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At least 1,261 records · Page 70Linked to original sources
PubMed1998

Organization and structure of NADH-dependent glutamate synthase gene from rice plants.

Genomic clones for NADH-dependent glutamate synthase (NADH-GOGAT; EC 1.4.1.14) were obtained from a genomic library of rice (Oryza sativa L. cv. Sasanishki). A genomic clone (lambdaOS42, 14 kb) covered an entire structural gene and a 3.7 kb 5'-upstream region from the first methionine. Another clone (lambdaOS23, 14 kb) contained a 2.8 kb 3'-downstream region from the stop codon. A 7047 bp long clone (lambdaOSR51) consisting of full length cDNA for NADH-GOGAT was isolated from a cDNA library prepared using mRNA from roots of rice seedlings treated with 1 mM NH4Cl for 12 h. The presumed transcribed region (11.7 kb) consisted of 23 exons separated by 22 introns. Rice NADH-GOGAT is synthesized as a 2166 amino acid protein with a molecular mass of 236.7 kDa that includes a 99 amino acid presequence. DNA gel blot analysis suggested that NADH-GOGAT occurred as a single gene in rice. Primer extension experiments map the transcription start of NADH-GOGAT to identical positions. The 3. 7 kb 5'-upstream region was able to transiently express a reporter gene in cultured rice cells. Putative motifs related to the regulation of NADH-GOGAT gene expression were looked for within the 5'-upstream region by database.

Amino Acid Oxidoreductases↗
PubMed2004

[Sequence and organization of Muntiacus reevesi mitochondrial genome].

A shot-gun DNA sequence strategy was employed,in which the mitochondrial genome library of Muntiacus reevesi has been constructed to obtain the complete mitochondrial genome sequence. The Chinese Muntjac's mitochondrial genome, consisting of 16354 base pairs which encode genes for 13 proteins, 2 rRNAs, and 22 tRNAs, is similar to those mammals in both order and orientation. The sequence of rRNA gene, some of the protein-coding regions and tRNAs are highly homologous in mammals. Differences existing in the length and sequence of the D-loop regions account for the variations in mammals mitochondrial genomes.

Animals↗
PubMed1991

Agarose entrapment method for the production of SfiI linking library for Theileria parva.

We have developed a simple method for isolation of SfiI linking clones from a eukaryotic genomic DNA. The method involves the physical separation of the small proportion of plasmids in a plasmid genomic library that are linearized by SfiI digestion, from the bulk of molecules that remain circular, by ordinary electrophoresis through high-percentage gels of SeaPlaque agarose. Following the isolation of linearized molecules, their recircularization, and introduction into Escherichia coli, 55% of recovered plasmids contained inserts of the expected size, and 73% of these had SfiI sites. This represented a 25-fold enrichment of linking clones expected to be present at a frequency of 1/60 in the original library of 4- 6-kb fragments of genomic DNA of the protozoan parasite Theileria parva. This approach is rapid and obviates the need for introduction of a selectable marker. It is uniquely appropriate for linking clones spanning SfiI sites as this enzyme leaves degenerate 3' overhanging ends that preclude the direct ligation into vector sites required by most alternative strategies, but that favor the recircularization reactions used here.

Animals↗
PubMed1998

Genomic structure of the regulatory region of the voltage-gated calcium channel alpha 1D.

In excitable and endocrine organs, calcium influxes through the L-type voltage-gated calcium channel (VGCC) which is composed of four (alpha 1, alpha 2, beta, and gamma) subunits. Temporal and spatial expression of calcium channel activity is regulated by the transcription of alpha 1 subunit. To elucidate the genomic organization of the VGCC alpha 1D subunit gene, a genomic clone was isolated from the human genomic library and its sequence was analyzed. A 12 kb genomic clone contained the 5'-flanking regulatory region and first two exons was selected and the initiation site for alpha 1D mRNA synthesis was examined by primer extension analysis. The major initiation site was found at the -523 NT position in the translation initiation site. The TATA box could not be found above the transcription initiation site. The CAT vector construct containing the 2.5 kb upstream region had high CAT activity on transfection to NG108-15 and PC12 cells, which confers the neuronal expression of the alpha 1D gene.

Amino Acid Sequence↗
PubMed1995

Cloning and characterization of three Aspergillus niger promoters.

An Aspergillus niger (An) genomic library was constructed using the promoter-trap vector, pLX2A, which contains a hygromycin B (Hy) phosphotransferase-encoding gene (hph) for selection of DNA fragments with promoter activity. This library was transformed in Escherichia coli and 80,000 colonies were obtained, 94% of which contained inserts. Transformations of plasmid DNA from the library into An resulted in 53 Hy-resistant (HyR) colonies. Southern blot analysis of 21 transformants confirmed the integration of hph into the An genome. Using the sib selection procedure, three functional promoters, PX6, PX18 and PX21, were identified from this library. Both DNA strands of all three fragments were sequenced and their sequences showed no significant homology to those in the database. Comparison of the sequences of all known promoters from An suggested that C+T-rich stretches are probably important for promoter structures. The promoter activity was analysed further using beta-galactosidase (beta Gal) as a quantitative marker. The results suggest that while PX21 is a much stronger promoter than the known alpha-amylase promoter of A. oryzae, PX6 promotes only weak expression of beta Gal.

Aspergillus niger↗
PubMed1988

Cell-cell adhesion in Dictyostelium discoideum.

Three separate mechanisms of cell-cell adhesion have been shown to appear at different stages of development in Dictyostelium discoideum. During the first few hours of development, the cells synthesize and accumulate a glycoprotein of 24,000 daltons (gp24) that is positioned in the membrane. The time of appearance of gp24 correlates exactly with the time of appearance of cell-cell adhesion in two strains in which temporal control varies by several hours. Antibodies specific to gp24 are able to block cell-cell adhesion during the first few hours of development but not during later development. By 8 hr of development, another glycoprotein, gp80, that is not recognized by antibodies to gp24 accumulates on the surface of cells. This membrane protein mediates an independent adhesion mechanism during the aggregation stage that is resistant to 10 mM EDTA. Antibodies specific to gp80 can block EDTA-resistant adhesion during this stage. During subsequent development, gp80 is removed from the cell surface and replaced by another adhesion mechanism that is insensitive to antibodies to either gp24 or gp80. A lambda gt11 expression vector carrying a Dictyostelium cDNA insert was isolated that directs the synthesis of a fusion protein recognized by antibodies specific to gp24. This cDNA was used to probe a genomic library. A clone carrying a 1.4-kb insert of genomic DNA was recognized by the cDNA and shown to hybridize to a 0.7-kb mRNA that accumulates early in development. This unusually small RNA could code for the small protein, gp24. Southern analysis of restriction fragments generated by various enzymes on Dictyostelium DNA with both the cDNA and genomic clones indicated the presence of two tandem copies of the gene. This may account for the failure to recover mutations resulting in the lack of gp24. Mutations have been recovered that result in the lack of accumulation of gp80, and cells carrying these mutations have been shown to be missing the second adhesion mechanism. These mutant strains are able to complete development because the other adhesion mechanisms are not impaired. Sequential addition of adhesion mechanisms provides a means for the formation of multicellular organisms from previously solitary cells.

Cell Adhesion↗
PubMed1987

A complex gene superfamily encodes actin in petunia.

We have shown by several independent criteria that actin is encoded by a very large and complex superfamily of genes in Petunia. Several cDNA and genomic probes encoding actins from diverse organisms (Dictyostelium, Drosophila, chicken and soybean) hybridize to hundreds of restriction fragments in the petunia genome. Actin-hybridizing sequences were isolated from a petunia genomic library at a rate of at least 200 per genome equivalent. Twenty randomly selected actin-hybridizing clones were characterized in more detail. DNA sequence data from four representative and highly divergent clones, PAc2, PAc3, PAc4 and PAc7, demonstrate that these actin-like sequences are related to functional actin genes. Intron positions typical of other known plant actin genes are conserved in these clones. Four of six clones analyzed (PAc1, PAc2, PAc3, PAc4) hybridize to leaf mRNA of the same size (1.7 kb) as that reported for other plant actin mRNAs and to a slightly smaller mRNA species (1.5 kb). Five distinct subfamilies of actin-related genes were characterized which varied in size from a few members to several dozen members. It is clear from our data that other actin gene subfamilies must also exist within the genome. Possible mechanisms of actin gene amplification and genome turnover are discussed.

Actins↗
PubMed1996

The structure of the gene encoding the human skeletal muscle alpha 1 subunit of the dihydropyridine-sensitive L-type calcium channel (CACNL1A3).

The structure of the gene encoding the human skeletal muscle alpha 1 subunit (CACNL1A3) of the dihydropyridine-sensitive voltage-dependent calcium channel was determined by isolation of overlapping genomic DNA clones from human cosmid, phage, and P1 libraries. Genomic fragments containing exons were subcloned, and the sequences of the exons and flanking introns were defined. Knowledge of the genomic structure of the CACNL1A3 gene, which spans 90 kb and consists of 44 exons, will facilitate the search for additional mutations in CACNL1A3 that cause neuromuscular disease.

Base Sequence↗
PubMed1989

Isolation and characterization of a fruit-specific cDNA and the corresponding genomic clone from tomato.

Differential screening of a cDNA bank constructed from ripe tomato fruit mRNA allowed the isolation of cDNA clone 2A11 which is entirely fruit-specific, is expressed at steadily increasing levels from anthesis to breaker, and accounts for approximately 1% of the messenger RNA in mature tomato fruit. A genomic clone corresponding to the 2A11 cDNA was isolated from a tomato genomic library. Sequence comparison of the cDNA clone with the genomic clone shows they are identical over the shared region with the genomic clone possessing a single large intron near the 5' end of the message. The open reading frame of 2A11 would encode a sulfur-rich polypeptide 96 amino acids in length. The identity of the putative protein is unknown. In situ hybridization shows that the 2A11 message is found throughout the pericarp cells in a tomato fruit. In contrast, in situ hybridization of early ripening stages with a polygalacturonase probe shows higher mRNA levels in cells of the outer pericarp and cells surrounding the vascular regions of the pericarp.

Amino Acid Sequence↗
PubMed1996

Organization of the histone H3 genes in soybean, barley and wheat.

Several variants of the replacement histone H3 genes from soybean, barley and wheat have been cloned and sequenced. Analysis of segregating populations in barley and soybean, as well as analysis of clones isolated from a soybean genomic library, suggested that these genes are dispersed throughout the genome. Several genes contains introns located in similar positions, but of different lengths and sequence. Comparison of mRNA levels in different tissues revealed that the intron-containing and intronless genes have different expression patterns. The distribution of the introns in the histone H3 genes across several plant species suggests that some of the introns might have been lost during the evolution of the gene family. Sequence divergence among introns and gene-flanking sequences in cloned gene variants allowed us to use them as specific probes for localizing individual gene copies and analyzing the genomic distribution of these variants across a range of genotypes.

Base Sequence↗
PubMed1992

Characterization of the promoter region of the murine fibroblast growth factor receptor 1 gene.

To obtain some clue for the regulatory mechanism by which fibroblast growth factor (FGF) receptor 1 (FGFR 1) gene is expressed, we have cloned the promoter region of this gene from genomic library of mouse FGF-responsive cell lines. The genomic clone isolated here includes the FGFR 1 gene from position -868 to +697 relative to transcription initiation site. Sequence analysis reveals the presence of various consensus sequences for the binding sites of transcriptional factors such as SP 1, GCF, Oct-I, AP 1 and AP 2, but the absence of TATA and CAAT sequence motif. The transfection of this promoter-CAT constructs into NIH 3T3 cells demonstrates its promoter activity which is at least located between base -106 and +104.

3T3 Cells↗
PubMed1994

A delayed rectifier potassium channel cloned from bovine adrenal medulla. Functional analysis after expression in Xenopus oocytes and in a neuroblastoma cell line.

Using a cDNA library from bovine adrenal medulla, and, subsequently, a bovine genomic library, we have isolated the gene coding for a non inactivating potassium channel. This gene encodes a 597-amino acid protein which we have called BAK5 as its sequence is very similar to members of Kv1.5 potassium channel family. Neuroblastoma cells (Neuro-2a cell line) were stably transfected with BAK5 DNA. Protein expression was under the control of a heat-shock promoter. Transfected cells showed a current highly selective for potassium, insensitive to tetraethylammonium but reversibly blocked by 4-aminopyridine. Oocytes injected with BAK5 mRNA also expressed a potassium current with the same characteristics.

4-Aminopyridine↗
PubMed1989

Cloning and sequencing of the peroxisomal amine oxidase gene from Hansenula polymorpha.

We have cloned the AMO gene, encoding the microbody matrix enzyme amine oxidase (EC 1.4.3.6) from the yeast Hansenula polymorpha. The gene was isolated by differential screening of a cDNA library, immunoselection, and subsequent screening of a H. polymorpha genomic library. The nucleotide sequence of a 3.6 kilobase stretch of DNA containing the amine oxidase (AMO) gene was determined. The AMO gene contains an open reading frame of 692 amino acids, with a relative molecular mass of 77,435. The 5' and 3' ends of the gene were mapped and show that the transcribed region measures 2134 nucleotides. The derived amino-acid sequence was confirmed by sequencing an internal proteolytic fragment of the purified protein. Amine oxidase contains the tripeptide sequence Ser-Arg-Leu, located 9 residues from the carboxy terminus, which may represent the topogenic signal for protein import into microbodies.

Amine Oxidase (Copper-Containing)↗
PubMed1988

Isolation and structural analysis of embryonic chicken pepsinogen gene: avian homologue of prochymosin gene.

Embryonic chicken pepsinogen gene was isolated from a chicken genomic library. This gene occupied approximately 3.5 kb of the genomic DNA and was separated into nine exons by eight introns. The positions of exon-intron junctions coincided with those in the human pepsinogen A gene and the bovine prochymosin gene. Southern blot analysis of chicken genomic DNA revealed that the structure of the isolated gene reflects the original structure in the chicken chromosome. At the same time, the presence of another copy of embryonic pepsinogen gene was suggested. 5'-flanking region of the isolated ECPg gene was analyzed.

Animals↗
PubMed1998

Sequence and expression pattern of the Drosophila melanogaster mitochondrial porin gene: evidence of a conserved protein domain between fly and mouse.

We have recently cloned a cDNA encoding mitochondrial porin in Drosophila melanogaster and shown its chromosomal localization (Messina et al., FEBS Lett. (1996) 384, 9-13). Such cDNA was used as a probe for screening a genomic library. We thus cloned and sequenced a 4494-bp genomic region which contained the whole gene for the mitochondrial porin or VDAC. It was found that this D. melanogaster porin gene contains five exons, numbered IA (115 bp), IB (123 bp), II (320 bp), III (228 bp) and IV (752 bp). The exons II, III and IV contain the protein coding sequence and the 3' untranslated sequence (3'-UTR). The first base in exon II precisely corresponds to the first base of the starting ATG codon. Exon IA corresponds to the 5'-UTR sequence reported in the published cDNA sequence. Exon IB corresponds to an alternative 5'-UTR sequence, demonstrated to be transcribed by 5'-RACE experiments. The exon-intron splicing borders and the length of the exon III perfectly match a homologous internal exon detected in the mouse genes. Such exon encodes a protein domain predicted by sequence transmembrane arrangement models to contain major hydrophilic loops and it is thus suspected to have a conserved distinct function. In situ hybridization experiments confirmed the localization of the genomic clone on the chromosome 2L at region 32B3-4. Together with genomic Southern blotting at various stringencies, the same experiment did not confirm the presence of a second genetic locus on D. melanogaster chromosomes. Northern blots demonstrated that the porin gene is a housekeeping one: three messages of approx. 1.2-1.6 kbp are transcribed in every fly developmental stage that was studied. They were shown to derive by an alternative usage of different promoters and polyadenylation sites.

Alternative Splicing↗
PubMed1983

Isolation and characterization of Drosophila melanogaster U2 small nuclear RNA genes.

We describe here the organization of DNA sequences complementary to Drosophila melanogaster U2 small nuclear (sn) RNA. From a genomic library we isolated two recombinants containing two genes each. Genomic reconstruction experiments and Southern analysis revealed that D. melanogaster possesses only four to five U2 snRNA genes or very closely related sequences. The nucleotide sequence of one of the clones analysed shows 77% homology with rat U2 snRNA. A stretch of 12 nucleotides that has been implicated in heterogeneous nuclear RNA splicing is conserved between rat and Drosophila. The genomic organization of these genes is very similar in different melanogaster strains but diverges highly in different Drosophila species.

Animals↗
PubMed2004

Development of a DNA microarray chip for the identification of sludge bacteria using an unsequenced random genomic DNA hybridization method.

A tool, based upon the DNA microarray chip, for the identification of specific bacteria from activated sludge, using the hybridization of genomic DNA with random probes, is described. This chip was developed using the genomic DNAs from Gordonia amarae, the natural filamentous actinomycete that causes sludge foaming and bulking, as well as a nonfilamentous floc forming bacterium (Zoogloea ramigera) and the skin pathogen Mycobacterium peregrinum without any sequence information. The sets of target probes on amine-coated glass were made from a genomic library, constructed with PCR products derived from randomly fragmented genomic DNAs extracted from pure cultures of the three strains. Initial hybridization results, when pure cultures were employed, showed the specificity of the probes as well as the resolution of the system, demonstrating the capabilities of this system to identify specific bacterial strains. The microarray was also tested for its ability to distinguish specific bacteria from among mixed bacterial communities, such as in sludge, soil, or spiked genomic DNA samples. The results showed that the probes are specific, with only mild cross-hybridization occurring in a small number of cases. Furthermore, the chip clearly discriminated the presence of all three strains when they were present alone or together within mixed samples. Moreover, using the spot intensity and DNA hybridization kinetics, the starting genomic DNA concentrations could be estimated relatively well, which would make it possible to predict the number of specific bacteria present within the test samples. Therefore, the random genomic hybridization approach, i.e., without any sequence information available for the probes, is a practical protocol for the identification of and screening for specific bacteria within any complex bacterial community from the environmental samples, such as in activated sludge, although the possibility of cross-hybridization may still exist.

Bacteria↗
PubMed1981

Structural variation among human beta-tubulin genes.

A chicken beta-tubulin cDNA probe has been used to screen two independently generated human genomic libraries. Of 13 EcoRI fragments detectable in a human genomic Southern blot experiment, 7 correspond in size to EcoRI fragments isolated from recombinant bacteriophage. The location of beta-tubulin-specific regions and the direction of transcription were determined within each cloned fragment. One clone (5 beta) contained a beta-tubulin-specific region of 6.8 kilobase pairs (kbp) that included three intervening sequences as well as a number of inverted repeat structures. The remaining clones contained beta-tubulin-specific sequences that were close to or, in two cases, substantially less than 1.9 kbp long. Because mature human beta-tubulin mRNA is approximately 1.9 kbp long, these short DNA regions cannot on their own encode a functional beta-tubulin mRNA. Analysis using 3'- and 5'-specific probes derived from the chicken cDNA clone showed the presence of both of these end regions within one truncated tubulin-like sequence. A second short tubulin-specific region failed to hybridize with a 3'-specific probe. These short sequences are therefore likely to be examples of pseudogenes that have arisen by loss of a portion of DNA essential to the production of functional human beta-tubulin mRNA.

Animals↗