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At least 1,423 records · Page 79Linked to original sources
PubMed1988

Characterization of the Azorhizobium sesbaniae ORS571 genomic locus encoding NADPH-glutamate synthase.

Sixteen independent Azorhizobium sesbaniae ORS571 vector insertion (Vi) mutants defective in ammonium assimilation (Asm-) were selected; genomic DNA sequences flanking the insertion endpoints were cloned directly. Resulting recombinant plasmids were used to identify, by hybridization, corresponding wild-type DNA sequences from an A. sesbaniae lambda EMBL3 genomic library (lambda Asm phages). All 16 Asm- Vi mutants physically mapped to a single genomic locus. Plasmid subclones of recombinant phage lambda Asm152 were able to complement both Escherichia coli gltB and A. sesbaniae Asm- Vi mutants; NADPH-glutamate synthase activity was detected in all such strains complemented to Asm+. Heterologous and homologous complementations required both A. sesbaniae gltA+ and (inferred) gltB+ genes. Eleven A. sesbaniae Asm- Vi mutants mapped to a 4-kilobase-pair (kbp) DNA region that exhibited homology with Bacillus subtilis gltA+. In E. coli maxicell labeling experiments, this 4-kbp DNA region encoded a 165-kilodalton polypeptide that was inferred to be the product of the A. sesbaniae gltA+ gene (glutaminase NADPH-dependent L-glutamate synthase subunit). Site-directed Tn5-lacZ mutagenesis of a glt plasmid subclone identified a region that bisected this locus into (at least) two cistrons. Because the remaining five A. sesbaniae Asm- mutants mapped to a 1.5-kbp region adjacent to gltA+, these mutants probably define a single gltB+ gene (glutamate dehydrogenase NADPH-dependent L-glutamate synthase subunit); this region did not exhibit homology with the B. subtilis gltB+ gene.

Ammonia↗
PubMed1988

Role of a phenazine antibiotic from Pseudomonas fluorescens in biological control of Gaeumannomyces graminis var. tritici.

Pseudomonas fluorescens 2-79 (NRRL B-15132) and its rifampin-resistant derivative 2-79RN10 are suppressive to take-all, a major root disease of wheat caused by Gaeumannomyces graminis var. tritici. Strain 2-79 produces the antibiotic phenazine-1-carboxylate, which is active in vitro against G. graminis var. tritici and other fungal root pathogens. Mutants defective in phenazine synthesis (Phz-) were generated by Tn5 insertion and then compared with the parental strain to determine the importance of the antibiotic in take-all suppression on wheat roots. Six independent, prototrophic Phz- mutants were noninhibitory to G. graminis var. tritici in vitro and provided significantly less control of take-all than strain 2-79 on wheat seedlings. Antibiotic synthesis, fungal inhibition in vitro, and suppression of take-all on wheat were coordinately restored in two mutants complemented with cloned DNA from a 2-79 genomic library. These mutants contained Tn5 insertions in adjacent EcoRI fragments in the 2-79 genome, and the restriction maps of the region flanking the insertions and the complementary DNA were colinear. These results indicate that sequences required for phenazine production were present in the cloned DNA and support the importance of the phenazine antibiotic in disease suppression in the rhizosphere.

Antifungal Agents↗
PubMed1997

Regulation of the formate dehydrogenase gene, FDH1, in the methylotrophic yeast Candida boidinii and growth characteristics of an FDH1-disrupted strain on methanol, methylamine, and choline.

The structural gene (FDH1) coding for NAD(+)-dependent formate dehydrogenase (FDH) was cloned from a genomic library of Candida boidinii, and the FDH1 gene was disrupted in the C. boidinii genome (fdh1 delta) by one-step gene disruption. In a batch culture experiment, although the fdh1 delta strain was still able to grow on methanol, its growth was greatly inhibited and a toxic level of formate was detected in the medium. In a methanol-limited chemostat culture at a low dilution rate (0.03 to 0.05 h[-1]), formate was not detected in the culture medium of the fdh1 delta strain; however, the fdh1 delta strain showed only one-fourth of the growth yield of the wild-type strain. Expression of FDH1 was found to be induced by choline or methylamine (used as a nitrogen source), as well as by methanol (used as a carbon source). Induction of FDH1 was not repressed in the presence of glucose when cells were grown on methylamine, choline, or formate, and expression of FDH1 was shown to be regulated at the mRNA level. Growth on methylamine or choline as a nitrogen source in a batch culture was compared between the wild type and the fdh1 delta mutant. Although the growth of the fdh1 delta mutant was impaired and the level of formate was higher in the fdh1 delta mutant than in the wild-type strain, the growth defect caused by FDH1 gene disruption was small and less severe than that caused by growth on methanol. As judged from these results, the main physiological role of FDH with all of the FDH1-inducing growth substrates seems to be detoxification of formate, and during growth on methanol, FDH seems to contribute significantly to the energy yield.

Amino Acid Sequence↗
PubMed1999

Growth hormone releasing substances: types and their receptors.

A series of structurally diverse growth hormone (GH) releasing substances have been synthesized that are distinct from the naturally occurring GH releasing hormone (GHRH). These synthetic molecules range from the family of GH releasing peptides and mimetics such as MK-0677. The physiological importance of these molecules and their receptor is exemplified by studies in the elderly. For example, when MK-0677 was administered chronically to 70- to 90-year-old subjects, once daily, the age-related reduced amplitude of GH pulses was reversed to that of the physiological profile typical of young adults. In 1996, the synthesis of (35)S-MK-0677 was reported and used as a ligand to characterize a common receptor (GH secretagogue receptor [GHS-R]) for the GH releasing substances. The GHS-R is distinct from the GHRH receptor. Subsequently, the GHS-R gene was cloned and shown to encode a unique G-protein coupled receptor with a deduced protein sequence that was 96% identical in human and rat. Because of the physiological importance of the GHS-R, a search for family members (FMs) was initiated and its molecular evolution investigated. Three FMs GPR38, GPR39 and FM3 were isolated from human genomic libraries. To accelerate the identification of other FMs, a vertebrate organism with a compact genome distant in evolutionary terms from humans was exploited. The pufferfish (Spheroides nephelus) genome provides an ideal model for the discovery of human genes. Three distinct full-length clones encoding proteins of significant sequence identity to the human GHS-R were cloned from the pufferfish. Remarkably, the pufferfish gene with highest sequence homology to the human receptor was activated by the hexapeptide and non-peptide ligands. These intriguing results show that the structure and function of the ligand binding pocket of the human GHS-R has been highly conserved in evolution ( approximately 400 million years) and strongly suggests that an endogenous natural ligand has been conserved. This new information is consistent with a natural ligand for the GHS-R playing a fundamentally important and conserved role in physiology.

Aged↗
PubMed1999

Association of the glucocorticoid receptor alternatively-spliced transcript 1A with the presence of the high molecular weight membrane glucocorticoid receptor in mouse lymphoma cells.

Using the combination of a cDNA library prepared from membrane glucocorticoid (mGR)-enriched S-49 cells and a mouse leukocyte genomic library, we have cloned a 7.3 kb full-length glucocorticoid receptor 1A cDNA. Primer extension, 5'RACE, and long distance PCR identified the transcription start site as being located at 1026 bp from the ATG codon. The first 1,013 nucleotides (nts) of the full length sequence constitute 5' UTR sequence (exon 1), the next 2349 bp, the coding region, and the last 3,907 bp, the 3'UTR. The entire 5'UTR sequence is unique to transcript 1A. The 3'UTR sequence is approximately 88.5 % conserved with the rat 3'UTR. Western blot analysis compared the molecular weight of in vitro translation products from the cloned 1A cDNA with partially purified cellular mGR. Both preparations contained the novel 150 KD and the 94 KD classical GR peptides, suggesting that transcript 1A encodes both receptor forms. Transfection of mGR-less and glucocorticoid lysis-resistant AtT-20 and HL-60 cells with full-length GR 1A cDNA imparted both mGR expression and glucocorticoid lysis-sensitivity to these cells.

3' Untranslated Regions↗
PubMed1990

Characterization of the human gene that encodes the peptide core of secretory granule proteoglycans in promyelocytic leukemia HL-60 cells and analysis of the translated product.

Based upon the deduced amino acid sequence of a cDNA (cDNA-H4) that had been proposed to encode the peptide core of an eosinophil and a HL-60 cell secretory granule proteoglycan, a 16-amino acid peptide was synthesized. This peptide was then used to elicit rabbit antibodies for study of the translation and post-translational modification of this gene product in hematopoietic cells. When HL-60 cells were radiolabeled for 2 min with [35S]methionine, a protein that migrated in a sodium dodecyl sulfate-polyacrylamide electrophoresis gel with a Mr of 20,000 was immunoprecipitated with the IgG fraction of the anti-peptide serum. Kinetic experiments revealed that within 10 min this radiolabeled precursor protein was converted in HL-60 cells into an Mr approximately 150,000 chondroitin sulfate proteoglycan intermediate. After a 20-min to 1-h chase, this [35S]methionine- or [35S]sulfate-labeled proteoglycan intermediate lost its antigenicity, presumably due to proteolysis of its N terminus. A human genomic library was probed under conditions of high stringency with cDNA-H4 to isolate genomic clones that contain the gene that encodes this proteoglycan peptide core. This gene spans approximately 15 kilobases and consists of three exons. The first exon encodes the 5'-untranslated region of the mRNA transcript, as well as the entire 27-amino acid signal peptide of the translated molecule. The second exon encodes a 49-amino acid region of the peptide core, predicted to be the N terminus of the molecule after its proteolytic processing in the endoplasmic reticulum. The third exon encodes the remainder of the molecule, including its glycosaminoglycan attachment, serine-glycine repeat region. As assessed by S1 nuclease mapping and primer extension analysis, the transcription-initiation site in HL-60 cells for this gene resides 53 base pairs upstream from the translation-initiation site.

Amino Acid Sequence↗
PubMed1988

The laminin B2 chain promoter contains unique repeat sequences and is active in transient transfection.

We previously isolated cDNA clones coding for the entire murine laminin B2 chain. In this report, we have screened a mouse genomic library with a 5' portion of the laminin B2 chain cDNA and isolated two genomic clones which contain the first and second exons. The transcription initiation site was determined by primer extension and S1 nuclease mapping. Exon 1 contained 641 bp (base pairs) including 229 bp of 5'-untranslated segment, sequences coding for the signal peptide and the N-terminal portion of the protein, while exon 2 contained 305 bp. Nucleotide sequencing of 830 bp of the 5'-flanking region of the gene showed several interesting features including the presence of 9 "GC" boxes, a stretch of 9 nearly identical repeats of 11 nucleotides between -200 and -450, and a sequence which is similar to the cAMP consensus sequence. There was no TATA box or CAAT box. A recombinant plasmid containing the 830 bp promoter segment coupled to the chloramphenicol acetyltransferase gene was constructed and transfected into various cells. Differentiated F9 cells transfected with this construct showed twice as much chloramphenicol acetyltransferase activity as the undifferentiated cells. The 830-bp B2 laminin promoter was also active in NIH-3T3 cells which produce little laminin, but was not active in human HT-1080 cells. These results indicate that this structurally unique promoter contains DNA sequences that help regulate the gene during differentiation.

Animals↗
PubMed1994

A novel human homeobox gene distantly related to proboscipedia is expressed in lymphoid and pancreatic tissues.

A novel human homeobox gene, HB9, was isolated from a cDNA library prepared from in vitro stimulated human tonsil B lymphocytes and from a human genomic library. The HB9 gene is composed of 3 exons spread over 6 kilobases of DNA. An open reading frame of 1206 nucleotides is in frame with a diverged homeodomain. The predicted HB9 protein has a molecular mass of 41 kilodaltons and is enriched for alanine, glycine, and leucine. The HB9 homeodomain is most similar to that of the Drosophila melanogaster homeobox gene proboscipedia. Northern blot analysis of poly(A) RNA purified from the human B cell line RPMI 8226 and from activated T cells revealed a major mRNA transcript of 2.2 kilobases. Similar analysis of poly(A) RNA from a variety of adult tissues demonstrated HB9 transcripts in pancreas, small intestine, and colon. Reverse transcriptase-polymerase chain reaction was used to examine HB9 RNA transcripts in hematopoietic cell lines. HB9 RNA transcripts were most prevalent in several human B cell lines and K562 cells. In addition, transcripts were detected in RNA prepared from tonsil B cells and in situ hybridization studies localized them in the germinal center region of adult tonsil. These findings suggest the involvement of HB9 in regulating gene transcription in lymphoid and pancreatic tissues.

Adult↗
PubMed1990

Cloning and characterization of the histidine biosynthetic gene cluster of Streptomyces coelicolor A3(2).

Biochemical and genetic data indicate that in Streptomyces coelicolor A3(2) the majority of the genes involved in the biosynthesis of histidine are clustered in a small region of the chromosome [Carere et al., Mol. Gen. Genet. 123 (1973) 219-224; Russi et al., Mol. Gen. Genet. 123 (1973) 225-232]. To investigate the structural organization and the regulation of these genes, we have constructed genomic libraries from S. coelicolor A3(2) in pUC vectors. Recombinant clones were isolated by complementation of an Escherichia coli hisBd auxotroph. A recombinant plasmid containing a 3.4-kb fragment of genomic DNA was further characterized. When cloned in the plasmid vector, pIJ699, this fragment was able to complement S. coelicolor A3(2) hisB mutants. Overlapping clones spanning a 15-kb genomic region were isolated by screening other libraries with labeled DNA fragments obtained from the first clone. Derivative clones were able to complement mutations in four different cistrons of the his cluster of S. coelicolor A3(2). Nucleotide sequence analysis of a 4-kb region allowed the identification of five ORFs which showed significant homology with the his gene products of E. coli. The order of the genes in S. coelicolor A3(2) (5'--hisD-hisC-hisBd-hisH-hisA-3') is the same as in the his operon of E. coli.

Amino Acid Sequence↗
PubMed2000

Genomic exploration of the hemiascomycetous yeasts: 3. Methods and strategies used for sequence analysis and annotation.

The primary analysis of the sequences for our Hemiascomycete random sequence tag (RST) project was performed using a combination of classical methods for sequence comparison and contig assembly, and of specifically written scripts and computer visualization routines. Comparisons were performed first against DNA and protein sequences from Saccharomyces cerevisiae, then against protein sequences from other completely sequenced organisms and, finally, against protein sequences from all other organisms. Blast alignments were individually inspected to help recognize genes within our random genomic sequences despite the fact that only parts of them were available. For each yeast species, validated alignments were used to infer the proper genetic code, to determine codon usage preferences and to calculate their degree of sequence divergence with S. cerevisiae. The quality of each genomic library was monitored from contig analysis of the DNA sequences. Annotated sequences were submitted to the EMBL database, and the general annotation tables produced served as a basis for our comparative description of the evolution, redundancy and function of the Hemiascomycete genomes described in other articles of this issue.

Amino Acid Sequence↗
PubMed2001

Development and mapping of Oryza glumaepatula-derived microsatellite markers in the interspecific cross Oryza glumaepatula x O. sativa.

Wild germplasm of domesticated crops is a source of genetic variation little utilized in breeding programs. Interspecific crosses can potentially uncover novel gene combinations that can be important for quantitative trait analysis. The combined use of wide crosses and genetic maps of chromosomal regions associated with quantitative traits can be used to broaden the genetic basis of rice breeding programs. Oryza glumaepatula is a diploid (AA genome) wild rice species native from South and Central America. A genetic map was constructed with 162 PCR-based markers (155 microsatellite and 7 STS markers) using a backcross population derived from the cross O. glumaepatula, accession RS-16 from the Brazilian Amazon Region x O. sativa BG-90-2, an elite rice inbred line. The map included 47 new SSR markers developed from an O. glumaepatula genomic library enriched for AG/TC sequences. All SSR markers were able to amplify the O. sativa genome, indicating a high degree of SSR flanking region conservation between O. glumaepatula and O. sativa species. The map covered 1500.4 cM, with an average of one marker every 10 cM. Despite some chromosomes being more densely mapped, the overall coverage was similar to other maps developed for rice. The advantage to construct a SSR-based map is to permit the combination of the speed of the PCR reaction, and the codominant nature of the SSR marker, facilitating the QTL analysis and marker assisted selection for rice breeding programs.

Chromosome Mapping↗
PubMed1988

Regional mapping of unique DNA sequences from human chromosome 3 derived from a flow-sorted chromosome library.

Eight single-copy DNA probes specific for human chromosome 3 were isolated by screening a human chromosome 3-derived genomic library. Southern blot analyses of DNAs isolated from a panel of somatic cell hybrids allowed us to regionally assign all probes to subregions on chromosome 3. Three clones were localized to the short arm of chromosome 3 (3p21----pter), two to the long arm (3q21----qter), and three to the 3q21----3p21 subregion. Six of these DNA sequences map to regions overlapping a segment of chromosome 3 (3p14----p23) frequently deleted in small cell lung cancer cells. Restriction fragment length polymorphism analyses indicate that at least three of the eight single-copy probes studies show MspI or BglII polymorphisms. This library is a useful source of chromosome 3-specific probes.

Chromosome Mapping↗
PubMed1987

Molecular cloning of rat renin cDNA and its gene.

Renin (EC 3.4.23.15) is an aspartyl protease that cleaves its only known substrate, angiotensinogen, to release the vasopressor hormone angiotensin. We have isolated full-length cDNAs for renin from a rat kidney cDNA library. The cDNAs are complementary to a 1434-nucleotide rat kidney mRNA that encodes preprorenin, the 402-amino acid precursor of renin. This rat cDNA was used to isolate the complete copy of a renin gene from a rat genomic library, and a comparison of this genomic clone with rat genomic DNA showed that renin is a single-copy gene in the rat. Rat renin is 85% identical to one mouse renin isozyme (renin-1) and 81% identical to the second mouse renin isozyme (renin-2), suggesting that the duplication of the mouse renin genes is a more recent event than the speciation of rats and mice. Analyses of rat, human, and mouse renin sequences revealed that the potential to form two-chain renin is apparently peculiar to mouse renin, and the expression of a tenth exon (which results in a three-amino acid insertion) is observed only in the human renin gene.

Amino Acid Sequence↗
PubMed1993

The human prohibitin (PHB) gene family and its somatic mutations in human tumors.

Five cosmid clones, isolated by procedures to screen genomic libraries for homologous variants of the human prohibitin gene (PHB), were analyzed to determine their genomic structures. Four of these (PHBP1-4) were found to be processed pseudogenes, each located on a different chromosome from their counterparts on chromosome 17q21. The DNA sequence of one clone (PHBP1, on chromosome 6q25) shared a 91.3% identity at the nucleotide level with the cDNA of functional prohibitin. A large number of human tumors of the breast, ovary, liver, and lung were examined for somatic mutations in the PHB gene. Although mutations were observed in a few sporadic breast cancers, none were identified in any of the other cancers.

Base Sequence↗
PubMed1996

Structure, sequence, expression, and chromosomal localization of the human V1a vasopressin receptor gene.

We recently reported the structure and functional expression of a human V1a vasopressin receptor (V1aR) cDNA isolated from human liver cDNA libraries. To understand further the expression and regulation of the V1aR, we now describe the genomic characteristics, tissue expression, chromosomal localization, and regional mapping of the human V1aR gene, AVPR1A. Tissue distribution of the human V1aR mRNA explored by Northern blot analysis of various human tissues or organs revealed the presence of a 5.5-kb mRNA transcript expressed in the liver and to a lesser degree in the heart, the kidney, and skeletal muscle. Screening of human genomic libraries revealed that the human AVPR1A gene is included entirely within a 6.4-kb EcoRI fragment and comprises two coding exons separated by a 2.2-kb intron located before the corresponding seventh transmembrane domain of the receptor sequence. The first exon also contains 2 kb of 5'-untranslated region, and the second exon includes 1 kb of 3'-untranslated region. 5'-RACE analysis of human liver mRNA by PCR localized the V1aR mRNA transcription start site 1973 bp upstream of the translation initiation site. Specific oligonucleotides derived from the intron sequence were used as primers in polymerase chain reaction (PCR) analysis of human/rodent somatic cell hybrids. AVPR1A was localized by PCR analysis of a somatic cell hybrid panel to chromosome 12. Fluorescence in situ hybridization using a yeast artificial chromosome physically mapped AVPR1A to region 12q14-q15.

Animals↗
PubMed1998

The mouse chondroadherin gene: characterization and chromosomal localization.

The mouse chondroadherin gene was isolated from a cosmid genomic library by the use of a rat chondroadherin cDNA probe. Southern blot analysis of mouse genomic DNA revealed a simple pattern of hybridization indicating a single copy gene for chondroadherin. The mouse chondroadherin gene encompasses 4.1 kb and consists of four exons separated by one large intron of 1929 bp followed by two smaller introns of 247 and 225 bp, respectively. Most of the translated region, including the start codon and the main part of a leucine-rich region, is contained within the first exon. Two small exons of 164 and 146 bp encode the rest of the protein. Interestingly, 4 bases from the stop codon, in the 3'-UTR, a third intron is located. A putative promoter region of 669 bp was sequenced and shown to contain a potential TATAA-box signal 29 bp upstream of the transcription start site and several recognition sites for transcription factors. The exon/intron organization of the chondroadherin gene differs from those of the other known genes of the leucine-rich repeat (LRR) family in the extracellular matrix. Taken together with comparison of protein sequences of other members of the LRR family in the extracellular matrix, the data suggest that chondroadherin has evolved along a different pathway. The chondroadherin gene was mapped to mouse chromosome 11, near D11Mit14, by single-strand conformation polymorphism linkage analysis.

Amino Acid Sequence↗
PubMed1998

Isolation and functional characterization of the mouse p75 TNF receptor promoter.

Tumor necrosis factor (TNF) is a pleiotropic cytokine that plays an important role in immunological and inflammatory responses. It exerts its biological effects via two distinct membrane receptors of apparent molecular weight of 55 (p55TNFR) and 75 kDa (p75TNFR), respectively. Most cell lines and primary tissues express both receptor types. While the p55TNFR gene is constitutively expressed at rather low levels, the transcription of p75TNFR is strongly modulated by a number of stimulatory agents. To characterize the mouse p75TNFR gene expression on a molecular level, we screened a mouse genomic library using the 5' end of the p75TNFR cDNA as a probe. A 6.3kb genomic clone containing about 6 kb of 5' flanking region and 300 bp of 3' sequence including the translational start site and the first exon was isolated and subcloned. Primer extension analysis revealed three transcriptional start sites located at -35, -39, and -564 bp upstream of the ATG-containing first exon. To determine whether the 5' flanking region exerts functional promoter activity, we generated deletion mutants fused to the luciferase reporter gene. Transfection of mouse fibroblasts (NIH3T3) with these constructs showed functional promoter activity of the isolated 5' region. By further sequence analysis of the 5' flanking region a number of putative DNA-binding sites for transcription factors, e.g., Sp1, CREB, Yi, YY1, and IFN gamma-responsive element, were identified.

3T3 Cells↗
PubMed1996

A second and differentially expressed glutamyl-tRNA reductase gene from Arabidopsis thaliana.

5-Aminolevulinic acid (ALA) is the universal precursor of tetrapyrroles (e.g., chlorophylls and hemes). In the chloroplasts of plants and in several eubacterial species ALA is formed in a two-step process known as the C5 pathway. In the first step, glutamyl-tRNA reductase (GluTR), converts glutamate of glutamyl-tRNA to glutamate 1-semialdehyde (GSA) which is rearranged to ALA by glutamate 1-semialdehyde-2,1-aminomutase (GSA-A) in the second step. Since ALA formation is a limiting step in chlorophyll biosynthesis, GluTR, which is encoded by the HEMA gene in Arabidopsis thaliana plays a vital role in that biosynthesis. Here we report the occurrence of a second functional HEMA gene (HEMA2) in A. thaliana. This gene was isolated by screening a genomic library with a probe from HEMA1. The nucleotide sequence of the cDNA and the corresponding genomic DNA indicates that the Arabidopsis HEMA2 gene contains two short introns (285 bp and 159 bp). The deduced amino acid sequence predicts a HEMA2 protein of 530 amino acids with 79% identity to the HEMA1-encoded GluTR. The 5'-flanking sequence of the HEMA2 gene includes several motifs (e.g., GT-1 boxes, GATA motifs) similar to light-responsive regulatory elements found in light-inducible genes. Unlike the HEMA1 transcript, which is present in all parts of the plant, HEMA2 is expressed in low levels in roots and flowers. The presence of a second functional HEMA gene in Arabidopsis raises the possibility that two C5 pathways exist in chloroplasts.

Aldehyde Oxidoreductases↗