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At least 1,765 records · Page 98Linked to original sources
PubMed1984

Structure of a chromosomal Phaseolus vulgaris lectin gene and its transcript.

A genomic library of Phaseolus vulgaris DNA was screened using a lectin cDNA clone that includes the entire coding region to obtain a lambda clone containing the corresponding nuclear lectin gene. Comparison of the cDNA and genomic nucleotide sequences showed that the gene has no intervening sequences. The 5' untranslated region was found to be only 10-16 base pairs long by S1 nuclease mapping. The lectin transcriptional unit is flanked by sequences which are exceptionally high (72-75%) in A + T content and its 5' flanking region contains potential transcription control elements.

Amino Acid Sequence↗
PubMed1995

Identification and inheritance of (GA/TC)n and (AC/GT)n repeats in the European flat oyster Ostrea edulis (L.).

Twelve microsatellites were isolated from a partial genomic library of Ostrea edulis using (GA/TC)n and (AC/GT)n probes and were subsequently sequenced. We estimate that, on average, 12,700 (GA/TC)n and 3900 (AC/GT)n microsatellites could be found in the genome assuming a random distribution. These estimates are high enough for the construction of a saturated genetic map. Primers were designed for three microsatellite loci, and analyses of polymorphism in a wild cohort revealed that one was suitable for population genetics studies (5 alleles), while the other two were highly polymorphic (between 17 and 48 alleles) and thus were more useful for paternity testing. Mendelian inheritance was tested on two full-sib families, and significant distortions of genotypic frequencies were found, although the gametic distributions seemed to be in agreement with Mendelian expectations. We interpret this as evidence for zygotic selection.

Animals↗
PubMed1986

Isolation and characterization of sarcomeric actin genes expressed in Xenopus laevis embryos.

A Xenopus laevis complementary DNA (cDNA) library prepared from messenger RNAs extracted from embryos has been screened for actin-coding sequences. Two cDNA clones corresponding to an alpha cardiac and an alpha skeletal muscle actin mRNA have been identified and characterized. From a genomic library, we have furthermore isolated the genes that correspond to the characterized cDNAs. In addition we have identified an actin processed gene which seems to be derived from a second type of skeletal muscle actin gene. Southern blot analysis of X. laevis DNA reveals that each of the three genes is present in at least two copies. In Xenopus tropicalis, a similar Southern blot analysis demonstrates that the three alpha actin genes exist as single copy. This result correlates with the genome duplication that has been proposed to have occurred recently in a X. laevis ancestor. A sequence comparison of the X. laevis cardiac and skeletal muscle actin cDNAs shows that the encoded peptides are highly conserved. Nevertheless, the numerous nucleotide changes at silent mutation sites suggest that the genes originated before the amphibia/reptile-bird divergence, more than 350 million years ago. Comparison of the promoters of the cardiac and skeletal actin genes, which are co-expressed in embryos, reveals a few common structural sequence elements.

Actins↗
PubMed1996

Genomic structure of the human bradykinin B1 receptor gene and preliminary characterization of its regulatory regions.

We report on the isolation of the human BK B1 receptor gene from a human lung fibroblast genomic library. The gene is present as a single copy, spans more than 10 kilobases and includes three exons interrupted by two introns. The relative position of the exons was mapped using RNase protection assay, and genomic DNA and cDNA sequence matches. Exon and intron-exon boundaries, and 5', 3' flanking regions were sequenced. While the 5' untranslated region is distributed on all three exons, the coding region is located entirely on the third exon. The exon-intron junction sequences are highly conserved. Primer extension analysis mapped the transcriptional initiation site 21 base pairs downstream of a TATA sequence. Two Aluc sequences and two distinct functional promoters were found in the human BK B1 receptor gene.

Base Sequence↗
PubMed1994

Murine and bovine blue cone pigment genes: cloning and characterization of two new members of the S family of visual pigments.

Two novel visual pigment genes, mouse blue and bovine blue, have been isolated from mouse and bovine genomic libraries, respectively, using a human blue cone pigment cDNA as probe. Corresponding cDNA clones have also been obtained from mouse retinas. The intron-exon boundaries for the mouse gene were determined by comparing the genomic and cDNA sequences. The visual pigments encoded by the mouse and bovine blue pigment genes are highly homologous to each other (89% amino acid identity) and to human blue and chicken violet cone pigments (greater than 80% identity), but are less homologous to chicken or goldfish blue cone pigments (less than 50% identity). These results indicate that phylogenetically both mouse and bovine blue pigments belong to the S branch of visual pigments, rather than to the M branch.

Amino Acid Sequence↗
PubMed1991

Derivation of a DNA clone corresponding to the viral agent of sheep-associated malignant catarrhal fever.

Malignant catarrhal fever is a fatal lymphoproliferative and degenerative disease of ruminants. One causative agent is the gammaherpesvirus alcelaphine herpesvirus 1 (AHV-1), which produces no disease in its natural host, the wildebeest (Connochaetes species). Epidemiological evidence implicates sheep as the carrier of a similar virus. However, attempts to culture this virus from sheep or from animals affected with sheep-associated malignant catarrhal fever (SA-MCF) have failed. Lymphoblastoid cells have been propagated from cattle, deer and rabbits with SA-MCF. Although these cells show no evidence of viral particles or antigens, hybridisation experiments now show that they contain DNA sequences homologous to those of AHV-1. A genomic library was constructed from one of these lymphoblastoid cell lines and a clone identified which hybridised to cloned AHV-1 DNA. The authors believe that this clone contains part of the SA-MCF viral genome, and that the SA-MCF virus and AHV-1 are closely related gammaherpesviruses.

Animals↗
PubMed2004

Identification of two mariner-like elements in the genome of the mosquito Ochlerotatus atropalpus.

Two distinct mariner-like elements, Atmar-1 and Atmar-2, were isolated from the genome of the mosquito Ochlerotatus atropalpus. Full-sized Atmar-1 elements, obtained by screening a genomic library, have a 1293-bp consensus sequence with 27-bp inverted terminal repeats and a 1047-bp open reading frame (ORF) encoding the transposase. The Atmar-2 elements were amplified by polymerase chain reaction from genomic DNA and contain the central part of the transposase ORF. Individual clones of both mariner elements contain deletions, frameshifts, and stop codons. The Atmar-1 elements are present in 370-1200 copies, while the Atmar-2 elements are present in approximately 100-300 copies per haploid genome. One of the Atmar-1 elements, Atmar-1.33, could be mobilized, suggesting the presence of functional Atmar-1 elements elsewhere in the genome. Phylogenetic analysis demonstrated that Atmar-1 elements belong to the irritans subfamily and Atmar-2 elements to the cecropia subfamily of mariner elements.

Amino Acid Sequence↗
PubMed1992

The genomic organization of the rat AT1 angiotensin receptor.

The AT1 receptor subtype modulates all of the hemodynamic effects of the vasoactive peptide, angiotensin II. In this report, we investigate the genomic organization of this important receptor. A rat genomic library was screened with fragments from the 5' region of a previously cloned cDNA, pCa18b, encoding the rat AT1 receptor. Two lambda clones were isolated and the hybridizing restriction fragments were sequenced. Comparison of the genomic and cDNA sequences reveals that the rat AT1 receptor has three exons. Two of the exons encode 5' untranslated sequence while the third exon encompasses the entire coding region, a small portion of the 5' untranslated region and the entire 3' untranslated sequence. Further analysis of the genomic sequence 5' to the start site of pCa18b demonstrates typical sequence motifs found in many eukaryotic promoters including a TATA box, a cap site and a potential Sp1 binding site. Southern analysis of genomic DNA indicates that the AT1 receptor subtype represented by pCa18b is encoded by one gene within the rat genome.

Amino Acid Sequence↗
PubMed2000

Microsatellite frequency and size variation in the parthenogenetic parasitic wasp Venturia canescens (Gravenhorst) (Hymenoptera: Ichneumonidae).

Nine genomic libraries of the parthenogenetic wasp Venturia canescens were screened for microsatellite loci. In contrast to other Hymenoptera (GT)n and not (CT)n, was the predominant repeat category found with 14 kb and 28 kb genomic DNA between loci, respectively. Mono- and trinucleotide microsatellites were rarer, occurring at frequencies between 231 kb and 589 kb of genome, whilst tetranucleotide repeats are scarce, with (ATTC)n and (CCGG)n loci occurring every 692 kb and 983 kb, respectively, and only one small imperfect (GATA)n locus and no (GACA)n loci were revealed. Over 70% of the dinucleotide, and all the trinucleotide microsatellites were small (less than eleven repeats), whilst 60% to 80% of loci were imperfect. Moreover, very few compound microsatellites and only a single association between different microsatellites were observed.

Animals↗
PubMed1996

Cloning, restriction endonuclease mapping and partial sequence analysis of the genome of human herpesvirus 7 strain JI.

Human herpesvirus 7 (HHV-7) is a recently isolated herpesvirus that has been shown to be related to human cytomegalovirus and human herpesvirus 6 and to be a member of the betaherpesvirus subgroup. Here we report the cloning, restriction endonuclease mapping and partial sequence analysis of HHV-7 strain JI DNA. Virus particles were obtained from the supernatant of infected SupT1 cells, the DNA isolated by proteinase K treatment-phenol extraction, and full-length viral DNA was purified and isolated on a pulsed-field gel. Aliquots of this highly purified material were treated in the following ways: (i) sonicated and end-repaired to create short randomly sheared fragments for cloning into M13mp 18-Smal vector DNA; (ii) cut with EcoRI for cloning into EcoRI-cut lambda ZAPII or lambda DASHII vectors; (iii) cut with BamHI for cloning into BamHI-cut lambda ZAP-Express or lambda DASHII vectors. Partial nucleotide sequencing of the M13 clones followed by detection of open reading frames and their translation allowed the identification of homologues through FASTA searches of the database. Relevant M13 clones were used as probes to isolate corresponding lambda phage clones, which could tentatively be mapped to the genome on the basis of presumed genetic collinearity between HHV-7 and HHV-6. Genomic "walking' between EcoRI and BamHI lambda genomic libraries enabled overlapping neighbouring clones to be identified and mapped. Each of these clones was analysed to map BamHI, EcoRI, Sa/l, Smal and Xhol restriction endonuclease sites to provide complete endonuclease maps for the entire genome.

Amino Acid Sequence↗
PubMed1995

Cloning, sequencing, and expression of a xylanase gene from the extreme thermophile Dictyoglomus thermophilum Rt46B.1 and activity of the enzyme on fiber-bound substrate.

A genomic library of the Dictyoglomus sp. strain Rt46B.1 was constructed in the phage vector lambda ZapII and screened for xylanase activity. A plaque expressing xylanase activity, designated B6-77, was isolated and shown to contain a genomic insert of 5.3 kb. Subcloning revealed that the xylanase activity was restricted to a internal 1,507-bp PstI-HindIII fragment which was subsequently sequenced and shown to contain a single complete open reading frame coding for a single-domain xylanase, XynA, with a putative length of 352 amino acids. Homology comparisons show that XynA is related to the family F group of xylanases. The temperature and pH optima of the recombinant enzyme were determined to be 85 degrees C and pH 6.5, respectively. However, the enzyme was active across a broad pH range, with over 50% activity between pH 5.5 and 9.5. XynA was shown to be a true endo-acting xylanase, being capable of hydrolyzing xylan to xylotriose and xylobiose, but it could not hydrolyze xylobiose to monomeric xylose. XynA was also shown to hydrolyze xylan present in Pinus radiata kraft pulp, indicating that it may be of use as an aid in pulp bleaching. The equivalent xylanase gene was also isolated from the related bacterium Dictyoglomus thermophilum, and DNA sequencing showed these genes to be identical, which, together with the 16S small-subunit rRNA gene sequencing data, indicates that Rt46B.1 and D. thermophilum are very closely related.

Amino Acid Sequence↗
PubMed1996

Characterization of cwl1+, a gene from Schizosaccharomyces pombe whose overexpression causes cell lysis.

From a Schizosaccharomyces pombe genomic library we have isolated the gene cwl1+ that causes cell lysis when it is overexpressed in the absence of an osmotic stabilizer. Southern hybridization showed that cwl1+ exists as a single copy in the S. pombe genome. The cwl1+ gene nucleotide sequence revealed a putative open reading frame of 924 bp encoding a polypeptide of 308 amino acids with a calculated Mt of 27000. The cwl1+ DNA hybridizes to a major RNA transcript of 1.5 kb whose 5' end maps at a position 452 bp upstream from the predicted translation start. Comparison of the amino acid sequence with those included in the current databases, showed no significant similarity to any known sequences. Cells overexpressing the cwl1+ gene under the control of the S. pombe nmt inducible promoter displayed a reduced cell wall content, were unable to separate after division and lysed drastically in the absence of osmotic stabilizer. Disruption of the cwl1+ gene caused no noticeable phenotype.

Amino Acid Sequence↗
PubMed2000

Brain-specific expression of novel G-protein-coupled receptors, with homologies to Xenopus PSP24 and human GPR45.

From mouse genomic libraries and human brain cDNA, we cloned three novel G-protein-coupled receptors (GPCRs), which have about 55-70% homologies with Xenopus PSP24 (xPSP24). Together with another human cDNA (GPR45) cloned by Marchese et al. (Genomics 56, 12-21, 1999). they comprise a family of mammalian PSP24s. Therefore, we termed these clones mouse PSP24alpha, beta, and human PSP24alpha, beta. The homologies between alpha and beta isoforms were 54% for human and 51% for mouse clones. None of these clones shares sequence similarities with any known mammalian GPCRs, thus forming a unique gene family. Northern blot demonstrated that both of the mouse transcripts were predominantly expressed in the brain. In situ hybridization of brain sections showed that the expression was observed in neuronal cells, such as olfactory mitral cells, cortical neurons, hippocampal pyramidal cells, and Purkinje cells in the cerebellum. We suggest that mammalian PSP24 is a distinct GPCR family and plays a role in the brain function.

Amino Acid Sequence↗
PubMed1989

Isolation and characterization of the nitrate reductase structural gene of Chlamydomonas reinhardtii.

The nitrate reductase structural gene of Chlamydomonas reinhardtii has been isolated from a genomic library by using a nitrate reductase cDNA probe from barley. Restriction fragment length polymorphism analyses mapped the Chlamydomonas clone (B6a) to the nitrate reductase structural gene locus nit-1. Overlapping inserts cover a region of the genome of about 24 kilobases containing the entire gene, which spans approximately 5-8 kilobases. Sequence analysis of DNA fragments from the B6a clone demonstrated a high degree of sequence similarity at the amino acid level with regions corresponding to portions of the heme and FAD/NADH-binding domains of tobacco and Arabidopsis thaliana nitrate reductases and human NADH cytochrome b5 reductase. The identity of the cloned gene as nitrate reductase was confirmed by its ability to complement a nit-1 mutation upon transformation. The nitrate reductase gene produced a 3.4-kilobase transcript in cells derepressed with nitrate; the transcript was undetectable in cells grown in the presence of ammonium. In cells that contain a mutation in the putative regulatory gene nit-2, significantly lower levels of the 3.4-kilobase transcript were found, indicating that the wild-type nit-2 gene is involved in the control of nitrate reductase transcript levels.

Amino Acid Sequence↗
PubMed1991

CYP52 (cytochrome P450alk) multigene family in Candida maltosa: molecular cloning and nucleotide sequence of the two tandemly arranged genes.

Southern blot analysis under low-stringency conditions using a previously isolated n-alkane-inducible cytochrome P450 (P450alk) gene as a probe revealed the presence of multiple P450alk-related genes in the genome of Candida maltosa. Nine P450alk-related genes (one reported previously and eight in the present report) were isolated from a genomic library constructed from this strain, and these were classified on the basis of sequence similarities into three pairs of putative allelic genes and three nonallelic genes. Two pairs of these alleles were tandemly arranged in the genome. The complete nucleotide sequences of one of these pairs were determined and compared to other members of this P450 family (CYP52) in C. maltosa and C. tropicalis. Northern blot analysis further showed that these genes were regulated by carbon sources. These results provide evidence for a P450alk (CYP52) multigene family in C. maltosa.

Amino Acid Sequence↗
PubMed1997

Cloning of genes coding for L-sorbose and L-sorbosone dehydrogenases from Gluconobacter oxydans and microbial production of 2-keto-L-gulonate, a precursor of L-ascorbic acid, in a recombinant G. oxydans strain.

We have purified L-sorbose dehydrogenase (SDH) and L-sorbosone dehydrogenase (SNDH) from Gluconobacter oxydans T-100 that showed an ability to convert D-sorbitol to 2-keto-L-gulonate (2-KLGA). A genomic library of Gluconobacter oxydans T-100 was screened with a probe, a 180-bp PCR product which was obtained from degenerate oligodeoxyribonucleotides based on the elucidated sequence of the purified SDH (used as primers) and the genomic DNA of G. oxydans T-100 (used as a template). From sequencing of the DNA from a clone positive to the probe, the SNDH and the SDH were estimated to be coded in sequential open reading frames with 1,497 and 1,599 nucleotides, respectively, which was confirmed by expression of the DNA in Escherichia coli that showed both enzymatic activities. The DNA was introduced to a shuttle vector which was prepared from a plasmid of G. oxydans T-100 and pHSG298 to obtain an expression vector designated pSDH155. The production of 2-KLGA by pSDH155 in G. oxydans G624, an L-sorbose-accumulating strain, was improved to 230% compared to that of G. oxydans T-100. Chemical mutation of the host strain to suppress the L-idonate pathway and replacement of the original promoter with that of E. coli tufB resulted in improving the production of 2-KLGA. Consequently, high-level production from D-sorbitol to 2-KLGA (130 mg/ml) was achieved by simple fermentation of the recombinant Gluconobacter.

Acetobacteraceae↗
PubMed1988

Internal quadruplication in the structure of human interstitial retinol-binding protein deduced from its cloned cDNA.

Interstitial retinol-binding protein (IRBP) is a glycoprotein that shuttles retinoids between the retina and pigment epithelium and is secreted by the photoreceptor cells of the vertebrate eye. Human retina cDNA libraries in lambda gt10 were screened with a previously isolated human IRBP probe (H.4 IRBP), yielding five overlapping cDNA clones generating a 4223-base sequence. A 17-kilobase pair clone (HGL.3) isolated by screening a human genomic library in EMBL3 with H.4 IRBP yielded a 2.5-kilobase pair SstI fragment that overlapped the 5' end of the cDNA sequence by 329 nucleotide residues. An open reading frame encoded the N-terminal sequence of human IRBP and predicted a protein consisting of 1262 amino acids with a molecular mass of 136,600. Two putative N-linked glycosylation sites were identified. The translated sequence suggests that there is a 16-amino acid presumptive signal peptide rich in hydrophobic residues and with a high alpha-helix probability preceding the N terminus of the mature protein. The amino acid sequence of human IRBP could be aligned with 87% identity with the amino acid sequences of 31 peptides (605 residues) purified from a tryptic digest of bovine IRBP. The protein sequence of human IRBP contains four duplicated segments (302-310 residues in length) with 33-38% identity. From the degree of identity between the bovine and human sequences, it is possible that IRBP evolved by several gene duplications that occurred 600-800 million years ago, before the emergence of the vertebrates.

Amino Acid Sequence↗
PubMed1997

Hamster ribosomal protein S24 multigene family: genomic organization and molecular structure of two pseudogenes.

A cDNA coding for the hamster S24 ribosomal protein was used to isolate homologous genes from a Syrian hamster fibroblast genomic library. Southern analysis, using S24 ribosomal protein cDNA and two probes derived from the 5' and 3' ends, suggests that the S24 ribosomal protein family is composed of at least 3 related members in the hamster genome, and of 6-10 members in the mouse genome. I describe the isolation of nine independent lambda recombinant phages that altogether carry two different genes encoding S24 ribosomal proteins. Sequence analysis indicates that each of these two genes contain sequences related to the S24 ribosomal protein but lack introns and differ in their flanking sequences. On the basis of these features, I propose that these two genes are processed pseudogenes. Interestingly, one of them is flanked by two different repetitive sequences, homologous to satellite DNA, whose functions are unknown. I also show that in the hamster genome the S24 ribosomal protein mRNA is transcribed from a unique gene using a precise initiation site.

Aniline Compounds↗