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PubMed2000

Assessment of the relationship between genotypic status of a DT-diaphorase point mutation and enzymatic activity.

DT-diaphorase, a cytosolic reductase, has been implicated as an activator of chemotherapeutic prodrugs and a detoxifier of certain potentially carcinogenic xenobiotics. A common C to T nucleotide 609 substitution in DT-diaphorase cDNA has been associated with protein instability and reduced catalytic activity. The degree to which the allelic status of the substitution correlates with enzymatic activity was assessed in 45 normal human skin fibroblast strains using a PCR-RFLP assay. Included in this study was the 3437T strain, which is unique in that it is heterozygous for the polymorphism yet contains undetectable enzymatic activity. An allele-specific RT-PCR-RFLP technique attributed this phenomenon to exclusive DT-diaphorase mRNA expression from the variant allele. Overlap in activities was observed between individual strains homozygous for the wild-type allele and heterozygotes, but the former group displayed enzymatic activity that was on average 2-fold higher. Western blot analysis of the two strains in this panel that are homozygous for the variant allele revealed that they express relatively low amounts of DT-diaphorase protein, consistent with the role of the substitution in protein instability. This work confirms that genotypic status is a reliable initial estimate of DT-diaphorase activity.

Adolescent↗
PubMed1997

Libraries for genomic SELEX.

An increasing number of proteins are being identified that regulate gene expression by binding specific nucleic acidsin vivo. A method termed genomic SELEX facilitates the rapid identification of networks of protein-nucleic acid interactions by identifying within the genomic sequences of an organism the highest affinity sites for any protein of the organism. As with its progenitor, SELEX of random-sequence nucleic acids, genomic SELEX involves iterative binding, partitioning, and amplification of nucleic acids. The two methods differ in that the variable region of the nucleic acid library for genomic SELEX is derived from the genome of an organism. We have used a quick and simple method to construct Escherichia coli, Saccharomyces cerevisiae, and human genomic DNA PCR libraries that can be transcribed with T7 RNA polymerase. We present evidence that the libraries contain overlapping inserts starting at most of the positions within the genome, making these libraries suitable for genomic SELEX.

Binding Sites↗
PubMed1996

Characterization of a prolinase gene and its product and an adjacent ABC transporter gene from Lactobacillus helveticus.

A prolinase (pepR) gene was cloned from an industrial Lactobacillus helveticus strain (53/7). Three clones, hybridizing with a gene probe specific for a peptidase shown to have activity against di- and tripeptides, were detected from a L. helveticus genomic library constructed in Escherichia coli. None of the three clones, however, showed enzyme activity against the di- or tripeptide substrates tested. One of the clones, carrying a vector with a 5.5 kb insert, was further characterized by DNA sequencing. The sequence analysis revealed the presence of two ORFs, ORF1 and ORF2 of 912 and 1602 bp, respectively. ORF2, located upstream of and in the opposite orientation to ORF1, had a promoter region overlapping that of ORF1. ORF1 had the capacity to encode a 35083 Da protein. When amplified by PCR, ORF1 with its control regions specified a 35 kDa protein in E. coli that was able to hydrolyse dipeptides, with highest activity against Pro-Leu, whereas from the tripeptides tested, only Leu-Leu-Leu was slowly degraded. By the substrate-specificity profile and protein homologies, the 35 kDa protein was identified as a prolinase. The activity of the cloned prolinase was inhibited by p-hydroxymercuribenzoate. Northern and primer-extension analyses of ORF1 revealed a 1.25 kb transcript and two adjacent transcription start sites, respectively, thus confirming the DNA sequence data. ORF2 had encoding capacity for a 59.5 kDa protein that showed significant homology to several members of the family of ABC transporters. Determination of the mRNA levels at different growth phases revealed that the pepR gene and ORF2 are transcribed in L. helveticus at the exponential and stationary phases of growth, respectively. Furthermore, two ORF2 deletion constructs, carrying the intact pepR gene, showed that this upstream operon adversely affected PepR activity in E. coli, which explains the enzymic inactivity of the original clones.

ATP-Binding Cassette Transporters↗
PubMed1996

Rat pristanoyl-CoA oxidase. cDNA cloning and recognition of its C-terminal (SQL) by the peroxisomal-targeting signal 1 receptor.

The composite pristanoyl-CoA oxidase cDNA sequence, derived from two overlapping clones from a rat liver cDNA library and a 5'-RACE (rapid amplification of cDNA ends) PCR fragment, consisted of 2600 bases and contained an open reading frame of 2100 bases, encoding a protein of 700 amino acids with a calculated molecular mass of 78445 Da. This value is somewhat larger than the reported molecular mass of 70 kDa as determined earlier by SDS-gel electrophoresis. The amino acid identity with rat palmitoyl-CoA oxidase was rather low (28%) and barely higher than that with the yeast acyl-CoA oxidases (20%), suggesting that the palmitoyl-CoA oxidase/pristanoyl-CoA oxidase duplication occurred early in evolution. The carboxy-terminal tripeptide of pristanoyl-CoA oxidase was SQL. In vitro studies with the bacterially expressed human peroxisomal-targeting signal-1 import receptor indicated that SQL functions as a peroxisome-targeting signal. Northern analysis of tissues from control and clofibrate treated rats demonstrated that the pristanoyl-CoA oxidase gene is transcribed in liver and extrahepatic tissues and that transcription is not enhanced by treatment of rats with peroxisome proliferators. No mRNA could be detected by northern analysis of human tissues, suggesting that the human pristanoyl-CoA oxidase gene, if present, is only poorly or not transcribed.

Amino Acid Sequence↗
PubMed2001

[Genomic structure and proteins sequence analysis of full-length of segment A of three infections bursal disease viruses].

The full-length of segment A of three infectious bursal disease viruses (IBDV), including an attenuated strain HZ2, an attenuated vaccine strain JD1 and a virulent field isolate ZJ2000, were cloned by long RT-PCR and sequenced respectively. All the three results revealed the identity of IB-DV with two overlapping open reading frames (ORF) flanked by 5'- and 3'-noncoding regions(NCR) in 3259 bp long. The strains shared high identity with each other at nucleotide or deduced amino acid level, and also had four unique sites H253, N279, T284, R330 which are common in other attenuated and some classic or highly virulent strains. The virulent strain ZJ2000 had several key amino acid mutations located in hypervariant region of VP2 and near the VP2-VP4 cleavage site of polypeptide, which is probably related to the virulence. Sequence comparison supported that VP2 is not the sole determinant of the virulence. The highly conservation in 5'- and 3'-NCR of different strains indicated the NCR may be not responsible for the virulence. But the same conservation appeared in VP5 revealed another complex relationship between VP5 and the virulence.

Amino Acid Sequence↗
PubMed2006

[Legionella pneumophila lvgA and Hsp60 gene splicing and the fusion gene expression in E.coli].

OBJECTIVE: To fuse Legionella virulence gene (lvgA) with heat shock protein 60 gene (Hsp60) by PCR and detect the fusion gene expression in E.coli. METHODS: The fragments of lvgA and Hsp60 genes having matching sequences at their ends to be fused were amplified from the genomic DNA of Legionella pneumophila by PCR, and the PCR products were mixed, denatured, reannealed, so that the strands with matching sequences at their 3' ends overlapped to serve as primers for each other. Extension of this overlap by DNA polymerase produced recombinant products. After amplification with outer primers, sufficient product of the fusion gene was harvested, which was inserted into the prokaryotic expression vector pGEX-4T-1 to construct the prokaryotic expression recombinant plasmid. After identification with restriction enzyme analysis, polymerase chain reaction and nucleotide sequence analysis, the E.coli BL21 containing the recombinant plasmid pGlvgA/Hsp60 was induced with IPTG and the expression of lvgA/Hsp60 was detected by SDS-PAGE and Western blot analysis. RESULTS: The lvgA/Hsp60 fusion gene of 2,292 bp was amplified and the recombinant plasmid pGlvgA/Hsp60 was constructed successfully. A 117-kD GST-lvgA-Hsp60 fusion protein was detected in the E.coli containing the recombinant plasmid. CONCLUSION: The recombinant plasmid for Legionella pneumophila lvgA/Hsp60 fusion gene is constructed successfully and this fusion protein can be expressed in prokaryotic cells efficiently, which make possible the immunological characterization of this fusion gene.

Alternative Splicing↗
PubMed1996

IL-12-induced activation of NK and T cells occurs in the absence of immediate-early activation gene expression.

The responses of lymphocytes to IL-2 and IL-12, involving proliferation, differentiation, and cytokine production, are only partially overlapping, and may depend on induced differential expression of specific sets of genes. Using reverse-transcription PCR differential display, we isolated an mRNA species expressed in IL-2- but not IL-12-stimulated NK cells. This was identified as the mRNA encoding the transcription factor egr-1, which is expressed with fast kinetics in T and NK cells upon IL-2, but not IL-12, stimulation. Analysis of the accumulation of mRNA-encoding members of the AP-1 transcription factor family demonstrated that c-fos and junB are also expressed upon stimulation of NK and T cells with IL-2, but not IL-12, whereas expression of c-jun and junD is not modified by either cytokine. Accordingly, increased AP-1 DNA-binding activity and AP-1-dependent transcriptional activity were detected exclusively in IL-2-stimulated cells. Analysis of the expression of genes reported to regulate cytokine-induced proliferation demonstrated that both IL-2 and IL-12 induce c-myc mRNA accumulation in NK and T cells, whereas only IL-2 induces bcl-2 expression. Our data provide the first demonstration that IL-12-mediated activation of T and NK cells does not involve expression of members of the immediate-early activation genes family (egr-1, c-fos, and junB), AP-1 transcriptional activity, or bcl-2 expression. This indicates that functional differences observed in IL-2- and IL-12-stimulated cells may depend, at least in part, on differential gene regulation.

DNA-Binding Proteins↗
PubMed2003

RNaseCut: a MALDI mass spectrometry-based method for SNP discovery.

MALDI mass spectrometry is an established platform for high-throughput genotyping of single nucleotide polymorphisms (SNPs). For many species and also for specific ethnic groups, the number of described SNPs is far from sufficient. Here we present a method for SNP discovery that can use existing MALDI genotyping platforms and is automation-compatible. The method is based on in vitro RNA transcripts from PCR products, that can be used to obtain highly informative sequence fingerprints by digestion with the guanosine- specific ribonuclease T1. In these fingerprints, a mutation can be detected as either a mass shift, absence of an existing peak or appearance of an additional peak. Due to mass-degeneracy of fragments and multiple presence of shorter fragments in a given sequence, a certain fraction of possible mutations will remain undetected with this method. Screening of both strands from one PCR product is possible by using T3- and T7-tailed primers and the respective RNA polymerases, and markedly decreases the probability of missing an existing SNP. The use of mass-shifted nucleotides can significantly reduce fragment overlaps and hence increase detectability. We have used a simulation of RNase digests of a set of randomly generated sequences to provide estimates for the general detection probability in dependence on PCR product length. A software package is provided that helps to design PCR primers by plotting out regions with a high SNP discovery score, calculates expected mass fingerprints and peaklists from the target sequence selected for screening and helps in interpretation of digest spectra.

Animals↗
PubMed2005

Molecular characterization of phytoplasmas in lilies with fasciation in the Czech Republic.

Lilium spp. with symptoms of severe fasciation were observed in Southern and central Bohemia during the period 1999-2003. Nucleic acids extracted from symptomatic and asymptomatic plants were used in nested-PCR assays with primers amplifying 16S-23S rRNA sequences specific for phytoplasmas. The subsequent nested-PCR with phytoplasma group-specific primers followed by RFLP analyses and the 16S ribosomal gene sequencing, allowed classification of the detected phytoplasmas in the aster yellows group, subgroups 16SrI-B and 16SrI-C alone, and in mixed infection. Samples infected by 16SrI-C phytoplasmas showed different overlapping RFLP profiles after TruI digestion of R16F2/R2 amplicons. Two of these amplicons were sequenced, one of them directly and the other after cloning; sequence analyses and blast alignment confirmed the presence of two different overlapping patterns in samples studied. The sequences obtained were closely related, respectively, to operon A and operon B ribosomal sequences of the clover phyllody phytoplasma. Direct PCR followed by RFLP analyses of the tuf gene with two restriction enzymes showed no differences from reference strain of subgroup 16SrI-C. Infection with aster yellows phytoplasmas of 16SrI-B subgroup in asymptomatic lilies cv. Sunray was also detected.

Czech Republic↗
PubMed1998

Dominant expression of rat prostanoid DP receptor mRNA in leptomeninges, inner segments of photoreceptor cells, iris epithelium, and ciliary processes.

Prostaglandin (PG) D2 is one of the major prostanoids in the mammalian brain and eye tissues. Its function is mediated by the prostanoid DP receptor, which is specific for PGD2 among the various prostanoids. In this study, we cloned the full-length cDNA for the rat DP receptor and used it for detection of DP receptor mRNA in various rat tissues. Northern blotting and RT-PCR analyses revealed that this DP receptor was expressed most intensely in the eye tissues, moderately in the leptomeninges and oviduct, and weakly in the epididymis. The tissue distribution profile of the mRNA for the rat DP receptor is overlapped with those of hematopoietic and lipocalin-type PGD synthases. Among rat eye tissues, the expression was the highest in the iris. In situ hybridization and in situ RT-PCR revealed DP receptor mRNA to be localized in the epithelium of the iris and ciliary body and in photoreceptor cells of the retina, suggesting the involvement of the receptor in the physiological regulation of intraocular pressure and the vision process. In the brain, DP receptor mRNA was dominantly expressed in the leptomeninges and was not detected in the brain parenchyma including the ventral rostral forebrain, the surface area of which is reportedly involved in sleep induction by PGD2.

Amino Acid Sequence↗
PubMed1992

cDNA cloning of new protein tyrosine phosphatases in the human colon.

Oligonucleotide probes corresponding to three invariant amino acid sequence motifs within the protein tyrosine phosphatase (PTPase) catalytic domain were synthesized and employed in the polymerase chain reaction (PCR). PCR products amplified from human colonic tissues were analyzed. Among 41 cDNA clones sequenced, two putative novel PTPases designated as CL-6 and CL-2B were isolated. cDNA cloning of CL-6 was performed, and three overlapped cDNA clones encoding part of the coding region, which was 2.1 kb long, were obtained. Expression of mRNAs of these clones was then investigated by Northern blot analysis or reverse transcriptase-PCR, suggesting that CL-6 mRNA may be expressed in a cell-type-specific manner, whereas the expression of CL-2B mRNA could be ubiquitous.

Base Sequence↗
PubMed2004

Comparative analysis of the CD19+ and CD138+ cell antibody repertoires in the cerebrospinal fluid of patients with multiple sclerosis.

Increased amounts of intrathecally synthesized IgG and oligoclonal bands have long been recognized as a hallmark of multiple sclerosis (MS). B cells and plasma cells are components of the inflammatory infiltrates in both active and chronic MS lesions, and increased numbers of these cells are present in MS cerebrospinal fluid (CSF). Single-cell RT-PCR was used to analyze both the CD19+ B cell and CD138+ plasma cell populations in CSF of two patients with clinically definite MS and of one MS patient whose CSF was obtained after a clinically isolated syndrome, but before the second episode. Sequence analysis of amplified IgG V region sequences identified the rearranged germline segments, extent of somatic mutation, and clonal relationships within and between the two cell populations in the three MS patients. Expanded B cell and plasma cell clones were detected in each MS CSF and in all three patients the CD138+ IgG repertoire was more restricted. However, little if any significant sequence overlap was observed between the CD19+ and CD138+ repertoires of each donor. Detection of plasma cell clones by single-cell PCR will facilitate the in vitro production of recombinant Abs useful in identifying disease-relevant Ags.

Adult↗
PubMed1998

Identification of ATM mutations using extended RT-PCR and restriction endonuclease fingerprinting, and elucidation of the repertoire of A-T mutations in Israel.

Ataxia-telangiectasia (A-T) is an autosomal recessive disorder characterized by neurodegeneration, immunodeficiency, cancer predisposition, and radiation sensitivity. The responsible gene, ATM, has an extensive genomic structure and encodes a large transcript with a 9.2 kb open reading frame (ORF). A-T mutations are extremely variable and most of them are private. We streamlined a high throughput protocol for the search for ATM mutations. The entire ATM ORF is amplified in a single RT-PCR step requiring a minimal amount of RNA. The product can serve for numerous nested PCRs in which overlapping portions of the ORF are further amplified and subjected to restriction endonuclease fingerprinting (REF) analysis. Splicing errors are readily detectable during the initial amplification of each portion. Using this protocol, we identified 5 novel A-T mutations and completed the elucidation of the molecular basis of A-T in the Israeli population.

Ataxia Telangiectasia↗
PubMed1999

The central part of the mouse immunoglobulin kappa locus.

At the present state of analysis the central part of the kappa locus comprises four contigs of together 1.2 Mb and contains 55 Vkappa genes. It is flanked by the 3' part of the locus with 22 Vkappa genes in 0.4 Mb (T. Kirschbaum et al., Eur. J. Immunol. 1998. 28: 1458-1466) and the 5' part with 63 Vkappa genes in six contigs of together 1.5 Mb (F. Röschenthaler et al., accompanying report). The 5' and the central regions have one large contig in common. A part of the central region is linked to the 3' region resulting in a 1.1-Mb contig. The structure of the contigs was established mainly by the analysis of overlapping cosmid clones derived from genomic DNA and yeast and bacterial artificial chromosomes (YACs and BACs) and by PCR techniques. Pulsed-field gel electrophoresis of YAC digests indicated that three gaps between the contigs of the central region are 10-40 kb in size, comprising together about 90 kb. Internal duplications in this part of the locus and rearranged YACs were the major problems of the structural work. Structural details are to be found on the Internet at http://www.med.uni-muenchen.de/biochemie/zach au/kappa.htm. In a concluding section of the report the mouse kappa locus is compared to the human one and some aspects of the evolution of the kappa locus are discussed.

Animals↗
PubMed2004

Extensive analysis of the 7q31 region in human prostate tumors supports TES as the best candidate tumor suppressor gene.

Loss of heterozygosity (LOH) on chromosome arm 7q31 is found in many prostate tumors. Such alterations are generally associated with inactivation of tumor suppressor genes. It has been shown previously that the main region of LOH at 7q31 spans the interval between the D7S486 and D7S2460 microsatellite loci, which contains several candidate tumor suppressor genes (TSG) such as TES, CAV2, CAV1, MET, CAPZA2, ST7 and WNT2. We tested 41 human sporadic prostate tumors for 7q31 LOH by using 5 polymorphic markers overlapping the critical region and used a real-time reverse transcriptase-polymerase chain reaction (RT-PCR) assay to study the expression of the 7 candidate TSGs located in this genomic region. We found that CAV1, CAV2, MET and TES mRNA expression was lower in prostate tumors than in normal prostate tissues. Our immunohistochemical results and previously published data on the compartmental expression of these messenger RNAs in stromal and epithelial cells suggest that TES is the best candidate tumor suppressor gene at 7q31.

Chromosomes, Human, Pair 7↗
PubMed2003

Myosin II in retinal pigmented epithelial cells: evidence for an association with membranous vesicles.

The goal of this study was to further characterize and identify possible functions for a cytoplasmic myosin II protein which we have isolated from retinal pigmented epithelial (RPE) cells. The nucleotide and deduced amino acid sequences are highly identical to non-muscle myosin heavy chain II-A (NMMHC II-A). However, this RPE myosin displays characteristics that are atypical of other myosins, including an affinity for carbohydrate and a C-terminal sequence extension, suggesting it may have a specialized function. In this study, reverse transcriptase-PCR using isoform-specific primers demonstrated that the RPE myosin and conventional NMMHC II-A have overlapping but distinguishable tissue expression profiles. To gain clues to function, subcellular distribution was determined in motile RPE cells using indirect immunofluorescence. In addition to subtle differences in localization that appeared to further distinguish this molecule from NMMHC II-A, these studies revealed a colocalization with phagocytosed intracellular vesicles. In vitro experiments suggest that the association in situ was not simply coincidental, because isolated vesicles interacted with the protein in cosedimentation assays. Taken together, our observations suggest the RPE myosin exhibits characteristics different from conventional myosin II-A and may function in intracellular vesicle transport.

Biological Transport, Active↗
PubMed2000

Gene expression profiling in human peripheral blood mononuclear cells using high-density filter-based cDNA microarrays.

Microarray technology has provided the ability to analyse the expression profiles for thousands of genes in parallel. The need for highly specialised equipment to use certain types of microarrays has restricted the application of this technology to a small number of dedicated laboratories. High-density filter-based cDNA microarrays provide a low-cost option for performing high-throughput gene expression analysis. We have used a model system in which filter-based cDNA microarrays representing over 4000 known human genes were used to monitor the kinetics of gene expression in human peripheral blood mononuclear cells (PBMCs) stimulated with phytohaemagluttinin (PHA). Using software-based cluster analysis, we identified 104 genes that altered in expression levels in response to PHA stimulation of PBMCs and showed that there was a considerable overlap between genes with similar temporal expression profiles and similar functional roles. Comparison of microarray quantitation with quantitative PCR showed almost identical expression profiles for a number of genes. Coupled with the fact that our findings are in agreement with a large number of independent observations, we conclude that the use of filter-based cDNA microarrays is a valid and accurate method for high-throughput gene expression profiling.

Cells, Cultured↗
PubMed1997

Structural analysis of a missense mutation (Val414Phe) in the catalytic core domain of the factor XIII(A) subunit.

Molecular analysis has been performed on a Malaysian patient with a severe bleeding disorder due to factor XIII(A) subunit deficiency. Total mRNA was isolated from the patient's leucocytes and four overlapping segments corresponding to the entire coding region of the A subunit cDNA were amplified by RT-PCR. The cDNA segments amplified efficiently and were of expected size. Direct sequencing of the complete reading frame revealed a single homozygous base change (nt 1327G-T) in exon 10 corresponding to a missense mutation, Val414Phe, in the catalytic core domain of the A subunit monomer. The mutation eliminates a BsaJ1 restriction site and family screening showed that both parents were heterozygous for the defect. The base substitution was absent in 55 normal individuals. Val414 is a highly conserved residue in the calcium-dependent transglutaminase enzyme family. Computer modelling based on 3D crystallographic data predicts that the bulky aromatic side chain of the substituted phenylalanine residue distorts protein folding and destabilizes the molecule. In addition, conformation changes in the adjacent catalytic and calcium binding regions of the A subunit are likely to impair the enzymatic activity of any protein synthesized.

Adult↗