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At least 1,621 records · Page 90Linked to original sources
PubMed1987

Type XII collagen: distinct extracellular matrix component discovered by cDNA cloning.

We have screened a cDNA library constructed from tendon fibroblast mRNA for the presence of collagenous coding sequences. Nucleotide sequence analysis of one isolated clone, pMG377, reveals that the clone encodes a polypeptide that is homologous to, yet distinctly different from, type IX short-chain collagen polypeptides. The structure of the conceptual translation product of the cDNA is also different from that of all other collagen types. Therefore, we have given the type IX-like collagen chain encoded by pMG377 the designation alpha 1(XII). Ribonuclease protection assays with single-stranded cRNA probes demonstrate that alpha 1(XII) mRNA is present in several tissues such as calvaria, tendon, and sternal cartilage of 17-day-old chicken embryo and in cornea from 6-day-old embryos. Using pMG377 as the hybridization probe, we isolated a fragment of the corresponding gene from a chicken genomic library. Partial nucleotide sequence analysis of the genomic clone DG12 shows that the exon/intron structure of the alpha 1(XII) collagen gene appears to be homologous to that of the alpha 1(IX) and alpha 2(IX) collagen genes. Our data demonstrate that types IX and XII collagen are two homologous members of a family of unique collagenous proteins that show tissue-specific patterns of expression. Based on their structure and the properties of their genes, we conclude that this family of collagens is distinctly different from that of fibrillar collagens.

Amino Acid Sequence↗
PubMed2005

Using siclopps for the discovery of novel antimicrobial peptides and their targets.

High throughput screening of SICLOPPS libraries afforded six distinct cyclic peptides that inhibit Escherichia coli growth both in liquid and solid media. One of these peptides (LN05) reduced both bacterial growth rate and caused cell aggregation in liquid media. Mutant bacteria immune to LN05 action were obtained at a frequency of 10(-7). Over-expression of an E. coli genomic library in the presence of LN05 production resulted in enrichment of a single genomic construct, a fragment of the NarZ gene.

Anti-Bacterial Agents↗
PubMed1995

Cloning and properties of a rice gene encoding phenylalanine ammonia-lyase.

Phenylalanine ammonia-lyase (PAL) genomic sequences were isolated from a rice (Oryza sativa L.) genomic library using a PCR-amplified rice PAL DNA fragment as a probe. There is a small family of PAL genes in the rice genome. The nucleotide sequence of one PAL gene, ZB8, was determined. The ZB8 gene is 4660 bp in length and consists of two exons and one intron. It encodes a polypeptide of 710 amino acids. The transcription start site was 137 bp upstream from the translation initiation site. Rice PAL transcripts accumulated to a high level in stems, with lower levels in roots and leaves. Wounding of leaf tissues induced ZB8 PAL transcripts to a high level. In rice suspension-cultured cells treated with fungal cell wall elicitors, the ZB8 PAL transcript increased within 30 min and reached maximum levels in 1-2 h. The transcription of the ZB8 gene was investigated by fusing its promoter to the reporter gene beta-glucuronidase (GUS) and transforming the construct into rice and tobacco plants, as well as rice suspension-cultured cells. High levels of GUS activity were observed in stems, moderate levels in roots and low levels in leaves of transgenic rice and tobacco plants. Histochemical analysis indicated that in transgenic rice the promoter was active in root apical tips, lateral root initiation sites, and vascular and epidermal tissues of stems and roots. In rice flowers, high GUS activity was observed in floral shoots, receptacles, anthers and filaments, occasionally GUS activity was also detected in lemma and awn tissues. In tobacco flowers, high GUS activity was detected in the pink part of petals. Consistent with the activity of endogenous PAL transcripts, wounding of rice and tobacco leaf tissues induced GUS activity from low basal levels. Tobacco mosaic virus (TMV) infection of tobacco leaves induced GUS activity to a high level. Fungal cell wall elicitors strongly induced GUS activity and GUS transcripts to high levels in transgenic rice suspension-cultured cells. We demonstrated that the promoter of ZB8 gene is both developmentally regulated and stress-inducible.

Amino Acid Sequence↗
PubMed1998

Organization of the human natriuretic peptide receptor A gene.

We have determined the structural organization of the human natriuretic peptide receptor A (hNPRA) gene without screening the genomic library. Based on the information for the cDNA of hNPRA, we amplified some fragments of the long polymerase chain reaction (PCR) products covering all genomic sequences of the gene and directly sequenced the products after extraction and purification. The hNPRA gene spans approximately 16 kb and contains 22 exons and 21 introns. All of the exon-intron junction sequences coincide with the GT/AG consensus sequence. The sequence encoding the transmembrane domain, one part of the hNPRA topological structure, exists in exon 7. The results of this first study, determination of the hNPRA gene structure, will facilitate further genetic analysis of the hNPRA gene and its related diseases.

Asian People↗
PubMed1988

Cloning, characterization and expression of the bacterial globin gene from Vitreoscilla in Escherichia coli.

The genomic locus responsible for production of the globin portion of Vitreoscilla hemoglobin (VtHb), the only well-characterized bacterial hemoglobin (Hb), has been cloned and expressed in Escherichia coli. A 17-mer oligodeoxynucleotide, corresponding to a region of the VtHb amino acid sequence was used as a hybridization probe to screen a Vitreoscilla genomic library constructed in broad-host-range cosmid vector pVK102. E. coli, carrying recombinant pVK102:H5 which contained a 16.5-kb insert of Vitreoscilla genomic DNA, produced three to four times more Hb than Vitreoscilla. Restriction mapping and subcloning revealed that the globin-coding gene (vgb) was completely localized on a 1.4-kb HindIII-SalI fragment of the 16.5-kb insert. Production of VtHb still occurred when this 1.4-kb fragment was cloned in plasmids pUC8 and pUC9 in opposite orientations, suggesting the presence of a Vitreoscilla promoter on this fragment. A single copy of this gene on the chromosome was indicated by Southern-blot analysis, and a 450-500-nt RNA transcript specific for the globin gene was detected after Northern hybridization. A partially purified Hb preparation from E. coli harboring the recombinant plasmid had identical spectral properties and subunit molecular size as authentic VtHb. The Hb in respiring cells of E. coli was in the physiologically functional oxyHb form.

Blotting, Northern↗
PubMed1992

Cloning of a full-length cDNA encoding bovine interleukin 4 by the polymerase chain reaction.

A human interleukin 4 (hIL-4)-encoding cDNA (hIL4) probe was used to screen a bovine genomic library, and three clones containing sequences with homology to the human and mouse IL4 cDNAs were isolated. Sequence information obtained from one of these genomic clones was used to design an oligodeoxyribonucleotide primer corresponding to the transcription start point region for use in the polymerase chain reaction (PCR). The PCR-RACE protocol, designed for the rapid amplification of cDNA ends, was successfully used to generate a full-length bovine IL4 (bIL4) cDNA clone from polyadenylated RNA isolated from concanavalin A-stimulated bovine lymph node cells. The bIL4 cDNA is 570 bp in length and contains an open reading frame of 405 nucleotides (nt), coding for a 15.1-kDa precursor of 135 amino acids (aa), which should be reduced to 12.6 kDa for unglycosylated bIL4 after cleavage of a putative hydrophobic leader sequence of 24 aa. The aa sequence contains one possible Asn-linked glycosylation site. Bovine IL4 is shorter than mouse (mIL4) and hIL4, because of a 51-nt deletion in the coding region. Comparison of the overall nt and deduced aa sequences shows a greater homology of bIL4 with hIL4 than with mIL4. This homology is not evenly distributed, however, with the nt sequences 5' and 3' of the coding region showing a much greater homology between all three species than the coding sequence.

Amino Acid Sequence↗
PubMed1996

Molecular cloning of a new member of the putative G protein-coupled receptor gene from barnacle Balanus amphitrite.

An intronless gene encoding a putative G protein-coupled receptor was isolated from the genomic library of barnacle Balanus amphitrite Darwin, with probes obtained from degenerate polymerase chain reaction (PCR) primers used to amplify putative transmembrane regions. The cloned genome DNA specifies an open reading frame of 1431 bp encoding 476 amino acids with seven hydrophobic transmembrane (TM)-spanning regions. The predicted protein contains potential asparagine-linked glycosylation and serine/threonine phosphorylation sites in the N-terminal and intracellular loops, respectively. Moreover, the protein has a consensus G protein-binding motif (Ala-Ile-Ser-Leu-Asp-Arg-Tyr-Leu-Ala) in TM domain III. This receptor is most closely related to human alpha 2-adrenergic receptor with 36.9% identity in 409 amino acids overlap. It is also homologous to human serotonin1A (5HT), snail pond 5HT and mouse D2-dopamine receptors with 33-36% identities. Within TM regions among these biogenic amine receptors, the cloned receptor shows considerable amino acid homology with more than 40% overall identities.

Animals↗
PubMed1992

Organization of the gene encoding the mouse T-cell-specific serine proteinase "granzyme A".

The mouse serine protease granzyme A is a member of a closely related family of T-cell-associated proteolytic enzymes, designated granzymes A-G. Previous studies have indicated that granzymes A and B are involved in various T-cell-mediated processes. Here we report the genomic organization of the granzyme A gene. We have cloned a 15-kb DNA fragment from a genomic library of a cloned CD8+ T-cell line and sequenced the exon-intron boundaries. The gene consists of five exons, and its genomic organization is very similar to that described for granzymes B, C, and F. In addition, we have sequenced 1.4 kb of the 5'-region and 1.1 kb of the 3'-region flanking the granzyme A gene. Putative promoter and enhancer elements were identified by sequence comparison with known consensus sequences. Some of these regulatory elements seem to be associated exclusively with granzyme A, whereas others are shared by members of the granzyme family.

Amino Acid Sequence↗
PubMed1998

Cloning and structure of a rabbit protein inhibitor of neuronal nitric oxide synthase (PIN) gene and its pseudogene.

Neuronal nitric oxide synthase (nNOS), the biosynthetic enzyme for the free radical neurotransmitter nitric oxide, was found to be inhibited by the protein inhibitor of nNOS, designated PIN (Jaffrey, S.R. and Snyder, S.H., (1996) Science 274, 774-777). The cDNA clone encoding a rabbit PIN was isolated, and the translated PIN protein was89 amino acid long sharing 100% of its deduced amino acid sequence with rat PIN. Using a radiolabelled riboprobe derived from the rabbit PIN cDNA, the rabbit PIN gene was isolated from a rabbit genomic library and the structural organization of the gene was determined. The gene contains three exons separated by two introns spanning approx. 2.3kb of genomic DNA. 5' RACE analysis mapped the transcriptional initiation site 98bp upstream of the initiator methionine codon. Characterization of the 5' flanking genomic region revealed that the rabbit PIN promoter is TATA-less, but contains a CCAAT box as well as various putative transcription factor-binding elements. The 3' untranslated region contains consensus polyadenylation signal (AATAAA). We also isolated an intronless gene with 93% nucleotide sequence similarity to the rabbit PIN cDNA. Sequence analysis indicates that the open reading frame was interrupted by a premature stop codon and frameshift which resulted in a processed pseudogene of the rabbit PIN.

Amino Acid Sequence↗
PubMed1999

The structure of the rat amiloride-sensitive epithelial sodium channel gamma subunit gene and functional analysis of its promoter.

Prolonged dietary Na+ depletion and chronic administration of adrenal steroids increase steady-state mRNA levels of the gamma subunit of the epithelial sodium channel (gammaENaC) in rat colon. This increase correlates with a marked increase in transepithelial Na+ transport and is thought to occur via transcriptional regulation. To begin to evaluate these mechanisms in detail, we determined the organization of the rat gammaENaC gene. A rat genomic library was screened and overlapping lambda clones that together span the gene (approximately 36 kb) and contain at least 1 kb of 5' flanking genomic DNA were isolated. As in the human gene, the rat gammaENaC gene contains 13 exons and a CpG island at the 5' end of the gene. A single transcription start site was identified in rat kidney by nuclease protection assay defining a 5' untranslated region of 126 nt. The translation initiation codon was identified within the second exon and the entire 3' UTR (approximately 1 kb) was within the last exon. 800 bp of 5' flanking sequence, as well as the 3.4 kb first intron, were sequenced and analyzed for transcriptional regulatory motifs. Analogous to the human gammaENaC gene [Thomas, C.P., Doggett, N.A., Fisher, R., Stokes J.B., 1996. Genomic organization and the 5' flanking region of the gamma subunit of the human amiloride-sensitive epithelial sodium channel. J. Biol. Chem. 271, 26 062--26 066], two GC boxes were seen at -30 and -61 to the transcription start site. In addition, putative AP-1, AP-2, CRE, Sp1 and GATA-1 and GRE motifs were identified elsewhere in the 5' flanking region or the first intron. Two mammalian-wide interspersed repeats and a rodent-specific B1 repeat were also identified within the first intron. Fragments containing the putative GRE motifs coupled to luciferase did not confer a glucocorticoid-stimulated response in two cell lines that contained a functional glucocorticoid receptor. However, a 76 nt rat gammaENaC 5' flanking fragment (-76 to +68) directed expression of luciferase in the epithelial cell lines H441 and FRTL5, suggesting that this minimal region that contained both GC boxes was sufficient for promoter activity.

Animals↗
PubMed1996

Nucleotide sequence of the Kaposi sarcoma-associated herpesvirus (HHV8).

The genome of the Kaposi sarcoma-associated herpesvirus (KSHV or HHV8) was mapped with cosmid and phage genomic libraries from the BC-1 cell line. Its nucleotide sequence was determined except for a 3-kb region at the right end of the genome that was refractory to cloning. The BC-1 KSHV genome consists of a 140.5-kb-long unique coding region flanked by multiple G + C-rich 801-bp terminal repeat sequences. A genomic duplication that apparently arose in the parental tumor is present in this cell culture-derived strain. At least 81 ORFs, including 66 with homology to herpesvirus saimiri ORFs, and 5 internal repeat regions are present in the long unique region. The virus encodes homologs to complement-binding proteins, three cytokines (two macrophage inflammatory proteins and interleukin 6), dihydrofolate reductase, bcl-2, interferon regulatory factors, interleukin 8 receptor, neural cell adhesion molecule-like adhesin, and a D-type cyclin, as well as viral structural and metabolic proteins. Terminal repeat analysis of virus DNA from a KS lesion suggests a monoclonal expansion of KSHV in the KS tumor.

Base Sequence↗
PubMed1996

Single locus microsatellites isolated using 5' anchored PCR.

Microsatellites are widely used as genetic markers because they are co-dominant, multiallelic, easily scored and highly polymorphic. A major drawback of microsatellite markers is the time and cost required to characterise them. We have developed a novel technique to reduce this cost by producing a microsatellite-rich PCR profile from genomic DNA which was cloned to yield a genomic library enriched for microsatellites. Sequence data and subsequent allele scoring within pedigrees revealed that these microsatellites retained their original repeat length and segregated normally. This technique permits genomic amplification with only one specific primer. Together with enrichment, the savings in primer costs reduces the cost of microsatellite characterisation considerably.

DNA Primers↗
PubMed2000

Cloning and sequencing of the triacylglycerol lipase gene of Aspergillus oryzae and its expression in Escherichia coli.

Aspergillus oryzae produces at least three extracellular lipolytic enzymes, L1, L2 and L3 (cutinase, mono- and diacylglycerol lipase, and triacylglycerol lipase, respectively). We cloned the triacylglycerol lipase gene (provisionally designated tglA) by screening a genomic library using a PCR product obtained with two degenerate oligonucleotide primers corresponding to amino acid sequences of L3 as probes. Nucleotide sequencing of the genomic DNA and cDNA revealed that the L3 gene (tglA) has an open reading frame comprising 954 nucleotides, which contains three introns of 47, 83 and 62 bp. The deduced amino acid sequence of the tglA gene corresponds to 254 amino acid residues including a signal sequence of 30 amino acids and, in spite of the difference in substrate specificity, it is homologous to those of cutinases from fungi. Three residues presumed to form the catalytic triad, Ser, Asp and His, are conserved. The cloned cDNA of the tglA gene was expressed in Escherichia coli, and enzyme assaying and zymography revealed that the cloned cDNA encodes a functional triacylglycerol lipase.

Amino Acid Sequence↗
PubMed1991

Cloning and characterization of the plasma membrane H(+)-ATPase from Candida albicans.

The Candida albicans PMA1 gene was isolated from a genomic library by using a hybridization probe obtained from the PMA1 gene of Saccharomyces cerevisiae. The gene was localized to chromosome III of the Candida genome. An open reading frame of 2,685 nucleotides predicts an amino acid sequence of 895 amino acids that is 83% homologous at both the DNA and protein levels to its S. cerevisiae equivalent. A polyadenylated mRNA transcript of about 4,000 nucleotides contains a highly folded AU-rich leader of 242 nucleotides. The structure of the gene, codon bias, and levels of approximately 100-kDa H(+)-ATPase protein recovered in plasma membranes indicate a highly expressed gene. The plasma membrane ATPase was purified to about 90% homogeneity and appeared to be blocked at the amino terminus. Three hydrophobic membrane sector tryptic fragments from the partially digested ATPase provided internal sequence information for over 50 amino acids, which agrees with the sequence predicted by the cloned gene. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis indicated that the C. albicans enzyme is about 3 kDa smaller than its Saccharomyces counterpart and was consistent with a predicted Mr of 97,398. Antibodies to the S. cerevisiae whole ATPase or its carboxyl terminus bound to the C. albicans enzyme but with lower avidity. Kinetic analysis showed that the Candida and Saccharomyces ATPases respond to glucose activation-starvation in nonidentical fashions. The amino-terminal domain of the C. albicans ATPase is marked by a net deletion of 23 amino acids in comparison with the S. cerevisiae ATPase. These differences maintain net charge, occur in nonconserved regions of fungal ATPases, and are sufficient to account for the observed difference in electrophoretic mobility between the two yeast ATPases.

Amino Acid Sequence↗
PubMed1991

Sequence and structure of a phenylalanine ammonia-lyase gene from Glycine max.

The gene encoding a key enzyme in anthocyanin biosynthesis, phenylalanine ammonia-lyase (PAL), was cloned from soybean (Glycine max). The purpose was to obtain a molecular probe to study the organization of this gene family in soybean and to examine novel regulatory mechanisms present in the anthocyanin biosynthetic pathway of this system. A soybean genomic library was constructed in the bacteriophage vector lambda Charon 35. A PAL cDNA clone from Phaseolus vulgaris was used in screening the library, and two PAL genes were isolated. One gene was sequenced entirely and analyzed by sequence homology to the PAL2 gene of Phaseolus vulgaris. Genomic analysis indicates that PAL sequences of Glycine max exist as a small gene family consisting of only two to three members. The representative PAL gene sequenced (PAL1) has a coding region of 2142 basepairs divided among two exons. The single intron is 1519 basepairs and splits the 131st codon.

Amino Acid Sequence↗
PubMed1999

Microsatellites in the silkworm, Bombyx mori: abundance, polymorphism, and strain characterization.

We have isolated and characterized microsatellites (simple sequence repeat (SSR) loci) from the silkworm genome. The screening of a partial genomic library by the conventional hybridization method led to the isolation of 28 microsatellites harbouring clones. The abundance of (CA)n repeats in the silkworm genome was akin to those reported in the other organisms such as honey bee, pig, and human, but the (CT)n repeat motif is less common compared to bumble bee and honey bee genomes. Detailed analysis of 13 diverse silkworm strains with a representative of 15 microsatellite loci revealed a number of alleles ranging from 3 to 17 with heterozygosity values of 0.66-0.90. Along with strain-specific microsatellite markers, diapause and non-diapause strain-specific alleles were also identified. The repeat length did not show any relationship with the degree of polymorphism in the present study. The co-dominant inheritance of microsatellite markers was demonstrated in F1 offspring. A list of primer sequences that tag each locus is provided. The availability of microsatellite markers can be expected to enhance the power and resolution of genome analysis in silkworm.

Alleles↗
PubMed1992

Human gene S31 encodes the pharmacologically defined serotonin 5-hydroxytryptamine1E receptor.

The gene encoding a human 5-hydroxytryptamine (5-HT)1 receptor subtype was isolated from a human placental genomic library by using oligonucleotide probes derived from transmembrane regions of the cloned human 5-HT1D beta receptor. The deduced amino acid sequence of the genomic clone hp75d is identical to that of the recently isolated, but uncharacterized, novel serotonin receptor gene S31. Transmembrane domain sequence comparison of clone hp75d with other guanine nucleotide-binding protein-coupled receptors revealed the highest degree of homology (64%) to the 5-HT1D alpha and 5-HT1D beta subtypes and lower degrees of homology (35-52%) to other serotonergic and catecholaminergic receptors. A stable cell line expressing this gene was established, using murine fibroblasts as the host cell, for pharmacological evaluation. High affinity (Kd = 9.7 nM), saturable (Bmax = 2.4 pmol/mg of protein) [3H]5-HT binding was detected using membranes derived from stable transfectants. Most compounds displayed low affinity (K(i) greater than 200 nM) for the expressed gene, with the exception of 5-HT (K(i) = 10 nM). The rank order of potency of ligands to compete for the [3H]5-HT-labeled site best matched the binding profile of the pharmacologically defined 5-HT1E binding site, 5-HT greater than methysergide greater than ergotamine greater than 8-hydroxy-2-(di-n-propylamino)tetralin greater than 5-carboxyamidotryptamine greater than ketanserin. 5'-Guanylylimidodiphosphate decreased high affinity agonist ([3H]5-HT) binding in a dose-dependent manner. 5-HT produced a dose-dependent inhibition of forskolin-stimulated cAMP accumulation in intact cells stably expressing the 5-HT1E gene. The response was blocked by the nonselective 5-HT1 receptor antagonist methiothepin. The molecular biological and pharmacological data are consistent with the designation that clone hp75d encodes a functional 5-HT1E receptor.

Adenylyl Cyclases↗
PubMed1991

The genes for the trophoblast interferons and the related interferon-alpha II possess distinct 5'-promoter and 3'-flanking sequences.

The genes for trophoblast interferons (IFN) bovine trophoblast protein-1 (bTP-1) and ovine trophoblast protein-1 (oTP-1) are expressed massively in the trophectoderm of preimplantation bovine and ovine concepti during the period of maternal recognition of pregnancy. These 172-amino acid IFN are closely related to the IFN-alpha II, a family of "long" IFN expressed in virus-induced leukocytes. Genomic Southern blotting with a full-length bTP-1 cDNA revealed about 15 genes that bind the probe with varying intensities. By using more specific probes for the 3'-ends of the cDNA, we have shown that only four to five of these represent bTP-1 genes, whereas no more than another four are IFN-alpha II. Genes for bTP-1 and IFN-alpha II, all of which are intronless, have been isolated from bovine genomic libraries, and their nucleotide sequences were compared. Additional bTP-1 genes and two distinct oTP-1 genes have been isolated from bovine and ovine genomic DNA by using the polymerase chain reaction procedure in conjunction with specific 3'- and 5'- primers (derived from the bTP-1 gene sequences determined above). The promoter region up to 100 bases upstream from the transcription start sites of the trophoblast IFN are almost completely conserved across different genes and across species, yet show only limited sequence identity with IFN-alpha II. Two putative binding regions for interferon regulatory factor-1 as well as several GAAANN motifs (where N is any nucleotide) that have been implicated in viral responsiveness of alpha 1- and beta-IFN genes are retained at identical positions in all of the trophoblast genes. Putative interferon regulatory factor-1-binding nucleotide hexamers and GAAANN motifs are also present in the IFN-alpha II genes, but these are organized very differently than in the trophoblast IFN genes. A GAAATG motif is present in IFN-alpha II promoters but is absent in trophoblast IFN genes. Based on the evidence presented, it is proposed that the trophoblast interferons constitute a separate subclass of IFN-alpha distinct from IFN-alpha II and IFN-alpha I.

Animals↗