A simple method for DNA restriction site mapping

Molecular structure and genetic stability of human hypoxanthine phosphoribosyltransferase (HPRT) gene duplications

We have determined the genetic stability of three independent intragenic human HPRT gene duplications and the structure of each duplication at the nucleotide sequence level. Two of the duplications were isolated as spontaneous mutations from the HL60 human myeloid leukemia cell line, while the third was originally identified in a Lesch-Nyhan patient. All three duplications are genetically unstable and have a reversion rate approximately 100-fold higher than the rate of duplication formation. The molecular structures of these duplications are similar, with direct duplication of HPRT exons 2 and 3 and of 6.8 kb (HL60 duplications) or 13.7 kb (Lesch-Nyhan duplication) of surrounding HPRT sequence. Nucleotide sequence analyses of duplication junctions revealed that the HL60-derived duplications were generated by unequal homologous recombination between clusters of Alu repeats contained in HPRT introns 1 and 3, while the Lesch-Nyhan duplication was generated by the nonhomologous insertion of duplicated HPRT DNA into HPRT intron 1. These results suggest that duplication substrates of different lengths can be generated from the human HPRT exon 2-3 region and can undergo either homologous or nonhomologous recombination with the HPRT locus to form gene duplications.

Cloning and expression of the canine interferon-gamma gene

The canine interferon-gamma (cIFN-gamma) chromosomal gene was isolated from a recombinant library, containing the entire dog genome, by screening with a rat IFN-gamma genomic probe. The structural organization of the cIFN-gamma gene closely resembles that of the human, murine, and rat IFN-gamma genes. It contains three intervening sequences and encodes a signal sequence of 23 amino acids followed by a mature protein of 143 amino acids. Two potential N-glycosylation sites are located at positions 16 and 83 of the mature protein. Comparison of the cIFN-gamma protein sequence with that of the corresponding murine, rat, human, and bovine proteins revealed a homology of 40%, 42%, 65%, and 76%, respectively. The cIFN-gamma gene was expressed under control of the simian virus 40 early promoter in Chinese hamster ovary (CHO) cells, deficient in dihydrofolate reductase (DHFR), after cotransformation with a plasmid containing the murine dhfr gene. Initial transformants with dhfr+ phenotype produced cIFN-gamma titers ranging from 10 to 10,000 laboratory units (LU)/ml of culture medium. A cIFN-gamma cDNA sequence was identified in a cDNA library constructed with partially purified RNA from a cIFN-gamma-producing CHO cell line. In vitro transcription of the cDNA and translation of the mRNA in Xenopus laevis oocytes resulted in secreted IFN-gamma with an antiviral activity specific for canine cells.

Genetic linkage analysis of bipolar affective disorder in an Old Order Amish pedigree

We have used genetic linkage analysis in an effort to identify a gene responsible for bipolar affective disorder (BAD) in an Old Order Amish pedigree. The initial study of this pedigree showed strong evidence for linkage of the chromosome 11p15 markers HRAS1 and the insulin gene (INS) to BAD, whereas a second report found no evidence for linkage. We have independently determined the INS and HRAS1 genotypes from 81 individuals in this pedigree. A polymerase chain reaction (PCR) assay was used to score INS alleles that are difficult to distinguish from one another by conventional agarose gel electrophoresis. In addition, we used four separate diagnostic models to score individuals with psychiatric illness as either affected or unaffected. No evidence of significant linkage between BAD and the markers was found with either two-point or multipoint analysis regardless of which diagnostic model was used. However, exclusion of the region of chromosome 11 between INS and RAS1 as a possible location for the BAD gene in this family depended on the diagnostic model. Further genetic linkage studies with additional DNA markers that span the genome are necessary to determine the chromosomal location of the BAD gene in this family.

Murine fumarylacetoacetate hydrolase (Fah) gene is disrupted by a neonatally lethal albino deletion that defines the hepatocyte-specific developmental regulation 1 (hsdr-1) locus

Homozygous deletion of the hepatocyte-specific developmental regulation 1 (hsdr-1) locus in mouse chromosome 7 results in perinatal death and a pleiotropic syndrome characterized by ultrastructural abnormalities of the liver and kidney, failure of induction of a number of specific transcription units in the liver and kidney during late gestation, and marked overexpression of an enzyme that defends against oxidative stress. Previously, the breakpoints of two albino (c) deletions (c14CoS and c1FAFyh) that genetically define hsdr-1 were localized, on a long-range map, in the vicinity of the distal breakpoint of a viable albino deletion (c24R75M) that breaks proximally within the c locus. Here we report the use of a probe derived from a deletion breakpoint fusion fragment cloned from c24R75M/c24R75M DNA to clone a breakpoint fusion fragment caused by the c14CoS deletion. The proximal breakpoint of the c14CoS deletion was discovered to disrupt a gene (Fah) encoding fumarylacetoacetate hydrolase, the last enzyme in the tyrosine degradation pathway. All of the extant c deletions eliciting the hsdr-1 phenotype prevent expression of the Fah gene in the liver, and all but one disrupt the coding segment of the gene. Therefore, the Fah gene maps within or proximal to the hsdr-1 locus, as defined by deletion breakpoints, and disruption of this gene may be partially or completely responsible for the phenotypes associated with the hsdr-1 deletion syndrome. These mouse mutants may also provide models for the human genetic disorder hereditary tyrosinemia, which is associated with fumarylacetoacetate hydrolase deficiency and liver and kidney dysfunction.

Molecular analysis of human chromosome 16 cosmid clones containing NotI sites

To test the feasibility of using cloned NotI sites as markers for physical mapping, we have screened for cosmid clones spanning the NotI sites on human Chromosome (Chr) 16. Fluorescence in situ hybridization analysis of these clones confirms the previously reported cluster of NotI sites on 16p13.3. Methylation status of the cloned NotI sites on genomic DNA was established by hybridization of the cosmids to Southern blots containing EcoRI and EcoRI/NotI digest of genomic DNA. These results indicated that four of six clones included in our study can be used as linking clones for physical mapping. Two clones have NotI sites which are not cleavable in the cell lines tested. In one clone, the NotI site exists as an isolated rare-cutting restriction enzyme site, whereas in the other clone the NotI site appears to be island-related.

Physical and biochemical characterization of the cloned LYS5 gene required for alpha-aminoadipate reductase activity in the lysine biosynthetic pathway of Saccharomyces cerevisiae

The LYS5 and LYS2 genes of Saccharomyces cerevisiae are required for the synthesis of alpha-aminoadipate reductase in the lysine pathway. The LYS5 gene, originally cloned as a DNA insert of the plasmid pSC5, has been subcloned on a 3.2 kb SphI-Sau3AI DNA fragment of the recombinant plasmid pSR7. An internal 2.1 kb HpaI-HpaI DNA fragment of the subclone, upon Southern hybridization, exhibits homology with HpaI-restricted wild-type S. cerevisiae genomic DNA. The lys5+ transformants exhibited alpha-aminoadipate reductase activity similar to that of wild-type cells. S1 nuclease analysis localizes the transcription initiation site relative to the detailed restriction map, and reveals the direction of transcription, as well as the transcript size of the LYS5 gene which can be no greater than 1.65 kb. From this it is estimated that the encoded polypeptide is appreciably smaller than the 4 kb LYS2 gene product. These results provide a physical and biochemical characterization of the cloned LYS5 gene. Based on these observations, it is concluded that the LYS5 gene encodes a relatively small polypeptide of the large heteropolymeric alpha-aminoadipate reductase.

Long-range physical map of the Ly-6 complex: mapping the Ly-6 multigene family by field-inversion and two-dimensional gel electrophoresis

The Ly-6 proteins are encoded by a recently identified multigene family. Much attention has been focused on these proteins because they may be involved in lymphocyte activation, and expression of some of them occurs at critical times in the differentiation of lymphocytes. These features make it important to investigate and to characterize further this family of molecules and the genes that encode them. To aid our investigation of these issues, we have constructed a physical map of the entire Ly-6 complex in the C57BL/6 murine genome using the combined techniques of field-inversion gel electrophoresis (FIGE), phage and cosmid genomic library screening, and two-dimensional DNA electrophoresis. This map spans approximately 1600 kb, and comparison of the FIGE map and cosmids indicates that most of the Ly-6 complex has been isolated in the cosmid clones.

Polymerase chain reaction primers and probes derived from flagellin gene sequences for specific detection of the agents of Lyme disease and North American relapsing fever

By cloning and sequencing the flagellin gene of Borrelia hermsii and comparing this sequence with that of the corresponding gene from B. burgdorferi, I identified a central region within the two genes which showed a reduced level of sequence similarity. Oligonucleotide sequences selected from this region produced species-specific amplimers when used in polymerase chain reaction experiments. Thus, primers derived from the B. burgdorferi sequence amplified a 276-bp fragment from 22 strains of B. burgdorferi of diverse geographic origin but not from 5 strains of B. hermsii, 5 other Borrelia species, 16 Treponema, Leptospira, and Spirochaeta species, or representatives of 10 other bacterial genera. However, when the amplified fragments were tested for hybridization with an oligonucleotide probe derived from the nonhomologous region, seven strains from either Germany or Switzerland did not hybridize. Cloning and sequencing of the amplified fragments from these strains revealed that the 22 strains of B. burgdorferi tested could be divided into three groups based on the nucleic acid sequence of the central region of the flagellin gene. With this information, oligonucleotide probes that hybridized to the amplified fragments and were able to differentiate the three groups of B. burgdorferi were designed. The corresponding primers, derived from the B. hermsii gene sequence, were tested for their ability to amplify DNA from this collection of strains. Although no amplification was obtained with representatives of the three groups of B. burgdorferi or various Treponema, Leptospira, and Spirochaeta species, amplification was obtained with the five other Borrelia species (B. parkeri, B. turicatae, B. crocidurae, B. anserina, and B. coriaceae) in addition to the five strains of B. hermsii. Sequencing of the amplified fragments from one strain of B. hermsii as well as B. parkeri and B. turicatae allowed the design of oligonucleotide probes that were able to differentiate the three species of North American relapsing fever spirochetes into two separate groups. These studies suggest that there is sufficient diversity within the flagellin gene sequences of closely related Borrelia species to differentiate them into groups and to pursue taxonomic studies both within and between species.

Detailed physical map and set of overlapping clones covering the genome of the archaebacterium Haloferax volcanii DS2

An integrated approach of "bottom up" and "top down" mapping has produced a minimal set of overlapping cosmid clones covering 96% of the 4140 kilobase-pairs (kbp) Haloferax volcanii DS2 genome and a completely closed physical map. This genome is partitioned into five replicons: a 2920 kbp chromosome and four plasmids, of 690 kbp (pHV4), 442 kbp (pHV3), 86 kbp(pHV1) and 6.4 kbp (pHV2). A restriction map for six infrequently-cutting restriction enzymes was constructed, representing a total of 903 sites in the cloned DNA. We have placed the two ribosomal RNA operons, the genes for 7 S RNA and for RNaseP RNA and 22 protein-coding genes on the map. Restriction site frequencies show significant variation in different portions of the genome. The regions of high site density correspond to halobacterial satellite or FII DNA which includes two small regions of the chromosome, the plasmids pHV1 and pHV2, and half of pHV4, but not pHV3.

The organization, localization and nucleotide sequence of the histone genes of the midge Chironomus thummi

Several histone gene repeating units containing the genes for histones H1, H2A, H2B, H3 and H4 were isolated by screening a genomic DNA library from the midge Chironomus thummi ssp. thummi. The nucleotide sequence of one complete histone gene repeating unit was determined. This repeating unit contains one copy of each of the five histone genes in the order and orientation mean value of H3 H4 mean value of H2A H2B H1 mean value of. The overall length is 6262 bp. The orientation, nucleotide sequence and inferred amino acid sequence as well as the chromosomal arrangement and localization are different from those reported for Drosophila melanogaster. The codon usage also shows marked differences between Chironomus and Drosophila. Thus the histone gene structure reported for Drosophila is not typical of all insects.

Construction and characterization of a NotI-BsuE linking library from the human X chromosome

We describe the construction and characterization of methylation-resistant sequence-tagged NotI linking clones specific for the X chromosome, referred to as NotI-BsuE linking clones. The approach consists of methylating the X-chromosome-specific cloned DNA with BsuE methylase (M. BsuE), an enzyme that methylates the first C residue in the CGCG sequence, followed by selection of the methylation-resistant NotI sites by insertion of a kanamycin-resistance gene in the clones cleavable by NotI. The frequent occurrence of NotI sites in CpG islands is expected to cause methylation of a large number of NotI sites with BsuE methylase, thereby rendering them resistant to NotI cleavage. Thus, the combination of M. BsuE and NotI yields less frequent cutting than the NotI alone. We have isolated, partially sequenced, and characterized 113 NotI-BsuE linking clones, and mapped 50 clones to various regions along the chromosome.

Chromosome structure: DNA nucleotide sequence elements of a subset of the minichromosomes of the protozoan Trypanosoma brucei

The genome of the protozoan Trypanosoma brucei contains a set of about 100 minichromosomes of about 50 to 150 kb in size. The small size of these chromosomes, their involvement in antigenic variation, and their mitotic stability make them ideal candidates for a structural analysis of protozoan chromosomes and their telomeres. We show that a subset of the minichromosomes is composed predominantly of simple-sequence DNA, with over 90% of the length of the minichromosome consisting of a tandem array of 177-bp repeats, indicating that these molecules have limited protein-coding capacity. Proceeding from the tip of the telomere to a chromosome internal position, a subset of the minichromosomes contained the GGGTTA telomere repeat, a 29-bp telomere-derived repeat, a region containing 74-bp G + C-rich direct repeats separated by approximately 155 bp of A + T-rich DNA that has a bent character, and 50 to 150 kb of the 177-bp repeat. Several of the minichromosome-derived telomeres did not encode protein-coding genes, indicating that the repertoire of telomeric variant cell surface glycoprotein genes is restricted to some telomeres only. The telomere organization in trypanosomes shares striking similarities to the organization of telomeres and subtelomeres in humans, yeasts, and plasmodia. An electron microscopic analysis of the minichromosomes showed that they are linear molecules without abnormal structures in the main body of the chromosome. The structure of replicating molecules indicated that minichromosomes probably have a single bidirectional origin of replication located in the body of the chromosome. We propose a model for the structure of the trypanosome minichromosomes.

Purification of BsuE methyltransferase and its application in genome mapping

We have used a combination of BsuE methyltransferase (M-BsuE) and NotI restriction enzyme to cut genomic DNA at a subset of NotI sites. The usefulness of this system is shown in a re-examination of the restriction map of the human MHC. Combinations of methylases and restriction enzymes can be used to generate cuts at different frequencies in genomic DNA, such that they generate ends complementary to NotI ends, and can be used in conjunction with NotI linking clones in chromosome jumping experiments. These enzyme combinations have the potential to produce cutting sites in genomic DNA spaced at intervals favorable for extensive mapping, fragment enrichment, and cloning efforts.

Chromosome structure: DNA nucleotide sequence elements of a subset of the minichromosomes of the protozoan Trypanosoma brucei

The genome of the protozoan Trypanosoma brucei contains a set of about 100 minichromosomes of about 50 to 150 kb in size. The small size of these chromosomes, their involvement in antigenic variation, and their mitotic stability make them ideal candidates for a structural analysis of protozoan chromosomes and their telomeres. We show that a subset of the minichromosomes is composed predominantly of simple-sequence DNA, with over 90% of the length of the minichromosome consisting of a tandem array of 177-bp repeats, indicating that these molecules have limited protein-coding capacity. Proceeding from the tip of the telomere to a chromosome internal position, a subset of the minichromosomes contained the GGGTTA telomere repeat, a 29-bp telomere-derived repeat, a region containing 74-bp G + C-rich direct repeats separated by approximately 155 bp of A + T-rich DNA that has a bent character, and 50 to 150 kb of the 177-bp repeat. Several of the minichromosome-derived telomeres did not encode protein-coding genes, indicating that the repertoire of telomeric variant cell surface glycoprotein genes is restricted to some telomeres only. The telomere organization in trypanosomes shares striking similarities to the organization of telomeres and subtelomeres in humans, yeasts, and plasmodia. An electron microscopic analysis of the minichromosomes showed that they are linear molecules without abnormal structures in the main body of the chromosome. The structure of replicating molecules indicated that minichromosomes probably have a single bidirectional origin of replication located in the body of the chromosome. We propose a model for the structure of the trypanosome minichromosomes.

Vectors containing infrequently cleaved restriction sites for use in BAL 31 nuclease-assisted and end-label-mediated analysis of cloned DNA fragments

Cloning vectors derived from plasmids pUC8 and pUC18 and phage M13mp10 were constructed so as to have multiple cloning sites (MCS) flanked by the recognition/cleavage sites for the Sfi I and Not I restriction nucleases. Cleavage of vectors containing cloned DNA fragments with either of the infrequently cleaving Sfi I or Not I endonucleases will usually yield linear DNAs cleaved only at the corresponding site in the MCS, so that the cloned insert can be degraded unidirectionally by the duplex exonuclease activity of the BAL 31 nucleases until an amount equal to the length of the vector has been degraded. The ends of the above constructs resulting from cleavage with Not I or Sfi I can readily be labeled, with labeling at only the terminus of the cloned DNA available for the Sfi I site. The BAL 31 nuclease-mediated procedures enhance a previous technique for mapping of restriction enzyme fragments, allow for localization of sequences in cloned segments for which a probe is available, and improve a method for sequencing cloned inserts through the production of sets of nested unidirectional deletions from either end of the parent cloned fragment. The advantages of end-label-mediated restriction site mapping using the above vectors over existing such procedures are also demonstrated.

Tn5cos: a transposon for restriction mapping of large plasmids using phage lambda terminase

A method for the rapid restriction mapping of large plasmids has been developed. A 400-bp fragment of phage lambda DNA containing the cos region has been inserted into Tn5. After in vivo transposition of this Tn5cos element into the plasmid of choice, the plasmid is isolated and linearized at its cos site with phage lambda terminase (Ter). Such Ter linearization was about 70% efficient. After partial digestion of the linear molecules with the appropriate restriction enzyme, the products are selectively labelled at the right or left cohesive phage lambda DNA termini by hybridization with digoxygenin (DIG)-11-dUTP-labelled (using terminal transferase) oligodeoxyribonucleotides complementary to the single-stranded cos ends. After pulsed field gel electrophoresis, the labelled fragments are visualized in the dried gel using a DIG-detection kit. The restriction map can be directly determined from the 'ladder' of partial digestion products.

Application of methylase-limited partial NotI cleavage for a long-range restriction map of the human ABL locus

The use of partial restriction digests for mapping complex genomes by pulsed-field gel electrophoresis has been limited by the difficulty of consistently obtaining these digests in agarose, which is a necessary matrix for high-molecular-weight DNA. Enzyme cleavage in agarose is faster then diffusion for most of the enzymes which cleave infrequently. We have developed a method for the production of partial digests in agarose for the endonuclease NotI (5' . . . GC/GGCCGC . . . 3') which circumvents the diffusion problem by using the blocking methylase M. BspRI (5' . . . GGmCC . . . 3'), which competes for the same sites. Using various ratios of the methylase and endonuclease results in partial digests in any size range desired. We report the successful application of this technique to the production of NotI partial digests of human genomic DNA for the mapping of the ABL locus of human chromosome 9.

Tandem arrangement of tRNA(Asp)-encoding genes in Phytophthora spp

We have cloned a region of repetitive DNA from the phytopathogenic fungus, Phytophthora parasitica. The cloned region consists of 17 highly homologous units arranged in tandem. The consensus sequence is 562 bp long and carries the information for a tRNA(Asp). All sequence motifs required for efficient RNA polymerase III transcription are present, and the tRNA derived from the nucleotide sequence is able to form a complete cloverleaf structure with high homology to previously characterized tRNA(Asp) molecules. The isolated tRNA(Asp) gene cluster is located at a distance of 20 kb from the TRP1 gene of P. parasitica. It comprises about 0.1% of the total genomic DNA. Similar clusters were detected in four other Phytophthora species.

Repeats and subrepeats in the intergenic spacer of rDNA from the nematode Meloidogyne arenaria

Ribosomal DNA (rDNA) repeats of the plant-parasitic nematode Meloidogyne arenaria are heterogeneous in size and appear to contain 5S rRNA gene sequences. Moreover, in a recA+ bacterial host, plasmid clones of a 9 kb rDNA repeat show deletion events within a 2 kb intergenic spacer (IGS), between 28S and 5S DNA sequences. These deletions appear to result from a reduction in the number of tandem 129 bp repeats in the IGS. The loss of such repeats might explain how rDNA length heterogeneity, observed in the Meloidogyne genome, could have arisen. Each 129 bp repeat also contains three copies of an 8 bp subrepeat, which has sequence similarity to an element found in the IGS repeats of some plant rDNAs.

Structure of the chromosomal gene and cDNAs coding for lactase-phlorizin hydrolase in humans with adult-type hypolactasia or persistence of lactase

Lactase-phlorizin hydrolase (LPH) splits lactose in the small intestine. LPH activity is high in the suckling; in many human populations the activity declines in adults, leading to adult-type hypolactasia, whereas in other populations the high LPH activity persists in adults. In the present work, we compared LPH sequences at the gene and cDNA level among adult subjects with high and low LPH activity. The complete intron-exon organization, including the sequences of all 17 exons and of the borders of all introns (as well as about 1,000 bp of 5' flanking region), was established for the cloned chromosomal LPH gene of a subject with persistence of lactase. Using PCR, we directly sequenced the exons of a hypolactasic subject. Except for silent mutations and the unknown linkage phase at two heterozygous positions, both coding sequences were identical. We further examined the LPH mRNA of a hypolactasic subject by S1 mapping and by sequencing a set of overlapping PCR products produced from cDNA templates. Except for allelic differences, the LPH sequence of the hypolactasic subject was identical to that of the LPH cDNAs of three subjects with persistence of lactase (one cDNA isolated previously by cloning and two characterized in the present work by PCR). No allele was peculiar to the hypolactasic subject. We conclude that humans with high or low levels of lactase can code for identical LPH enzymes.

A chimpanzee-derived chromosome-specific alpha satellite DNA sequence conserved between chimpanzee and human

We describe a cloned 2.7 kb alpha satellite sequence, Pan-3, from the pygmy chimpanzee (Pan paniscus) that specifically hybridizes in situ to chromosome 19 in the pygmy chimpanzee and to the homeologous human chromosome, no. 17. Using high stringency conditions of hybridization on Southern blots, this sequence hybridized to DNA from both species of chimpanzee (P. paniscus and P. troglodytes) and from human but not to DNA from gorilla (Gorilla gorilla) or orangutan (Pongo pygmaeus). Partial sequence analysis showed that Pan-3 and a previously described human chromosome 17-specific clone have up to 91% sequence identity. To our knowledge this is the highest sequence similarity reported between alphoid subsets from human and any other primate.

Enzymatic cleavage of a bacterial chromosome at a transposon-inserted rare site

The sequential use of the methylase M.Xbal (5'.TCTAGm6A) and the methylation-dependent endonuclease Dpnl (5'-Gm6A decreases TC) results in cleavage at 5'.TCTAGA decreases TCTAGA. This recognition sequence was introduced into a transposon derived from the Mu bacteriophage and transposed into the genome of the bacterium Salmonella typhimurium. M.Xbal methylation was provided in vivo by a plasmid containing the M.Xbal gene and the S. typhimurium genome was cleaved to completion by Dpnl at one or more sites, depending on the number of transposon insertions. The resulting genomic fragments were resolved by pulsed-field electrophoresis. The potential use of single M.Xbal/Dpnl cleavage sites as reference positions to map rare restriction sites is discussed.

Characterization and rapid analysis of the highly polymorphic VNTR locus D4S125 (YNZ32), closely linked to the Huntington disease gene

The highly polymorphic VNTR locus pYNZ32 has been more extensively characterized, and its analysis converted to a rapid PCR-based format. DNA sequencing in the areas within and flanking the repeated segment allowed the design of specific amplification primers. The repeated region of pYNZ32 consists of an imperfectly duplicated 27-bp motif, 16 bases of which are more highly conserved. Allelic products from PCR amplification were resolved into nine different size classes ranging from approximately 1400 to 2200 bp. Additional polymorphism was revealed when the amplified products were analyzed by restriction enzyme digestion. Both the overall size variation and the internal sequence polymorphism were used to determine a heterozygosity value of 86% for YNZ32 in 50 unrelated individuals. The rapid analysis and improved resolution of amplified alleles on agarose gels, and the internal variability within YNZ32, increase its diagnostic utility as a VNTR and as a linkage marker for the nearby Huntington disease gene.

Transcription regulates oxolinic acid-induced DNA gyrase cleavage at specific sites on the E. coli chromosome

Prominent DNA gyrase-mediated cleavage sites, induced by oxolinic acid, occur at specific, but infrequent, locations on the Escherichia coli chromosome. These sites, which we call toposites, may represent high affinity DNA gyrase binding sites or may mark chromosomal regions that accumulate superhelical stress. Toposites are usually grouped in 5 to 10 kb clusters that are mostly 50 to 100 kb apart. The total number of clusters on the chromosome is between 50 and 100. The location of sites depends on the local sequence. The extent of DNA gyrase cleavage at toposites can be strongly modulated by transcription occurring at as far as 35 kb away.

Production of Streptomyces clavuligerus isopenicillin N synthase in Escherichia coli using two-cistron expression systems

Streptomyces clavuligerus isopenicillin N synthase (IPNS) gene expression was achieved in Escherichia coli by the construction of two-cistron expression systems formed in the high copy number plasmid vector pUC119. These two-cistron constructions were composed of the IPNS gene and its flanking sequences which encoded an upstream open reading frame (ORF), the IPNS ribosome binding site and a putative transcription terminator. No E. coli- like Streptomyces promoter motif was present upstream of the IPNS gene therefore transcriptional regulation of the two-cistron system was provided by the lac promoter of pUC119. Enzymatically active IPNS was detected in E. coli cells harboring the recombinant plasmids thereby providing evidence for the activity of the IPNS ORF and for the feasibility of production of S. clavuligerus IPNS in E. coli. These results indicate that simple two-cistron constructions involving foreign gene flanking sequences may be used to express foreign proteins in E. coli.

Analysis of expression and evolutionary relationships of phosphoenolpyruvate carboxylase genes in Flaveria trinervia (C4) and F. pringlei (C3)

Phosphoenolpyruvate carboxylase (PEPCase) was shown to be encoded by a multigene family in various Flaveria species analysed. Several clones were isolated from genomic libraries of F. pringlei (C3 species) and F. trinervia (C4 species) and classified into four distinct groups according to their hybridization behaviour to a full-length cDNA clone encoding the PEPCase C4 isozyme of F. trinervia. A detailed cross-hybridization analysis demonstrated that the closest relative of most of the PEPCase genes isolated from F. trinervia and F. pringlei was not found in the same but in the other species. Northern analysis, using stringent conditions, allowed discrimination of class-specific PEPCase transcripts and revealed characteristic organ-specific expression patterns.

Restriction mapping of recombinant lambda DNA molecules using pulsed field gel electrophoresis

We have integrated pulsed field gel electrophoresis with the partial digestion strategy of Smith and Birnstiel (1976, Nucleic Acids Res. 3,2387-2398) to generate a rapid and accurate method of restriction endonuclease mapping recombinant lambda DNA molecules. Use of pulsed field gels dramatically improves the accuracy of size determination and resolution of DNA restriction fragments relative to standard agarose gels. Briefly, DNA is partially digested with restriction enzymes to varying extents and then hybridized with a radiolabeled oligonucleotide which anneals specifically to one of the lambda cohesive (cos) ends, effectively end labeling only those digestion products containing that cos end. In this study, we have used an oligonucleotide hybridizing to the right cos end. DNA is then fractionated by pulsed field gel electrophoresis, the gel dried down, and cos end containing fragments visualized by autoradiography. Fragment sizes indicate the distances from the labeled cos end to each restriction site for the particular restriction enzyme employed. This procedure requires only minimal quantities of DNA and is applicable to all vectors utilizing lambda cos ends.

Current methods for YAC clone characterization

Yeast artificial chromosome (YAC) cloning has allowed isolation of much longer DNA fragments than was previously possible. While this technology makes feasible the isolation of large regions of complex genomes in overlapping cloned segments, it has also required altered methods for manipulation of cloned DNAs. In particular, the isolation of insert sequences from YAC clones has been especially difficult. Methods for characterization of YAC inserts are described and compared.

A physical-genetic map of the lipid-containing bacteriophage PR4

A physical map of the bacteriophage PR4 genome was constructed which includes 59 sites for 10 restriction endonucleases. The average size of the phage PR4 genome estimated from the sum of DNA fragments generated with the restriction endonucleases Hphl, Mnll, Bgll, AlwNl, and BstXl is 15,170 +/- 240 bp. A collection of recombinant plasmids containing restriction fragments of PR4 DNA generated with Bgll, Hphl, Mnll, and Xmnl inserted into either the low copy number plasmid vector pHSG575 or the high copy number plasmid vector pUC19 was constructed. This collection of recombinant plasmids represents roughly 93% of the PR4 genome. We also constructed a bank of 136 recombinant plasmids containing PR4 DNA fragments resulting from Hpall partial digestion. We have localized 13 genes on the phage PR4 genome through marker rescue with these phage DNA clones. These genes include the structural genes for the major capsid protein (P2) and a nonstructural protein (P6A) implicated in virus assembly.

Isolation and sequence of the canine pancreatic phospholipase A2 gene

A genomic library has been constructed in EMBL3 lambda phage using high molecular mass DNA isolated from canine spleen. A cDNA clone, shown to code for preprophospholipase A2 which is processed to the prosecretory form prior to release from secretory cells, was used to identify a lambda clone which contains the complete phospholipase A2 gene. Restriction enzyme and DNA sequence analysis indicate that the primary transcriptional unit for the phospholipase gene, approximately 9.0 kb, is organized into four exon sequences. Exon 1 encodes the 5' nontranslated sequence, the ATG initiation codon, and the hydrophobic core of the signal peptide. Exons 2-4 encode regions of the peptide of residues -11 to 43, 43 to 86 and 86 to 124, respectively. The 5' flanking region shows a TATA box at position -29 and multiple CAAT boxes at positions -279, -206, -183 and -159. Regions of the 5' flanking sequence in the canine sequence, from nucleotides -47 to -74 and -91 to -129, show high similarity to similar regions in the human gene. However, an analysis of 400 nucleotides of the 5' flanking sequence in transient expression studies was unable to identify tissue-specific promoter or enhancer sequences. Within 5' nontranslated regions the canine and human genes share a pyrimidine-rich sequence which may be involved in differential regulation of mRNA translation.

Methylase-limited partial NotI cleavage for physical mapping of genomic DNA

Partial cleavage of DNA with the restriction endonuclease NotI (5'...GC/GGCCGC...3') is an important technique for genomic mapping. However, partial genomic cleavage with this enzyme is impaired by the agarose matrix in which the DNA must be suspended. To solve this problem we have purified the blocking methylase M. BspRI (5'...GGmCC...3') for competition digests with NotI. The resulting methylase-limited partial DNA cleavage is shown to be superior to standard techniques on bacterial genomic DNA.

ABBREVIATIONS

bp, base-pair; kb, one thousand base-pairs; Mb, one million base-pairs; Tris, Tris(hydroxy-methyl)aminomethane; EDTA, (ethylenedinitrilo)tetraacetic; beta-ME, beta-mercaptoethanol; PMSF, phenyl methyl-sulfonyl fluoride; PEG, polyethyleneglycol (MW = 8000); 3H, tritium; SAM, S-adenosylmethionine; KGB, potassium glutamate buffer; DTT, dithiothreitol; IPTG, isopropyl-beta-D-thiogalactopyranoside; BSA, bovine serum albumin.

Identification of tissue specific nuclear proteins: DNA sequence and protein binding regions in the T cell receptor beta J-C intron

We have determined the DNA sequences in the J2-C2 intron of the T cell receptor (TCR) beta gene and analyzed nuclear proteins binding to this region. Previously, we identified two tissue-specific DNase I hypersensitive regions, potential regulatory regions, in the J-C intron. The DNA sequence of the J2-C2 intron revealed that both DNase I hypersensitive regions have similar DNA sequences, suggesting that these regions are evolutionarily conserved. We have also identified tissue-specific nuclear-protein binding regions downstream of the DNase hypersensitive regions. Although transcriptional enhancer activity was not observed in the hypersensitive regions or the adjacent protein binding regions in the J-C intron, our findings suggest that the TCR-beta J-C intron may contain some other type of regulatory element.

Cloning and sequence analysis of linear plasmid telomeres of the bacterium Borrelia burgdorferi

Borrelia burgdorferi, the Lyme disease agent, has double-stranded linear plasmids with covalently closed ends. DNA at the ends, or telomeres, of two linear plasmids of B. burgdorferi strain B31 was examined. Telomeric sequences from both ends of a 16 kb linear plasmid and from one end of a 49 kb linear plasmid were cloned and sequenced. An 18 bp AT-rich inverted repeat was found at each end of the 16 kb linear plasmid. The sequences of the two ends of this plasmid were different beyond these short inverted terminal repeats. The cloned end of the 49 kb linear plasmid had sequence identity with one end of the 16 kb linear plasmid. The end sequence common to both plasmids contained a series of phased, short direct repeats and a 52 bp palindrome adjacent to a highly AT-rich region. These findings indicate that Borrelia linear plasmid telomeres have structural features different from those of other known replicons.

Multigene families in African swine fever virus: family 110

The genome of African swine fever virus was screened for the existence of repetitive sequences by hybridization between different cloned restriction fragments covering the viral DNA. Several sets of repeated sequences were detected in fragments located close to the DNA ends. One of these groups of repetitions involved fragments located at both ends of the genome. The remaining groups involved fragments that were located exclusively at the left end. The sequence of a 3.2-kilobase segment spanning from 7.5 to 11 kilobases from the left DNA end, which showed a complex pattern of cross-hybridizations, was determined. Two short and three long blocks of direct repeated sequences were found in this DNA region, which accounted for the hybridization results. The repeated sequences formed a family of five homologous genes with an average length of 116 codons (multigene family 110), one of which had a dimeric structure. Transcripts of the five members of the family were detected both in RNA synthesized in vitro by purified African swine fever virions and in RNA isolated at early times after infection. Comparison of the predicted protein sequences revealed a striking conservation of a cysteine-rich domain in the central part of the proteins. In addition, a highly hydrophobic NH2-terminal sequence present in all the proteins suggests that these proteins are processed through the endoplasmic reticulum.

Partial gene duplication involving exon-Alu interchange results in lipoprotein lipase deficiency

Major structural rearrangements are uncommon causes of mutation in human genetic diseases. We have previously described that a significant proportion of unrelated patients of western European descent who are deficient in lipoprotein lipase (LPL) activity have a major structural rearrangement in the LPL gene. Here we report the detailed characterization of this mutation. We show that this rearrangement is due to a duplication of approximately 2 kb which results from juxtaposition of intron 6 to a partially duplicated exon 6. We have sequenced both the junction fragment of this duplication and the corresponding wild-type regions and have found that the breakpoint in intron 6 is associated with the simple repeat found at the 3' end of an Alu element. The breakpoint within exon 6 shows no homology to this simple repeat. This result both suggests that this interchange arose as a nonhomologous recombination event and shows that such events resulting in duplication which occur in normal gene evolution may also lead to genetic disease. Cloning of the junction fragment has allowed synthesis of appropriate primers for rapid screening for this rearrangement in other families with LPL deficiency.

Simplified cosmid vectors for gene transfer to cultured mammalian cells: isolation of the gene for elongation factor 2 from the mouse

We constructed a series of cosmid vectors that carry two tandemly arranged lambda cos and mammalian selective markers. We achieved cloning efficiencies of 1-3 x 10(7) and greater than 10(6) colony-forming units per microgram of insert, using a cloned 42-kb BamHI fragment and Sau3AI fragments of 40-50 kb from mouse genomic DNA, respectively. The modified Ca.phosphate coprecipitation method [Ishiura et al., Mol. Cell. Biol. 2 (1982) 607-616] considerably improved the efficiency of gene transfer of cosmids into cultured mammalian cells: when genes encoding thymidine kinase from herpes simplex virus type 1 and aminoglycoside 3'-phosphoribosyltransferase from Tn5 were selected, the efficiencies of gene transfer into mouse L cells were about 10(-6). The mouse genome contains one copy of the functional gene for elongation factor 2 (EF2) per haploid genome and multiple copies of the EF2-related gene. We isolated a cosmid that carried functional full-length mouse EF2 from a cosmid library of L-cell genomic DNA, by colony hybridization and subsequent gene transfer of candidate cosmids into human 143B cells.

Primary structure and regulation of vegetative specific genes of Dictyostelium discoideum

We have examined the expression and structure of several genes belonging to two classes of vegetative specific genes of the simple eukaryote, Dictyostelium discoideum. In amebae grown on bacteria, deactivation of all vegetative specific genes occurred at the onset of development and very little mRNA exists by 8 to 10 hours. In contrast, when cells were grown in axenic broth, the mRNA levels remained constant until a dramatic drop occurred around 10 to 12 hours. Thus, regulation of both classes of genes during the first several hours of development is dependent upon the prior growth conditions. Analysis of genomic clones has resulted in the identification of two V genes, V1 and V18, as ribosomal protein genes. Several other V genes were not found to be ribosomal protein genes, suggesting that in Dictyostelium non-ribosomal protein genes may be coordinately regulated with the ribosomal protein genes. Finally, using deletion analysis we show that the promoters of two of the V genes are composed of a constitutive positive element(s) located upstream of sequences involved in the regulated expression of these genes and within the first 545 upstream bp for V18 and 850 bp for V14. The regions involved in regulated expression were localized between -7 and -222 for V18 and -70 and -368 for V14. The sequences conferring protein synthesis sensitivity were shown to reside between -502 and -61 of the H4 promoter.

The 5' end of U3 snRNA can be crosslinked in vivo to the external transcribed spacer of rat ribosomal RNA precursors

From previous work it was known that U3 RNA is hydrogen bonded to nucleolar 28 S to 35 S RNA and can be covalently crosslinked to RNA of greater than 28 S by irradiation in vivo with long-wave ultraviolet light in the presence of 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT psoralen). Here we use a novel sandwich blot technique to identify these large nucleolar RNA species as rRNA precursors and to map the site(s) of crosslinking in vivo. The crosslink occurs between one or more residues near the 5' end of U3 RNA and a 380 nucleotide region of the rat rRNA external transcribed spacer (ETS1). We have sequenced this region of the rat ETS and we show that it includes an RNA-processing site analogous to those previously mapped to approximately 3.5 kb upstream from the 5' end of mouse and human 18 S rRNAs.

Cloning of ligand-specific cell lines via gene transfer: identification of a D2 dopamine receptor subtype

Using rat genomic DNA, we have established a transfected mouse fibroblast cell line that expresses a spiperone binding site with the pharmacological characteristics of a D2 dopamine receptor. The expressed D2 receptors are the product of a gene that is distinct from that reported by Bunzow et al. [Bunzow, J. R., Van Tol, H. H. M., Granoly, D. K., Albert, P., Salon, J., Christie, M., Machida, C. A., Neve, K. A. & Civelli, O. (1988) Nature (London) 336, 783-787]. Flow cytometry with the Ca2+-sensitive dye indo-1 demonstrated that activation of the expressed D2 sites resulted in increases in intracellular calcium that were dependent on the influx of external Ca2+. These general cloning procedures should be applicable to the production of cell lines expressing a variety of genes for which only functional assays are available.

The DAL7 promoter consists of multiple elements that cooperatively mediate regulation of the gene's expression

Expression of the allantoin system genes in Saccharomyces cerevisiae is induced by allophanate or its analog, oxalurate. This work provides evidence for the involvement of distinct types of cis-acting elements in the induction process. The first element was found to have the properties of an upstream activation sequence (UAS). This element was localized to a 16-base-pair (bp) DNA fragment containing a short 5-bp sequence that occurred repeatedly in the upstream region of DAL7. When present in two or more copies, the 16-bp fragment supported high-level beta-galactosidase production in a CYC1-lacZ expression vector; there was, however, no response to the allantoin pathway inducer. The second element had the properties of a negatively acting element or upstream repression sequence (URS). This element was localized to a 16-bp DNA fragment containing an 8-bp sequence that was repeated four times in the upstream region of DAL7. A fragment containing the 8-bp repeated sequence placed adjacent to the UAS-containing fragment mediated inhibition of the ability of the UAS to support lacZ expression regardless of whether inducer was present. A third element, designated an upstream induction sequence (UIS), was required for response to inducer. The UIS was localized to a small DNA fragment containing an approximately 10-bp sequence that was repeated twice in the upstream region of DAL7. When a fragment containing the 10-bp repeated sequence was placed adjacent to these UAS and URS elements, the construction (UIS-UAS-URS) supported normal oxalurate-mediated induction of beta-galactosidase synthesis. These data are consistent with the suggestion that multiple, cis-acting elements participate in the induction process.

A versatile non-radioactive technique for restriction analysis of recombinant DNA

Restriction analysis of recombinant DNA is most frequently performed according to Smith and Birnstiel by labeling 5'-termini with 32P, followed by partial digestion, separation, and autoradiographic detection of labeled fragments. We describe a rapid, non-radioactive technique for restriction analysis of recombinant DNA which combines Southern blotting of partial restriction digests and hybridization with a vector-specific probe labeled with the steroid-hapten Digoxigenin for immunological detection. This technique has several advantages compared to conventional methods. Labeling with 32P is not necessary and as the labeled DNA-fragment used as probe is vector-specific, it can be applied for numerous constructs using the particular cloning vector (e.g.pBR322). Furthermore, the probe can be stored for several months and can be reused many times.

DNA amplification in Streptomyces achromogenes subsp. rubradiris is accompanied by a deletion, and the amplified sequences are conditionally stable and can be eliminated by two pathways

Southern blot analysis of BglII-digested DNA isolated from wild-type Streptomyces achromogenes, which harbors the 8.8-kilobase amplifiable unit of DNA, AUD-Sar 1, and of similarly digested DNA from 12 strains carrying an array of 200 to 300 tandem copies of a specific AUD-Sar 1-derived 8.0-kilobase DNA sequence, ADS-Sar 1, revealed the absence of the 12.4-kilobase BglII AUD-Sar 1-chromosome right junction band in the latter strains, whereas the corresponding 26.0-kilobase left junction band remained unaltered. Further Southern analyses indicated in all of the seven amplified strains tested the occurrence of a deletion of at least 10 kilobases of the DNA adjacent to the right side of the AUD. The deletion has one endpoint in the vicinity of the ADS array. Corroborating and expanding upon previously reported results, we found that the amplified DNA of strain C010 was stably maintained for at least 20 transfers when the transfers involved mycelia propagated in spectinomycin-free liquid medium. In contrast, when strain C010 was subjected separately to one cycle of protoplast formation and regeneration or to three cycles of spore germination, aerial mycelium formation, and sporulation on spectinomycin-free media, only approximately 20% of the protoplast regenerants and spores retained the reiterated DNA sequences and the ability subsequently to form colonies on media containing high levels of spectinomycin. Approximately 80% of these units completely deleted the reiterated DNA and left adjacent sequences and exhibited sensitivity to 25 micrograms of spectinomycin per ml. One among 24 protoplast-derived deletants apparently retained the left portion of the AUD-ADS left direct repeat plus left adjacent sequences.

DNA sequence and expression of the 36-kilodalton outer membrane protein gene of Brucella abortus

The cloning of the gene(s) encoding a 36-kilodalton (kDa) cell envelope protein of Brucella abortus has been previously described (T. A. Ficht, S. W. Bearden, B. A. Sowa, and L. G. Adams, Infect, Immun. 56:2036-2046, 1988). In an attempt to define the nature of the previously described duplication at this locus we have sequenced 3,500 base pairs of genomic DNA encompassing this region. The duplication represented two similar open reading frames which shared more than 85% homology at the nucleotide level but differed primarily because of the absence of 108 nucleotides from one of the two gene copies. These two genes were read from opposite strands and potentially encoded proteins which are 96% homologous. The predicted gene products were identical over the first 100 amino acids, including 22-amino-acid-long signal sequences. The amino acid composition of the predicted proteins was similar to that obtained for the Brucella porin isolated by Verstreate et al. (D. R. Verstreate, M. T. Creasy, N. T. Caveney, C. L. Baldwin, M. W. Blab, and A. J. Winter, Infect. Immun. 35:979-989, 1982) and presumably represented two copies of the porin gene, tentatively identified as omp 2a (silent) and omp 2b (expressed). The homology between the two genes extended to and included Shine-Dalgarno sequences 7 base pairs upstream from the ATG start codons. Homology at the 3' ends extended only as far as the termination codon, but both genes had putative rho-independent transcription termination sites. Localization of the promoters proved more difficult, since the canonical procaryotic sequences could not be identified in the region upstream of either gene. Promoter activity was demonstrated by ligation to a promoterless lacZ gene in pMC1871. However, only one active promoter could be identified by using this system. A 36-kDa protein was synthesized in E. coli with the promoter in the native orientation and was identical in size to the protein produced in laboratory-grown B. abortus. When the promoter-containing fragment was inverted, a 33-kDa protein was expressed. These results were consistent with the predicted sizes based on the nucleotide sequences of the open reading frames in omp 2b and omp 2a. Whether this locus contains one active and one silent or cryptic porin gene, or two active Brucella porin genes expressed under different environmental conditions, is discussed.