Detection of two restriction endonuclease activities in Haemophilus parainfluenzae using analytical agarose--ethidium bromide electrophoresis

Molecular cloning and physical mapping of the tupaia herpesvirus genome

Purified virion DNA of about 200 kilobase pairs of tupaia herpesvirus strain 2 was cleaved with EcoRI or HindIII restriction endonuclease. Restriction fragments representing the complete viral genome including both termini were inserted into the EcoRI, HindIII, and EcoRI-HindIII sites of the bacterial plasmid pAT153. Restriction maps for the restriction endonucleases EcoRI and HindIII were constructed with data derived from Southern blot hybridizations of individual viral DNA fragments or cloned DNA fragments which were hybridized to either viral genome fragments or recombinant plasmids. The analysis revealed that the tupaia herpesvirus genome consists of a long unique sequence of 200 kilobase pairs and that inverted repeat DNA sequences of greater than 40 base pairs do not occur, in agreement with previous electron microscopic data. No DNA sequence homology was detectable between the tupaia herpesvirus DNA and the genome of murine cytomegalovirus, which was reported to have a similar structure. In addition, seven individual isolates of tupaia herpesvirus were characterized. The isolates can be grouped into five strains by their DNA cleavage patterns.

Displacement synthesis of globin complementary DNA: evidence for sequence amplification

We have examined a cDNA displacement synthesis procedure in which the extent of precursor incorporation and the unusual kinetics of displacement synthesis suggest a unique replicative form of DNA and the occurrence of multiple rounds of displacement synthesis, leading to amplification of mRNA sequences. Globin double-stranded DNA containing a hairpin loop was extended by the addition of a homopolymer to the 3' end. This was followed by displacement synthesis with the Klenow fragment of DNA polymerase I that was primed by an oligonucleotide hybridized to the homopolymer. Thus, the hairpin cDNA was copied to form an open duplex with an inverted repetition of globin sequences. These molecules can then serve as templates for additional synthesis which would be primed from oligomers bound the homopolymer. Globin cDNA sequences appear to be amplified 10-fold or more by this procedure. Globin cDNA obtained by displacement synthesis was similar in size to the original template. However, displaced molecules associate to the extent that they are not readily resolved by electrophoresis or sedimentation under nondenaturing conditions. Restriction endonuclease digests of 32P-labeled displaced strands gave fragment patterns similar to rabbit globin cDNA hairpin molecules. S1 nuclease studies demonstrated that displaced complexes and replication intermediates are partially single stranded, which might account for their aggregation properties.

The expression of the SV40 early region in the transformed human cell line SV80

The one complete copy of the SV40 early region present in human cells of the transformed line SV80 carries a duplication of the 5' portion of the early region, including its transcriptional control region and splicing signals (W. Gish and M. Botchan, personal communication). Novel SV40-specific RNA species of sufficiently large size, 3.8 and 4.2 kb, to be expressed from the duplicated early transcriptional control region were detected in SV80 cytoplasmic and nuclear RNA preparations by blot hybridization. The results of transcription in a cell-free system of a plasmid, pSV80-04, representing this SV80 cell SV40 DNA integrate (W. Gish and M. Botchan, personal communication) and of nuclease protection experiments with end-labelled pSV80-04 DNA fragments support the conclusion that the duplicated early sequences are transcribed in SV80 cells. It has also been established that the duplicated early splicing signals are functional in SV80 cells. These results are discussed in relation to the large amounts of SV40 early mRNA and T-antigen synthesized in cells of the SV80 line.

RecBC enzyme nicking at Chi sites during DNA unwinding: location and orientation-dependence of the cutting

Homologous recombination by the E. coli RecBC pathway occurs at elevated frequency near Chi sites. We reported previously that Chi induces RecBC enzyme to cleave one DNA strand--that containing the Chi sequence 5'G-C-T-G-G-T-G-G3'. We report here that the Chi-dependent cleavage occurs four, five, or six nucleotides to the 3' side of the Chi octamer and produces nicks with 3'-OH and 5'-PO4 groups. Chi-dependent cleavage occurs if RecBC enzyme approaches the Chi sequence from the right, but not if it approaches only from the left, during unwinding of the duplex DNA substrate. A single RecBC enzyme molecule appears to cleave the DNA and to release part of it as a single-stranded fragment. These and previous results indicate that Chi-dependent cleavage is concomitant with DNA unwinding by RecBC enzyme and provide an enzymatic basis for the orientation-dependence of Chi recombinational hotspot activity. These observations demonstrate a key step of a proposed model of recombination in which RecBC enzyme produces a potentially invasive single-stranded DNA tail extending from Chi to its left. We discuss the relation between the action of Chi sites and that of special sites enhancing eukaryotic recombination.

A stable plasmid vector and control of its copy number in Bacillus brevis 47, a protein-producing bacterium

A low-copy-number plasmid vector, pHY481, was constructed by combining a macrolide resistance gene of a Staphylococcus aureus plasmid with a cryptic plasmid found in a Bacillus brevis strain isolated from soil. The plasmid introduced into B. brevis 47, an extensively investigated protein-producing bacterium, was maintained very stably in the absence of selective antibiotics. A Bacillus megaterium alpha-amylase gene subcloned into pHY481 was retained much more stably in B. brevis 47 than one subcloned into a plasmid of S. aureus origin. B. brevis 47 mutants were also isolated in which the copy number of pHY481 was amplified about 10-fold. The copy number of pHY481 with the inserted amylase gene also increased in the mutants. As a result, a severalfold-higher amount of the enzyme was produced in the mutants compared with that produced in wild-type B. brevis 47. Thus, the plasmid vector constructed here and the copy-number mutants of B. brevis 47 are useful for cloning foreign genes and performing genetic engineering in the protein-producing bacterium.

Isolation and characterization of the pMI10 plasmid from Bacillus subtilis, an alpha-amylase producer

The plasmid DNA pMI10 (5310 bp) was isolated from the alpha-amylase producing strain B. subtilis A18. Thirteen restriction endonucleases were used to digest pMI10 DNA and the restriction map of pMI10 DNA was constructed by mapping PstI (1), HindII (2), BglI (2), BspRI (3) and HindIII (3) sites.

Nucleotide sequence of a regulatory region of the uidA gene in Escherichia coli K12

Multiple regulatory events are involved in the expression of the uidA gene. A regulatory region of this gene has been located on a 460 base pair Sau3A-EcoRI fragment and its nucleotide sequence was determined by the dideoxy method using pEMBL plasmids. A preliminary analysis of this sequence revealed the presence of numerous palindromic structures with some overlaps.

A simple and rapid method for screening bacteria for type II restriction endonucleases: enzymes in Aphanothece halophytica

A method is described which allows a large number of bacterial strains to be rapidly and easily screened for the presence of site-specific endonucleases. The method involves selective permeabilization of the bacterial cell and analysis of the exuded material. Type II restriction endonucleases from cyanobacteria and Gram-negative eubacteria have been detected and new enzymes have been found. The method should be widely applicable and easy to modify for use in genera other than those tested. Three-site-specific endonuclease activities, detected by this method in Aphanothece halophytica PCC 7412, were purified and their recognition and cleavage specificities were determined AhaI and AhaII recognise and cleave the same DNA sequences as CauII and AcyI respectively; the specificity of AhaIII (TTT decreases AAA) has been reported previously (Whitehead and Brown, 1982, FEBS Letters 143:296-300).

Recognition sequences of restriction endonucleases and methylases--a review

The properties and sources of all known endonucleases and methylases acting site-specifically on DNA are listed. The enzymes are crossindexed (Table I), classified according to homologies within their recognition sequences (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 restriction endonucleases include relaxed specificities (Table III), the structure of the restriction fragment ends (Table IV), and the sensitivity to different kinds of DNA methylation (Table V). Table VI classifies the methylases according to the nature of the methylated base(s) within their recognition sequences. This table also comprises those restriction endonucleases, which are known to be inhibited by the modified nucleotides. Furthermore, this review includes a restriction map of bacteriophage lambda DNA based on sequence data. Table VII lists the exact nucleotide positions of the cleavage sites, the length of the generated fragments ordered according to size, and the effects of the Escherichia coli dam- and dcmI-coded methylases M X Eco dam and M X Eco dcmI on the particular recognition sites.

The use of gene fusions to study the expression of uidR, a negative regulatory gene of Escherichia coli K-12

The uidR regulatory gene of Escherichia coli codes for a repressor molecule that negatively controls the expression of the uidA gene. The uidR gene was fused in front of the lacZ gene in vitro on plasmid cloning vectors developed by Casadaban et al. [J. Bacteriol. 143 (1980) 971-980. The transcriptional direction of uidR was deduced from the restriction pattern and the phenotypic properties of the uidR-lacZ fusion plasmids. The gene is transcribed counterclockwise on the standard E. coli map, as is the uidA gene. The uidR-lacZ fusions were also used to examine the regulation of expression from the uidR promoter. It was observed that the uidR gene expression is repressed by its own product and is sensitive to catabolite control. The uidR-lacZ-encoded proteins of various sizes were isolated but attempts to obtain hybrid molecules possessing, in a single polypeptide, both the beta-galactosidase and UidR repressor activities were unsuccessful.

Anti-mRNA: specific inhibition of translation of single mRNA molecules

A plasmid was constructed to generate RNA complementary to the beta-galactosidase mRNA under control of the phage lambda PL promoter. When this anti-mRNA was produced, synthesis of beta-galactosidase was dramatically inhibited (98%). Syntheses of galactoside permease and transacetylase, whose coding sequences are downstream of the beta-galactosidase coding region, are inhibited to a lesser degree, 80% and 55%, respectively. The generation of anti-mRNA that can be targeted to inhibit a single species of mRNA molecule within cells provides a potent mechanism by which specific transcripts can be translationally inactivated. This can be used to determine the function of proteins as well as to select cloned genes in a single rapid and convenient step.

Recombination in adenovirus: analysis of crossover sites in intertypic overlap recombinants

Overlap recombination has been used as a means of generating intertypic recombinants with crossover sites located within a defined region of the adenovirus genome. Using terminal DNA fragments of adenovirus type 2 and type 5 that overlap within the vicinity of the hexon coding region (51.6-59.7 map units), two different crosses could be studied; in one the overlap entirely encompasses the hexon and there are homologous regions at either side of the overlap where recombination is expected, and in the other only one side of the overlap is capable of sustaining recombination. The overall distribution of crossover sites within the overlap has been determined by restriction endonuclease mapping, and analysed in terms of the extent of homology between Ad2 and Ad5 in this region as defined by the DNA sequences (R. Kinloch, N. Mackay, and V. Mautner (1984). J. Biol. Chem., 259, 6431-6436; G. Akusjärvi, P. Aleström, M. Pettersson, M. Lager, H. Jörnvall, and U. Pettersson (1984). Submitted). Crossovers are found only in regions of relatively high DNA homology, as previously shown for intertypic recombination between temperature-sensitive viruses (M. E. G. Boursnell and V. Mautner (1981). Virology 112, 198-209). The presence of a free DNA end within the heterologous zone is insufficient to overcome the barrier to recombination. In crosses where recombination is confined to a relatively small homologous zone (45.9-53.0 mu) there is no special distribution of crossovers within the interval; no "hot spot" is discernible at the free DNA end, suggesting that a free DNA end is not especially recombinogenic, nor at the junction between the homologous and heterologous zones, suggesting that branch migration up to the heterology does not always occur. A cross designed to furnish evidence for gene conversion gave rise to a "conventional" recombinant with a crossover located within a 21-nucleotide tract of homology.

Reverse transcription of Drosophila mobile dispersed genetic element RNAs: detection of intermediate forms

DNA-RNA complexes were detected in cultured Drosophila melanogaster cells. These complexes are practically perfect hybrid molecules of mobile dispersed genes DNA (mdg1 and mdg3) and suitable poly(A)+RNA. Three species of single-stranded DNA have been found in hybrid molecules: full-sized mdg DNA containing either one or two LTRs (both minus strands) and single LTR sequences (plus strand). The properties of hybrid molecules are consistent with those being expected from the model of reverse transcription pathway of transposition and amplification of mdg elements.

Cloning with tandem gene systems for high level gene expression

A method has been devised for increasing the copy number of a gene (or genes) cloned into a plasmid while minimizing the size of the plasmid. If n copies of a transcriptional unit are cloned, including the promoter, coding region and terminator, the size of the plasmid will increase by n times the total size of the unit. However, if we borrow the concept of polycistronic operon and sandwich n structural genes, each with its own ribosome binding-site, between a promoter and a transcription terminator, there will be a space saving equivalent to n-1 promoters and n-1 transcription terminators. We have constructed plasmids in which an E. coli lipoprotein promoter is followed by 1 to 4 human leukocyte interferon genes and a transcription terminator. The applications of this method in genetic engineering are discussed.

A physical and functional analysis of Tn917, a Streptococcus transposon in the Tn3 family that functions in Bacillus

The erythromycin-resistance (Emr)-conferring transposon Tn917, first isolated in the genus Streptococcus, has in previous work been shown to function efficiently in the spore-forming species Bacillus subtilis, where it has been developed as a tool for identifying and studying sporulation genes. In the present work, a physical analysis of Tn917 was undertaken, including detailed restriction mapping, chemical DNA sequencing, heteroduplex studies, and Southern hybridization analysis, as a first step in understanding the genetic organization of this useful insertion element. The location and transcriptional orientation of the transposon-borne erm gene (the gene responsible for the Emr phenotype) have been determined, and a partial sequence of DNA 5' to the coding sequence of this gene indicates that its inducibility is probably the result of "translational attenuation," a mechanism known to be responsible for the regulation of at least two other gram-positive erm genes. Restriction mapping and heteroduplex analysis have revealed extensive homology between Tn917 and the Staphylococcus transposon Tn551, throughout virtually their entire lengths, and DNA sequencing studies have revealed a remarkably high degree of sequence correspondence within the terminal inverted repeats of Tn917, Tn551 and the gram-negative transposon Tn3. Tn917 was also shown to generate a 5-bp duplication upon insertion, as do Tn3 and Tn551 (and all of the other Tn3-related elements studied thus far), strengthening the conclusion that these three transposons are members of a highly dispersed family of related insertion elements which populate both gram-positive and gram-negative genera.

Immunoprecipitation of some forms of simian virus 40 large-T antigen by antibodies to synthetic peptides

Antibodies were raised against six synthetic peptides corresponding to overlapping amino acid sequences (106 through 145) from a putative DNA binding domain in simian virus 40 (SV40) large-T antigens. All six antipeptide sera immunoprecipitated large-T from crude extracts of SV40-transformed cells, but the efficiency varied widely; in general, antibodies to the longer peptides produced the strongest anti-large-T activity. Antisera were purified by immunoaffinity chromatography on immobilized peptide. The purified antisera recognized only some forms of large-T; full-sized large-T from transformed cells, super-T from SV3T3 C120 cells, and 70,000-dalton T-antigen from Taq-BamHI cells were immunoprecipitated, whereas large-T from productively infected cells reacted irreproducibly, and the full-sized protein, synthesized in vitro or eluted from sodium dodecyl sulfate-containing gels, and the 33,000- and 22,000-dalton truncated large-Ts from Swiss SV3T3 and MES2006 cells, respectively, were not immunoprecipitated. This pattern of reactivity was explained when extracts were fractionated by sucrose density centrifugation, and it was found that only rapidly sedimenting forms of large-T were immunoprecipitated by the antipeptide sera; that is, large-T complexed with nonviral T antigen was detected, whereas lighter forms were not detected. Cascade immunoprecipitations did not support the view that this result was caused by the low affinity of the peptide antisera for large-T, and Western blotting experiments confirmed that the peptide antisera react directly with immobilized, monomeric large-T but not with nonviral T antigen. Immunoprecipitation assays to detect large-T:nonviral T antigen complexes bound specifically to fragments of SV40 DNA showed that under conditions of apparent antibody excess, DNA still bound to the complex.

Differences exist between viral transcripts in cottontail rabbit papillomavirus-induced benign and malignant tumors as well as non-virus-producing and virus-producing tumors

Five major cottontail rabbit papillomavirus-specific polyadenylated RNA species with sizes of 4.8, 2.6, 2.0, 1.3, and 0.9 kilobases (kb) were found in virus-producing tumors of cottontail rabbits (the natural host for the virus). Two of the RNA species (sizes, 2.0 and 1.3 kb) are indistinguishable with respect to size and map position from the RNA species detected previously in non-virus-producing benign and malignant tumors (Nasseri et al., J. Virol. 44:263-268, 1982). The 2.0-kb RNA in virus-producing benign tumors is more abundant than the 1.3-kb RNA. This, together with similar observations of benign non-virus-producing tumors, suggests that the predominance of the 2.0-kb RNA is a general feature of benign tumors. The change to a preferential synthesis of the 1.3-kb RNA appears to be a phenomenon of tumor progression from papillomas to carcinomas. Three transcripts of 4.8, 2.6, and 0.9 kb are unique to virus-producing tumors. The RNA molecules were mapped in two steps. First, hybridization of Northern blots with subgenomic probes revealed the approximate map position of the transcripts. Second, with nuclease S1 and exonuclease VII mapping procedures and end-labeled probes, the major exons of the 4.8-, 2.6-, 2.0-, and 1.3-kb RNAs were mapped precisely, and it is shown that all RNAs are transcribed from the same DNA strand. Both 1.3- and 2.0- kb RNAs consist of two exons which are separated by an identical 2.45-kb intron. The 5' ends of the 5'-proximal exons of the 2.0- and 1.3-kb RNAs map to positions 0.07 and 0.16, respectively. Some of the 2.0-kb RNA molecules, especially in the carcinoma, have an alternative 5' end at position 0.06. The 3' ends of both exons map to position 0.22, where two ends were found about seven nucleotides apart. The sizes of the 5'-proximal exons of the 2.0- and 1.3-kb RNAs are 1.23 and 0.48 kb, respectively. The 1.3- and 2.0-kb RNAs share a common 3'-proximal exon of 0.66 (0.61) kb. This exon has two 5' ends 50 nucleotides apart at map position 0.53 and a 3' end at map position 0.61. Only the 3'-proximal part of the 4.8- and 2.6-kb RNAs have been mapped precisely. Both RNAs share a common 3' end at position 0.99. The 2.6-kb RNA part consists of a single 1.59-kb exon which extends to map position 0.79.(ABSTRACT TRUNCATED AT 400 WORDS)

Identification of transfer RNA suppressors in Escherichia coli. IV. Amber suppressor Su+6 a double mutant of a new species of leucine tRNA

An Escherichia coli DNA fragment containing an Su+6 amber suppressor gene (supP) was cloned into a lambda gt lambda Ch vector by the shotgun method, selecting a Su+6 transducing phage lambda pSu+6. Through prophage integration followed by induction occurring at the transducing region of the lambda pSu+6 in Su- E. coli, a counterpart transducing phage carrying the wild-type allele (Su degrees 6) was isolated (lambda pSu degrees 6). The fingerprint of a tRNA encoded by lambda pSu degrees 6 was identical to that of an unidentified tRNAE previously reported (Ikemura & Ozeki, 1977). The cloverleaf structure of this tRNA was determined by combining the results of tRNA analysis and DNA sequencing of the gene. Judging from the anticodon of 5'-CAA-3', Su degrees 6 tRNA was identified as a new type of leucine isoacceptor in E. coli. Unlike other suppressors analyzed, Su+6 tRNA differed by two nucleotides from Su degrees 6 tRNA; one at the anticodon (CAA to CUA) and the other at the junction of D- and anticodon-stem (A27 to G27). DNA sequence analysis revealed that a single stretch of tRNA is flanked by the putative sequences of promoter and terminator. Thus a single copy of the Su degrees 6 tRNA gene constitutes a solitary tRNA transcription unit. Southern blotting showed only one copy of Su degrees 6 tRNA gene per haploid genome of E. coli. Since this single gene can mutate to the Su+6 suppressor, the Su degrees 6 leucine tRNA may be accounted as a dispensable species among the leucine isoacceptor tRNAs. Two possible open reading frames are found immediately following the Su degrees 6 tRNA gene.

Identification of transfer RNA suppressors in Escherichia coli. III. Ochre suppressors of lysine tRNA

Transducing phages of lambda carrying suppressors, lysT (Su+ beta), supG and and supL, were isolated in vivo. Upon infection with each of these phages, the production of tRNALys and tRNAVal1 was markedly enhanced. Fingerprint analysis of these tRNAs revealed that they consisted of normal tRNALys, mutant tRNALys and tRNAVal1 in equimolar ratios. The mutant tRNALys carried a single-base alteration at the anticodon, from 5'-UUU-3' to 5'-UUA-3', which makes it an ochre suppressor. DNA sequence analysis of the entire transducing fragment (730 base-pairs) of lambda pSu+ beta revealed that three tRNA genes are tightly clustered within a transcription unit in the following order; i.e. promoter-(48 base-pairs)-wild-type tRNALys-(132 base-pairs)-tRNAVal1-(2 base-pairs)-Su+ beta tRNALys-. In wild-type bacteria there are two identical tRNALys genes in one operon. Although we have shown that in Su+ beta it is the distal tRNALys that has been mutated to the ochre suppressor by a single base change at the anticodon (U36 to A36), we have not determined which of the two genes bears the supG or the supL mutation. The sequences following both tRNALys genes are highly homologous: both are about 100 base-pairs long and both terminate with an 18 base-pair sequence homologous to the last 18 bases of each tRNA. The sequences of tRNALys and tRNAVal1 are also very similar. Thus, including the 3'-portions of these tRNA genes, the 18 base-pair sequence is more or less periodically repeated five times in the DNA sequence.

Cytoskeletal involvement in cAMP-induced sensitization of chromatin to nuclease digestion in transformed Chinese hamster ovary K1 cells

The cAMP-induced reverse transformation of CHO-K1 cells, which restores fibroblastic morphology, normal nuclear structure, specific membrane structures and biochemical activities, and cell growth regulation, also restores the sensitivity of nuclear chromatin digestion by DNase I to that resembling the normal fibroblast. All of these aspects of the reverse-transformation reaction require integrity of the cytoskeleton. The nuclease-sensitivity effect is achieved only when the entire cell rather than the isolated nucleus is incubated with cAMP derivatives, indicating linkage between the cytoskeleton and nuclear components. Evidence is presented to show that the DNA sensitization to digestion involves interaction between DNA and other chromatin components and affects different regions of the genome in specific ways. Normal fibroblasts display greater endogenous nuclease activity than the transformed cell. The data are interpreted in terms of a genetic regulatory system extending from the membrane to the nucleus and utilizing the cAMP-induced cytoskeleton.

A novel method for the rapid cloning in Escherichia coli of Bacillus subtilis chromosomal DNA adjacent to Tn917 insertions

A rapid and general procedure has been devised for the pBR322-mediated cloning in Escherichia coli of Bacillus subtilis chromosomal DNA extending in a specified direction from any Tn917 insertion. Derivatives of Tn917 have been constructed that contain a pBR322-derived replicon, together with a chloramphenicol-resistance (Cmr) gene of Gram-positive origin (selectable in B. subtilis), inserted by ligation in two orientations into a SalI restriction site located near the center of the transposon. When linearized plasmid DNA carrying such derivatives was used to transform to Cmr B. subtilis bacteria already containing a chromosomal insertion of Tn917, the pBR322 sequences efficiently became integrated into the chromosomal copy of the transposon by homologous recombination. It was then possible to clone chromosomal sequences adjacent to either transposon insertion junction into E. coli, using a selection for ampicillin-resistance, by transforming CaCl2-treated cells with small amounts of insert-containing DNA that had been digested with various restriction enzymes and then ligated at a dilute concentration. Because pBR322 sequences may be inserted by recombination in either orientation with respect to the transposon arms, a single restriction enzyme (such as EcoRI or SphI) that has a unique recognition site in pBR322 DNA may be used to separately clone chromosomal DNA extending in either direction from the site of any transposon insertion. A family of clones generated from the region of an insertional spo mutation (spoIIH::Tn917) was used in Southern hybridization experiments to verify that cloned material isolated with this procedure accurately reflected the arrangement of sequences present in the chromosome. Strategies are discussed for taking advantage of certain properties inherent in the structure of clones generated in this way to facilitate the identification and study of promoters of insertionally mutated genes.

Petite induction in Saccharomyces cerevisiae by ethidium analogs. Action on mitochondrial genome

Petite induction of ethidium analogs was examined in both resting and growing yeast cells. All of the analogs used in these experiments were active in dividing cells of Saccharomyces cerevisiae; only the parent ethidium bromide was mutagenic under resting conditions. Incorporation of adenine into mitochondrial DNA appeared to be prevented completely by ethidium and partially inhibited by other analogs. Treatment of growing cells with analogs affected fragmentation of pre-existing DNA as seen by the loss of a mitochondrial antibiotic resistance marker. The rates of elimination of the marker were different; ethidium generated greater loss than the monoamino analogs (3-amino and 8-amino-); and the deaminated analog was least effective. However, in resting yeast the marker was partially eliminated only with treatment of the parent ethidium. The degradation of the mitochondrial DNA by exposure to ethidium compounds was confirmed by agarose gel electrophoresis. Electrophoretic patterns of the mitochondrial DNA treated with each of the analogs under growing conditions and only with ethidium under resting conditions showed degradation of the mitochondrial DNA.

Molecular cloning of a major cell wall protein gene from protein-producing Bacillus brevis 47 and its expression in Escherichia coli and Bacillus subtilis

Bacillus brevis 47 contains two major cell wall proteins. Each protein forms a hexagonal array in the cell wall. A 4.8-kilobase HindIII fragment of B. brevis 47 DNA cloned into Escherichia coli with pBR322 as a vector directed the synthesis of polypeptides cross-reactive with antibody to the middle wall protein. A 700-base-pair BamHI-HpaI fragment was shown to be the essential region for the synthesis of immunoreactive polypeptides. Furthermore, this fragment appeared to contain the promoter activity. The 3.5-kilobase BamHI fragment covering the essential region as well as its downstream sequence was subcloned into the corresponding restriction site of pUB110 by using Bacillus subtilis as the cloning host. Both E. coli and B. subtilis carrying the cloned DNA synthesized several immunoreactive polypeptides which were mainly found in the cytoplasm. B. subtilis secreted polypeptides cross-reactive with antibody to the middle wall protein. These extracellular polypeptides were degraded upon prolonged culture.

Ty1-promoted expression of aspartate transcarbamylase in the yeast Saccharomyces cerevisiae

An entire copy of a Ty1 yeast transposon has been found inserted between two regions comprising the single transcriptional and translational URA2 units in yeast that code respectively for carbamylphosphate synthetase (CPSase) and aspartate transcarbamylase (ATCase). The mutant Rev 16 was obtained from an ATCase- strain blocked by multiple nonsense mutations in the proximal CPSase region and submitted to selective pressure for recovery of the enzyme activity coded by the distal part of the gene. The inserted Ty1 has one XhoI site in both delta elements, delimiting a 5.6 kb piece of DNA that shows a classical Ty1 restriction pattern. The orientation of this sequence in URA2 is the same as in the previously described examples in which Ty1 has positive effects on the expression of adjacent genes. In this case the Ty1 is situated more than 1 kb from the URA2 region in which ATCase structural mutants have been mapped. Nevertheless, transcription of the entire sequence distal to the Ty1 is restored and has become subject to mating-type control, leading to a weak enzyme activity. Our observations are in agreement with generally accepted ideas regarding the way in which Ty1 elements affect gene expression, and additionally, represent the first example of a Ty1 -promoted reinitiation occurring in the middle of a single transcription unit.

Characterization of the DNA of a defective human parvovirus isolated from a genital site

An apparently helper-dependent parvovirus was isolated from a penile flat condylomatous lesion by inoculating the material into a culture of human fibroblasts, and by coinfecting these cells with adenovirus type 12. Upon addition of an adenovirus helper, the virus could be readily propagated in human KB cells. Analysis of its DNA revealed that it shares structural similarities with the DNA of the four defective parvoviruses (adeno-associated viruses, AAV) described so far, but that the cleavage pattern obtained after digesting the DNA with restriction enzymes is different from that of AAV 1-AAV 4. Nucleic acid hybridization data further support the assumption that the isolated defective parvovirus is not identical with the other four serotypes. When conditions of high stringency were used, only weak cross-reactivity was seen with the DNAs of AAV 1-AAV 4, whereas the latter showed strong cross-hybridization with each other. The organization of the DNA of the newly isolated parvovirus was investigated by mapping the cleavage sites of several restriction enzymes. It is proposed to designate the new isolate as AAV 5.

Direct evidence for specific binding of the replicative origin of the Escherichia coli chromosome to the membrane

The origin of replication of the Escherichia coli chromosomal DNA binds with high affinity to outer membrane preparations. This specific binding requires a 463-base-pair region of origin DNA between positions -45 and +417 of the oriC map. We show that binding does not require the presence of adjacent regions. From further analysis, we conclude that more than one binding site resides within the 325-base-pair fragment between positions +38 (BamHI) and +417 (XhoI). When this fragment is cut, two pieces bind with high affinity and one binds with lesser affinity. The binding ability of one of the high affinity sites is abolished by cutting it at position +92 with BamHI.

Balbiani ring 6 gene in Chironomus tentans: a diverged member of the Balbiani ring gene family

We describe the internal organization of a large part of the Balbiani ring (BR) 6 gene in Chironomus tentans. The BR6 gene is a diverged member of the BR gene family. It displays the characteristic hierarchic organization of repetitive sequences, but in the constant region of the repeat units the overall sequence homology is only 49% when compared to other BR genes. All four cysteines are among the few amino acids conserved in the constant region. In the subrepeat region the central part is built from a repeated tripeptide, Pro-Glu--Arg+. A similar charge distribution adjacent to prolines is found in other BR gene subrepeat regions, most pronouncedly in the BR2-encoded protein. These conserved properties of the BR gene products are relevant to the issue how the various BR gene products interact to form a supramolecular structure, the larval tube, and how functional demands influence the evolution of a eucaryotic gene family.

The DNA of bacteriophage 643: isolation and properties of the DNA of a bacteriophage infecting lactic Streptococci

The DNA extracted from bacteriophage 643, which infects group N strains of Streptococci, could be separated into four components by electrophoresis on agarose gels. Electron microscopy established the predominant form of the DNA to be a relaxed, circular molecule of molecular weight 14.9 X 10(6). The four species observed on electrophoresis are believed to be a circular monomeric form, a linear form derived from it, a circular dimeric form, and the corresponding linear dimer. Two DNA components were demonstrated by sedimentation velocity in the analytical ultracentrifuge and by zone sedimentation in sucrose gradients. These corresponded to a circular monomeric form and a circular dimeric form; no evidence for supercoiled forms was found by sedimentation in either neutral or denaturing solvents. Bacteriophage 643 DNA was sensitive to cleavage by single-strand-specific nuclease S1 and could be labeled in vitro by the PolI-catalyzed incorporation of [alpha-32P]dATP into the molecule under conditions that did not permit nick translation, suggesting that the circular duplex molecule is interrupted by a single-stranded gap.

U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells

The majority, and perhaps all, of the genes for human U1 small nuclear RNA (U1 RNA) were shown to be located on the short arm of human chromosome 1. These genes were mapped by Southern blot analysis of DNA from rodent-human somatic cell hybrids, using the 5' region of a human U1 RNA gene as a human-specific probe. This probe hybridized to DNA fragments present only in digests of total human DNA or to the DNAs of cell lines which contained human chromosome 1. The major families of human U1 RNA genes were identified, but some human genes may have gone undetected. Also, the presence of a few U1 RNA genes on human chromosome 19 could not be ruled out. In spite of the lack of extensive 5'-flanking-region homology between the human and mouse U1 RNA genes, the genes of both species were efficiently transcribed in the hybrid cells, and the U1 RNAs of both species were incorporated into specific ribonucleoprotein particles.

Molecular weight determination program

A computer program is described that will determine the molecular weight of DNA, RNA or protein molecules separated according to size by gel electrophoresis. It uses the sizes and migration distances of known molecules in a reference lane to compute a second or third order equation whose curve best fits the data points. It then computes the sizes of all molecules from this equation. Migration distances are measured and entered using an analog tablet. The program is written in Apple Pascal and designed to run on an Apple II Plus computer.

The function(s) provided by the adenovirus-specified, DNA-binding protein required for viral late gene expression is independent of the role of the protein in viral DNA replication

The adenovirus type 2 (Ad2) host range mutant Ad2hr400 grows efficiently in cultured monkey cells at 37 degrees C, but is cold sensitive for plaque formation and late gene expression at 32.5 degrees C. After nitrous acid mutagenesis of an Ad2hr400 stock, cold-resistant variants were selected in CV1 monkey cells at 32.5 degrees C. One such variant, Ad2ts400, was also temperature sensitive (ts) for growth in both CV1 and HeLa cells. Marker rescue analysis has been used to show that the two phenotypes, cold resistant and temperature sensitive, are due to two independent mutations, each of which resides in a different segment of the gene encoding the 72-kilodalton DNA binding protein (DBP). The cold-resistant mutation (map coordinates 63.6 to 66) is a host range alteration that enhances the ability of the virus to express late genes and grow productively in monkey cells at 32.5 degrees C. The temperature-sensitive mutation is in the same complementation group and maps to the same segment of the DBP gene (map coordinates 61.3 to 63.6) as the well-characterized DBP mutant Ad5ts125. Like Ad5ts125, Ad2ts400 is unable to replicate viral DNA or to properly shut off early mRNA expression at the nonpermissive temperature. Two sets of experiments with Ad2ts400 suggest that DBP contains separate functional domains. First, when CV1 cells are coinfected at the nonpermissive temperature with Ad2 plus Ad2ts400 (Ad2 allows DNA replication and entry into, but not completion of, the late phase of infection), normal late gene expression and productive growth occur. Second, temperature shift experiments show that, although DNA replication is severely restricted at the nonpermissive temperature in ts400-infected monkey cells, late gene expression occurs normally. These results indicate that the DBP activity required for normal late gene expression in monkey cells is functional even when the DBP's DNA replication activity is disrupted.

Cloning and expression of a thermophilic alpha-amylase gene from Bacillus stearothermophilus in Escherichia coli

A 6.4 Kb HindIII fragment of Bacillus stearothermophilus DY-5 DNA cloned in Escherichia coli using pBR322 as a vector was shown to direct the synthesis of a thermophilic alpha-amylase. In attempts to reduce the size of the insert, the alpha-amylase gene was shown to be contained in a 3.1 Kb HindIII - BamHI fragment of the donor strain DNA. The alpha-amylase gene was stably maintained and expressed efficiently in E. coli. The enzymic properties of alpha-amylase produced in E. coli closely resembled those of the donor strain alpha-amylase and the temperature range for the maximal activity was from 65 degrees C to 80 degrees C. Nearly 100% of the activity remained after heating at 80 degrees C for 15 min. The alpha-amylase was shown to be accumulated in the periplasmic space. It was purified to a nearly homogenous protein with a molecular weight of 61,000, which was very similar in size to that produced by B. stearothermophilus DY-5.

Isolation and bacterial expression of a murine alpha leukocyte interferon gene

A murine alpha interferon gene (MuIFN-alpha A) was isolated from a murine genomic DNA library in phage lambda. The gene was cloned and its sequence determined. It was expressed in Escherichia coli under the control of the trp promoter/operator which resulted in antiviral activity on mouse L-cells. MuIFN-alpha A exhibits 60% homology to HuIFN-alpha A at the amino acid level.

Molecular cloning of a Bacillus subtilis xylanase gene in Escherichia coli

A gene coding for xylanase synthesis in Bacillus subtilis was isolated by direct shotgun cloning using Escherichia coli as a host. Following partial digestion of B. subtilis chromosomal DNA with PstI or EcoRI restriction enzymes, fragments ranging from 3 to 7 kb were introduced into the PstI or EcoRI sites of pBR325. Transformed colonies having lost either the ampicillin or chloramphenicol resistance markers were screened directly on 1% xylan plates. Out of 8000 transformants, ten xylanase-positive clones were identified by the clearing zone around lysozyme-treated colonies. Further characterization of one of the clones showed that the xylanase gene was present in a 3.9-kb insert within the PstI site of the plasmid pBR325. Retransformation of E. coli strain with the xylanase-positive hybrid plasmid pRH271 showed 100% transformation to xylanase production. The intracellular xylanase produced by the transformed E. coli was purified by ion exchange and gel permeation chromatography. The electrophoretic mobility of the purified xylanase indicated an Mr of 22 000.

Isolation of the yeast structural gene for the membrane-associated enzyme phosphatidylserine synthase

The structural gene (CHO1) for phosphatidylserine synthase (CDPdiacylglycerol:L-serine O-phosphatidyltransferase, EC 2.7.8.8) was isolated by genetic complementation in Saccharomyces cerevisiae from a bank of yeast genomic DNA on a chimeric plasmid. The cloned DNA (4.0 kilobases long) was shown to represent a unique sequence in the yeast genome. The DNA sequence on an integrative plasmid was shown to recombine into the CHO1 locus, confirming its genetic identity. The cho1 yeast strain transformed with this gene on an autonomously replicating plasmid had significantly increased activity of the regulated membrane-associated enzyme phosphatidylserine synthase. Partial purification of phosphatidylserine synthase from microsomes of this transformed strain confirmed that the membrane-bound enzyme was overproduced 6- to 7-fold as compared with the wild-type strain. The strain also synthesized the product phospholipid, phosphatidylserine, at an increased rate. The transformed strain had altered proportions of a variety of other phospholipids, suggesting that their synthesis is affected by the rate of synthesis of phosphatidylserine in yeast.

U1 small nuclear RNA genes are located on human chromosome 1 and are expressed in mouse-human hybrid cells

The majority, and perhaps all, of the genes for human U1 small nuclear RNA (U1 RNA) were shown to be located on the short arm of human chromosome 1. These genes were mapped by Southern blot analysis of DNA from rodent-human somatic cell hybrids, using the 5' region of a human U1 RNA gene as a human-specific probe. This probe hybridized to DNA fragments present only in digests of total human DNA or to the DNAs of cell lines which contained human chromosome 1. The major families of human U1 RNA genes were identified, but some human genes may have gone undetected. Also, the presence of a few U1 RNA genes on human chromosome 19 could not be ruled out. In spite of the lack of extensive 5'-flanking-region homology between the human and mouse U1 RNA genes, the genes of both species were efficiently transcribed in the hybrid cells, and the U1 RNAs of both species were incorporated into specific ribonucleoprotein particles.

A gene affecting accumulation of the RNA moiety of the processing enzyme RNase P

The level of 10Sb (M1) RNA, the RNA of RNase P, is very low in growing cultures of rnpB mutants. Northern transfer experiments suggested that these strains accumulate no more than 10% of the wild-type level of 10Sb RNA. However, there is no indication that there is a limiting amount of RNase P activity in these mutants in vivo. A plasmid that directs the synthesis of 10Sb RNA does not complement the rnpB mutants, even though there is only a single gene for 10Sb RNA in the Escherichia coli genome. The 10Sb RNA synthesized from this plasmid is equivalent to wild-type 10Sb RNA since it can replace it in the reconstitution of RNase P. The 10Sb RNA, which is a rather stable molecule, is unstable in the presence of the rnpB mutation. This could explain why rnpB mutants do not accumulate 10Sb RNA. An F' plasmid that contains DNA from the rnpB region of the chromosome complements an rnpB mutant in vivo and in vitro, and it also contains the 10Sb RNA gene. A number of possible explanations for these phenomena are discussed.

Isolation of a functional exuR-repressor-beta-galactosidase hybrid protein by use of in vitro gene fusions

The exuR regulatory gene of Escherichia coli codes for a repressor molecule that controls negatively the expression of the exu regulon genes involved in the hexuronate degradation. The exuR gene was fused to the lacZ gene in vitro on plasmid cloning vectors developed by Casadaban et al. [J. Bacteriol. 143 (1980) 971-980]. The exuR-lacZ fusion gene allows the production of hybrid molecules possessing in a single polypeptide beta-galactosidase activity as well as the capacity to bind in vivo specifically to the operators of the exu operons. However, the affinity of ExuR hybrid protein for the exu operators seems to be reduced in comparison with the native repressor since, even overproduced in the cell, the chimeric polypeptide was not able to completely repress the expression of the exu operons. The other functions of the ExuR repressor, i.e., repression of the uxuAB operon and inactivation by the inducers, were not retained in the chimeric protein. This particular chimaera of Mr about 120 000 was purified by chromatography on phosphocellulose from strains carrying the fusion plasmids. The purified polypeptide was able to repress in vitro the synthesis of an exu gene product in a cell-free transcription and translation system. The implications of the repressor activity in the chimeric protein are discussed. The NH2-terminus of ExuR repressor probably recognizes the exu operators specifically, and this region represents less than 20% of the entire ExuR molecule.

Suppression of a VP1 mutant of simian virus 40 by missense mutations in serine codons of the viral agnogene

We isolated second-site revertants of a partially defective VP1 mutant of simian virus 40. The suppressing mutation in each of these pseudorevertants was mapped to the viral agnogene. Of six independently isolated pseudorevertants, all had a missense mutation in a serine codon, near the beginning of the agnogene, that would cause replacement of serine at position 7, 11, or 17 in the agnoprotein by a hydrophobic amino acid. Our results suggest that the agnoprotein interacts in a specific way with VP1 during the late stages of viral development.

A site-specific endonuclease essential for mating-type switching in Saccharomyces cerevisiae

We have detected two site-specific endonucleases in strains of Saccharomyces cerevisiae. One endonuclease, which we call YZ endo, is present only in yeast strains that are undergoing mating-type interconversion. The site at which YZ endo cleaves corresponds to the in vivo double-strand break occurring at the mating-type locus in yeast undergoing mating-type interconversion. YZ endo generates a site-specific double-strand break having 4-base 3' extensions terminating in 3' hydroxyl groups. The site of cleavage occurs in the Z1 region near the YZ junction of the mating-type locus. Mutant mating-type loci known to decrease the frequency of mating-type interconversion are correspondingly poor substrates for YZ endo in vitro. In vitro analysis of a number of such altered recognition sites has delimited the sequences required for cleavage. The molecular genetics of mating-type interconversion is discussed in the context of this endonucleolytic activity. The second endonuclease, which we refer to as Sce II, is present in all strains of S. cerevisiae we have examined. The cleavage site of Sce II has been determined and proves to be unrelated to the cleavage site of YZ endo.

The pattern of integration of viral DNA sequences in the adenovirus 5-transformed human cell line 293

The pattern of integrated adenovirus 5 DNA in the adenovirus 5-transformed human cell line 293 was analyzed by DNA blot hybridization. In contrast to a previous report, only sequences from the left end of the genome were detected. The viral DNA was contained in a unique DNA fragment generated by cleavage of 293 DNA with either EcoRI or BamHI, two enzymes which do not cut the integrated viral DNA. Further mapping studies indicated that the integrated sequence was probably colinear with viral DNA. The joining to host cell sequences occurred between viral nucleotide base pairs 1 and 270 (a site for BalI) on one end and 4123 (SmaI site) and 5372 (BalI site) at the other end. The viral DNA was not tandemly repeated. These results suggest that integration of viral sequences into the host genome probably occurred at a single site. If any subsequent duplications of viral DNA took place, then duplication of extensive cellular sequences also must have occurred.

Transcription renders chromatin resistant to micrococcal nuclease digestion

When isolated HeLa cell nuclei were preincubated under transcription conditions with excess E. coli RNA polymerase, chromatin DNA became relatively resistant to digestion by micrococcal nuclease. Quantitation of the DNA content in nuclei after enzyme digestion revealed that approximately twice as much nuclease was required to give the same levels of release of DNA fragments from transcribed as from untranscribed nuclei. Resistance increased with the amount of polymerase and with the time of preincubation. Since the resistance to nuclease was not observed in the presence of rifampicin or by preincubation without UTP, both RNA chain initiation and elongation were considered to be essential for the manifestation of resistance. However, when DNase 1 was used as a probe, such a change in chromatin DNA was not detected.

Complex organization of a cryptic satellite DNA in the genome of the marine invertebrate Rapana thomasiana Grosse (Gastropoda)

Isopicnic centrifugation in Cs2SO4-Ag+ gradients at pH 7.0 reveals that the genome of the marine snail Rapana thomasiana Grosse (Gastropoda) contains an AT-rich satellite fraction comprising 5% of the DNA. Restriction enzyme analysis shows that the satellite DNA is composed of a number of related subsets arranged in tandem arrays. They have evolved from the segmental amplification of an 1460 bp long monomer unit with a complex inner organization. Most probably, the present basic repeat originates from an ancestral 400-500 bp long sequence in which some insertions and/or deletions have occurred.

Cloning and expression of a porcine prorelaxin gene in E. coli

A porcine prorelaxin gene has been constructed partly by synthetic means and partly from its natural messenger RNA. A gene coding for the 32 N-terminal amino acids including a chain initiator methionine codon (B gene) was synthesised and inserted in a plasmid at a site downstream from a tryptophan promoter in such a way that its expression is under the control of the trp promoter. DNA corresponding to the rest of the prorelaxin was prepared using reverse transcriptase extension of a primer complementary to relaxin mRNA and joined at a suitable restriction site to the B gene. Transformation of E. coli with this plasmid followed by suitable induction resulted in the synthesis of a new protein identified as prorelaxin by its size and its antigenic similarity to relaxin.