Limited growth PCR screening of a plasmid library.
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Cloning, Molecular↗
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Results for “Plasmid library”
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High-efficiency generation of plasmid cDNA libraries using electro-transformation.
A simple and efficient method for the construction of large cDNA libraries in plasmid vectors is described. Cloning efficiencies of greater than 1 x 10(6) recombinants per microgram starting RNA are easily obtained using electroporation. A detailed protocol for determining the optimal conditions using this novel approach is presented.
Base Sequence↗
Isolation of a tomato alcohol dehydrogenase 2-encoding cDNA using phage-promoted antibody screening of a plasmid cDNA library.
We describe the cloning of a cDNA encoding tomato alcohol dehydrogenase 2 (Adh2) by screening plasmid cDNA clones in phage plaques. A cDNA library constructed in a plasmid vector containing a unique SstI site at the 5' end of the cDNA insert was transferred into the SstI site of the lacZ gene of phage lambda Charon16, and screened by anti-Adh2 antibody to identify reactive plaques. Plasmid cDNA clones were recovered by SstI digestion, ligation, and transformation from phage minipreps for subsequent characterization. This system preserves the original plasmid library for subsequent screening with nucleic acid probes to identify full-length, multiple independent, or related cDNA clones not subject to the selection pressure of phage growth or lysogeny, or negative antibody reactivity. Thirty-two cDNA clones were identified with polyclonal antiserum to Adh2. Three of these reacted with monoclonal anti-Adh2 and only those three hybridized to maize adh1 sequence. One of these cDNAs, Adh31, was further characterized as encoding Adh2 by hybrid-selected translation and high sequence homology with the maize adh1 gene.
Alcohol Dehydrogenase↗
Magnetic bead capture of cDNAs from double-stranded plasmid cDNA libraries.
We have developed a cDNA library screening method which allows the simultaneous screening of >10 ( 12 ) double-stranded plasmid cDNA molecules with minimal a priori sequence knowledge. A biotinylated, gene-specific oligonucleotide probe along with abutting 'blocking' oligos is hybridized to the plasmid cDNA library and the target plasmid retrieved with paramagnetic streptavidin beads and transformed into Escherichia coli. Multiple rounds of enrichment with a target plasmid represented at 0.002-0.0001% resulted in over one-third positive clones. Our method will be useful for isolating even the rarest cDNAs starting from ESTs, isolated exons or homologous sequence information.
Bacterial Proteins↗
Use of peptides-on-plasmids combinatorial library to identify high-affinity peptides that bind rhodopsin.
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Amino Acid Sequence↗
Identification of ZipA, a signal recognition particle-dependent protein from Neisseria gonorrhoeae.
A genetic screen designed to identify proteins that utilize the signal recognition particle (SRP) for targeting in Escherichia coli was used to screen a Neisseria gonorrhoeae plasmid library. Six plasmids were identified in this screen, and each is predicted to encode one or more putative cytoplasmic membrane (CM) proteins. One of these, pSLO7, has three open reading frames (ORFs), two of which have no similarity to known proteins in GenBank other than sequences from the closely related N. meningitidis. Further analyses showed that one of these, SLO7ORF3, encodes a protein that is dependent on the SRP for localization. This gene also appears to be essential in N. gonorrhoeae since it was not possible to generate null mutations in the gene. Although appearing unique to Neisseria at the DNA sequence level, SLO7ORF3 was found to share some features with the cell division gene zipA of E. coli. These features included similar chromosomal locations (with respect to linked genes) as well as similarities in the predicted protein domain structures. Here, we show that SLO7ORF3 can complement an E. coli conditional zipA mutant and therefore encodes a functional ZipA homolog in N. gonorrhoeae. This observation is significant in that it is the first ZipA homolog identified in a non-rod-shaped organism. Also interesting is that this is the fourth cell division protein (the others are FtsE, FtsX, and FtsQ) shown to utilize the SRP for localization, which may in part explain why the genes encoding the three SRP components are essential in bacteria.
Amino Acid Sequence↗
Construction of a cosmid library and physical mapping of Bombyx mori nucleopolyhedrovirus genome.
Bombyx mori nucleopolyhedrovirus (BmNPV) DNA was partially digested with BamHI and BglII, or EcoRI, and cloned into the cosmid pWE15. Eight cosmid clones possessing viral DNA fragments with a size range from 34.9 kb to 45.1 kb were obtained, and they covered the entire viral DNA sequence. Using the cosmid library and plasmid libraries obtained previously, physical maps of BmNPV DNA were constructed for EcoRI, SmaI, PstI, SacI and SacII.
Baculoviridae↗
A rapid and improved method for generating cDNA libraries in plasmid and phage lambda vectors.
We have developed a fast and efficient procedure for generating cDNA libraries in plasmid or phage lambda vectors. We used Mo-MuLV reverse transcriptase to synthesize the first strand and directly added Escherichia coli DNA polymerase I with RNase H to synthesize the second strand. A special advantage of our procedure is the use of oligodeoxynucleotide adapters to insert the cDNA into the vector, avoiding the use of methylating enzymes and subsequent digestion with massive amounts of restriction endonucleases. This also obviates the need to tail the cDNA molecules with homopolymers, simplifying subsequent procedures such as sequencing or transfer to other vectors. Finally, we have used a rapid screening procedure to isolate full-length clones with oligodeoxynucleotide probes recognizing conserved regions at the 5' termini of the mRNA. The system is ideal for cloning and analyzing polymorphic alleles of genes, such as those of the major histocompatibility complex.
Bacteriophage lambda↗
Efficient construction of cDNA libraries in plasmid expression vectors using an adaptor strategy.
We describe a method for the construction of large DNA fragment libraries in plasmid vectors, in which complementary, single-stranded extensions are ligated onto both vector and insert DNA using un-phosphorylated adaptor oligonucleotides. Special consideration has been taken of the requirements of expression screening as follows: cDNA synthesis using random oligonucleotide primers is described which maximises the probability of obtaining open reading frame fragments from large mRNA molecules, the adaptors use codons found in high abundance E. coli proteins to minimise problems of premature termination when using strong promoters, and the sequence encoded by the adaptors, when cloned into the bacterial expression vector pEX1, promotes a surface location for the foreign antigenic determinant where it is accessible to antibodies used for screening.
Bacterial Proteins↗
[Study on a downstream signal molecule of human CASK/LIN-2].
OBJECTIVE: To elucidate the function of human CASK/LIN-2, a novel member of membrane-associated guanylate kinase homologs family (MAGUK), by using the yeast two-hybrid system(LexA) to screen the protein interacting with the guanylate kinase-like domain(GK) of hCASK and identify possible protein that might involve downstream signal transduction of hCASK. METHODS: PCR strategy was used to amplify GK domain cDNA fragment of hCASK. The DNA was subcloned into pLexA to construct bait vector pLexA-GK. The pLexA-GK was transformed into yeast host strain EGY48; through testing the bait protein and a repression assay, it was demonstrated that the bait protein did not have transcription activation for leu and lacZ reporter genes, however it could enter nucleus, bind LexA operator. Human fetus brain cDNA library plasmids were transformed into EGY48 containing pLexA-GK and p8op-lacZ, and screened on plates of Gal/Raf his- trp- ura- leu- and Gal/Raf his- trp- ura-X-gal. The clones with galactose dependent leu+ and lacZ+ were isolated; their library plasmids were rescued by means of transforming E.coli KC8. These library plasmids were transformed into the yeast again to re-screen. The remaining positive clones were analyzed by PCR and restriction endonuclease. Finally two kinds of target DNA fragments were obtained. RESULTS: The specificity testing indicated that the two target proteins could specially bind GK domain of hCASK. After DNA sequencing and BLASTn analysis on NCBI, it was shown that the two target DNA fragments, 732 and 683 bp, had high sequence similarity with human inhibitors of differentiation 1(Id1) mRNA, with identities of 97%(630/645) and 98%(656/666), respectively. CONCLUSION: GK domain of hCASK could specially interact with Id1 in yeast. Id1 might be a downstream signal molecule of hCASK, which might involve in regulation of cell differentiation.
Base Sequence↗
High-throughput screening of cellulase F mutants from multiplexed plasmid sets using an automated plate assay on a functional proteomic robotic workcell.
BACKGROUND: The field of plasmid-based functional proteomics requires the rapid assay of proteins expressed from plasmid libraries. Automation is essential since large sets of mutant open reading frames are being cloned for evaluation. To date no integrated automated platform is available to carry out the entire process including production of plasmid libraries, expression of cloned genes, and functional testing of expressed proteins. RESULTS: We used a functional proteomic assay in a multiplexed setting on an integrated plasmid-based robotic workcell for high-throughput screening of mutants of cellulase F, an endoglucanase from the anaerobic fungus Orpinomyces PC-2. This allowed us to identify plasmids containing optimized clones expressing mutants with improved activity at lower pH. A plasmid library of mutagenized clones of the celF gene with targeted variations in the last four codons was constructed by site-directed PCR mutagenesis and transformed into Escherichia coli. A robotic picker integrated into the workcell was used to inoculate medium in a 96-well deep well plate, combining the transformants into a multiplexed set in each well, and the plate was incubated on the workcell. Plasmids were prepared from the multiplexed culture on the liquid handler component of the workcell and used for in vitro transcription/translation. The multiplexed expressed recombinant proteins were screened for improved activity and stability in an azo-carboxymethylcellulose plate assay. The multiplexed wells containing mutants with improved activity were identified and linked back to the corresponding multiplexed cultures stored in glycerol. Spread plates were prepared from the glycerol stocks and the workcell was used to pick single colonies from the spread plates, prepare plasmid, produce recombinant protein, and assay for activity. The screening assay and subsequent deconvolution of the multiplexed wells resulted in identification of improved CelF mutants and corresponding optimized clones in expression-ready plasmids. CONCLUSION: The multiplex method using an integrated automated platform for high-throughput screening in a functional proteomic assay allows rapid identification of plasmids containing optimized clones ready for use in subsequent applications including transformations to produce improved strains or cell lines.
Journal Article↗
A versatile bait vector allowing rapid isolation of prey vectors in Gal4-dependent yeast two-hybrid screens.
Two-hybrid screens have been widely used in recent years for identifying and isolating new interaction partners to known proteins. Current Gal4-dependent two-hybrid screens employ mostly bait and library vectors, which both have the ampicillin gene as a selection marker in bacteria. The isolation of the library plasmids takes several days, because library and bait plasmid cannot be separated easily. We have replaced the ampicillin gene by a kanamycin gene in a Gal4 DNA binding domain bait vector. This vector reduces four- to fivefold the time period required for the isolation of library plasmid DNA. In addition we have changed the multicloning site in the modified vector for easy cloning of cDNA inserts. This vector is advantageous not only in standard two-hybrid screens, but also in mass screens that require multiple screening rounds in order to characterize networks of protein-protein interactions.
Base Sequence↗
Identification of promoter regions in the human genome by using a retroviral plasmid library-based functional reporter gene assay.
Attempts to identify regulatory sequences in the human genome have involved experimental and computational methods such as cross-species sequence comparisons and the detection of transcription factor binding-site motifs in coexpressed genes. Although these strategies provide information on which genomic regions are likely to be involved in gene regulation, they do not give information on their functions. We have developed a functional selection for promoter regions in the human genome that uses a retroviral plasmid library-based system. This approach enriches for and detects promoter function of isolated DNA fragments in an in vitro cell culture assay. By using this method, we have discovered likely promoters of known and predicted genes, as well as many other putative promoter regions based on the presence of features such as CpG islands. Comparison of sequences of 858 plasmid clones selected by this assay with the human genome draft sequence indicates that a significantly higher percentage of sequences align to the 500-bp segment upstream of the transcription start sites of known genes than would be expected from random genomic sequences. We also observed enrichment for putative promoter regions of genes predicted in at least two annotation databases and for clones overlapping with CpG islands. Functional validation of randomly selected clones enriched by this method showed that a large fraction of these putative promoters can drive the expression of a reporter gene in transient transfection experiments. This method promises to be a useful genome-wide function-based approach that can complement existing methods to look for promoters.
3T3 Cells↗
cDNA suppression subtraction library for screening down-regulated genes in gastric carcinoma.
AIM: To establish cDNA suppression subtraction library with a high subtraction efficiency by counterpart normal gastric mucosa mixture mRNA subtracting gastric cancer cells mixture mRNA for screening down-regulated genes in gastric carcinoma. METHODS: RNA of gastric cancer tissues and counterpart normal gastric mucosa were respectively isolated in five patients with gastric cancer, and their mRNA was purified. cDNA suppression subtraction library was established by counterpart normal gastric mucosa mixture mRNA (tester) subtracting gastric cancer tissues mixture mRNA (driver) of five patients with gastric carcinoma. The library plasmids were transformed into competent bacteria DH5a after ligation of the library cDNA fragments with T vectors. Library plasmids were extracted after picking colonies and shaking bacteria overnight. Its subtraction efficiency was confirmed by PCR and reverse hybridization of a nylon filter onto which the colonies of bacteria were transferred with probes of reverse transcription products cDNA of gastric cancer tissues mRNA and counterpart normal gastric mucosa mRNA labeled with alpha- (32)P dCTP. RESULTS: mRNA purified from total RNA of gastric cancer tissues and counterpart normal gastric mucosa in five patients with gastric carcinoma revealed a good quality. cDNA suppression subtraction library constructed for screening down-regulated genes in gastric carcinoma represented a high subtraction efficiency. 86 % of differential expression in down-regulated genes between counterpart normal gastric mucosa and gastric carcinoma was confirmed. CONCLUSION: cDNA suppression subtraction library with a high subtraction efficiency for screening down-regulated genes in gastric carcinoma is successfully established.
Cloning, Molecular↗
Epitope selection from an uncensored peptide library displayed on avian leukosis virus.
Phage display libraries have provided an extraordinarily versatile technology to facilitate the isolation of peptides, growth factors, single chain antibodies, and enzymes with desired binding specificities or enzymatic activities. The overall diversity of peptides in phage display libraries can be significantly limited by Escherichia coli protein folding and processing machinery, which result in sequence censorship. To achieve an optimal diversity of displayed eukaryotic peptides, the library should be produced in the endoplasmic reticulum of eukaryotic cells using a eukaryotic display platform. In the accompanying article, we presented experiments that demonstrate that polypeptides of various sizes could be efficiently displayed on the envelope glycoproteins of a eukaryotic virus, avian leukosis virus (ALV), and the displayed polypeptides could efficiently attach to cognate receptors without interfering with viral attachment and entry into susceptible cells. In this study, methods were developed to construct a model library of randomized eight amino acid peptides using the ALV eukaryotic display platform and screen the library for specific epitopes using immobilized antibodies. A virus library with approximately 2 x 10(6) different members was generated from a plasmid library of approximately 5 x 10(6) diversity. The sequences of the randomized 24 nucleotide/eight amino acid regions of representatives of the plasmid and virus libraries were analyzed. No significant sequence censorship was observed in producing the virus display library from the plasmid library. Different populations of peptide epitopes were selected from the virus library when different monoclonal antibodies were used as the target. The results of these two studies clearly demonstrate the potential of ALV as a eukaryotic platform for the display and selection of eukaryotic polypeptides libraries.
Amino Acid Sequence↗
Genomic organization of Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus.
The genome organization of the Helicoverpa armigera single-nucleocapsid nucleopolyhedrovirus (HearNPV) was investigated and compared to that of other baculoviruses. A detailed physical map was constructed for the restriction enzymes BamHI, BglII, EcoRI, HindIII, KpnI, PstI, SacI and XhoI. The 130.1-kilobase pairs (kb) long viral genome was cloned as restriction fragments into a plasmid library, which covered 97.5% of the viral genome. From this plasmid library about 45 kb of dispersed sequence information was generated. Fifty-three putative open reading frames (ORFs) with homology to ORFs of other baculoviruses were identified and their location on the genome of HearNPV was determined. The arrangement of the ORFs along the HearNPV genome is significantly different from the multiple-nucleocapsid NPVs, AcMNPV, BmNPV and OpMNPV, which have a highly collinear genome, and the granulovirus XcGV. In contrast the genomes of HearNPV and SeMNPV are highly collinear. This close relatedness between an MNPV and an SNPV is supported by the phylogeny of specific genes of these two viruses and suggests that the morphotype (S or M) is only a taxonomic and not a phylogenetic denominator. The data presented here also give further support to the view that the gene distribution along baculovirus genomes can be used as a character to describe baculovirus relatedness independent of gene phylogeny. Five homologous regions (hrs) were located on the genome of HearNPV. This is also the first report of the existence of hrs in SNPVs and this observation suggests that hrs are a common feature of baculovirus genomes.
Animals↗
Identification of a Mycobacterium tuberculosis gene that enhances mycobacterial survival in macrophages.
Intracellular survival plays a central role in the pathogenesis of Mycobacterium tuberculosis. To identify M. tuberculosis genes required for intracellular survival within macrophages, an M. tuberculosis H37Rv plasmid library was constructed by using the shuttle vector pOLYG. This plasmid library was electroporated into Mycobacterium smegmatis 1-2c, and the transformants were used to infect the human macrophage-like cell line U-937. Because M. smegmatis does not readily survive within macrophages, any increased intracellular survival is likely due to cloned M. tuberculosis H37Rv DNA. After six sequential passages of M. smegmatis transformants through U-937 cells, one clone (p69) was enriched more than 70% as determined by both restriction enzyme and PCR analyses. p69 demonstrated significantly enhanced survival compared to that of the vector control, ranging from 2.4- to 5.3-fold at both 24 and 48 h after infection. DNA sequence analysis revealed three open reading frames (ORFs) in the insert of p69. ORF2 (1.2 kb) was the only one which contained a putative promoter region and a ribosome-binding site. Deletion analysis of the p69 insert DNA showed that disruption of ORF2 resulted in complete loss of the enhanced intracellular survival phenotype. This gene was named the enhanced intracellular survival (eis) gene. By using an internal region of eis as a probe for Southern analysis, eis was found in the genomic DNA of various M. tuberculosis strains and of Mycobacterium bovis BCG but not in that of M. smegmatis or 10 other nonpathogenic mycobacterial species. Sodium dodecyl sulfate-polyacrylamide gel electrophoretic analysis showed that all M. smegmatis eis-containing constructs expressed a unique protein of 42 kDa, the predicted size of Eis. The expression of this 42-kDa protein directly correlated to the enhanced survival of M. smegmatis p69 in U-937 cells. These results suggest a possible role for eis and its protein product in the intracellular survival of M. tuberculosis.
Amino Acid Sequence↗
Subtraction of cap-trapped full-length cDNA libraries to select rare transcripts.
The normalization and subtraction of highly expressed cDNAs from relatively large tissues before cloning dramatically enhanced the gene discovery by sequencing for the mouse full-length cDNA encyclopedia, but these methods have not been suitable for limited RNA materials. To normalize and subtract full-length cDNA libraries derived from limited quantities of total RNA, here we report a method to subtract plasmid libraries excised from size-unbiased amplified lambda phage cDNA libraries that avoids heavily biasing steps such as PCR and plasmid library amplification. The proportion of full-length cDNAs and the gene discovery rate are high, and library diversity can be validated by in silico randomization.
Gene Expression Profiling↗