A knockdown of the herpes simplex virus type-1 gene in all-in-one CRISPR vectors

INTRODUCTION

Herpes simplex virus type 1 (HSV-1) is a virus that causes serious human disease and establishes a long-term latent infection. The latent form of this virus has shown to be resistant to antiviral drugs. Clustered Regularly Interspace Short Palindromic Repeats (CRISPR), is an important tool in genome engineering and composed of guide RNA (gRNA) and Cas9 nuclease that makes an RNA-protein complex to digest exclusive target sequences implementation of gRNA. Moreover, CRISPR-Cas9 system effectively suppresses HSV-1 infection by knockout of some viral genes.

MATERIALS AND METHODS

To survey the efficacy of Cas9 system on HSV-1 genome destruction, we designed several guide RNAs (gRNAs) that all packaged in one vector. Additionally, we performed a one-step restriction using BamHI and Esp3I enzymes.

RESULTS

CRISPR/Cas9 system targeted against the gD gene of HSV-1 was transfected into HEK-AD cells that showed a significant reduction of HSV-1 infection by plaque assay and real-time PCR.

CONCLUSION

The pCas-Guide-EF1a-GFP CRISPR vector can create a fast and efficient method for gRNA cloning by restriction enzymes (Esp3I (BsmBI) and BamHI). Therefore, the CRISPR/Cas9 system may be utilized for the screening of genes critical for the HSV-1 infection and developing new strategies for targeted therapy of viral infections caused by HSV-1.

Temporal dynamics of methyltransferase and restriction endonuclease accumulation in individual cells after introducing a restriction-modification system

Type II restriction-modification (R-M) systems encode a restriction endonuclease that cleaves DNA at specific sites, and a methyltransferase that modifies same sites protecting them from restriction endonuclease cleavage. Type II R-M systems benefit bacteria by protecting them from bacteriophages. Many type II R-M systems are plasmid-based and thus capable of horizontal transfer. Upon the entry of such plasmids into a naïve host with unmodified genomic recognition sites, methyltransferase should be synthesized first and given sufficient time to methylate recognition sites in the bacterial genome before the toxic restriction endonuclease activity appears. Here, we directly demonstrate a delay in restriction endonuclease synthesis after transformation of Escherichia coli cells with a plasmid carrying the Esp1396I type II R-M system, using single-cell microscopy. We further demonstrate that before the appearance of the Esp1396I restriction endonuclease the intracellular concentration of Esp1396I methyltransferase undergoes a sharp peak, which should allow rapid methylation of host genome recognition sites. A mathematical model that satisfactorily describes the observed dynamics of both Esp1396I enzymes is presented. The results reported here were obtained using a functional Esp1396I type II R-M system encoding both enzymes fused to fluorescent proteins. Similar approaches should be applicable to the studies of other R-M systems at single-cell level.

Clinical usefulness of serum EBV DNA levels of BamHI W and LMP1 for Nasal NK/T-cell lymphoma

Quantitative real-time polymerase chain reaction (PCR) was utilized to measure serum EBV DNA levels of BamHI W fragment and latent membrane protein 1 (LMP1) in 20 nasal natural killer (NK)/T-cell lymphoma patients. Both serum EBV DNAs were detected at high levels in all patients, but the levels were below the limit of detection in all healthy controls. The BamHI Z fragment, Epstein-Barr-replication activator (ZEBRA) expression was detected in a small proportion (0.1-3%) of lymphoma cells from 10 (50%) of the patients. Patients with ZEBRA expression showed significantly higher DNA levels of BamHI W and LMP1 (P = 0.0081, P = 0.004), suggesting that EBV DNA may be caused by EBV replication from lymphoma cells. Kaplan-Meier and univariate analyses revealed that high DNA levels of BamHI W and LMP1 at pre-treatment and high BamHI W DNA level at post-treatment were associated with short disease-free survival and overall survival (P < 0.05, each). Although the DNA levels of BamHI W and LMP1 correlated significantly, their dynamics were not always parallel. Patients with low pre-treatment level of both EBV DNAs showed a favorable course, in contrast to patients with high pre-treatment level of both EBV DNAs who showed an aggressive course (P = 0.0085). More importantly, the high pre-treatment level of both EBV DNAs was determined as the only independent prognostic factor among various prognostic factors. These data suggest that simultaneous measurement of serum levels of both BamHI W and LMP1 DNAs may be useful for diagnosis, disease monitoring, and prediction of prognosis for nasal NK/T-cell lymphoma patients.

Infection of Epstein-Barr virus in colorectal cancer in Chinese

BACKGROUND & OBJECTIVE

Except for the tight correlation to nasopharyngeal carcinoma, accumulating evidences show that Epstein-Barr virus (EBV) is correlated to other carcinomas. This study was to investigate the correlation of EBV to colorectal carcinoma in Chinese.

METHODS

EBV DNA was detected by polymerase chain reaction (PCR) in 90 specimens of primary colorectal carcinoma and 25 specimens of corresponding adjacent non-cancerous tissue, with the primers covering 2 different regions of EBV genome, BamH I W fragment and latent membrane protein 1 (LMP1) exon 3. The expression of EBV nuclear antigen 1 (EBNA1) and LMP1 were determined by immunohistochemistry, and the expression of EBV-encoded RNAs (EBERs) was detected by in situ hybridization.

RESULTS

EBV LMP1 exon 3 and W fragment were detected in 27.7% and 32.2% of the 90 colorectal carcinoma specimens, which were significantly higher than the positive rate of EBV gene in the 25 adjacent non-cancerous tissues (4.0%, P<0.001). Of the 29 W fragment-positive tumors, 23 (79.3%) were EBNA1-positive, 1 (3.4%) was EBERs-positive; most EBNA1-positive cells were tumor cells with positive signals gathered in the nuclei. No expression of EBNA1 and EBERs were detected in the 8 W fragment-negative tumors. No expression of LMP1 was detected in all tumor specimens.

CONCLUSION

EBV infection might be associated with colorectal carcinoma in Chinese.

Chromosomal Localization, Copy Number Assessment, and Transcriptional Status ofBamHI Repeat Fractions in Water BuffaloBubalus bubalis

Higher eukaryotes contain a wide variety of repetitive DNA, although their functions often remain unknown. We describe cloning, chromosomal localization, copy number assessment, and transcriptional status of 1378- and 673-bp repeat fractions in the buffalo genome. The pDS5, representing the 1378-bp fragment, showed FISH signals in the centromeric region of acrocentric chromosomes only, whereas pDS4, corresponding to 673 bp, detected signals in the centromeric regions of all the chromosomes. Crosshybridization studies of pDS5 and pDS4 with genomic DNA from different sources showed signals only in buffalo, cattle, goat, and sheep. Real-time PCR analysis uncovered 1234 and 3420 copies of pDS5 and pDS4 fragments per the haploid genome, corresponding to 30 and 68 copies per chromosome, respectively. Analysis of cDNA from different tissues of buffalo with Real-time PCR showed maximum expression of pDS5 and pDS4 in the spleen and liver, respectively. Phylogenetic analysis of these sequences showed a close relationship between buffalo and cattle. The prospect of this approach in comparative genomics is highlighted.

A Comparison Study of Different PCR Assays in Measuring Circulating Plasma Epstein-Barr Virus DNA Levels in Patients with Nasopharyngeal Carcinoma

PURPOSE

To compare the performance of three PCR assays in measuring circulating Epstein-Barr virus (EBV). DNA levels in nasopharyngeal carcinoma patients and to confirm its prognostic significance.

EXPERIMENTAL DESIGN

Plasma from 58 newly diagnosed nasopharyngeal carcinoma patients were collected before, during, and every 3 to 6 months after radiotherapy. EBV DNA levels were determined by real-time quantitative PCR using primer/probe sets for polymerase-1 (Pol-1), latent membrane protein 2 (Lmp2), and BamHI-W. Pretreatment levels from the three assays were correlated with each other and serial measurements from the Pol-1 assay were correlated with clinical variables.

RESULTS

Pol-1 was more accurate than BamHI-W in predicting EBV DNA concentrations in cell lines. Of the three assays, BamHI-W yielded the highest concentrations followed by Pol-1 in plasmas (n = 23). The correlation coefficient was 0.99 (P < 0.0001) for Pol-1 and Lmp2, 0.66 (P < 0.0001) for Pol-1 and BamHI-W, and 0.55 (P < 0.0001) for BamHI-W and Lmp2. Elevated pretreatment DNA levels as detected by Pol-1 were correlated with advanced nodal stage (P = 0.04) and overall stage (P = 0.028). There was no correlation between pretreatment EBV DNA levels and freedom-from-relapse or overall survival; however, there was a significant correlation between posttreatment levels and these variables. The 2-year freedom-from-relapse and overall survival rates were 92% and 94% for patients with undetectable, and 37% and 55% for those with detectable, posttreatment levels (P < 0.0001 and P < 0.002).

CONCLUSIONS

The three PCR assays yielded similar results in detecting EBV DNA in plasmas. The Pol-1-detected posttreatment EBV DNA level was the strongest predictor for treatment outcomes.

Stress-dependent regulation of the gene encoding gamma-glutamylcysteine synthetase from the fission yeast

Glutathione (GSH), an important antioxidant involved in stress response, is synthesized in two sequential reactions. Gamma-glutamylcysteine synthetase (GCS) catalyzes the first step in GSH biosynthesis, which is usually known to be rate-limiting. In this work, regulatory patterns of the GCS gene from the fission yeast Schizosaccharomyces pombe have been investigated. The 607 bp upstream region from the translational initiation point was amplified by the two synthetic primers. The amplified DNA was ligated into the BamHI/HindIII site of the shuttle vector YEp367R to generate the fusion plasmid pUGCS101. The GCS-lacZ fusion gene construct was confirmed by restriction mapping and nucleotide sequencing. The GCS-lacZ fusion gene was used to study effects of various agents on the transcription of the GCS gene. The synthesis of beta-galactosidase from the fusion plasmid pUGCS101 was enhanced by metals, oxidative and nitrosative stresses, and glutathione-depleting agents. The GCS mRNA level in the wildtype S. pombe cells was significantly elevated by the treatment with sodium nitroprusside or menadione, which was detected by RT-PCR. It was also induced by low concentrations of glucose and sucrose. These results suggest that the expression of S. pombe GCS gene is regulated by various stresses and carbon sources.

Design and Synthesis of Photochemically Controllable Restriction EndonucleaseBamHI by Manipulating the Salt-Bridge Network in the Dimer Interface

The strategy for the design of photochemically controllable enzymes by manipulating the dimer interface is described. Employing a restriction endonuclease BamHI, the selective incorporation of amino acids having a photoremovable 6-nitroveratryl group into the specific position (Lys132) in the dimer interface of the BamHI mutant (H133A) was performed. The activity of the photofunctionalized BamHI mutant was significantly suppressed, and the following photoirradiation induced the recovery of the activity. In addition, uncaging of the 6-nitroveratryl group introduced to Lys132 did not seriously reduce the catalytic activity and affinity for the substrate. These results indicate that the activity of the enzyme can be effectively regulated by caging and uncaging of the specific amino acid in the dimer interface using the photoremovable group.

Crystal structure of BstYI at 1.85A resolution: a thermophilic restriction endonuclease with overlapping specificities to BamHI and BglII

We report here the structure of BstYI, an "intermediate" type II restriction endonuclease with overlapping sequence specificities to BamHI and BglII. BstYI, a thermophilic endonuclease, recognizes and cleaves the degenerate hexanucleotide sequence 5'-RGATCY-3' (where R=A or G and Y=C or T), cleaving DNA after the 5'-R on each strand to produce four-base (5') staggered ends. The crystal structure of free BstYI was solved at 1.85A resolution by multi-wavelength anomalous dispersion (MAD) phasing. Comparison with BamHI and BglII reveals a strong structural consensus between all three enzymes mapping to the alpha/beta core domain and residues involved in catalysis. Unexpectedly, BstYI also contains an additional "arm" substructure outside of the core protein, which enables the enzyme to adopt a more compact, intertwined dimer structure compared with BamHI and BglII. This arm substructure may underlie the thermostability of BstYI. We identify putative DNA recognition residues and speculate as to how this enzyme achieves a "relaxed" DNA specificity.

Presence of Copalyl Diphosphate Synthase Gene in an Actinomycete Possessing the Mevalonate Pathway

We have previously shown that gene clusters for biosyntheses of terpentecin and BE-40644, a diterpene antibiotic and a sesquiterpene antibiotic, respectively, were located in the adjacent mevalonate pathway gene clusters. In this study, a mevalonate pathway gene cluster was cloned from Streptomyces sp. strain KO-3988, which was known to produce furaquinocin A, employing a hybridization experiment using a 3-hydroxy-3-methyl glutaryl CoA (HMG-CoA) reductase gene, which had been previously cloned from the strain KO-3988, as a probe. By sequencing flanking regions, we found four open reading frames that could encode a putative cytochrome P450 (ORF1), an isoprenoid cyclase (ORF2), an unknown protein (ORF3), and a polyprenyl diphosphate synthase gene (ORF4) in the upstream region of the mevalonate pathway gene cluster, though we did not find any genes related to furaquinocin A biosynthesis. The two ORFs (ORF2 and 4) were expressed as recombinant enzymes in E. coli and used for studies to investigate functions of these products. The ORF4 product was confirmed to be a geranylgeranyl diphosphate (GGDP, C20) synthase. The ORF2 product proved to catalyze a conversion of GGDP into copalyl diphosphate, the first example of an enzyme with this function of prokaryotic origin. These results again showed that actinomycetes possessing the mevalonate pathway usually produce an isoprenoid and that its biosynthetic gene cluster exists in adjacent the mevalonate pathway gene cluster.

Evaluation of a whole-genome amplification method based on adaptor-ligation PCR of randomly sheared genomic DNA

High-throughput genetic studies often require large quantities of DNA for a variety of analyses. Developing and assessing a whole-genome amplification method is thus important, especially with the current desire for large-scale genotyping in previously collected samples for which limited DNA is available. The method we have developed, called PRSG, is based on an adaptor-ligation-mediated PCR of randomly sheared genomic DNA. An unbiased representation was evaluated by performing PCR on 2,607 exons of 367 genes, which are randomly distributed throughout the genome, on PRSG products of hundreds of individuals. An infrequent loss (<1%) of the exon sequence on the PRSG products was found. Out of 307 microsatellites on various chromosomes, 258 (84%) were amplified in both the PRSG product and an original DNA, whereas 49 (16%) microsatellites were lost only in the PRSG product. Array CGH analysis of 287 loci for measuring the relative gene copy number demonstrated that a low bias was detected. Moreover, this method was validated on 100-1,000 laser-captured cells from paraffin-embedded tissues. These data show that PRSG can provide a sufficient amount of genomic sequence for a variety of genetic analyses as well as for long-term storage for future work.

[Analysis of the N-acetyltransferase 2 gene polymorphism in the patients with chronic obstructive pulmonary disease and in populations of the Volga-Ural region]

Restriction fragment-length polymorphism of the gene coding for N-acetyltransferase 2 (NAT2) was typed in populations of the Volga-Ural region (Bashkirs, Tatars, Chuvashes, Udmurts, and Russians) as well as in patients with chronic obstructive pulmonary disease (COPD) and in healthy individuals. Rapid and slow acetylator phenotypes were determined based on the presence or absence of the KpnI, TaqI, and BamHI restriction endonuclease recognition sites. The proportion of slow acetylators in the populations examined varied from 40.00% in Bashkirs to 64.15% in Chuvashes with statistically significant difference between these two ethnic groups (chi 2 = 5.7; p = 0.02). Overall, in the Volga-Ural populations slow acetylators represented 56.25% of the subjects examined. This value was similar to those presented in other studies of Caucasoid populations. In the COPD patients a statistically significant decrease of the slow acetylator frequency to 48.28% compared to healthy individuals (62.18%) was observed (chi 2 = 4.60; p = 0.036). The data obtained suggest a possible association between the drug resistance in the COPD patients with the rapid acetylator phenotype, which can lead to the development of the chronic form of the disease.

An alternative approach for screening active bam HI variants: overexpression in T-7 RNA polymerase based system

The type II restriction endonuclease, Bam HI, has been overexpressed in E. coli by cloning the Bam HI gene in frame with an E. coli Ribosome Binding Site (RBS) under the T7 promoter of an E. coli expression vector pRSET A. The expression level of Bam HI endonuclease using this construct was found to be higher than that reported of the overexpressing clone pAEK14. Our overexpressing clone, pAABRw in BL21 cells in presence of Bam HI methylase in pMAP6 following induction with IPTG yields about 9.2 x 10(6) units per gram wet cell paste. In vivo activity of the recombinant endonuclease could be confirmed by the SOS induction assay in JH139 cells even in the absence of T7 polymerase and cognate Bam HI methylase because of leaky expression in E. coli. This provides an alternate way to screen the active endonuclease and its variants.

Reduced activity of bamhi variants c54i, c64w, and c54d/c64r is consistent with the substrate-assisted catalysis model

Three specific mutants, C54I, C54W, and a double-mutant C54D:C64R of restriction endonuclease BamHI, were generated and studied to investigate the role, if any, of the 54th and 64th cysteine residues in the catalysis of BamHI. The mutation was achieved using the megaprimer approach for PCR. The mutant genes were cloned and characterized by sequencing. The mutant and the wild-type proteins were expressed and purified and their kinetic parameters were determined using short synthetic oligonucleotides as substrates. All mutants had higher K(m) values than that of the wild-type enzyme suggesting a decrease in the affinity of the enzyme for its substrate. The mutant protein C54W showed significant changes in the CD spectra vis-a-vis wild-type enzyme and had the lowest K(m)/K(cat) value among the mutants indicative of changes in the secondary structure of the protein. The melting curves of the mutant proteins overlapped that of the wild-type enzyme. Analysis of the K(cat) values in the context of cocrystal structure suggests that the effect of Cys54 mutation is probably through the perturbation of the local structure whereas reduced activity of the double mutant is consistent with the substrate-assisted catalysis mechanism.

Activity of the EBNA1 promoter associated with lytic replication (Fp) in Epstein-Barr virus associated disorders

BACKGROUND/AIMS

In Epstein-Barr virus (EBV) positive cell lines that are stably infected, three different promoters are known to direct the transcription of EBV nuclear antigen 1 (EBNA1). These are located in the BamHI-C, BamHI-Q, and BamHI-F regions of the viral genome (Cp, Qp, and Fp, respectively). Fp is activated upon induction of the viral lytic cycle. The aim of this study was to investigate the activity of Fp in EBV associated diseases.

METHODS

Using reverse transcriptase polymerase chain reaction, a qualitative analysis of EBNA1 promoter usage in various EBV associated diseases was performed.

RESULTS

Fp driven transcription was detected in the context of primary infection and/or lytic replication; at least a portion of the Fp driven transcripts encoded EBNA1. Qp driven EBNA1 transcripts were detected in most samples across the range of disorders tested. Cp driven EBNA1 transcripts were detected in the context of immune suppression and in samples containing EBV positive (non-neoplastic) lymphoid cells.

CONCLUSIONS

These results confirm the previously proposed "housekeeping" function of the Qp promoter.

A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data

The development and assessment of a prediction method for gel retardation and sequence dependent curvature of DNA based on dinulcleotide step parameters are described. The method is formulated using the Babcock-Olson equations for base pair step geometry (1) and employs Monte Carlo simulated annealing for parameter optimization against experimental data. The refined base pair step parameters define a stuctural construct which, when the width of observed parameter distributions is taken into account, is consistent with the results of DNA oligonucleotide crystal structures. The predictive power of the method is demonstrated and tested via comparisons with DNA bending data on sets of sequences not included in the training set, including A-tracts with and without periodic helix phasing, phased A4T4 and T4A4 motifs, a sequence with a phased GGGCCC motif, some "unconventional" helix phasing sequences, and three short fragments of kinetoplast DNA from Crithidia fasiculata that exhibit significantly different behavior on non-denaturing polyacrylamide gels. The nature of the structural construct produced by the methodology is discussed with respect to static and dynamic models of structure and representations of bending and bendability. An independent theoretical account of sequence dependent chemical footprinting results is provided. Detailed analysis of sequences with A-tract induced axis bending forms the basis for a critical discussion of the applicability of wedge models,junction models and non A-tract, general sequence models for understanding the origin of DNA curvature at the molecular level.

The transposon A(R)4-24P[white, rosy] in Drosophila melanogaster is subject to position-effect variegation at a non-centromeric insertion site

The white gene within the transposon A(R)4-24P[white,rosy] inserted at cytological location 24D1-2 in the euchromatic portion of the Drosophila melanogaster genome exhibits a mosaic pattern of expression which is modified by temperature and Y-chromosome number, as in cases of classical position-effect variegation (PEV). The eye colour of the flies in this variegated stock remains mosaic in the presence of the PEV modifier Su(var)3-6, slightly less so with Su(var)3-9 and Su(var)2-5, and full suppression of variegation occurs in the presence of Su(var)3-7. We have induced further transposition of A(R)4-24 and isolated two mosaic stocks with this transgene at new cytological locations. In these stocks, the A(R)4-24 transposon was flanked by the same genomic DNA fragments as in the original location. Spontaneous loss of these fragments leads to reversion of the variegated eye colour to wild-type. We suggest that the flanking DNA fragments from 24D1-2 are capable of inducing position-effect variegation without any association with centromeric heterochromatin. In situ hybridisation and Southern analysis demonstrate that the 5' flanking genomic fragment contains repeated sequences which are abundantly present in heterochromatin.

The activity of the Epstein-Barr virus BamHI W promoter in B cells is dependent on the binding of CREB/ATF factors

The programme of Epstein-Barr virus (EBV) gene expression that leads to virus-induced growth transformation of resting B lymphocytes is initiated through activation of the BamHI W promoter, Wp. The factors regulating Wp, and the basis of its preferential activity in B cells, remain poorly understood. Previous work has identified a B cell-specific enhancer region which is critical for Wp function and which contains three binding sites for cellular factors. Here we focus on one of these sites and show, using bandshift assays, that it interacts with three members of the CREB/ATF family of cell transcription factors, CREB1, ATF1 and ATFa. A mutation which abrogates the binding of these factors reduces Wp reporter activity specifically in B cell lines, whereas a mutation which converts the site to a consensus CREB-binding sequence maintains wild-type promoter function. Furthermore Wp activity in B cell, but not in non-B cell, lines could be inhibited by cotransfection of expression plasmids expressing dominant negative forms of CREB1 and ATF1. Increasing the basal activity of CREB/ATF proteins in cells by treatment with protein kinase A or protein kinase C agonists led to small increases in Wp activity in B cell lines, but did not restore promoter activity in non-B cell lines up to B cell levels. We conclude that CREB/ATF factors are important activators of Wp in a B cell environment but require additional B cell-specific factors in order to mediate their effects.

An improved integration replacement/disruption method for mutagenesis of yeast essential genes

We improved the integration replacement/disruption method (Shortle, D., Novic, P., and Botstein, D. Proc. Natl. Acad. Sci. USA 81: 4889-4893, 1984) for isolating mutants in any of essential genes of the yeast Saccharomyces cerevisiae by integrating mutagenized DNA into the wild type gene of interest. We adopted this method to isolate temperature-sensitive mutants of the MPC1 gene encoding the YLL031C ORF. To facilitate integration of the mutagenic plasmid at a site near the 5' end of the ORF, a BamHI site was created at 300 bp downstream of the 5' end of the truncated ORF to be mutagenized. The MPC1 gene was disrupted in the wild type haploid strain by integrating a 5'-truncated derivative of the gene with mutations induced by in vitro mutagenesis. Transformants thus obtained were subjected for diagnosis of conditional lethality by replica-plating onto an appropriate selection medium to detect mutants. A primary mutant isolated by this method reverted in a high frequency due to a tandem repeat created by mutagenic integration. We deviced a method to obtain a stable temperature-sensitive strain by disrupting the tandem duplication. Two stable temperature-sensitive mutants thus obtained were found to be remedial either with 1 M sorbitol or with 0.1 M Mg2+ and to be sensitive to local anestheticum, tetracaine, at 25 degrees C.

Promoter interference in a bacteriophage lambda control region: effects of a range of interpromoter distances

The p(R) and p(RM) promoters of bacteriophage lambda direct transcription in divergent directions from start sites separated by 83 phosphodiester bonds. We had previously shown that the presence of an RNA polymerase at p(R) interfered with open complex formation at p(RM) and that this effect was alleviated by the deletion of 10 bp between the two promoters. Here we present a detailed characterization of the dependence of the interference on the interpromoter distance. It was found that the reduced interference between the two promoters is unique to the 10-bp deletion. The relief of interference was demonstrated to be due to the facilitation of a step subsequent to RNA polymerase binding to the p(RM) promoter. A model to explain these observations is proposed. A search of known Escherichia coli promoters identified three pairs of divergent promoters with similar separations to those investigated here.

Identification and characterization of brt1, a gene down-regulated during B-regulated development in Schizophyllum commune

To identify genes regulated by the B mating-type genes a differential RNA display was established for the homobasidiomycete Schizophyllum commune and a gene, brt1, was identified. The mRNA concerned is highly abundant in monokaryotic mycelia and is down-regulated in matings in which either the B genes alone or else both the A and B genes are different between the mates. This places the gene brt1 under the control of the pheromone response system of S. commune encoded by the B mating-type loci. Sequence analysis revealed similarity to a novel protein family, two members of which have been shown to inhibit translational re-initiation.

Strand interruptions confer strand preference during intracellular correction of a plasmid-borne mismatch in Saccharomyces cerevisiae

Site-directed mutagenesis was used to construct yeast centromere plasmids in which a strand nick or gap could be placed 5' or 3', on either strand, to a reporter gene (SUP4-o) carrying defined base mismatches. The plasmids were then transformed into yeast cells and the direction and efficiency of mismatch repair were assayed by scoring colouring of the transformant colonies. Strands that were nicked were consistently corrected more often than intact strands, but the effect was very small. However, placement of a small gap at the same positions as the nicks resulted in a marked increase in selection for the gapped strand and an enhanced efficiency of mismatch repair. Both the preference for the gapped strand and correction of the mismatch were offset by deletion of the mismatch repair gene PMS1. Together, the results suggest that strand interruptions can direct intracellular mismatch correction of plasmid-borne base mispairs in yeast.

Identification of enhancer-like elements in the ribosomal intergenic spacer of Odontophrynus americanus 2n and 4n (Amphibia, Anura)

Repetitive elements are found in the ribosomal intergenic spacer (IGS) of most organisms. A particularly complex pattern of internal repetition occurs in the IGSs of O. americanus 2n and 4n, which are composed of several types of BamHI subrepeats (B-SRs). The most repetitive one is approximately 87 bp long, and is highly represented in the IGS variants of these amphibians. Sequence analyses of six diploid and two tetraploid B-SRs show 87% and 86% homology, respectively, and related secondary structure predictions. The comparison of the 2n and 4n B-SR sequences aligned with the 81 bp enhancer of Xenopus laevis reveals 36% homology. Furthermore, other B-SR features like size, number, and secondary structures resemble those of Xenopus enhancers, suggesting that B-SRs may function as regulators of O. americanus rDNA transcription. The present data also corroborate the close evolutionary relationship between 2n and 4n O. americanus species.

A mutant of BamHI restriction endonuclease which requires N6-methyladenine for cleavage

Amino acid residues Asn116 and Ser118 of the restriction endonuclease BamHI make several sequence-specific and water-bridged contacts to the DNA bases. An in vivo selection was used to isolate BamHI variants at position 116, 118 and 122 which maintained sequence specificity to GGATCC sites. Here, the variants N116H, N116H/S118G and S118G were purified and characterized. The variants N116H and N116H/S118G were found to have lost their ability to cleave unmethylated GGATCC sequences by more than two orders of magnitude, while maintaining nearly wild-type levels of activity on the N6-methyladenine-containing sequence, GGmATCC. In contrast, wild-type BamHI and variant S118G have only a three- to fourfold lower activity on unmethylated GGATCC sequences compared with GGmATCC sequences. The N116 to H116 mutation has effectively altered the specificity of BamHI from an endonuclease which recognizes and cleaves GGATCC and GGmATC, to an endonuclease which only cleaves GGmATCC. The N116H change of specificity is due to the lowered binding affinity for the unmethylated sequence because of the loss of two asparagine-DNA hydrogen bonds and the introduction of a favorable van der Waals contact between the imidazole group of histidine and the N6-methyl group of adenine.

Genetic analysis of the base-specific contacts of BamHI restriction endonuclease

Here, we investigate the highly specific interaction of the BamHI endonuclease with its cognate recognition sequence GGATCC by determining which amino acid residues can be substituted at the DNA interface while maintaining specificity. Mutational studies, together with the structural determination of the restriction endonuclease BamHI have revealed the amino acid residues which are involved in DNA catalysis and those which play a role in the specific binding of the enzyme to its cognate DNA recognition sequence. Amino acid residues N116, S118, R122, D154 and R155 are involved in DNA sequence recognition and are located in the major groove in close proximity to the nucleotide bases comprising the recognition sequence. Cassette mutagenesis of these amino acids, together with in vivo transcriptional interference selection, was used to identify an array of substitutions which maintain site-specific binding to the cognate GGATCC sequence. This approach has demonstrated the extent of acceptable variation among amino acid residues which are directly involved in site-specific binding. One variant, double mutant N116H, S118G was found to cleave DNA only when the adenine base in the recognition site is methylated.

Protein engineering of BamHI restriction endonuclease: replacement of Cys54 by Ala enhances catalytic activity

Chemical modification studies of BamHI endonuclease indicated the importance of the cysteine residue in catalysis [Nath, K. (1981) Arch. Biochem. Biophys, 212, 611-617]. Of the three cysteine residues at positions 34, 54 and 64 in the BamHI endonuclease Cys54 and Cys64 are at the DNA-protein interface. The co-crystal structure of the BamHI-DNA complex, however, does not indicate any role of cysteines either in binding or catalysis. In the context of strong biochemical evidence, Cys54 in BamHI was changed to Ala54 to investigate its role in catalysis. The mutation was carried out by PCR overlap extension, the mutant gene was cloned and characterized by sequencing. The mutant BamHI was expressed and purified to homogeneity and the kinetic parameters (K(M) and kcat) of the wild type and the C54A mutant were determined. The mutation results in up to approximately 40% enhancement of kcat and some increase in K(M). These in vitro results were also supported by in vivo SOS induction assays: the C54A mutant gene under the T7 promoter caused complete lysis in JH139 in absence of T7 RNA polymerase whereas the wild-type gene gave deep blue colonies under the same conditions. The results suggest no direct role of Cys54 in catalysis, but it can influence the catalytic activity through Val57 backbone contact seen in the co-crystal structure.

[The variability of mitochondrial DNA in eastern Slavs]

Geographical distributions of three mitochondrial DNA markers (BamHI-1/AvaII-5(3), BamHI-2/AvaII-5(3), and BamHI-3/MspI-4) were analyzed in Caucasian populations of Europe and Middle East. Considerable genetic similarity between eastern Slavs and southern European populations (r = 0.995) has been found. It is assumed that the basic components of the mitochondrial gene pool of eastern Slavs are of southern European origin.

Ribonuclease-charged vector for facile direct cloning with positive selection

Plasmid vectors for positive selection of cloned inserts in Escherichia coli were devised, based on an expression plasmid (pMT416) for the bacterial ribonuclease barnase. In addition to the barnase gene under control of a synthetic tac promoter, these plasmids carry the gene for the barnase inhibitor, barstar, the constitutive expression of which protects the bacterium from the detrimental effects of moderate barnase production. Full expression of the barnase gene overcomes protection by barstar and becomes lethal. Having a unique SmaI/XmaI site in the barnase structural gene, pMT416 itself can be used as a selective vector: uncut or religated pMT416 will preclude growth while plasmids with inserts in the barnase gene will allow the cells to survive. The entire pUC polylinker was inserted into the barnase gene in place of the Val-36 codon. This insert of nineteen largely hydrophilic amino acids does not prevent the lethal effect of full expression of the gene. The resulting plasmid, pMT440, is a generally useful selective cloning vector representing the "kill-the-rest" approach.

Structural, functional, and evolutionary relationships between lambda-exonuclease and the type II restriction endonucleases

lambda-exonuclease participates in DNA recombination and repair. It binds a free end of double-stranded DNA and degrades one strand in the 5' to 3' direction. The primary sequence does not appear to be related to any other protein, but the crystal structure shows part of lambda-exonuclease to be similar to the type II restriction endonucleases PvuII and EcoRV. There is also a weaker correspondence with EcoRI, BamHI, and Cfr10I. The structure comparisons not only suggest that these enzymes all share a similar catalytic mechanism and a common structural ancestor but also provide strong evidence that the toroidal structure of lambda-exonuclease encircles its DNA substrate during hydrolysis.

Molecular structure of the rDNA intergenic spacer (IGS) in Triturus: implications for the hypervariability of rDNA loci

Ribosomal DNA (rDNA) variation in the species Triturus vulgaris meridionalis (Amphibia, Urodela) is remarkable because of unusually high intraspecific variability in the number and distribution of ribosomal loci in the karyotype; in addition, portions of the intergenic spacer (IGS) are clustered at chromosomal loci where they are not associated with ribosomal 18S and 28S RNA genes. These clusters are referred to as extraribosomal, and they appear to consist mostly of repetitive BamHI elements. In this paper, we report the complete nucleotide sequence of an IGS of T. v. meridionalis; this structural analysis is aimed to get insight into the molecular mechanism(s) of spreading of the ribosomal cistrons as well as its possible functional significance. We found that the IGS of T. vulgaris has a modular structure: modular repetitive elements contain sequences possibly related to the regulation of transcription of the ribosomal units. In particular, both ribosomal and extraribosomal IGS elements contain presumptive enhancers. Interestingly, the enhancer-containing region is mostly conserved between ribosomal and extraribosomal elements, while mutations accumulate in a region characterized by repetitions of a simple sequence motif, that we consider as a possible recombination hotspot. Our data suggest that extraribosomal elements most probably originated from ribosomal enhancer-containing elements able to move independently from the ribosomal unit at novel chromosomal positions, perhaps with the aid of the simple repetitive motif. We argue that a similar mechanism may lead to the spreading of complete repetition units as well, giving rise to multiple, and variable, ribosomal sites. We propose that hypervariability in the number and distribution of the rDNA loci, as seen in T. vulgaris, is a further mechanism to ensure redundancy, which seems to be an intrinsic property of rDNA biology, the occurrence of IGS elements independently clustered at separate chromosomal loci being a by-product of this mechanism.

Mapping of the mouse Tdgf1 gene and Tdgf pseudogenes

Teratocarcinoma-derived growth factor-1 (Tdgf1), a member of the "EGF family" of growth factors, is expressed during mouse gastrulation in the forming mesoderm and later in the truncus arteriosus of the developing heart. In humans, TDGF1 is highly expressed in germ cell tumors and in colon and mammary carcinomas. In mouse, one gene (Tdgf1) and two pseudogenes (Tdgf1-ps1 and Tdgf1-ps2) have been isolated and characterized. Tdgf1 corresponds to the gene expressed in F9 teratocarcinoma cells. Tdgf1-ps1 and Tdgf1-ps2 are two intronless sequences with all the characteristics of retroposons. In the present paper, we assign the chromosomal location for Tdgf1, Tdgf1-ps1, and Tdgf1-ps2 sequences to Chromosomes (Chrs) 9, 16, and 17, respectively. Two previously described mouse mutants, scant hair (sch) and fur deficient (fd), map near the Tdgf1 gene. Analysis of their DNA coding region provided no evidence that Tdgf1 could be the responsible gene for these phenotypes. Finally, analysis of the DNA from several Mus musculus strains and from Mus spretus mice revealed a highly variable restriction pattern and the absence of the Tdgf1-ps1 genomic sequence from the Mus spretus genome.

A serine-to-proline mutation in the copper-transporting P-type ATPase gene of the macular mouse

We have investigated the cDNA sequence of the copper-transporting P-type ATPase (Atp7a) gene of the macular mouse, a model for human Menkes disease. A point mutation (T to C) that results in substitution of proline for serine in a putative eighth transmembrane domain of the ATP7A was identified. This contrasts with abnormalities identified in the Atp7a of other mottled mouse strains: lack of expression of Atp7a mRNA in the dappled mouse, and a splicing mutation in the blotchy mouse.

[Similarity of geographic distribution of frequencies of p(c) allele of erythrocyte acid phosphatase and BamHI-3/MspI-4 types of mitochondrial DNA in Caucasoid human populations]

The frequencies of the pC allele of red cell acid phosphatase (AcPI) and a group of mitochondrial DNA (mtDNA) types BamHI-3/MspI-4 were shown to have similar geographic distribution in Caucasoid populations of six regions of Europe and Asia. The maximum frequency values of these markers were revealed in southern and southeastern Europe. The possibility of associations between these variants of polymorphism in the genotype-mitotype system is discussed. The geographical gradients of pC and BamHI-3/MspI-4 correlate with the directions of neolithic migrations of Caucasoids from the Near East to Europe. The region of maximum frequency values of pC and BamHI-3/MspI-4 is supposed to be largely consistent with the area where considerable enhancing of the population size of neolithic migrants from the Near East and their mixing with the ancient population of Europe occurred.

Isolation of temperature-sensitive mutants of the BamHI restriction endonuclease

Two heat-sensitive R.BamHI mutants, T157I and P173L, and one cold-sensitive R.BamHI mutant, T114I, were isolated after chemical mutagenesis of the bamhIR gene that codes for the restriction endonuclease BamHI (R.BamHI). The thermosensitivity of T114I, T157I and P173L is revealed by the 10(2)-10(3) lower plating efficiency at the non-permissive temperature of strains bearing these alleles. The conditional-lethal phenotype can be rescued by introduction of the cognate bamhIM gene into the same cell. The mutant enzymes induce the SOS response in vivo and display reduced phage restriction activity. The P173L protein, when expressed at 30 degrees C and purified, shows reduced thermostability at 65 degrees C. T157I and P173L mutants yield different intermediates during partial trypsin digestion. The conditional-lethal BamHI mutants could be used to deliver in vivo DNA cleavage and for further isolation of relaxed-specificity mutants.

Purification and characterization of C.BamHI, a regulator of the BamHI restriction-modification system

The bamHIC gene, controlling the BamHI restriction-modification (R-M) system can functionally be replaced by providing pvuIIC or smaIC in trans. C.BamHI, the protein product encoded by bamHIC, has been purified and shown to bind a 345-bp DNA fragment within the BamHI R-M system.

Expression of the complementary-strand transcripts from BamHI-A region of the Epstein-Barr virus genome in various induced virus-carrying B cell lines

The complementary-strand transcripts from Epstein-Barr virus BamHI-A-I fragments (also called the BARF0 RNAs) were first found in a nasopharyngeal carcinoma passaged in nude mice, c15, and soon proved to exist in various EBV-associated tumors and virus-carrying B cell lines. The data from previous studies revealed that the BARF0 transcripts have a highly spliced structure, whereas the evidence about their in vivo translational products remains few. The BARF0 RNA is also somehow considered as a new member of the viral latent transcripts. In order to know further about its transcriptional profile, we investigated its transcription in several EBV-carrying B cell lines during different viral stages. Our results show that (1) at least some of the BARF0 transcripts are transcribed during the viral lytic stage in the tested inducible lines; (2) the major lytic BARF0 mRNA appears heterogeneous in size (2.5 to 4.2 kb) among different lines; (3) in P3HR1 and Akata lines, the major BARF0 transcript is highly spliced and sensitive to both an inhibitor of the viral DNA polymerase and of protein synthesis. The identification of such lytic BARF0 RNAs may help us to understand further about their complex gene expression.

Cloning of HindIII digested bovine herpesvirus-1 DNA fragments from an Indian respiratory isolate

The DNA from an Indian isolate of Bovine Herpesvirus-1 was isolated and analysed with restriction endonucleases. On shot gun cloning seven HindIII digested BHV-1 DNA fragments could be cloned in pBR322 vector. Recombinant clones with viral DNA insert was identified by insertional inactivation of the selection marker and restriction analysis of recombinant plasmids with HindIII. Further, recombinant plasmids were analysed with HindIII, EcoRI and BamHI restriction endonucleases to identify the different viral DNA inserts. The restriction site map of recombinant plasmids were correlated with the map reported earlier. The southern blot of restriction digested recombinant plasmids was hybridized with radio-labelled BHV-1 DNA as probe.

Structure of restriction endonuclease bamhi phased at 1.95 A resolution by MAD analysis

BACKGROUND

Type II restriction endonucleases recognize DNA sequences that vary between four to eight base pairs, and require only Mg2+ as a cofactor to catalyze the hydrolysis of DNA. Their protein sequences display a surprising lack of similarity, and no recurring structural motif analogous to the helix-turn-helix or the zinc finger of transcription factors, has yet been discovered.

RESULTS

We have determined the crystal structure of restriction endonuclease BamHI at 1.95 A resolution. The structure was solved by combining phase information derived from multi-wavelength X-ray data by algebraic and maximum likelihood methods. The BamHI subunit consists of a central beta-sheet with alpha-helices on both sides. The dimer configuration reveals a large cleft which could accommodate B-form DNA. Mutants of the enzyme that are deficient in cleavage are located at or near the putative DNA-binding cleft. BamHI and endonuclease EcoRI share a common core motif (CCM) consisting of five beta-strands and two helices. It remains to be determined if other restriction enzymes also contain the CCM.

CONCLUSIONS

The structure of BamHI provides the first clear evidence that there may be substantial structural homology amongst restriction enzymes, even though it is undetectable at the sequence level.

Location and rapid analysis of the intragenic BamHI polymorphic site of the factor IX gene

We report the precise location and a polymerase chain reaction (PCR)-based method for the analysis of the intragenic BamHI polymorphism of the factor IX (FIX) gene. After screening DNA samples from the Brazilian Black population by a selective amplification of a segment of the FIX gene containing entire exon 2, intron 2, and exon 3 followed by digestion of PCR products with BamHI, we were able to identify individuals presenting the polymorphic BamHI site. By DNA sequencing of selected samples, the dimorphic base was located at nucleotide number 6575 (intron 2). The PCR method outlined here allows rapid and easy analysis of this polymorphism. Its application may be particularly useful for carrier detection and prenatal diagnosis of hemophilia B in the Black population, thus far the only one that has been shown to be polymorphic for this site. Because of its apparent restrictive pattern it may also be used in combination with other markers for estimates of racial admixture in mixed populations in which the Black population is present (as is the case for most countries in the American continent).

Direct selection of binding proficient/catalytic deficient variants of BamHI endonuclease

Variants of BamHI endonuclease in which the glutamate 113 residue has been changed to lysine or the aspartate 94 to asparagine were shown to behave as repressor molecules in vivo. This was demonstrated by placing a BamHI recognition sequence, GGATCC, positioned as an operator sequence in an antisense promoter for the aadA gene (spectinomycin resistance). Repression of this promoter relieved the inhibition of expression of spectinomycin resistance. This system was then used to select new binding proficient/cleavage deficient BamHI variants. The BamHI endonuclease gene was mutagenized either by exposure to hydroxylamine or by PCR. The mutagenized DNA was reintroduced into E. coli carrying the aadA gene construct, and transformants that conferred spectinomycin resistance were selected. Twenty Spr transformants were sequenced. Thirteen of these were newly isolated variants of the previously identified D94 and E113 residues which are known to be involved in catalysis. The remaining seven variants were all located at residue 111 and the glutamate 111 residue was shown to be involved with catalysis.

Protecting recognition sequences on DNA by a cleavage-deficient restriction endonuclease

This report describes the use of a biochemical tool that has been developed to aid in the manipulation of DNA. A DNA binding-proficient and cleavage-deficient BamHI mutant protein, E113K, was used in vitro to protect its recognition sequence (5'-GGATCC-3') against the catalytic action of site-specific endonuclease, exonuclease and methylase. In vitro conditions are reported here in which the E113K protein protects BamHI sites (5'-GGATCC-3') from cleavage by BamHI endonuclease or Sau3AI endonuclease (5'-GATC-3'); protects a neighboring restriction site 5'-CCCGGG-3' from SmaI endonuclease digestion; blocks methylation of 5'-GGATCC-3' by Dam methylase (5'-GATC-3'); and blocks Bal31 exonuclease progression at a BamHI site. The Bal31 procedure could be used to generate unidirectional deletions of a DNA fragment. The use of mutant endonucleases that are binding-proficient and cleavage-deficient to shield DNA from nuclease digestion or methylase modification expands the repertoire of methods to manipulate DNA in vitro.

Clonal heavy chain isotype switching within the proliferation centers of a small lymphocytic lymphoma: implications regarding the origin of proliferation centers

We describe an unusual case of small lymphocytic lymphoma with multiple prominent pseudofollicular proliferation centers in which immunohistochemistry reveals that the small cells are surface IgM kappa positive and the large pseudofollicular cells are surface IgA kappa positive. We further show by genomic DNA analysis that the tumor tissue contains two JH rearrangements, one Cmu rearrangement, one C alpha rearrangement, and a single C kappa rearrangement, strongly suggesting that the large cells within the proliferation centers have arisen from the small cells via a clonal heavy chain immunoglobulin isotype switch. Isotype switching in human lymphoma and leukemia appears to be an uncommon event. However, there are reports that strongly support isotype switching in pre-B-cell leukemia, Richter's syndrome, lymphoid blast crisis of chronic myelogenous leukemia, and multiple myeloma. To our knowledge, there have been no previous reports demonstrating isotype switching within the proliferation centers of small lymphocytic lymphoma. We present evidence of in vivo intratumoral isotype switching within the proliferation centers of a small lymphocytic lymphoma documented at the level of immunohistochemistry and DNA rearrangement.

[Cleft lip and palate in the Chilean population: association with BamH1 polymorphism of the transforming growth factor alpha (TGFA) gene]

In recent studies we have demonstrated that the model that better explains the genetic etiology of non syndromic cleft lip/palate (CL/P) in the Chilean population is one that postulates the existence of a major dominant autosomic locus with low penetrance, without discarding the possible influence of polygenes. Similar conclusions have been communicated by others authors in different populations. Thus, investigations have been initiated to seek possible associations between candidate genes and restriction length polymorphisms (RFLP's), specifically between Transforming Growth Factor Alpha (TGFA) gene RFLP's and CL/P, in caucasian populations. Results thus far obtained have been inconclusive. Therefore, the aim of this work was to study this association in the Chilean population, that is ethnically different. The gene and phenotype frequencies of the TGFA gene BamH1 polymorphism in CL/P probands (n = 21) and controls (n = 16) were determined. No significant differences were detected in the frequencies of the A1 and A2 alleles of the TGFA gene between probands and controls. These results do not support an association between the cleft palate phenotype and TGFA RFLP.

Regulation of the BamHI restriction-modification system by a small intergenic open reading frame, bamHIC, in both Escherichia coli and Bacillus subtilis

BamHI, from Bacillus amyloliquefaciens H, is a type II restriction-modification system recognizing and cleaving the sequence G--GATCC. The BamHI restriction-modification system contains divergently transcribed endonuclease and methylase genes along with a small open reading frame oriented in the direction of the endonuclease gene. The small open reading frame has been designated bamHIC (for BamHI controlling element). It acts as both a positive activator of endonuclease expression and a negative repressor of methylase expression of BamHI clones in Escherichia coli. Methylase activity increased 15-fold and endonuclease activity decreased 100-fold when bamHIC was inactivated. The normal levels of activity for both methylase and endonuclease were restored by supplying bamHIC in trans. The BamHI restriction-modification system was transferred into Bacillus subtilis, where bamHIC also regulated endonuclease expression when present on multicopy plasmid vectors or integrated into the chromosome. In B. subtilis, disruption of bamHIC caused at least a 1,000-fold decrease in endonuclease activity; activity was partially restored by supplying bamHIC in trans.

[The genome localization of the plasmid pAP27 fin N system]

Plasmid transfer genetic regulatory system fin N of F-like plasmid pAP27 have been localized on BamHI-restriction fragment f3 (length 8.7 kb). Plasmid pUC19 Fin-activity have been cleared up and characterized from the point of view of its specificity of action on some plasmid transfer functions.

Cofactor requirements of BamHI mutant endonuclease E77K and its suppressor mutants

A mutant BamHI endonuclease, E77K, belongs to a class of catalytic mutants that bind DNA efficiently but cleave DNA at a rate more than 10(3)-fold lower than that of the wild-type enzyme (S. Y. Xu and I. Schildkraut, J. Biol. Chem. 266:4425-4429, 1991). The preferred cofactor for the wild-type BamHI is Mg2+. BamHI is 10-fold less active with Mn2+ as the cofactor. In contrast, the E77K variant displays an increased activity when Mn2+ is substituted for Mg2+ in the reaction buffer. Mutations that partially suppress the E77K mutation were isolated by using an Escherichia coli indicator strain containing the dinD::lacZ fusion. These pseudorevertant endonucleases induce E. coli SOS response (as evidenced by blue colony formation) and thus presumably nick or cleave chromosomal DNA in vivo. Consistent with the in vivo result, the pseudorevertant endonucleases in the crude cell extract display site-specific partial DNA cleavage activity. DNA sequencing revealed two unique suppressing mutations that were located within two amino acid residues of the original mutation. Both pseudorevertant proteins were purified and shown to increase specific activity at least 50-fold. Like the wild-type enzyme, both pseudorevertant endonucleases prefer Mg2+ as the cofactor. Thus, the second-site mutation not only restores partial cleavage activity but also suppresses the metal preference as well. These results suggest that the Glu-77 residue may play a role in metal ion binding or in enzyme activation (allosteric transition) following sequence-specific recognition.

[Structural organization of a segment of chromosome, containing the vir gene of Bordetella pertussis]

To study the structural arrangement of the chromosomal region containing vir genes of Bordetella pertussis the corresponding 15 kb fragment of Bordetella pertussis chromosomal DNA has been cloned. The sequence homology to an earlier characterized Bordetella pertussis genetical element RSBP1 and flanked by two 400 bp inverted repeats has been shown to be located at an end of a BamHI fragment. The restriction map of Bordetella pertussis 475 coincides with the previously published maps of Bordetella pertussis Tohama and 18323 permitting one to conclude the definite conservatism of the cloned sequence. The preliminary data obtained make possible mapping of the RSBP1 homologous sequence adjacent to adenylate cyclase, agglutinin 2 and pertussis toxin genes. The possible role of RSBP1 elements in the regulation of Bordetella virulence is suggested.