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At least 1,603 records · Page 89Linked to original sources
PubMed1997

Homologous sequences in the Campoletis sonorensis polydnavirus genome are implicated in replication and nesting of the W segment family.

Polydnaviruses (PDVs) are double-stranded DNA viruses with segmented genomes that replicate only in the oviducts of some species of parasitic wasps and are required for the successful parasitization of lepidopteran insects. PDV DNA segments are integrated in the genomes of their associated wasp hosts, and some are nested; i.e., smaller segments are produced from and largely colinear with larger segments. To determine the internal structure of nested viral segments, the first complete nucleotide sequence of a PDV genome segment and its integration locus was determined. By restriction mapping, Southern blot, and sequence analyses, we demonstrated that the Campoletis sonorensis PDV segment W is integrated into wasp genomic DNA. DNA sequence analysis revealed that proviral segment W terminates in two 1,185-bp direct long terminal repeats (LTRs) in the wasp chromosome, while only one LTR copy is present in the extrachromosomal (viral) W. The results suggest that terminal direct repeats are a general feature of PDV DNA segment integration but that the homology and size of the repeats can vary extensively. Segment W contains 12 imperfect direct repeats of six different types between 89 bp and 1.9 kbp with 65 to 90% homology. The orientation and structure of the repeats suggest that W itself may have arisen through sequence duplication and subsequent divergence. Mapping, hybridization, and sequence analyses of cloned R and M demonstrated that these segments are nested within segment W and that internal imperfect direct repeats of one type are implicated in the homologous intramolecular recombination events that generate segments R and M. Interestingly, segment nesting differentially increases the copy number of genes encoded by segment W, suggesting that the unusual genomic organization of PDVs may be directly linked to the unique functions of this virus in its obligate mutualistic association with parasitic wasps.

Animals↗
PubMed1987

Cloning and characterization of the Escherichia coli K-12 alanine-valine transaminase (avtA) gene.

avtA, which encodes the alanine-valine transaminase, transaminase C, was cloned in vivo with high- and low-copy-number mini-Mu cloning vectors. The phenotype conferred by the cloned avtA+ gene usually depended upon the plasmid copy number; most high-copy-number avtA+ plasmids permitted isoleucine-requiring ilvE strains to grow in the absence of isoleucine (multicopy suppression), while low-copy-number avtA+ plasmids did not. avtA was mapped to a 1.25-kilobase segment by comparison of the restriction maps of 24 independent mini-Mu plasmids and then by gamma-delta (Tn1000) mutagenesis of a pBR322-avtA+ plasmid. The direction of transcription of avtA on the cloned fragment was determined with fusions to a promoterless lac gene.

Chromosome Mapping↗
PubMed1996

Deficiency of cox1 gene expression in wheat plants with Aegilops columnaris cytoplasm.

Wheat plants with Aegilops columnaris cytoplasm are characterized by growth inhibition and partial male sterility and show an impaired mitochondrial cytochrome c oxidase activity. We designed this study to clarify the functional relationship between this impaired cytochrome c oxidase activity and possible structural alterations to the mitochondrial genes cox1, cox2 and cox3 that encode three subunits of the cytochrome c oxidase. Using restriction mapping and DNA sequencing, we found major rearrangements in the flanking regions of the cox1 and cox3 genes. In Northern-blot analysis, we detected two different cox3 transcripts and a reduced level of a cox2 transcript, whereas we could not detect a transcript of cox1. These results suggest that rearrangements of the flanking regions of the cox1 gene may result in the severe suppression of its transcription, and subsequently, may lead to the impaired cytochrome c oxidase activity.

Base Sequence↗
PubMed1992

Multiple mRNA forms of human GTP cyclohydrolase I.

To isolate full length cDNA clones encoding human GTP cyclohydrolase I, the first and rate-limiting enzyme in tetrahydrobiopterin biosynthesis, a cDNA library generated from human liver was screened by plaque hybridization. Analysis of the clones, hybridized with rat cDNA fragment, by restriction mapping and partial sequencing showed the existence of three kinds of cDNAs. All three cDNAs were identical in their central and 5' regions. They were, however, found to diverge at 3' ends. Furthermore, the three species of mRNAs corresponding to the three cDNAs were detected in human liver by reverse transcription-polymerase chain reaction (RT-PCR) analysis. These results indicate that, in humans, GTP cyclohydrolase I molecules are encoded by at least three distinct mRNAs.

Amino Acid Sequence↗
PubMed1994

A middle-repetitive DNA sequence element in the sheep parasitic nematode, Trichostrongylus colubriformis.

A novel repetitive DNA sequence in the sheep parasitic nematode Trichostrongylus colubriformis was cloned and sequenced. A 1.1 kb repetitive sequence (Tc15) which hybridized with DNA from T. colubriformis but not with DNA from two other parasitic nematodes, Haemonchus contortus and Ostertagia circumcincta, or sheep was further characterized. Southern blot analysis showed that the repeat hybridized to a range of fragments in restriction digested T. colubriformis DNA and existed in multiple copy number tandem arrays. However, to define clearly the repetitive monomeric unit further screening of phagemid libraries containing BamH I restriction fragments using a subclone of Tc15 as a probe was carried out. Restriction map and sequence data were compiled for 3 clones containing a 145 bp highly repetitive sequence (designated TcREP) which shared homology with the original pTc15 clone. TcREP hybridized to a tandemly repeating sequence monomer of 145 bp in T. colubriformis DNA which was cloned from various genetic environments in the T. colubriformis genome. TcREP homologous sequences were also found in the genomes of two other species of the same genus (Trichostrongylus axei and Trichostrongylus vitrinus) but not in a fourth species (Trichostrongylus rugatus).

Animals↗
PubMed1989

Multiple amylase genes in two strains of Bacillus stearothermophilus.

Plasmid DNA fragments from Bacillus stearothermophilus ATCC29609 (BR135) and chromosomal DNA fragments from B. stearothermophilus ATCC31195 (BR132) were cloned into pBR322 and transformed into Escherichia coli strain HB101. Clones were selected which demonstrate extracellular expression of thermostable amylase. The DNA inserts from both strains showed similar restriction maps. Examination of the parental strains revealed plasmids of approx. 100 kb and 35 kb for BR135 and no discernible plasmids for BR132. Hybridization experiments showed that the amylase gene is contained within a 3.2-kb HindIII fragment on both plasmids, and to be present in multiple copies in the BR135 chromosome. Multiple chromosomal copies of the amylase gene were also observed for BR132. Purification of the alpha-amylase produced by the cloned plasmid amy gene yielded a homogeneous 58-kDa protein with thermostable amylase activity.

Blotting, Southern↗
PubMed1989

Structure and expression of the human motilin gene.

The human motilin gene was isolated from a human genomic library and its structure was determined by restriction mapping and DNA sequence analysis. The gene consists of five exons separated by four introns spanning approximately 9 kb of genomic DNA. Exon I encodes the 5' untranslated portion of the motilin mRNA. Exons II and III encode the signal peptide and the 22-amino-acid motilin peptide; codons encoding the motilin moiety are split by an intron. The carboxy-terminal motilin-associated peptide (MAP) is largely encoded by Exons III and IV with the last two amino acids of the motilin precursor and the 3' untranslated region encoded by Exon V. Thus, the motilin gene has an unusual structure in which a small bioactive peptide is encoded on two distinct exons. Examination of the expression of the human and nonhuman primate motilin gene by Northern hybridization analysis indicates that it is expressed in a number of gastrointestinal and extragastrointestinal tissues.

Animals↗
PubMed1996

Cloning of the fliI gene from Rhodobacter sphaeroides WS8 by analysis of a transposon mutant with impaired motility.

A transposon mutant of Rhodobacter sphaeroides WS8 was isolated that showed reduced swarming on soft agar plates. Liquid cultures of this mutant (M18) showed a low percentage of motile swimming cells in mid-exponential phase and a low level of extracellular flagellin protein by Western blotting. M18 was complemented by a clone from a library of R. sphaeroides WS8 DNA, and restriction mapping of the site of TnphoA insertion in the mutant, coupled with DNA sequencing, showed that it had a defect in the fliI gene. To determine if a partly functional fliI gene was giving the low-motility phenotype of M18, a drug resistance omega cartridge was inserted into the gene to give a complete null mutant. This null strain also produced a low percentage of motile cells. Possible reasons for this apparent fliI-independent flagellar formation are discussed.

Amino Acid Sequence↗
PubMed1993

Cloning, expression, and sequence analysis of a cytolytic enterotoxin gene from Aeromonas hydrophila.

The structural gene and regulatory element for a cytolytic enterotoxin of a diarrheal isolate, SSU, of Aeromonas hydrophila was cloned and its DNA sequence was determined. A complementary, mixed synthetic oligonucleotide based on the first 10 NH2-terminal amino acid residues of the Aeromonas cytolytic enterotoxin was used as a probe to screen a genomic library constructed in bacteriophage EMBL3. Cell lysates of Escherichia coli (lambda CH4), containing the cytolytic enterotoxin gene, lysed rabbit red blood cells and destroyed Chinese hamster ovary cells, caused fluid secretion in rat ileal loops, and were lethal to mice when injected intravenously. All biological activities associated with the cytolytic enterotoxin were neutralized by rabbit homologous polyclonal antibodies. Sodium dodecyl sulfate polyacrylamide gel electrophoresis and subsequent Western blot analysis of the cell lysate of E. coli (lambda CH4) revealed a protein band of approximately 52 kDa, using antisera to the cytolytic enterotoxin or antibodies generated against a synthetic peptide to the toxin. DNA sequence analysis of a 2.8-kb SalI-BamHI fragment revealed the presence of one large open reading frame (1479 bp) that would encode a protein of 54.5 kDa, a precursor form of the cytolytic enterotoxin, with a 23 amino acid leader peptide. Despite a significant amount of homology at the DNA and amino acid levels between our cytolytic enterotoxin and two aerolysins of Aeromonas species, variation in the restriction maps of these three toxin genes was prominent. Likewise, considerable divergence in DNA sequence was observed upstream of the structural genes for the reported aerolysins and our cytolytic enterotoxin, suggesting that these structurally similar toxin molecules may be regulated differently. Finally, our data showed that the cytolytic enterotoxin from a diarrheal isolate, SSU, of A. hydrophila exhibited characteristics that were unique compared with those of the reported aerolysins.

Aeromonas hydrophila↗
PubMed1993

Cloning of a human platelet-activating factor receptor gene: evidence for an intron in the 5'-untranslated region.

A clone encoding a gene for a human platelet-activating factor (PAF) receptor has been isolated from a human genomic library. A 6-kb Hind III fragment was subcloned and was found to contain a full coding sequence identical with that previously reported for cDNA clones encoding PAF receptors from leukocyte cDNA libraries. Sequencing of the 6-kb Hind III fragment upstream from the start codon revealed that the 5'-untranslated region deviated from reported cDNA sequences beginning at base -39, suggesting the presence of an intron in this region. Consensus sequences for a splice junction appear appropriately located at the predicted 3' end of the purported intron. Restriction map analysis of the region revealed that the size of the intron in the 5'-untranslated region was at least 16 kb. These data indicate that a gene for a human PAF receptor is present in the genome without introns in the coding sequence and that splicing of mRNA encoding PAF receptors appears to occur in the 5'-untranslated region.

Amino Acid Sequence↗
PubMed1994

Genomic cloning of the mouse LDL receptor related protein/alpha 2-macroglobulin receptor gene.

The LDL receptor-related protein (LRP) or alpha 2-macroglobulin receptor (A2mr) is encoded by a 15-kb mRNA in mouse and human. Probes encompassing different regions of the mouse cDNA were used to isolate clones from a cosmid library of mouse strain 129. Four overlapping cosmids were used for restriction mapping and Southern blot analysis. This map and hybridization data obtained with oligonucleotide probes from the 5' and 3' ends of the Lrp cDNA demonstrated that the mouse gene is approximately 85 kb in size. The Lrp promoter region was sequenced and reveals strong evolutionary conservation of putative regulatory elements between mouse and human. The present study will facilitate detailed elucidation of the function of LRP in vivo.

Animals↗
PubMed1992

Characterization of the novel nisin-sucrose conjugative transposon Tn5276 and its insertion in Lactococcus lactis.

A novel, chromosomally located conjugative transposon in Lactococcus lactis, Tn5276, was identified and characterized. It encodes the production of and immunity to nisin, a lanthionine-containing peptide with antimicrobial activity, and the capacity to utilize sucrose via a phosphotransferase system. Conjugal transfer of Tn5276 was demonstrated from L. lactis NIZO R5 to different L. lactis strains and a recombination-deficient mutant. The integration of Tn5276 into the plasmid-free strain MG1614 was analyzed by using probes based on the gene for the nisin precursor (nisA) and the gene for sucrose-6-phosphate hydrolase (sacA). The transposon inserted at various locations in the MG1614 chromosome and showed a preference for orientation-specific insertion into a single target site (designated site 1). By using restriction mapping in combination with field inversion gel electrophoresis and DNA cloning of various parts of the element including its left and right ends, a physical map of the 70-kb Tn5276 was constructed, and the nisA and sacA genes were located. The nucleotide sequences of Tn5276 junctions in donor strain NIZO R5 and in site 1 of an MG1614-derived transconjugant were determined and compared with that of site 1 in recipient strain MG1614. The results show that the A + T-rich ends of Tn5276 are flanked by a direct hexanucleotide repeat in both the donor and the transconjugant but that the element does not contain a clear inverted repeat.

Base Sequence↗
PubMed1993

[Molecular-genetic analysis of expression features of the evolutionary-conservative neurogene Nc73EF of Drosophila melanogaster].

Molecular-genetic analysis of the Nc (neural conserved) genome sequence of Drosophila melanogaster located at the position 73EF of Drosophila melanogaster was performed. The Nc73EF sequence was shown to be expressed in the nervous system of Drosophila. We constructed the restriction map of this sequence and revealed the main RNA-coding fragment in the 5'-3' orientation. The RNA-dot analysis data demonstrated that expression of the Nc73EF transcripts took place mainly in the nervous system. Hybridization with the human brain poly(A)+RNA confirmed the basic RNA-coding fragment to be evolutionary conservative. Southern blot analysis showed this fragment to be unique in the Drosophila genome. Northern blots detected three transcripts of this DNA fragment.

Animals↗
PubMed1992

Oligonucleotide-directed site-specific mutagenesis in Drosophila melanogaster.

An efficient technique has been developed for performing in vivo site-directed mutagenesis in Drosophila melanogaster. This procedure involves directed repair of P-element-induced DNA lesions after injection of a modified DNA sequence into early embryos. An oligonucleotide of 50 base pairs, whose sequence spans the P-element insertion site, mediates base replacement in the endogenous gene. Restriction mapping, DNA sequencing, and polymerase chain reaction analysis demonstrate that base substitutions present in an injected oligonucleotide are incorporated into genomic sequences flanking a P insertion site in the white gene. This analysis suggests that progeny bearing directed mutations are recovered with a frequency of about 0.5 x 10(-3). Because Drosophila remains a premier organism for the analysis of eukaryotic gene regulation, this system should find strong application in that analysis as well as in the analysis of DNA recombination, conversion, repair, and mutagenesis.

Animals↗
PubMed1996

A novel plasmid from Staphylococcus epidermidis specifying resistance to kanamycin, neomycin and tetracycline.

The naturally occurring plasmid pSTS7 from Staphylococcus epidermidis mediated resistance to tetracycline via a tetL gene and to kanamycin and neomycin via an aadD gene. Plasmid pSTS7 showed partial restriction map and sequence homology to the previously described tetracycline resistance plasmid pNS1981 from Bacillus subtilis and to the kanamycin/neomycin/bleomycin resistance plasmid pUB110 from S. aureus. Sequence analysis of the regions flanking the two resistance genes in pSTS7 led to the identification of a novel site for interplasmid recombination which could explain the derivation of pSTS7 from the incompatible pNS1981- and pUB110-like parental plasmids under tetracycline-selective pressure.

Amino Acid Sequence↗
PubMed1992

Evidence of incorporation of the chromosomal beta-lactamase gene of Enterococcus faecalis CH19 into a transposon derived from staphylococci.

We recently reported the chromosomal location of the staphylococcal beta-lactamase gene in four strains of Enterococcus faecalis. Transfer of this gene from strain CH19 to an enterococcal recipient was accompanied by transfer of numerous other antimicrobial resistance determinants in the absence of detectable plasmid DNA. A restriction map developed by comparing digestions of the regions surrounding the beta-lactamase gene in donor and recipient chromosomes resembles published maps of previously described staphylococcal beta-lactamase transposons, particularly in the area of the structural gene and its downstream region. In addition, DNA sequence analysis of the region immediately downstream of the beta-lactamase gene from both CH19 and its transcipient, CX19, revealed the presence of a 121-bp inverted repeat region found in Tn552 and Tn4002, two previously described staphylococcal beta-lactamase transposons. These results suggest that the chromosomal beta-lactamase gene of E. faecalis CH19 is incorporated into a transposonlike element derived from staphylococci.

Base Sequence↗
PubMed1991

The first analysed archegoniate mitochondrial gene (COX3) exhibits extraordinary features.

The first mitochondrial-encoded gene of an archegoniate has been identified, cloned and sequenced. The cytochrome oxidase III gene (cox3) of the moss Physcomitrella patens consists of a 618 bp open reading frame with high homology (around 72%) to known cox3 sequences of higher plants. Nevertheless, it is a quarter shorter than these. The cox3 gene of P. patens contains no introns and reveals a G + C-content of 41.3%. The region containing the cox3 gene exists as a single copy in the mitochondrial genome as shown by restriction mapping. In the 5' flanking sequence a putative ribosome binding site and a putative secondary structure were found. Two main transcripts of 2.4 kb and 2.6 kb were detected indicating a complex mitochondrial transcription pattern possibly due to co-transcription. Additional open reading frames were found downstream from, as well as upstream of, the cox3 gene. In Western blots a polyclonal cox3 antibody from yeast detected one single band with an apparent molecular weight of 22 kDa.

Amino Acid Sequence↗
PubMed1990

Disruption of the gene XRN1, coding for a 5'----3' exoribonuclease, restricts yeast cell growth.

As a step toward determining the metabolic role(s) of a 5'----3' exoribonuclease (XRN1), a yeast gene, XRN1, encoding XRN1, was first cloned, then disrupted to test its essentially or effect on yeast cell growth. Clones in the high-copy-number plasmid YEp24 cause overproduction (fivefold) of XRN1 in yeast cells, as measured by either poly(A) hydrolytic activity or immunoreactivity. Restriction mapping and deletion analysis showed that the XRN1 gene is located on a 6.7-kb XbaI-XhoI fragment of chromosome VII. The normal gene was disrupted in two haploid yeast strains by integrating a fragment with a BglII-deleted segment replaced with the yeast URA3 gene, and the disrupted strains lack XRN1. Successful transformation of haploid cells showed that the gene is not essential, but its absence markedly affected the cell growth rate. The growth defect is corrected by introduction of the XRN1 gene on a plasmid back into the disrupted yeast.

Blotting, Southern↗