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PubMed2002

Molecular cloning, characterisation, and expression of a neutral trehalase from the insect pathogenic fungus Metarhizium anisopliae.

A neutral trehalase gene (NTH1) was isolated from a lambdaEMBL3 genomic library of the insect pathogenic fungus Metarhizium anisopliae. Sequencing of the gene revealed extensive homology with other fungal neutral trehalases. The NTH1 gene exists as a single copy in the genome. Two STREs exist in the 5'UTR of NTH1, which may mediate transcriptional activation of the NTH1 gene in response to various stresses. The NTH1 gene encodes a protein of 737 amino acids with a calculated M(r) of 83.1kDa. A cyclic adenosine 3',5'-monophosphate-dependent phosphorylation consensus site and a putative calcium binding site were found in the amino-terminal domain of NTH1, consistent with a regulatory enzyme. Expression of the trehalase cDNA was achieved in Saccharomyces cerevisiae. Southern blot analysis of RT-PCR products indicated that the neutral trehalase gene is transcribed in vitro in cell-free haemolymph of the tobacco hornworm Manduca sexta and in vivo in the early stage of infection.

Animals↗

PubMed2003

Exploiting the yeast Saccharomyces cerevisiae for the study of the organization and evolution of complex genomes.

Yeast artificial chromosome (YAC) cloning systems have advanced the analysis of complex genomes considerably. They permit the cloning of larger fragments than do bacterial artificial chromosome systems, and the cloned material is more easily modified. We recently developed a novel YAC cloning system called transformation-associated recombination (TAR) cloning. Using in vivo recombination in yeast, TAR cloning selectively isolates, as circular YACs, desired chromosome segments or entire genes from complex genomes. The ability to do that without constructing a representative genomic library of random clones greatly facilitates analysis of gene function and its role in disease. In this review, we summarize how recombinational cloning techniques have advanced the study of complex genome organization, gene expression, and comparative genomics.

Chromosomes, Artificial, Yeast↗

PubMed2003

The minimum LOH region defined on chromosome 17p13.3 in human hepatocellular carcinoma with gene content analysis.

Hepatocellular carcinoma (HCC) is one of the most common human cancers in Asia. Previous studies have shown that in addition to aberrations of the p53 gene on chromosome 17p13.1, other gene(s) on chromosome 17p13.3 may also play a role in HCC. To detect the status of loss of heterozygosity (LOH) in HCC and to determine the minimum region of LOH on 17p13.3, we analyzed 22 paired HCC and non-cancerous liver samples with 14 polymorphic markers plus TP53 (p53 gene) as a comparison. The data revealed a high level of LOH (>68%) in a minimum region between D17S1866 and D17S1574, spanning over a 1.5 Mb region. Genomic library screening using markers in the region has resulted in the isolation of a cluster of BAC/PAC clones. We created a physical map in this region. Using large-scale genome sequencing, gene annotation, cDNA screening, and exon trapping, we identified 17 known genes and 13 novel genes in the minimum region. The function of these genes was analyzed and the possibility of several putative tumor suppressor genes was discussed.

Base Sequence↗

PubMed1997

Molecular cloning of a putative serotonin receptor gene from barnacle, Balanus amphitrite.

We isolated a putative serotonin receptor gene from a genomic library of the barnacle, balanus amphitrite Darwin, using an Ncol fragment of the barnacle G protein-coupled receptor gene that is homologous to the alpha 2-adrenoceptor. The cloned genomic DNA had no intron and specified an open reading frame of 1137 base pairs encoding 379 amino acids (aa). The predicted aa sequence has a typical seven hydrophobic transmembrane spanning region and a consensus G protein-binding motif. This receptor was most homologous to the human 5HT1A receptor and closely related to other 5HT1 receptor subtypes.

Amino Acid Sequence↗

PubMed1998

Genetic transformation of astaxanthin mutants of Phaffia rhodozyma.

Stable red astaxanthin-producing transformants were obtained after genetic transformation of two Phaffia rhodozyma mutants. A yellow mutant, accumulating beta-carotene, and an albino mutant, accumulating phytoene, from P. rhodozyma were transformed using a genomic library of wild-type strain UCD 67-385 in the pBluescript vector. Hybridization assays, using the pBluescript DNA as a radioactive probe, indicate integration of vector sequences into the genome of the transformants. Transformants DNA was digested with restriction endonucleases, ligated with T4 DNA ligase and then used to transform E. coli. Ampicillin resistant plasmids, containing 0.1, 0.2, and 2.5 kb DNA inserts of P. rhodozyma, were rescued from the yeast red transformants. The molecular analysis indicate that transformation has occurred by an integration event of donor DNA into the genome of the host strains.

Basidiomycota↗

PubMed1993

(CT)n and (GT)n microsatellites: a new class of genetic markers for Salmo trutta L. (brown trout).

Thirteen (GT)n and four (CT)n microsatellite loci (n = 10 or more and n = 20 or more, respectively) have been isolated from a partial genomic library of brown trout and sequenced. On average, a (GT)n repeat sequence occurs approximately every 23 kb and a (CT)n repeat sequence every 76 kb in brown trout genome. Primers for DNA amplifications using the polymerase chain reaction (PCR) were synthesized for three single locus microsatellites. Mendelian inheritance of the observed polymorphisms was confirmed in full-sib families. Four brown trout populations (10 unrelated individuals per population) were screened for polymorphism with these three microsatellite loci. The total number of alleles detected in the four populations is five at one locus, six at the other two microsatellite loci and is three, on average, per population. Heterozygosities range from 0.18 to 0.74. The largest differences in allelic frequencies occurred between the Mediterranean and the Atlantic populations: this result is congruent with previous allozymic data. The gene-centromere distances of the three microsatellite markers were determined on gynogenetic lines: post-reduction rates range from 0.17 to 0.60. For all the three microsatellite loci, the primers designed from brown trout sequences can be used in another closely related species of salmonid, the rainbow trout (Oncorhynchus mykiss). This last aspect supports the view that microsatellite markers may have wide application in genetic studies in salmonid species and fishes in general.

Animals↗

PubMed1985

Gene encoding human growth hormone-releasing factor precursor: structure, sequence, and chromosomal assignment.

We have isolated and characterized overlapping clones from phage lambda and cosmid human genomic libraries that predict the entire structure of the gene encoding the precursor to human growth hormone-releasing factor. The gene includes five exons spanning 10 kilobase pairs of human genomic DNA. There appears to be a segregation of distinct functional regions of the GRF precursor and its mRNA into the five exons of the gene. The DNA sequences of all exons, intron/exon boundaries, and 5' and 3' flanking regions are presented. Dot-blot analysis of DNA from high resolution dual-laser-sorted human chromosomes indicates that the single-copy growth hormone-releasing factor gene is located on human chromosome 20.

Amino Acid Sequence↗

PubMed1992

Molecular cloning and chromosomal localization of a human gene encoding D-amino-acid oxidase.

Genomic clones covering the entire sequence of the gene encoding human D-amino-acid oxidase (DAO) (EC 1.4.3.3), one of the principal and characteristic flavoenzymes of peroxisomes, were isolated from human placental genomic libraries with the aid of a previously cloned cDNA for human DAO as a probe. Nucleotide sequence analysis revealed that the gene, present as a single copy in the human genome, comprises 11 exons and spans 20 kilobase pairs. The protein sequences containing the catalytically important residues, Tyr-228 and His-307, are coded for by separate exons. Heterologous transcription initiation sites were identified by primer extension analysis, and the sequence of the 5'-flanking region of the DAO gene was found to show some features common to other mammalian genes, such as those of glucocorticoid and the cAMP-responsive element. An additional noteworthy feature is the presence of promoter-like sequences in the first intron of the gene. In addition, two sequences of alternating pyrimidine and purine nucleotides, (CA)20 and (CA)17, are also present in the first intron. Such sequences may play some role in the expression of the DAO gene in human tissues. With the use of genomic DNAs prepared from human and Chinese hamster somatic hybrid cells as templates for the polymerase chain reaction, the gene for DAO was localized to human chromosome 12.

Animals↗

PubMed1995

Towards the finer mapping of facioscapulohumeral muscular dystrophy at 4q35: construction of a laser microdissection library.

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal-dominant disorder which has been mapped to the 4q35 region. In order to saturate this distal 4q region with DNA markers, a laser-based chromosomal microdissection and microcloning procedure was used to construct a genomic library from the distal 20% of chromosome 4, derived from a single human metaphase spread. Of the 100 microclones analyzed from this library, 94 clones contained inserts sized from 80-800 bp, with an average size of 340 bp. Less than 20% of these clones hybridized to human repeat sequences. Seventy-two single-copy clones were further characterized by Southern blot hybridization against a DNA panel of somatic cell hybrids, containing various regions of chromosome 4. Forty-two clones mapped to chromosome 4, of which 8 clones mapped into the relevant 4q35 region. Twenty of these chromosome 4-specific clones were screened against "zoo-blots"; 11 clones, of which 3 mapped to 4q35, identified conserved sequences. This is the first report to describe the isolation of potential expressed sequences derived from the FSHD region. These chromosome region-specific microclones will be useful in the construction of the physical map of the region, the positional cloning of potential disease-associated genes, and the identification of additional polymorphic markers from within the distal 4q region.

Biomarkers↗

PubMed1992

Gene structure and expression of the mouse 5-HT2 receptor.

Serotonin (5-hydroxytryptamine, 5-HT) is an important neurotransmitter which mediates numerous physiological functions. Using the SacI-EcoRI restriction fragment of the rat brain 5-HT2 receptor cDNA as a probe, we have screened a mouse brain cDNA library, created by random priming and constructed in SWAJ vectors, and have isolated a cDNA encoding a 1.4 kb open reading frame which codes for a functional mouse 5-HT2 receptor identified from pharmacological binding profiles and coupling of phosphoinositide formation in a stably transfected fibroblast cell line. The deduced amino acid sequence is 97.4% identical to the rat 5-HT2 receptor. Using the same 5-HT2 receptor cDNA probe, ten positive genomic clones were isolated from two mouse genomic libraries constructed in the pWE15 cosmid vector and the EMBL-3 phage vector. Extensive mapping and sequencing of these genomic clones indicate the mouse 5-HT2 receptor coding region spans over 20 kb and is composed of three exons split by two introns. Northern blot analysis shows one band of 5-6 kb in the mouse brain, but not in the heart, lung, liver, or kidney total RNA. Southern analysis of mouse liver genomic DNA shows a simple pattern of digestion by several restriction enzymes, which suggests that one copy of the 5-HT2 receptor gene may exist in the mouse genome.

3T3 Cells↗

PubMed1987

Retropseudogenes for human chromosomal protein HMG-17.

The human genome contains multiple copies of sequences homologous to the cDNA coding for non-histone chromosomal protein HMG-17. To study the mechanism of generation and dispersion of the HMG-17 multigene family a human genomic library was screened and 70 clones isolated and studied by Southern transfer and restriction site analysis. The results suggest that most of the clones contain unique sequences. Sequence analysis of two genomic clones indicates that they contain elements typical of processed retropseudogenes. Even though both sequences contained open reading frames the sequences lacked introns, were flanked by short, direct repeats and lacked elements associated with functional genes. The sequences of the two pseudogenes were 85% homologous to each other and each was 90% homologous to the human cDNA. Based on the sequence difference in the open reading frame between the pseudogenes and the cDNA it can be estimated that the sequences arose approximately ten million years ago from a common precursor. The present paper, which is the first study on genes coding for this nucleosomal binding protein, indicates that the HMG-17 multigene family is the largest known human retropseudogene family.

Base Sequence↗

PubMed1982

Cloning and sequence analysis reveal structural variation among related zein genes in maize.

We have isolated a gene encoding one of the 19,000 dalton zein proteins from a maize genomic library constructed in Charon 4A. This gene occurs on a 7.7 kb Eco RI fragment, and based on Southern hybridization analysis, represents one of several homologous sequences present in the maize genome. The nucleotide sequence of the gene predicts a protein composed of 235 amino acids, including a signal peptide of 21 amino acids. There are no intervening sequences in the gene. By comparing the nucleotide sequence of this gene with that of a homologous cDNA clone, we have identified a basis for microheterogeneity within the gene family. The 5' nucleotide sequences of the genomic and cDNA clones are identical, but they differ in the center of the protein, where repeated amino acid sequences occur. A nucleotide sequence encoding a conserved peptide of 20 amino acids is repeated nine times in the center of both of these clones.

Base Sequence↗

PubMed1994

The genomic organization of the rat angiotensin II receptor AT1B.

Expression of two subtypes of angiotensin type 1 receptor (AT1A and AT1B) seems to be controlled by different mechanisms. As a step toward the elucidation of difference in the mechanism in their gene expression, the genomic organization of rat angiotensin II type 1B receptor was investigated. Rat genomic DNA fragments were cloned by screening a genomic library with fragments from two cDNA clones (2.3 and 2.2 kb) encoding the rat AT1B receptor. Three lambda clones were isolated, and the hybridizing restriction fragments were sequenced. Comparison of the genomic clone DNA and cDNA sequences revealed that the rat AT1B receptor gene contains three exons and two introns. Two of the exons encoded 5' untranslated sequences while the third exon contained the entire coding region. The 5'-flanking region contained the typical sequence motifs found in many eukaryotic promoters including a TATA box and a potential SP1 binding site. The transcription initiation site was located at -8 bp upstream the 5' end of the cDNA in the 5'-flanking region.

Animals↗

PubMed1990

High-frequency nuclear transformation of Chlamydomonas reinhardtii.

By using a method in which cell-wall-deficient Chlamydomonas reinhardtii cells were agitated in the presence of DNA, glass beads, and polyethylene glycol, nuclear transformation rates of approximately 10(3) transformants per micrograms of plasmid DNA were achieved. The nitrate reductase gene from wild-type Chlamydomonas was used to complement a mutation in the corresponding gene of a strain containing nit1-305. Transformants were selected by growth with nitrate as sole source of nitrogen. The transforming DNA integrated into the genome at a low-copy number in nit+ transformants. When cells carrying nit1-305 were agitated in the presence of two plasmids, one with the gene for nitrate reductase and the second with an unselected gene, the unselected gene was present in 10-50% of nit+ transformants. This high frequency of cotransformation will allow any cloned gene to be introduced into Chlamydomonas. Moreover, the overall efficiency of transformation should be high enough to permit isolation of genes from genomic libraries by complementation of stable nuclear mutants. The availability of efficient nuclear and chloroplast transformation in Chlamydomonas provides specific advantages for the study of chloroplast biogenesis, photosynthesis, and nuclear-chloroplast genome interactions.

Cell Nucleus↗

PubMed1992

Gene structure of Bombyx mori larval serum protein (BmLSP).

To understand the molecular mechanisms of the larval-specific transcription of Bombyx mori larval serum protein (BmLSP), we isolated a clone of the BmLSP gene from a genomic library and sequenced a 3.5-kb fragment. An intron was found in the 5' noncoding region of the BmLSP gene. A putative transcription start point was determined by primer extension analysis. Genomic Southern hybridization showed that there is one copy of the BmLSP gene in a haploid genome. A database search revealed that the BmLSP gene has presumptive repetitive sequences found in other B. mori genes, the sequence homologous to ecdysone-responsive elements and a heptamer sequence found in storage protein genes.

Amino Acid Sequence↗

PubMed1998

Isolation and characterization of an auxin-inducible SAUR gene from radish seedlings.

A gene homologue to the auxin-inducible SAUR (Small Auxin Up RNAs) of soybean was isolated from a cDNA and a genomic library of radish. The cDNA clone was about 470 bp in length and contained a DST (Down STream) element that was involved in mRNA instability in the 3'-untranslated region. The genomic clone contained two short sequences that related to auxin-responsible core sequences (AGTCTC and TATCCCAC) in its promoter region. The radish SAUR transcript was accumulated by auxin and cycloheximide treatments in the same way as that in other plant species. However, the NDE and DUE elements that were reported in all of the other SAUR gene promoters were not conserved in this radish SAUR gene. The results suggest that the promoter activity of the SAUR gene will be regulated by only two short sequences.

Amino Acid Sequence↗

PubMed1991

Gene characterization and promoter analysis of the human 5-lipoxygenase-activating protein (FLAP).

The human gene for the recently identified 5-lipoxy-genase-activating protein (FLAP) has been cloned. The gene was isolated from two different genomic libraries and is contained within four overlapping bacteriophage clones. The gene spans greater than 31 kilobases and consists of five small exons and four large introns. Southern blot analysis of human genomic DNA suggests the presence of a single FLAP gene per haploid genome. A restriction site polymorphism was identified in intron II of the gene. This restriction fragment length polymorphism appears to be present in the normal population at a fairly high frequency. The transcription initiation site was located, at an adenine residue, 74 base pairs upstream of the ATG initiation codon. Examination of the sequence of the gene 5' to the mRNA start site revealed the presence of a possible TATA box (TGTAAT) 22 base pairs upstream and potential AP-2 and glucocorticoid receptor binding sites. Functional analysis of the FLAP gene promoter was assayed by transient transfection of mouse P388D1 cells (macrophage) and human HepG2 cells (hepatoma) with 5'-flanking sequences of the FLAP gene fused upstream of the chloramphenicol acetyltransferase reporter gene. Expression in the mouse macrophage cell line of the various FLAP gene promoter constructs revealed both tissue specificity and enhancer-like activities whereas in the hepatoma cell line only a minimum level of activity was obtained.

5-Lipoxygenase-Activating Proteins↗

PubMed1989

Cloning and characterization of the mouse gene that encodes the peptide core of secretory granule proteoglycans and expression of this gene in transfected rat-1 fibroblasts.

A mouse liver genomic library was probed with a 450-base pair AccI----3' gene-specific fragment of a mouse bone marrow-derived mast cell proteoglycan cDNA to isolate 15-18-kilobase (kb) genomic clones containing the gene that encodes the peptide core of mouse secretory granule proteoglycans. Based on the nucleotide sequences of its 2.0-3.5-kb subcloned fragments, this mouse gene consists of three exons. The first exon contains 41 base pairs of untranslated nucleotides that are present in the 5' region of the transcript and also encodes the hydrophobic 25-amino acid signal peptide. The second exon encodes a 48-amino acid sequence that would be predicted to be the N terminus of the peptide core after the signal peptide has been removed in the endoplasmic reticulum. The third exon encodes a 79-amino acid sequence that includes the 15 amino acids immediately preceding an alternating serine-glycine 21-amino acid sequence for glycosaminoglycan attachment, and the subsequent C-terminal 43 amino acids; this exon also contains the 424 untranslated nucleotides present in the 3' region of the transcript. Primer extension and S1 nuclease protection analyses were performed to determine the transcription initiation site of the mouse gene. Rat-1 fibroblasts were cotransfected with the selectable marker pSV2 neo and a lambda clone (lambda MG-PG1) to obtain two rat-1 fibroblast cell lines that had the mouse secretory granule proteoglycan gene integrated into their genomes. RNA blot analysis of both cell lines revealed the presence of the 1.0-kb secretory granule proteoglycan peptide core mRNA transcript, indicating that lambda MG-PG1 contained the entire mouse secretory granule proteoglycan peptide core gene including some of the regulatory elements in its promoter region. The gene that encodes the peptide core of mouse secretory granule proteoglycans is the first proteoglycan gene to have its complete exon/intron organization determined and to be transfected and expressed in another cell type.

Amino Acid Sequence↗