Lambda ZAP Research Articles

Genomic Structure and Organization of the HumanrBATGene (SLC3A1)

Cystinuria is an autosomal recessive disorder of amino acid transport, manifesting as three phenotypes (I, II, and III). An amino acid transport gene,rBAT,is responsible for cystinuria. Mutation and linkage analyses have demonstrated the disease to be heterogeneous, withrBATbeing the defective gene in type I cystinuria. The genomic structure of the humanrBATgene (HGMW-approved symbol SLC 3A1) has been established via two strategies: (i) construction of two different genomic libraries by subcloning the MegaYAC921B6 (CEPH), containingrBAT,in Lambda ZAP and screening usingrBATcDNA and different PCR products; and (ii) generation and sequencing of genomic fragments by long PCR usingrBATcDNA-derived primers. TherBATgene spans approximately 45 kb and consists of 10 exons. The introns range from 500 to 13,000 bp. All splice sites conform to the GT/AG rule. The promoter region has been further analyzed, and a predicted TATA box 98 bp upstream of the first coding ATG was identified. In addition anAlurepeat has been detected 72 bp upstream of the predicted TATA box.

Transcription of the Campylobacter jejuni cell division gene ftsA

As part of a study of genes whose transcription is maintained in stationary phase, cloned segments of DNA were selected from a Lambda ZAP II library of Campylobacter jejuni NCTC 11168. One such clone was found to encode a homologue of the Escherichia coli cell division gene ftsA. Examination of mRNA by transcription mapping revealed that the Campylobacter gene has one major and three minor transcription start sites. There were several significant differences in the structure and organisation of the C. jejuni ftsA promoter compared to that of E. coli.

Analysis of a genomic DNA expression library of Mycobacterium tuberculosis using tuberculosis patient sera: evidence for modulation of host immune response.

DNA obtained from a human sputum isolate of Mycobacterium tuberculosis, NTI-64719, which showed extensive dissemination in the guinea pig model resulting in a high score for virulence was used to construct an expression library in the lambda ZAP vector. The size of DNA inserts in the library ranged from 1 to 3 kb, and recombinants represented 60% of the total plaques obtained. When probed with pooled serum from chronically infected tuberculosis patients, the library yielded 176 recombinants with a range of signal intensities. Among these, 93 recombinants were classified into 12 groups on the basis of DNA hybridization experiments. The polypeptides synthesized by the recombinants were predominantly LacZ fusion proteins. Serum obtained from patients who were clinically diagnosed to be in the early phase of M. tuberculosis infection was used to probe the 176 recombinants obtained. Interestingly, some recombinants that gave very strong signals in the original screen did not react with early-phase serum; conversely, other whose signals were extremely weak in the original screen gave very intense signals with serum from recently infected patients. This indicates the differential nature of either the expression of these antigens or the immune response elicited by them as a function of disease progression.

Molecular cloning and characterization of Coccidioides immitis antigen 2 cDNA

Previous experiments have provided evidence that Coccidioides immitis antigen 2 (Ag2) is a major T-cell-reactive component of mycelia and spherule cell walls. Here we report the identification and cloning of the cDNA that encodes Ag2 from a lambda ZAP cDNA expression library constructed from spherule-derived RNA. DNA sequence analysis established that the 1,255-bp clone contains a 174-bp 5' untranslated region, a 582-bp open reading frame which encodes for a protein consisting of 194 amino acids, and a 375-bp 3' untranslated region, including a poly(A) tail. The recombinant Ag2 protein has a predicted molecular mass of 19.5 kDa and contains an 18-amino-acid N terminus which has been tentatively identified as a signal peptide. The Ag2 cDNA was ligated into the pGEX-4T-3 vector and expressed in Escherichia coli TG-1 cells as a glutathione S-transferase fusion protein. The recombinant fusion protein showed reactivity with sera from patients with coccidioidomycosis and elicited delayed-type footpad hypersensitivity responses in Coccidioides-immune mice. These results suggest that the Ag2 cDNA can be used for the large-scale production of this immunologically important protein.

Lathyrus Dehydrin : A Drought Inducible cDNA Clone — Isolation and Characterization

Dehydrin like transcripts (drought inducible mRNA) accumulated in drought stressed shoots and roots of Lathyrus sativus. ABA also induced the expression of dehydrin in unstressed seedlings but to a lower extent. A cDNA expression library was prepared in lambda ZAP vector from mRNA of drought stressed shoots of Lathyrus sativus cv P-24 and screened with pea dehydrin cDNA probe. One positive clone (∼ 500 bp) was purified and characterised. The partial nucleotide sequence of the clone Lsd, contained a possible open reading frame which would encode a polypeptide with region of significant amino acid sequence similarity to dehydrin from other plant species. The genomic counterpart of Lsd cDNA was found to be present within a fragment of ∼ 3.4 and ∼ 3.2 kb in parent as well as in the somaclones of Lathyrus sativus, by using different restriction enzymes.

Isolation and characterization of a clone encoding a major allergen ( Bla gBd90K) involved in IgE-mediated cockroach hypersensitivity

Previous studies have established that atopic individuals living in cockroach-infested housing become sensitized to cockroach aeroallergens and produce IgE antibodies to a variety of proteins. We describe the isolation of a complementary DNA clone from an expression library, constructed with messenger RNA from German ( Blattella germanica) cockroaches, which encodes a major allergen involved in mediating cockroach hypersensitivity. Approximately 0.2% of the clones from a lambda ZAP XR cDNA library bound IgE from a patient with cockroach sensitivity. A randomly selected subset of these clones revealed that they were either different isolates of the same gene or members of a closely related gene family. One of the largest clones (a 4 kb insert) from this subset, Bla g Bd90K hybridized to a single mRNA of approximately the same size. DNA sequence analysis showed that this gene consisted of seven 576 bp tandem repeats with a short unique region at either end. No significant sequence homologies were found between the cockroach clone and any other gene reported in the GenBank database. Serum from 17 of 22 (77%) patients with cockroach hypersensitivity identified IgE-binding recombinant protein expressed from clone Bla g Bd90K in Escherichia coli XL-Blue cells as determined by sodium dodecylsulfate–polyacrylamide gel electrophoresis/immunoblot analysis. This recombinant protein migrates with a molecular weight (90 kd) apparently similar to one identified in whole body extracts. We have identified and isolated a cDNA that encodes a major cockroach allergen ( Bla g Bd90K) present in German cockroaches. (J A LLERGY C LIN I MMUNOL 1996;98:172-80.)

Evaluation and characterization of a porcine small intestine cDNA library: analysis of 839 clones.

A porcine small intestine directionally cloned cDNA library was constructed in the vector lambda Zap II. Clones were hybridized with total labeled cDNA such that putative high-copy number transcripts could be differentiated from middle- and low-copy number transcripts prior to selection and characterization by DNA sequencing. More than 2000 non-hybridizing and 242 hybridizing clones were collected. In total, 839 clones were sequenced from the 3' end of the cDNA, and after inter-clone comparison, the unique clones were sequenced from the 5' end of the cDNA. The 5' data were used to query the sequence in databases and resulted in the identification of 630 different gene transcripts, of which 604 are new porcine genes. The identity of 361 transcripts could be identified from sequence comparison studies. The validity of this semi-random selection approach was verified by the identification of a large number of unique transcripts.

Characterization of the cytoplasmic filament protein gene (cfpA) of Treponema pallidum subsp. pallidum.

Treponema pallidum and other members of the genera Treponema, Spirochaeta, and Leptonema contain multiple cytoplasmic filaments that run the length of the organism just underneath the cytoplasmic membrane. These cytoplasmic filaments have a ribbon-like profile and consist of a major cytoplasmic filament protein subunit (CfpA, formerly called TpN83) with a relative molecular weight of approximately 80,000. Degenerate DNA primers based on N-terminal and CNBr cleavage fragment amino acid sequences of T. pallidum subsp. pallidum (Nichols) CfpA were utilized to amplify a fragment of the encoding gene (cfpA). A 6.8-kb EcoRI fragment containing all but the 5' end of cfpA was identified by hybridization with the resulting PCR product and cloned into Lambda ZAP II. The 5' region was obtained by inverse PCR, and the complete gene sequence was determined. The cfpA sequence contained a 2,034-nucleotide coding region, a putative promoter with consensus sequences (5'-TTTACA-3' for -35 and 5'-TACAAT-3' for -10) similar to the sigma70 recognition sequence of Escherichia coli and other organisms, and a putative ribosome-binding site (5'-AGGAG-3'). The deduced amino acid sequence of CfpA indicated a protein of 678 residues with a calculated molecular mass of 78.5 kDa and an estimated pI of 6.15. No significant homology to known proteins or structural motifs was found among known prokaryotic or eukaryotic sequences. Expression of a LacZ-CfpA fusion protein in E. coli was detrimental to survival and growth of the host strain and resulted in the formation of short, irregular filaments suggestive of partial self-assembly of CfpA. The cytoplasmic filaments of T. pallidum and other spirochetes appear to represent a unique form of prokaryotic intracytoplasmic inclusions.

Molecular cloning and sequence analysis of the gene encoding LipL41, a surface-exposed lipoprotein of pathogenic Leptospira species

We report the cloning of the gene encoding a surface-exposed leptospiral lipoprotein, designated LipL41. In a previous study, a 41-kDa protein antigen was identified on the surface of Leptospira kirschneri (D. A. Haake, E. M. Walker, D. R. Blanco, C. A. Bolin, J. N. Miller, and M. A. Lovett, Infect. Immun. 59:1131-1140, 1991). We obtained the N-terminal amino acid sequence of a staphylococcal V8 proteolytic-digest fragment in order to design an oligonucleotide probe.A Lambda ZAP II library containing EcoRI fragments of L. kirschneri DNA was screened, and a 2.3-kb DNA fragment which contained the entire structural lipL41 gene was identified. The deduced amino acid sequence of LipL41 would encode a 355-amino-acid polypeptide with a 19-amino-acid signal peptide, followed by an L-X-Y-C lipoprotein signal peptidase cleavage site. A recombinant His6-LipL41 fusion protein was expressed in Escherichia coli in order to generate specific rabbit antiserum. LipL41 is solubilized by Triton X-114 extraction of L. kirschneri; phase separation results in partitioning of LipL41 exclusively into the detergent phase. At least eight proteins, including LipL41 and the other major Triton X-114 detergent phase proteins, are intrinsically labeled during incubation of L. kirschneri in media containing [3H] palmitate. Processing of LipL41 is inhibited by globomycin, a selective inhibitor of lipoprotein signal peptidase. Triton X-100 extracts of L. kirschneri contain immunoprecipitable OmpL1 (porin), LipL41, and another lipoprotein, LipL36. However, in contrast to LipL36, only LipL41 and OmpL1 were exposed on the surface of intact organisms. Immunoblot analysis of a panel of Leptospira species reveals that LipL41 expression is highly conserved among leptospiral pathogens.

Molecular cloning and characterization of the Coccidioides immitis complement fixation/chitinase antigen.

Detection of anti-Coccidioides complement-fixing (CF) antibody is a valuable diagnostic and prognostic aid in coccidioidomycosis. The CF antibody response is directed against a heat-labile antigen that has chitinase activity, hereafter referred to as the CF/chitinase protein. To identify and clone this immunoreactive enzyme, we constructed a Coccidioides immitis cDNA lambda ZAP expression library from spherule RNA and detected fusion peptides expressing CF epitopes by immunoscreening. A cDNA clone consisting of 1,623 bp was identified, sequenced, and found to contain a single open reading frame that encodes a protein of 47 kDa with 427 amino acids. Deduced amino acid sequence analyses showed that the cloned CF/chitinase cDNA contains a 35-amino-acid region, beginning at Ser-18 and ending at and ending at Arg-52 which has 92% homology with the reported N-terminal amino acid sequence of authentic CF/chitinase protein. The first 17 amino acids in the deduced sequence of the cloned cDNA are not present on the mature CF/chitinase protein, suggesting that it may be a signal peptide. Expression of the CF/chitinase cDNA insert by using the pGEX-4T-3 vector yields a fusion peptide that bears CF-specific epitopes and shows chitinase activity. The CF/chitinase clone will enable large-scale production of the recombinant CF antigen for use in immunoassays and facilitate studies on the role of chitinase in the morphogenesis of C. immitis.

Cysticercosis: Identification and Cloning of Protective Recombinant Antigens

We describe the cloning and the evaluation of the protective capacity of 5 recombinant antigens expressed during the cysticercus stage of both Taenia crassiceps and Taenia solium. A cDNA library was constructed in bacteriophage lambda ZAP using mRNA isolated from larvae of T. crassiceps of the ORF strain. The recombinant phage library was screened with polyclonal antibodies against 56- and 74-kDa protective antigen fractions. This screening identified 13 recombinant clones, 5 of which were also strongly recognized by pooled sera from pigs experimentally infected with T. solium. The native antigens are proteins of 56 (clones KETcl, 4, 7) and 74 and 78 kDa (clones KETc11, 12) of T. crassiceps cysticerci. Vaccination experiments using these 5 recombinant clones against murine cysticercosis point to the relevance of KETcl, 4, 7, and 12 in host protection, whereas immunization with the clone KETc11 does not modify the parasite load in females and facilitates the parasitosis in males. We report here the DNA and the deduced amino acid sequence (100 amino acids) of the first protective antigen (KETc7) of potential interest for T. solium pig cysticercosis prevention.

Cloning and sequencing of a human cDNA encoding a putative transcription factor containing a bromodomain

A 2985 by cDNA was isolated from a Lambda Zap Express library and sequenced. The cDNA appeared to represent a previously unknown gene that encodes an acidic 757 amino acid protein containing a bromodomain, several potential sites for phosphorylation by casein kinase-II and small proline-rich segments. The results suggest that the encoded protein might be a novel transcription factor.

The structural gene encoding human enterotoxigenic Escherichia coli PCFO20 is homologous to that for porcine 987P.

Putative colonization factor PCFO20 was recently identified in an enterotoxigenic Escherichia coli (ETEC) strain of serogroup O20 isolated from a child with diarrhea in Argentina. The gene encoding the structural subunit of PCFO20 fimbriae, fotA, was cloned from strain ARG-2 in the expression phage vector lambda ZAP Express. One positive clone, pGV29, that carried a 3.3-kb fragment was identified on the basis of fimbrillin production by using a monospecific rabbit anti-PCFO20 serum. Nucleotide sequencing of a 1.3-kb Sau3A-ClaI fragment of the subclone pGV292 containing the region coding for PCFO20 fimbrillin revealed two open reading frames of which one was complete. A western blot (immunoblot) showed that the cloned protein, FotA, migrated like the PCFO20 fimbrial subunit protein did. Fimbriae were not detected on the surface of E. coli host bacteria containing pGV292 or pGV29, suggesting that the genes needed for assembly of PCFO20 fimbriae are lacking in both clones. The fotA gene encodes a 20,574-Da prefimbrillin protein which contains a 21-amino-acid signal sequence; the mature protein has a size of 18.1 kDa. The subunit protein FotA was found to be more homologous to the subunit of porcine 987P than to any fimbrial subunit produced by human ETEC. Alignments of the amino acid sequences of the two proteins indicate that they are partly identical, with an overall similarity of 82%. FotA fimbrillin was shown to be transported and assembled by the fimbria assembly machinery in porcine ETEC strain 987. PCFO20 and 987P may have evolved from a common ancestral gene. They are immunologically related but have affinity for different host cell receptors, since PCFO20-producing bacteria do not bind to neonatal piglet enterocytes.

Molecular cloning, expression and characterization of a recombinant glutathione S-transferase from Echinococcus multilocularis

We report the identification and characterization of the first cestode glutathione S-transferase (GST) cDNA sequence. A fragment of an Echinococcus multilocularis glutathione S-transferase cDNA was isolated by the polymerase chain reaction. Subsequently, a Lambda zap cDNA library prepared from mRNA from protoscolices of E. multilocularis was screened with this PCR fragment. A complete cDNA clone was isolated and the nucleotide sequence determined. Analysis of the E. multilocularis GST-deduced amino acid sequence indicates that it is clearly related to the mammalian μ-class GSTs. The E. multilocularis GST cDNA was expressed in Escherichia coli, using a protocol designed to produce the native enzyme rather than a fusion protein. The 25.5-kDa enzyme subunit was purified to homogeneity using glutathione-sepharose chromatography. Gel filtration demonstrated that this GST is enzymatically active as a homodimer. The recombinant enzyme had conjugating activity with organic hydroperoxides and with members of the trans, trans-2,4 alkadienal and trans-2-alkenal series, which are secondary products of lipid peroxidation.

Intracellular membrane proliferation in E. coli induced by foot-and-mouth disease virus 3A gene products.

During picornavirus infection replication of genomic RNA occurs in membrane-associated ribonucleoprotein complexes. These replication complexes contain different nonstructural viral proteins with mostly unknown function. To examine the function of nonstructural picornaviral proteins in more detail, cDNA of foot-and-mouth-disease virus (FMDV) strain O1 Lausanne was cloned into lambda ZAP II, and different parts of the P3-coding sequence were expressed in E. coli by the T7 polymerase system. Expression products constituted (a) fusion proteins composed of N-terminal leader peptide of bacteriophage T7 phi 10 protein fused to FMDV P3-sequences of different lengths, (b) translation products of authentic P3-region genes, and (c) carboxy-terminally truncated 3A proteins. Expression products were characterized by NaDodSO4-polyacrylamide gel electrophoresis, immunoblotting, as well as electron and immunoelectron microscopy. We show here that in the T7 polymerase system a high level of expression of 3A-containing peptides is achieved in E. coli. Remarkably, the expression of 3A-derived proteins induced a dramatic intracellular membrane proliferation in E. coli cells, similar to the vesicle induction observed in FMDV-infected cells. By immunoelectron microscopy, 3A-reactive material was found associated with these membranes. We hypothesize that the FMDV 3A protein is instrumental in eliciting intracellular membrane proliferation in infected cells as a prerequisite for viral RNA replication.

An allergenic polypeptide representing a variable region of hsp 70 cloned from a cDNA library of Cladosporium herbarum.

Extracts of Cladosporium herbarum, a major source of fungal aeroallergens, exhibit a complex profile of IgE-binding proteins. Yields of conventionally purified allergens from this mold have been insufficient to permit further molecular analyses. To enhance and simplify the purification of allergens from C. herbarum, we have sought to use recombinant DNA techniques to clone, identify and bacterially express immunoselected C. herbarum allergens. We constructed a cDNA library in lambda ZAP II using mRNA isolated from C. herbarum. From this library, phage clones encoding a new allergen were immunoselected using pooled human atopic IgE. The cloned cDNA was excised from the phage vector as a recombinant pBluescript II SK-phagemid and sequenced. Expression of the recombinant allergen was carried out in E. coli XL1-blue transformants of the phagemid. Bacterial lysates from cells induced to express the cloned allergen were immunoblotted and probed with individual human atopic IgEs. The cDNA clone encodes a 278 amino acid polypeptide homologous to the C-terminal portion of 70 kDa heat shock protein (hsp 70). The polypeptide possesses features common to other hsps 70, i.e. a similar hydropathic profile and a variable C-terminal region with conserved sequence at the very C-terminus. Binding of the recombinant peptide to IgE from 38% of atopic sera or plasma from individuals allergic to C. herbarum was demonstrated. These results indicate that amino acid substitutions are relatively conserved even in the variable C-terminal regions of hsp 70 species. Thus, this study should draw attention to the possibility of induction of anaphylactic responses in a sensitized individual when hsp 70 from any pathogenic species is administered for vaccination.

Characterization of a cDNA Encoding Murine Coagulation Factor VII

The cDNA encoding murine coagulation factor VII (mfVII) was isolated and reconstructed from a lambda Zap cDNA library generated from murine liver mRNA. The cDNA contains 1903 nucleotides spanning 15 bases upstream of the 5'-translation initiation codon, an open reading frame of 1338 nucleotides, 550 nucleotides downstream of the first stop codon and a 3' poly(A) tail. The translation product is composed of a 41-amino acid signal/propeptide region followed by a 405-residue mature protein. The latter is highly homologous to that of human, rabbit, bovine, Rhesus monkey, and canine fVII. All protein domains of hfVII are strictly conserved in mfVII.

Cloning and expression of a cDNA encoding bovine retinal pigment epithelial 11-CIS retinol dehydrogenase.

Identification of a 32-kd protein in the bovine retinal pigment epithelium.A bovine retinal pigment epithelium cDNA library was constructed in the bacteriophage lambda ZAP Express. A monoclonal antibody, designated 21-C3/AV, was used to isolate the cDNA encoding the 21-C3/AV antigen. A positive full-length clone, designated 21-C3RDH/CD, was sequenced. Northern blot analysis was used to determine the length of the mRNA and the tissue expression pattern. The entire open reading frame of clone 21-C3RDH/CD was used to isolate a recombinant baculovirus clone and expressed in Spodoptera frugiperda insect cells. Enzymatic activity toward 11-cis retinaldehyde was investigated.The complete nucleotide sequence of 21-C3RDH/CD was obtained. The deduced amino acid sequence reveals homology with short-chain alcohol dehydrogenases. Northern blot analysis detected a 1.2-kb transcript. Although the monoclonal antibody used to isolate 21-C3RDH/CD also reacts with other ocular and nonocular tissues, the authors were unable to demonstrate any reactivity with RNA samples isolated from different (non)ocular tissues. Recombinant baculovirus-infected insect cells synthesized the 21-C3/AV antigen. This protein showed 11-cis retinol dehydrogenase activity.Homology to the human D-beta-hydroxybutyrate dehydrogenase precursor and other alcohol dehydrogenases shows that 21-C3RDH/CD encodes a short-chain alcohol dehydrogenase. Furthermore, tissue specificity and molecular weight of the antigen suggest that 21-C3RDH/CD encodes the bovine retinal pigment epithelial 11-cis retinol dehydrogenase. Direct proof came from experiments in which we used the baculovirus-based expression system for in vitro synthesis of the protein encoded by 21-C3RDH/CD. Protein extracts obtained from recombinant baculovirus-infected insect cells were found capable of reducing 11-cis retinaldehyde.

Lack of serological specificity of recombinant heat shock protein of Leishmania donovani.

In order to identify a specific recombinant antigen of Leishmania donovani with potential use for diagnosis, a cDNA library was constructed in lambda ZAP II expression vector. On screening the cDNA library using pooled sera from Indian patients with kala azar, 20 antibody reactive clones were identified. These were subcloned into pBluescript phagemid by an in vivo excision procedure. The molecular weights of the expressed recombinant proteins varied from 15 to 70 kDa and the cDNA insert sizes varied from 0.5 kb to the largest size of approximately 2.0 kb which was designated as the E2b clone. The nucleotide sequencing revealed that 50% of the clones had sequence homology to the heat shock protein gene of L. donovani. The serological studies conducted with the kala azar positive sera and sera from healthy laboratory workers using the recombinant protein from the E2b clone and having sequence homology to Ldhsp 70, indicated that although all the kala azar sera was positive, 12 of 20 healthy individuals also showed antibodies against the recombinant hsp70, indicating that this antigen is not suitable for serological diagnosis of kala azar.

Repression of P53-Dependent Sequence-Specific Transactivation by MEF2C

Lambda ZAP cDNA library constructed from spleen of a p53-deficient mouse was screened by South-Western technique using Fragment A, a DNA sequence that p53 specificaly binds to, as a probe. One (clone 2) of six clones isolated was identical to MEF2c, a MADS-family transcription factor. Transcripts of the mef2c gene was also detected in spleen where the expression has not been reported so far. Isolated clones except clone 2 had a growth-suppression activity on p53-deficient osteosarcoma cell line (Saos II). Clone 2 repressed the transactivation from Fragment A by p53, suggesting that MEF2c may act as a negative regulator of p53-responsive element.