acetylated in the presence of TraX.

Genome size in bacteria

This manuscript examines genome size in bacteria. The opposing capability of bacteria to alter their genome sizes and order of genes within limits yet remain somewhat constant provides a mechanisms for diversity and evolution in bacterial populations. Bacteria may have evolved by increasing their genome size and changing gene orders with the assistance of restriction endonucleases cleaving foreign DNA and providing a diverse pool of DNA sequences for recombination. These aspects and selected information on physically mapping bacterial genomes will be discussed.

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

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

Identification of Bifidobacterium strains by rRNA gene restriction patterns

Total DNA from 21 collection or industrial Bifidobacterium strains was cleaved with various restriction endonucleases. Following electrophoresis, the fragments were subjected to Southern blot hybridization with a heterologous [alpha-32P]dCTP-labeled rDNA (genes coding for rRNA) 23S gene probe. The ribosomal patterns allowed all tested strains to be differentiated and previous classifications to be confirmed. The same method was used to characterize DNA from 121 Bifidobacterium isolates collected from the intestinal flora of five human volunteers after the induction of colonic bacterial imbalance by antibiotics and absorption of a resistant exogenous Bifidobacterium strain. Hybridizations with the ribosomal probe revealed 11 different ribosomal patterns in addition to that of the exogenous strain. They permitted the Bifidobacterium populations belonging to the dominant colonic flora to be monitored over time. This experiment revealed significant and sustained alterations of the endogenous intestinal flora; indeed, some strains were eliminated, while others, probably belonging to subdominant flora, replaced them. Furthermore, even 2 months after the end of antibiotic treatment, the colonic flora remained different from that observed before treatment. Finally, our results showed that antibiotherapy did not allow colonic colonization by the exogenous strain.

Supernumerary heterochromatic segments associated with the nucleolar chromosomes of Pyrgomorpha conica (Orthoptera) contain methylated rDNA sequences

The two nucleolus organizing chromosome pairs of the grasshopper Pyrgomorpha conica can carry a proximal supernumerary heterochromatic segment. We employed different cytological techniques to characterize and analyze the possible origin of this segment. The supernumerary segment and the nucleolus organizing regions (NORs) show similar responses after C-banding plus either Giemsa or acridine orange, and chromomycin A3/distamycin A staining to detect GC-rich chromosome regions. Fluorescence in situ hybridization with a biotinylated rDNA probe demonstrated that the segment originated by amplification of the rDNA genes. However, as the silver staining indicates, the ribosomal genes present in the segment are not active since no nucleolus is formed. The use of in situ digestion with the isoschizomeric MspI and HpaII restriction endonucleases and subsequent Giemsa, ethidium bromide or chromomycin A3/distamycin A staining, suggests that the segment has been inactivated by DNA methylation.

Comparative analysis of the genomes of mycobacteriophages infecting saprophytic and pathogenic mycobacteria

The genomes of a series of mycobacteriophages have been analyzed to disclose possible relationships between genetic characteristics and host range. The percent guanine-plus-cytosine in the DNA of 14 phages was found to be 34.4 to 47.5, as determined by a double-labelling procedure, which is unaffected by the presence of modified bases. The DNA of few mycobacteriophages yielded discordant values when the G + C content was estimated by buoyant density determination and by the double labelling procedure. This observation suggests the possible presence of modified bases in these genomes. The reduced susceptibility of viral DNAs to several restriction endonucleases is suggestive of the occurrence of both methyladenine and methylcytosine in the genome of all the mycobacteriophages studied. Heterologous annealing among the 14 DNAs analyzed yielded 6 hybridization groups. Within one group, the homology level among viral genomes was estimated by comparing the electrophoretic mobilities of restriction fragments: values of 0.8 to 1.3% base substitution have thus been found. A comparison of the genomic characteristics and host range of the mycobacteriophages analyzed suggests a possible relationship between restriction pattern, G + C content, crosshybridization level and host range.

Analysis of restriction enzyme-induced chromosomal aberrations by fluorescence in situ hybridization

Fluorescence in situ hybridization and Giemsa staining of metaphase chromosomes were used to determine the relative frequencies of symmetric exchange aberrations (translocations) and asymmetric exchange aberrations (rings, dicentrics, and polycentrics) after exposure of human lymphoblastoid cells to restriction enzymes or X-rays. The yield of symmetric exchanges was determined with the use of chromosome-specific probes for human chromosomes 2 or 4, which were hybridized to metaphase chromosomes from cells exposed to the enzymes PvuII, SacI, or XbaI or 3 or 5 Gy of X-rays. The yield of asymmetric exchanges was determined in Giemsa-stained metaphase chromosomes from the same enzyme-treated or irradiated cell population. About 1.5- to 3-fold more symmetric than asymmetric exchanges were induced after restriction enzyme treatment. However, after X-ray treatment the yield of dicentrics relative to the yield of reciprocal translocations was close to the expected 1:1 ratio.

Chromosome jumping from flanking markers defines the minimal region for alf/hsdr-1 within the albino-deletion complex

The locus alf/hsdr-1, defined by the albino-deletion complex on mouse chromosome 7, is essential for neonatal survival. Animals homozygous for a subset of the deletions die shortly after birth due to impaired gene expression in liver parenchymal cells and kidney proximal tubular cells. Here, we describe a detailed analysis of the region containing alf/hsdr-1 by means of chromosome jumping from flanking markers. Three chromosome jumping libraries based on the restriction enzymes XmaI and SalI were constructed. Isolation of eight jumping clones distributed over 450 kb allowed more than 240 kb to be cloned in genomic lambda and cosmid libraries. Five of the probes map within the minimal genetic interval for alf/hsdr-1, which is defined by the proximal borders of the deletions c10R75M and c11DSD. The breakpoints of these deletions were precisely mapped, which allowed alf/hsdr-1 to be localized to a 310-kb interval.

The distribution of restriction fragment lengths for non-overlapping restriction sites in a random DNA sequence model

Overlapping subsequences in a DNA sequence are not independent even if independence is supposed for the single nucleotides. Therefore the often used geometric distribution for the length of restriction fragments is not exact. The exact distribution of this random variable is derived for non-overlapping restriction sites in a DNA sequence with an infinite (or very large) number of nucleotides. Correction to the finite case is easy. It is shown that the simple geometric distribution is a good approximation as long as the basic probability for the occurrence of the recognition sequence at a given site is small.

The modification and expression of 21-hydroxylase gene in normal human adrenal gland and adrenal cancer

Genomic DNA and total RNA from three adrenal cancer tissues were analyzed by hybridization with human 21-hydroxylase gene. Southern blot analysis with restriction enzyme Eco RI revealed major fragments at 18, 13 and 9 kilobase (kb) in normal adrenal glands. In two of three adrenal cancers, however, the band at 18 kb was either absent or decreased and the 9 kb fragment showed an increase in its intensity. Normal liver, kidney and leucocytes has only 18 and 13 kb while lacking the 9 kb fragment. Using Taq I, Bam HI or Bgl II, we found no difference in restriction fragment patterns between adrenal cancer and normal tissues. Cleavage with Hpa II after digestion with Bgl II showed that significantly more DNA was digested into low-molecular weight fragments in adrenal cancer and the normal adrenal gland than those in other normal tissues. By Northern blot analysis, there was difference of signal intensity of hybridizing mRNA between the adrenal cancers and normal adrenal glands. These results suggest that the Eco RI site in the flanking region of the 21-hydroxylase gene may be modified in adrenal cancer tissue, and that inadequate 21-hydroxylase is present in some forms of adrenal cancers.

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)

Characterization of a temperate actinophage, MPphiWR-1, capable of infecting Micromonospora purpurea ATCC 15835

A temperate actinophage was isolated from soil using the gentamicin-producing microorganism, Micromonospora purpurea ATCC 15835 as host. The characterization of the phage represents the initial step in its development as a cloning vector. The phage isolated, MPphiWR-1, formed red- to purple-pigmented turbid plaques. Cells isolated from these plaques were resistant to superinfection with lytic mutants of MPphiWR-1. Southern blots of genomic DNA from a resistant culture showed that MPphiWR-1 integrated into the host genome. The phage was UV- or Mitomycin C-inducible. The integration, resistance to superinfection and inducibility indicated a lysogenic relationship with the host. Using MPphiE-RCPM, a lytic derivative, the phage host range was demonstrated to include members of three genera: one species each of Ampullariella and Catellatospora, and 12 species of Micromonospora. The phage belonged to Ackerman's B1 morphotype having an isometric head and a flexible noncontractile tail. The density of the phage was 1.525 g/cc. Restriction site mapping demonstrated that the phage DNA was 57.9 kb long and had cohesive ends. Using EDTA enrichment, viable mutants with deletions of at least 3.5 kb were isolated and mapped. Phage adsorption, sensitivities and plating efficiency were investigated. Non-liposome PEG-mediated transfection was demonstrated.

Characteristics and restriction analysis of the 4-chlorobiphenyl catabolic plasmid, pSS50

The plasmid pSS50 is a 53-kilobase self-transmissible plasmid of broad host range that has been isolated from several Alcaligenes and Acinetobacter species. This plasmid has previously been shown to mediate the mineralization of 4-chlorobiphenyl to carbon dioxide and water. Physical characterization of this plasmid by restriction analysis indicates that most hexanucleotide cleavage sites are clustered in a 5-kilobase region, leaving large regions without restriction sites. The paucity of restriction sites is not due to DNA methylation.

The GTm6AC sequence is overwound and bent

By a combination of distance constraints obtained from NMR spectra and molecular mechanics calculations we have determined the three dimensional structure of the self-complementary decanucleotide d(CGCGTm6ACGCG). Methylation of an adenine at a position 3' to T induces significant conformational changes relative to B-DNA. This arises from the close proximity of the four methyl groups in the large groove in the centre of the sequence. The helical twist between the two T.m6A base pairs is found to be 45 degrees, as for D-DNA, and is accompanied by a high negative value of the wedge roll angle between these base pairs. The overall nonzero wedge roll observed shows that the helix is bent. These constraints appear to be material for the absence of the sequence T-m6A in natural DNAs.

Nucleotide sequence and genetic organization of the NgoPII restriction-modification system of Neisseria gonorrhoeae

The NgoPII restriction endonuclease, which recognizes the sequence 5'-GG decreases CC-3', differs from its isoschizomer HaeIII in being sensitive to methylation at the external cytosine residue. The entire nucleotide sequence of a cloned 3.3 kb segment of Neisseria gonorrhoeae strain P9 chromosomal DNA which harbours the NgoPII restriction-modification system has been determined. This data, coupled with sub-cloning experiments, indicates that the restriction endonuclease (R.NgoII) and modification (M.NgoII) genes are transcribed from separate promoters but are arranged in tandem, with the R.NgoPII gene being located on the 5' side of the M.NgoPII gene. Unlike all previously reported restriction systems the 3' end of the endonuclease open reading frame overlaps the 5' end of the methylase open reading frame by 8 codons. This overlap may have implications for the regulation of the NgoPII restriction-modification system.

Applications of molecular genetics to gastrointestinal and liver diseases. I. Technical approaches

Recent developments in recombinant DNA techniques have allowed an understanding of the molecular genetics of many diseases, some affecting the gastrointestinal tract and liver. DNA probes which detect sequences within or near disease genes can be selected by direct approaches, if the gene product or primary gene function is known, or by indirect methods when the chromosomal location is known. Such probes have resulted in extensive family studies which can now define risks to family members of developing a genetic disease. The development of the polymerase chain reaction will also be of considerable use in clinical genetics and in the diagnosis of some infectious diseases. The techniques are summarized and examples of their use are given. A glossary of terms is also provided.

Location and methylation pattern of a nuclear matrix associated region in the human pro alpha 2(I) collagen gene

Using both a 25 mM Lithium di-iodosalicylic acid (LIS) and a 2M NaCl extraction procedure to extract nuclear matrices from white cells we have identified a 0.9 kb nuclear matrix associated region (MAR) in the human pro alpha 2(I) collagen gene. The MAR is located towards the 3' coding end of the gene, it is completely associated with the matrix in transcriptionally inactive white cells but is incompletely associated with the matrix in transcriptionally active fibroblasts. Furthermore the methylation state of the fibroblast gene in the region coinciding with the MAR showed unique differences when compared to adjacent sites in the fibroblast gene and corresponding sites of the white cell gene.

Deletion of a 55-kilobase-pair DNA element from the chromosome during heterocyst differentiation of Anabaena sp. strain PCC 7120

The filamentous cyanobacterium Anabaena sp. strain PCC 7120 produces terminally differentiated heterocysts in response to a lack of combined nitrogen. Heterocysts are found approximately every 10th cell along the filament and are morphologically and biochemically specialized for nitrogen fixation. At least two DNA rearrangements occur during heterocyst differentiation in Anabaena sp. strain PCC 7120, both the result of developmentally regulated site-specific recombination. The first is an 11-kilobase-pair (kb) deletion from within the 3' end of the nifD gene. The second rearrangement occurs near the nifS gene but has not been completely characterized. The DNA sequences found at the recombination sites for each of the two rearrangements show no similarity to each other. To determine the topology of the rearrangement near the nifS gene, cosmid libraries of vegetative-cell genomic DNA were constructed and used to clone the region of the chromosome involved in the rearrangement. Cosmid clones which spanned the DNA separating the two recombination sites that define the ends of the element were obtained. The restriction map of this region of the chromosome showed that the rearrangement was the deletion of a 55-kb DNA element from the heterocyst chromosome. The excised DNA was neither degraded nor amplified, and its function, if any, is unknown. The 55-kb element was not detectably transcribed in either vegetative cells or heterocysts. The deletion resulted in placement of the rbcLS operon about 10 kb from the nifS gene on the chromosome. Although the nifD 11-kb and nifS 55-kb rearrangements both occurred under normal aerobic heterocyst-inducing conditions, only the 55-kb excision occurred in argon-bubbled cultures, indicating that the two DNA rearrangements can be regulated differently.

Constitutive and light-induced DNAseI hypersensitive sites in the rbcS genes of pea (Pisum sativum)

The chromatin structure of pea (Pisum sativum) rbcS genes in inactive (root), potentially active (dark-grown leaf), and active states (light-grown leaf) was analysed using (a) pancreatic DNAseI to detect general DNAseI sensitivity and DNAseI-hypersensitive sites, and (b) methyl-sensitive restriction endonucleases to probe for cytosine methylation within the promoter region. We showed that within the same organ individual members of the pea rbcS multigene family are differentially sensitive to DNAseI suggesting differential protection in nuclei. During light activation general DNAseI sensitivity increases in some genes, especially their 5' upstream regulatory sequences. DNAseI-hypersensitive sites are constitutively present in 5' upstream regulatory sequences around positions -335, -465, -650, and -945 (5' constitutive domain) and in the coding region around position +340, +450, +530, +640, and +810 (3' constitutive domain). One additional hypersensitive site appears after light induction (inducible site). This region is centred around position -190 and flanked by light-responsive elements (LREs). In spite of changes in the chromatin structure of rbcS genes during their transition from an inactive to an active state, their cytosine methylation at Alu I, Fnu 4HI, Hae III, Sau 3AI and Sau 96I sites in the promoter region remains uniform.

Use of plasmid profiles in epidemiologic surveillance of disease outbreaks and in tracing the transmission of antibiotic resistance

Plasmids are circular deoxyribonucleic acid molecules that exist in bacteria, usually independent of the chromosome. The study of plasmids is important to medical microbiology because plasmids can encode genes for antibiotic resistance or virulence factors. Plasmids can also serve as markers of various bacterial strains when a typing system referred to as plasmid profiling, or plasmid fingerprinting is used. In these methods partially purified plasma deoxyribonucleic acid species are separated according to molecular size by agarose gel electrophoresis. In a second procedure, plasmid deoxyribonucleic acid which has been cleaved by restriction endonucleases can be separated by agarose gel electrophoresis and the resulting pattern of fragments can be used to verify the identity of bacterial isolates. Because many species of bacteria contain plasmids, plasmid profile typing has been used to investigate outbreaks of many bacterial diseases and to trace inter- and intra-species spread of antibiotic resistance.

Restriction analysis and quantitative estimation of methylated bases of filamentous and unicellular cyanobacterial DNAs

The DNAs of strains of three cyanobacterial genera (Anabaena, Plectonema, and Synechococcus) were found to be partially or fully resistant to many restriction endonucleases. This could be due to the absence of specific sequences or to modifications, rendering given sequences resistant to cleavage. The latter explanation is substantiated by the content of N6-methyladenine and 5-methylcytosine in these genomes, which is high in comparison with that in other bacterial genomes. dcm- and dam-like methylases are present in the three strains (based on the restriction patterns obtained with the appropriate isoschizomeric enzymes). Their contribution to the overall content of methyladenine and methylcytosine in the genomes was calculated. Partial methylation of GATC sequences was observed in Anabaena DNA. In addition, the GATC methylation patterns might not have been random in the three cyanobacterial DNA preparations, as revealed by the appearance of discrete fragments (possibly of plasmid origin) withstanding cleavage by DpnI (which requires the presence of methyladenine in the GATC sequence).

Novel densitometric method for endonuclease analysis of Escherichia coli DNA samples containing multiple plasmids

We developed a novel method whereby the digestion pattern of each plasmid was distinguished in a sample of endonuclease-digested plasmid DNAs which contained multiple plasmids extracted from a bacterial strain. This method consisted of two procedures. (i) The concentration ratio of each undigested plasmid DNA and of each digested DNA fragment was calculated on the basis of densitometric scanning of an electrophoretogram, and the concentration ratio was then compared with the theoretical concentration ratio to determine from which plasmid each fragment was generated. (ii) The second procedure involved rapid visual identification with a scanning graph. We thus analyzed five strains of Escherichia coli that harbored several cryptic plasmids. The two procedures made it possible to analyze the restriction digestion pattern of each plasmid without the need to isolate the individual plasmids, except in the case of certain fragments. Even when the digested patterns of these exceptional fragments could not be distinguished completely, however, our method had the advantage that peak patterns of plasmids could be compared visually among different bacterial strains.

Widespread occurrence of the restriction endonuclease YenI, an isoschizomer of PstI, in Yersinia enterocolitica serotype O8

The cold-active restriction endonuclease YenI, an isoschizomer of PstI, was found in 12 of 14 Yersinia enterocolitica serotype O8 strains of different origins, but not in other serotypes of Y. enterocolitica, Yersinia pseudotuberculosis, or Yersinia pestis. In spite of the limited number of strains tested, the result suggests that the detection of YenI endonuclease or the gene might result in more rapid determination of the prominently pathogenic serotype of Y. enterocolitica.

Sequence requirements of Escherichia coli attTn7, a specific site of transposon Tn7 insertion

Transposon Tn7 transposes at high frequency to a specific site, attTn7, in the Escherichia coli chromosome. We devised a quantitative assay for Tn7 transposition in which Tn7-end derivatives containing the cis-acting transposition sequences of Tn7 transpose from a bacteriophage lambda vector upon infection into cells containing the Tn7-encoded transposition proteins. We used this assay to identify a 68-base-pair DNA segment containing the sequences essential for attTn7 target activity. This segment is positioned asymmetrically with respect to the specific point of Tn7 insertion in attTn7 and lacks obvious homology to the sequences at the ends of Tn7 which participate directly in transposition. We also show that some sequences essential for attTn7 target activity are contained within the protein-coding sequence of a bacterial gene.

DNA methylation in leprosy-associated bacteria: Mycobacterium leprae and Corynebacterium tuberculostearicum

The DNAs of two kinds of microorganisms from human leprosy lesion, Mycobacterium leprae and Corynebacterium tuberculostearicum (also known as "leprosy-derived corynebacterium" or LDC), have been analysed and compared with the genomes of reference bacteria of the CMN group (genera Corynebacterium, Mycobacterium and Nocardia). The guanine-plus-cytosine content (% GC) of DNA was determined by a double-labelling procedure, which is unaffected by the presence of modified and unusual bases (that alter both buoyant density and mid-melting-point determinations). Accordingly, the DNAs of seven LDC strains had GC values of 54-56 mol %, and that of armadillo-grown M. leprae a value of 54.8 +/- 0.9 mol %. Restriction patterns disclosed no methylated cytosine in the DNA sequences CCGG, GGCC, AGCT and GATC of either LDC or M. leprae DNA. N6-methyl adenine was present in the sequence GATC of all LDC strains, but was missing from the genomes of all others CMN organisms analysed, including M. leprae. By HPLC analysis of LDC-DNA hydrolysates, it was found that N6-methyladenine amounted to 1.8% of total DNA adenine, and was present exclusively within GATC sequences, which appeared all to be methylated. It is concluded that LDC represent a group of corynebacteria endowed with high genetic homogeneity and a unique restriction pattern, whereby their genome is easily distinguished from that of M. leprae, which has a similar base composition.

Cleavage of methylated CCCGGG sequences containing either N4-methylcytosine or 5-methylcytosine with MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases

The cleavage specificity of R.Cfr9I was determined to be C decreases CCGGG whereas the methylation specificity of M.Cfr9I was C4mCCGGG. The action of MspI, HpaII, SmaI, XmaI and Cfr9I restriction endonucleases on an unmethylated parent d(GGACCCGGGTCC) dodecanucleotide duplex and a set of oligonucleotide duplexes, containing all possible substitutions of either 4mC or 5mC for C in the CCCGGG sequence, was investigated. It was found that 4mC methylation, in contrast to 5mC, renders the CCCGGG site resistant to practically all the investigated endonucleases. The cleavage of methylated substrates with restriction endonucleases is discussed.