Unique Cloning Sites Research Articles

Replication of a geminivirus derived shuttle vector in maize endosperm cells

A maize (Zea mays L.) endosperm cell culture has been shown to efficiently replicate DNA sequences derived from wheat dwarf virus (WDV), a monopartite monocot geminivirus. To analyze sequences necessary for viral replication and to verify their application for a plant gene expression vector, we have developed a 3.7 kilobase pairs Escherichia coli--plant cell shuttle vector, pWI-11. The p15A origin of replication, functional in E. coli, was introduced into the viral sequences. We have replaced the coding region of the coat protein gene by that of bacterial neomycin phosphotransferase II (NPT II) gene. The resulting NPT II gene fusion can serve as a selectable marker in both plant and E. coli systems. Into a unique cloning site in this pWI-11 vector, we introduced a gene fusion carrying the bacterial beta-glucuronidase (GUS) coding region under control of the cauliflower mosaic virus 35S (CaMV35S) gene promoter and terminator. By transferring these viral sequences into protoplasts derived from maize endosperm cell cultures, we have demonstrated that the plasmid pWI-11 can replicate in maize endosperm cells, that the GUS reporter gene introduced into pWI-11 can be expressed at high level in the transformed cells, and that the replicating viral DNA can be rescued from endosperm cells by transforming E. coli in the presence of kanamycin. The level of GUS gene expression increased progressively in transformed endosperm cells during a prolonged culture period, coinciding with replication of the viral sequences in these cells.

Insertion of DNA Sequences at a Unique Restriction Enzyme Site Engineered for Vector Purposes into the Genome of Herpes Simplex Virus Type 1

We describe the construction of a novel herpes simplex virus (HSV) vector containing a unique XbaI restriction enzyme cloning site in an intergenic position in the short unique genome region. Sequences can be inserted at this site with high efficiency by ligation with XbaI-digested vector DNA. A series of plasmids has been designed for use with this vector. These allow protein coding sequences to be placed under the control of various transcriptional regulation signals and then isolated as XbaI fragments ready for insertion into the vector. The XbaI fragments also contain the beta-galactosidase gene thereby facilitating selection of recombinant virus by screening for blue plaques. A variant of the vector has been made based on the temperature-sensitive (ts) mutant tsK, which expresses only immediate early (IE) genes at non-permissive temperatures. Chloramphenicol acetyltransferase was used as a reporter gene to assess the fidelity of expression of sequences cloned into this position. Under these circumstances IE and early HSV promoters were shown to behave as expected in both wild-type and ts vectors.

Mini-Tn5 transposon derivatives for insertion mutagenesis, promoter probing, and chromosomal insertion of cloned DNA in gram-negative eubacteria

A collection of Tn5-derived minitransposons has been constructed that simplifies substantially the generation of insertion mutants, in vivo fusions with reporter genes, and the introduction of foreign DNA fragments into the chromosome of a variety of gram-negative bacteria, including the enteric bacteria and typical soil bacteria like Pseudomonas species. The minitransposons consist of genes specifying resistance to kanamycin, chloramphenicol, streptomycin-spectinomycin, and tetracycline as selection markers and a unique NotI cloning site flanked by 19-base-pair terminal repeat sequences of Tn5. Further derivatives also contain lacZ, phoA, luxAB, or xylE genes devoid of their native promoters located next to the terminal repeats in an orientation that affords the generation of gene-operon fusions. The transposons are located on a R6K-based suicide delivery plasmid that provides the IS50R transposase tnp gene in cis but external to the mobile element and whose conjugal transfer to recipients is mediated by RP4 mobilization functions in the donor.

Nucleotide sequence of the phage λgt11 SacI- KpnI lacZ region

The nucleotide sequence of the λgt11 SacI- KpnI region, surrounding the unique EcoRI cloning site, was directly determined. This sequence previously had to be compiled from several diverse sources. The direct sequence confirms the sequence predicted from the compilation and pinpoints other unique restriction enzyme targets in the region for use in subcloning.

Expression of foreign epitopes in P-fimbriae ofEscherichia coli

Hypervariable regions (HRs) of the major subunit of F11 fimbriae were exploited for insertion of foreign epitopes. Two insertion vectors were created that contain a unique cloning site in HR1 or HR4 respectively. Several oligonucleotides, coding for antigenic determinants derived from different pathogens, were cloned in both insertion vectors. Hybrid fimbrial subunits were generally shown to be assembled in fimbriae when the length of the inserted peptide did not exceed 14 amino acids. The inserted peptides appeared to be exposed in the fimbrial filament. One hybrid fimbrial protein induced detectable levels of antibodies against the inserted epitope if injected into mice.

Biological and immunological characterization of influenza virus haemagglutinin expressed from the haemagglutinin locus of vaccinia virus

Plasmid vectors were constructed to facilitate the insertion and expression of a foreign gene in the haemagglutinin (HA) gene locus of vaccinia virus. Five unique cloning sites adjacent to the P7.5 promoter of vaccinia virus permit the rapid insertion of a foreign sequence coding for a protein into these plasmids. This vector system provides a simple procedure to select recombinant viruses because they can be readily identified on the basis of their HA-defective phenotype. Recombinant vaccinia viruses expressing influenza virus HA were constructed to characterize the possible use of this system. The recombinant viruses did express the influenza HA through the authentic pathway of biosynthesis. In addition to having immunological characteristics similar to the authentic influenza HA, the expressed HA was found to possess haemagglutinating, haemadsorption and acid-inducible fusion activities. These findings demonstrate the usefulness of this eukaryotic vector system.

Vectors for constructing kan gene fusions: direct selection of mutations affecting IS 10 gene expression

We describe several vectors for constructing translational fusions to the kan gene of Tn5. Fusions are constructed in vitro using multi-copy vectors containing unique cloning sites situated between upstream transcriptional terminators and a downstream kan gene lacking transcriptional and translational start signals. Multi-copy fusions can be converted to single-copy chromosomal fusions by in vivo recombination with specific phage λ vectors and vice versa. We find that kan fusions are often more suitable than lacZ fusions for the direct selection of mutations that increase fusion expression. These vectors were developed for isolating mutations that increase IS 10 transposase expression; we describe strategies used to isolate such mutations, which map to IS 10 or the Escherichia coli himA, himD(hip), dam or infC genes.

An inducible expression vector for both fission and budding yeast

We have developed a vector system for inducible gene expression in both fission yeast ( Schizosaccharomyces pombe) and budding yeast ( Saccharomyces cerevisiae). The autonomously replicating expression vector contains multiple glucocorticoid response elements, rendering a linked promoter inducible 20–70-fold by glucocorticoid hormones in the presence of the mammalian glucocorticoid receptor. A polylinker with several unique cloning sites allows insertion of cDNAs of interest. Glucocorticoids are gratuitous signalling molecules in yeast, exerting little or no effect on the expression of genes other than those fused to the regulated promoter.

Expression vectors for quatitating in vivo translational ambiguity: Their potential use to analyse frameshifting at the HIV gag-pol junction

Translational errors are necessary so as to allow gene expression in various organisms. In retroviruses, synthesis of pol gene products necessitates either readthrough of a stop codon or frameshifting. Here we present an experimental system that permits quantification of translational errors in vivo. It consists of a family of expression vectors carrying different mutated versions of the luc gene as reporter. Mutations include both an in-frame stop codon and 1-base-pair deletions that require readthough or frameshift, respectively, to give rise to an active product. This system is sensitive enough to detect background errors in mammalian cells. In addition, one of the vectors contains two unique cloning sites that make it possible to insert any sequence of interest. This latter vector was used to analyse the effect of a DNA fragment, proposed to be the target of high level slippage at the gag-pol junction of HIV. The effect of paromomycin and kasugamycin, two antibiotics known to influence translational ambiguity, was also tested in cultured cells. The results indicate that paromomycin diversely affects readthrough and frameshifting, while kasugamycin had no effect. This family of vectors can be used to analyse the influence of structural and external factors on translational ambiguity in both mammalian cells and bacteria.

A new vector using the human multidrug resistance gene as a selectable marker enables overexpression of foreign genes in eukaryotic cells

A new vector, pSK1.MDR, has been constructed for expressing nonselectable genes in eukaryotic cells. The vector uses the human multidrug resistance gene, MDR1, as a dominant selectable marker and contains an additional transcription unit plus a unique SalI cloning site for inserting nucleotide sequences to be expressed. To test this expression system, a cDNA ( IL2R) for the 55-kDa interleukin-2 receptor was inserted into the SalI site, and the resulting plasmid was transfected into NIH3T3 cells. Cells which acquired the MDR1 gene were selected with colchicine, and cells with high levels of MDR1 expression were selected by growth in increasing concentrations of the drug. Drug resistant cells also expressed the cotransferred, nonselected IL2R gene, and its expression was increased to 740000 receptors per cell by growing cells in high concentrations of colchicine. The MDR1 system represents a very efficient method for synthesizing large amounts of protein in a wide variety of eukaryotic cells.

A new bacteriophage vector for cloning in Bacillus subtilis and the use of ø105 for protein synthesis in maxicells

Zabarovsky and Allikmets [Gene 42 (1986) 119–123] have described a cloning procedure based on partial filling-in of vector and target DNA cohesive ends, which strongly enriches for recombinant molecules with single insertions. Improved Bacillus subtilis bacteriophage ø105 vectors containing unique cloning sites for SalI have been constructed to take advantage of the partial fill-in method. The new vectors have been used to construct B. subtilis genomic libraries from which several sporulation loci have been isolated, including five not previously cloned. On inserting a promoterless lacZ gene into the cloning site, β-galactosidase (βGal) was detected at a late stage in lytic phage growth, indicating that phage transcription is directed through the cloning site. When UV-irradiated cells (‘maxicells’) were infected with the recombinant phage containing the lacZ gene, in the presence of labelled amino acids, a protein of the expected M r for βGal was visualised, in addition to the phage proteins. This system should provide a useful general approach for the identification of the products of cloned genes from B. subtilis and other Gram-positive organisms.

Expression of Human Thymidylate Synthase in Escherichia coli

A cDNA clone encoding thymidylate synthase (TS) has been isolated from a human T-cell library and modified in the 5'-untranslated region to incorporate several unique cloning sites. The gene has been cloned as a cassette into several Escherichia coli expression vectors which did not provide detectable amounts of the enzyme. A successful approach used a constitutive E. coli expression vector developed for the enzyme from Lactobacillus casei. A 115-base pair 5'-untranslated region from the L. casei TS which contains a ribosomal binding site and other regulatory sequences has been fused to the coding region of the human TS gene to provide a construct that is expressed in E. coli. The level of expression was further enhanced by altering the nucleotide sequence of the first 90 base pairs to accommodate common codon use in E. coli. In our best expression system, catalytically active human TS is expressed to a level that represents about 1.6% of the total soluble protein. The recombinant human TS has been purified and characterized; except for the presence of an amino-terminal blocking group, the enzyme has physical and kinetic properties similar to the enzyme isolated from human cells.

Transposon tagging using Ty elements in yeast.

We have used the ability to induce high levels of Ty transposition to develop a method for transposon mutagenesis in Saccharomyces cerevisiae. To facilitate genetic and molecular analysis, we have constructed GAL1-promoted TyH3 or Ty917 elements that contain unique cloning sites, and marked these elements with selectable genes. These genes include the yeast HIS3 gene, and the plasmid PiAN7 containing the Tn903 NEO gene. The marked Ty elements retain their ability to transpose, to mutate the LYS2, LYS5, or STE2 genes, and to activate the promoterless his3 delta 4 target gene. Ty elements containing selectable genes are also useful in strain construction, in chromosomal mapping, and in gene cloning strategies.

Smart2, a cosmid vector with a phage lambda origin for both systematic chromosome walking and P-element-mediated gene transfer in Drosophila.

We describe a new phage-lambda-replicon-based cosmid vector suitable for both chromosome walking and P-element-mediated transformation in Drosophila. Its unique BamHI cloning site is flanked by the promoters for the SP6 and T7-encoded RNA polymerases, permitting the synthesis of probes complementary to the ends of the cloned inserts for library screening. The selectable marker is tet for bacterial cell transformation and neo for Drosophila transformation expressed under the control of the Drosophila hsp70 promoter.

A set of small bacterial plasmids with unique cloning sites.

A set of small bacterial plasmids with unique cloning sites.

Development of a new shuttle plasmid system for Escherichia coli and Clostridium perfringens.

We constructed a 7.9-kilobase-pair recombinant shuttle plasmid, designated pHR106, by combining desired segments of three plasmids: an Escherichia coli plasmid (pSL100) which provides a multiple cloning site, a Clostridium perfringens plasmid (pJU122) which provides a clostridial origin of replication, and an E. coli plasmid (pJIR62) which provides an E. coli origin of replication, an ampicillin resistance gene, and a chloramphenicol resistance gene of clostridial origin. The shuttle plasmid transformed E. coli HB101 with a frequency of 1 transformant per 10(4) viable cells and C. perfringens L-phase strain L-13 with a frequency of approximately 1 transformant per 10(6) viable cells. Because of the set of unique cloning sites and the chloramphenicol resistance marker, this shuttle plasmid should be particularly useful for studies of gene regulation and for enzyme production with C. perfringens.

Transient expression system to measure the efficiency of vaccinia promoter regions

A transient expression system has been developed to compare the relative efficiency of expression of various vaccinia virus DNA sequences containing transcriptional regulatory elements. A plasmid vector was constructed containing both the Escherichia coli galactokinase gene ( galK) and the guanine phosphoribosyltransferase gene ( gpt). To direct the expression of gpt within this vector, a vaccinia virus promoter region was isolated from the HindIII-F fragment of the genome and inserted 5′ to gpt coding sequence. Four unique cloning sites in front of galK allow simple and precise fusion of various vaccinia virus DNA fragments that contain the regulatory site of interest to galK. Sequences containing promoter regions were ligated to the coding segment of the galK to create four recombinant plasmids, which were introduced into vaccinia virus-infected cells by transfection. Both galK and gpt were thus expressed under the control of vaccinia virus transcriptional units, and the enzymatic activities were measured in the same cell extract with a filter-binding assay. The major advantage of this transient expression system is that the variations in galK expression are always measured relative to the internal gpt standard. Changes in the galK gpt ratio resulting from different vaccinia promoters of galK are thus a quantitative measurement of promoter strength.

Cosmid vectors for rapid genomic walking, restriction mapping, and gene transfer.

We have designed cosmid vectors for rapid genomic "walking" and restriction mapping. These vectors contain the transcription promoters from either bacteriophage SP6, T7, or T3 flanking a unique BamHI cloning site. Mammalian expression modules encoding the dominant marker neomycin phosphotransferase or the amplifiable dihydrofolate reductase gene expressed from SV40 promoters were inserted for use in gene transfer studies. Restriction sites for the enzymes Not I and Sfi I, which cut mammalian DNA very infrequently, have been engineered near the transcriptional promoters to enable the excision of most inserts as single, full-length fragments. Genomic libraries representative of mouse, human, and hamster genomes were constructed by inserting 33- to 44-kilobase-pair (kbp) DNA fragments, generated by partial cleavage of genomic DNA with Mbo I or Sau3A, into the unique BamHI site. Digestion of recombinant cosmids with restriction enzymes that cleave frequently but do not disrupt the transcriptional promoters generates two small DNA templates for the synthesis of end-specific RNA probes to facilitate directional "walking." Cosmid restriction maps can be determined rapidly by one of several methods. The cosmids and methods we describe should have wide utility in determining the functional and structural organization of complex eukaryotic genomes and for physically linking distant genetic loci.

The mapping of chromosomes in Saccharomyces cerevisiae: I. A cosmid vector designed to establish, by cloning into cdc-mutants, numerous start loci for chromosome walking in the yeast genome

A series of vectors for cosmid cloning in yeast has been derived from cosmid pHC79. Vectors pMT4 through pMT6 contain two tandemly arranged cohesive end sites ( cos) from the genome of bacteriophage γ Their design allows the rapid and simple preparation of cosmid arms by linearizing a vector at the unique PvwII-restriction site located between the two cos-sequences and then cutting the linearized molecule at one of its unique cloning sites for BamHI, ClaI, PvuI, SalI or Scal. Cosmids generated with arms from the most advanced vector, pMT6, carry the origin of replication ( ori) and the Ap R gene from pBR322 and the TRP1/ARS1 and URA1 genes from Saccharomyces cerevisiae. A yeast genomic DNA library was established by packaging in vitro, into bacteriophage λ preheads, of partially restricted yeast DNA fragments ligated to cosmid arms of vector pMT6. About 80% of the clones thus obtained comprise inserts of contiguous genomic DNA over 30 kb in length. Unique DNA probes for the yeast genes CDC10, CDC39, HIS4, LEU2, and PGK1 have successfully been applied when testing for completeness of this library by isolating a series of overlapping cosmid clones that carry the respective genes. The library will thus be useful for the selection of cosmid clones which carry CDC genes from yeast by complementing first, with the vectorial yeast gene URA1, the pyrimidine auxotrophy of most cdc-strains and then, with the respective CDC wild-type genes, of the temperature-sensitive mutant alleles. Most CDC clones thus obtained will provide unique DNA probes which serve as randomly distributed start sequences within the yeast genome for overlap hybridization screening in chromosome mapping studies.

Vectors with restriction site banks V. pJRD215, a wide-host-range cosmid vector with multiple cloning sites

The construction of a new wide-host-range, restriction-site bank, cosmid-cloning vehicle (pJRD215) is described. The wide-host-range properties and the ability to be transferred by conjugation, extend genetic engineering to those Gram-negative species that cannot be transformed. The vector permits the cloning of genes from Gram-negative bacteria using a complementation screening procedure in a mutant host. This procedure is simplified by the possibility of construction of a cosmid gene bank so that only a few hundred clones need to be screened. Subsequent subcloning of the gene of interest is facilitated by the presence of at least 23 unique cloning sites.