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At least 109 records · Page 6Linked to original sources
PubMed1989

DNA sequence analysis of the 24.5 kilobase pair cytochrome oxidase subunit I mitochondrial gene from Podospora anserina: a gene with sixteen introns.

The DNA sequence of a 26.7 Kilobase pair (10(3) base pairs = 1 Kb) region of the mitochondrial genomes of races s and A from Podospora anserina was determined. Within this region, the 24.5 Kb cytochrome oxidase subunit I gene was located and its exon sequences determined by computer analysis comparisons with other fungal genes. The Podospora COI gene was interrupted by two group II introns (one in race s) and fourteen group I introns ranging in size from about 2.2 Kb to 404 bp. Earlier studies on secondary structure analysis, as well as comparison of their open reading frames (ORFs), showed that the two group II introns were closely related. The fourteen group I introns were representatives of three subgroupings (IB, C and a new category, subgroup ID). Two of these group I introns were separated by just a single exon codon. The analysis of all these introns is discussed in comparison with other fungal introns as well as with the known Podospora anserina introns.

Amino Acid Sequence↗
PubMed1989

DNA sequence analysis of the apocytochrome b gene of Podospora anserina: a new family of intronic open reading frame.

The 5,969 bp (base pair) DNA sequence of the apocytochrome b mitochondrial (mt) gene of race A Podospora anserina was located in a 8.5 Kbp region. This gene contained a 2,499 bp subgroup IB and a 1,306 bp subgroup ID intron as well as a 990 bp subgroup IB intron which is present in race A but not race s. The large subgroup IB intron and the race A specific IB intron both contained potential alternate splice sites which brought their open reading frames into phase with their upstream exon sequences. All three introns were compared with regard to their secondary structures and open reading frames to the other 30 group I introns in Podospora anserina, as well as to other fungal introns. We detected a new family of intronic ORFs comprising seven P. anserina introns, several N. crassa introns, as well as the T4td bacteriophage intron. Sequence similarities to intron-encoded endonucleases were noteworthy. The DNA sequences reported here and in the accompanying paper complete the analysis of race s and race A mitochondrial DNA.

Amino Acid Sequence↗
PubMed1985

Physical mapping and DNA sequence analysis of the rifampicin resistance locus in vaccinia virus.

Rifampicin has been shown to inhibit the maturation of poxviruses at a discrete step in envelope formation (Moss et al., 1969; Pennington et al., 1970; Nagayama et al., 1970; Grimley et al., 1970). A rifampicin-resistant vaccinia virus mutant (RifR) was selected for its ability to grow in the presence of 100 micrograms/ml of rifampicin. Utilizing intact DNA or endonuclease restricted cloned DNA subfragments derived from the RifR mutant virus, the locus specifying rifampicin resistance was physically mapped by marker rescue analysis leftward of the unique XhoI site within the HindIII D fragment. DNA sequencing of a 445 bp fragment encompassing this region revealed an AT to GC transition when compared with the equivalent wild-type DNA fragment. Analysis of the six potential open reading frames within the 445-bp fragment indicated only one available open reading frame. On this basis, the rifampicin-resistant vaccinia virus mutant was shown to have a codon transition from asparagine to aspartic acid.

Amino Acid Sequence↗
PubMed1987

DNA sequence analysis of two bovine immunoglobulin CH gamma pseudogenes.

A bovine calf liver DNA library in lambda 2001 bacteriophage has been screened with a human Ig gamma 4 heavy-chain constant-region gene probe. Four hybridizing clones have been identified, and the DNA sequences in two of these, which have high homology with CH gamma genes, are reported here. Within the bovine sequences, four separate exons can be identified, corresponding to the three CH domains and the hinge of gamma heavy-chain genes. Both of these genes contain atypical sequences around one or more of their exon/intron boundaries with consequent loss of splice sites, indicating that these are probably gamma pseudogenes. One sequence codes for a C-terminal peptide which matches the 18-mer C-terminal heavy-chain peptide of bovine serum IgG2, the other encodes a C-terminal peptide unknown in the bovine. These results suggest that evolutionary duplication of CH gamma genes has occurred in the bovine.

Amino Acid Sequence↗
PubMed1983

Random subcloning of sonicated DNA: application to shotgun DNA sequence analysis.

A method for producing random subclones using sonication to fragment the DNA is presented. The sonication is combined with enzymatic repair of the fragment ends and a rigorous size fractionation step to prepare subclones of relatively homogeneous and specific size. Under some conditions sonication is shown to shear A + T-rich sequences preferentially, although under most conditions it will create a random subclone library. The use of these subclone libraries for an improved "shotgun" DNA sequencing strategy is tested on a 17.2-kb (kilobase) fragment of Epstein-Barr virus.

Base Sequence↗
PubMed1991

Mutational specificities of environmental carcinogens in the lacl gene of Escherichia coli H. V: DNA sequence analysis of mutations in bacteria recovered from the liver of Swiss mice exposed to 1,2-dimethylhydrazine, azoxymethane, and methylazoxymethanolacetate.

The host-mediated assay (HMA) was used to determine the spectra of mutations induced in the lacl gene of Escherichia coli cells recovered from the livers of Swiss mice exposed to the carcinogens 1,2-dimethylhydrazine (SDMH), azoxymethane (AOM), and methylazoxymethanolacetate (MAMA). These spectra were further compared with changes induced by dimethylnitrosamine (DMNA) in the HMA methodology. A total of 177 independent lacl mutations arising in the HMA following exposure to SDMH, AOM, and MAMA were analyzed. Single-base substitutions accounted for 97% of all mutations analyzed. The vast majority of the single-base substitutions consisted of G:C----A:T transitions (94% of all mutations). The remaining mutations consisted of A:T----G:C transitions (3% of all mutations) while non-base substitutions accounted for only 3% of the total mutagenesis. The latter mutations consisted of one frameshift mutation and four lacO deletions. The distribution of G:C----A:T transitions induced by the three chemicals in the first 200 bp of the lacl gene was not random, but rather clustered at sites where a target guanine was flanked at the 5' site by a purine residue.

1,2-Dimethylhydrazine↗
PubMed1986

DNA sequence analysis of a 5.27-kb direct repeat occurring adjacent to the regions of S-episome homology in maize mitochondria.

The DNA sequence of the 5270-bp repeated DNA element from the mitochondrial genome of the fertile cytoplasm of maize has been determined. The repeat is a major site of recombination within the mitochondrial genome and sequences related to the R1(S1) and R2(S2) linear episomes reside immediately adjacent to the repeat. The terminal inverted repeats of the R1 and R2 homologous sequences form one of the two boundaries of the repeat. Frame-shift mutations have introduced 11 translation termination codons into the transcribed S2/R2 URFI gene. The repeated sequence, though recombinantly active, appears to serve no biological function.

Amino Acid Sequence↗
PubMed1990

DNA sequence analysis of endoglucanase genes from Pseudomonas fluorescens subsp. cellulosa and Pseudomonas sp. NCIB 8634.

The DNA of two previously isolated recombinant clones, one from Pseudomonas sp. NCIB 8634 (= Cellvibrio mixtus) (pPC71) and another from Pseudomonas fluorescens subsp. cellulosa (pPFC4) that express endoglucanase activity in E. coli was sequenced. Plasmid pPC71 had three open reading frames, two of which include portions of plasmid pBR322. The third open reading frame occurs entirely within the Pseudomonas DNA insert and encodes a protein with a molecular mass of 5845 Da. The DNA insert in pPFC4 was found to contain an open reading frame (PFC-ORF) that encodes a protein of 32189 Da. The major endoglucanase produced in E. coli cells carrying pPFC4 is about 30,000 Da. It is concluded that PFC-ORF encodes this endoglucanase. Both ribosome and catabolite gene activator protein binding sites lie upstream from the initiating codon of PFC-ORF. An interesting feature of the PFC-ORF protein is the presence of amino acid motifs Val-Ser-Ser-Ser-Ser and Val-Val-Ser-Ser-Ser-Ser-Ser that occur within a 25 amino acid span.

Amino Acid Sequence↗
PubMed1990

Chemical robot for enzymatic reactions and extraction processes of DNA in DNA sequence analysis.

A chemical robot capable of performing enzymatic reactions and extraction processes of DNA has been developed. The basic functions of this robot include handling of plastic tubes with caps, micropipetting, mixing, microcentrifuging and incubating. As a result, almost all of the pre-electrophoresis steps can be carried out. In addition, because these processes are automated, the working time of each process can be reduced. The reproducibility of the automated operation is equivalent to that of a skilled operator.

Base Sequence↗
PubMed1984

Restriction site bank vectors. II. DNA sequence analysis of plasmid pJRD158.

pJRD158 is a small plasmid vector (3903 bp) derived from pBR327 and specifying resistance to ampicillin and tetracycline. It contains 28 unique restriction sites (and 4 nonunique restriction sites) that can be used for cloning. The DNA sequence and computer-assisted restriction site analysis of pJRD158 are reported. Evidence is also presented that suggests a 2-bp revision of the DNA sequence of pBR322 in the RNA primer region.

Ampicillin↗
PubMed1990

Molecular cloning, genetic characterization and DNA sequence analysis of the recM region of Bacillus subtilis.

In Bacillus subtilis the recM gene, whose product is associated with DNA repair and recombination, has been located between the dnaX and rrnA genes. The recM gene has been cloned and analyzed. Analysis of the nucleotide sequence (3.741-kilobase) around recM revealed five open reading frames (orf). We have assigned recM and dnaX to two of this orf, given the gene order dnaX-orf107-recM-orf74-orf87. The organization of genes of the dnaX-orf107-recM region resembles the organization of genes in the dnaX-orf12-recR region of the Escherichia coli chromosome. Proteins of 24.2 and 17.0 kDa would result from translation of the wild type and in vitro truncated recM genes, and radioactive bands of proteins of molecular weights of 24.5 and 17.0 kDa were detected by the use of the T7promoter-expression system. The RecM protein contains a potential zinc finger domain for nucleic acid binding and a putative nucleotide binding sequence that is present in many proteins that bind and hydrolyze ATP. Strains, in which the recM gene has been insertionally inactivated, were generated and show a phenotype essentially the same as previously described recM mutants.

Adenosine Triphosphate↗
PubMed1994

DNA sequence analysis of the cytosolic acetaldehyde dehydrogenase gene (Ahd-2) in mouse strains with variable ethanol preferences.

Differences in Ahd-2 at the DNA sequence level were characterized in mouse strains with variable ethanol preferences. The 5' region and the region surrounding the active site of Ahd-2 were compared to detect differences which could affect ethanol sensitivity. Only minor differences were found among the strains in the two regions. These differences cannot explain their variable ethanol preference and the implications of sequence identities among the divergent strains in these regions has yet to be determined.

Alcohol Drinking↗
PubMed1982

DNA sequence analysis of a mouse pro alpha 1 (I) procollagen gene: evidence for a mouse B1 element within the gene.

In a 3.8-kilobase mouse DNA sequence encoding amino acid sequences for the pro alpha 1(I) chain of type I procollagen, 14 coding sequences were identified which specify a sequence 95% homologous to amino acid residues 568 to 963 of the bovine alpha 1(I) chain. All of these coding sequences were flanked by appropriate splice junctions following the GT/AG rule. These observations suggest, but do not prove, that this pro alpha 1(I) gene is transcriptionally active. Of the 14 coding sequences, 7 were 54 base pairs in length, whereas the remainder were higher multiples of 54 base pairs. Nonrandom utilization of codons pertained throughout all of the coding sequences showing a preference (56%) for U in the wobble position. Two of the intervening sequences encoded imperfect vestiges of coding sequences which exhibited a codon preference different from that of the pro alpha 1(I) gene proper and were not flanked by splice junctions. One intervening sequence encoded a member of the mouse B1 family of middle repetitive sequences. It was flanked by 8-base-pair direct repeats and had a truncated A-rich region, suggesting that it may be a mobile element. Within this element were sequences which could function as a RNA polymerase III split promoter.

Animals↗
PubMed1992

DNA sequence analysis of the dnaK gene of Escherichia coli B and of two dnaK genes carrying the temperature-sensitive mutations dnaK7(Ts) and dnaK756(Ts).

The DNA sequence of the dnaK gene of Escherichia coli was analyzed. The nucleotide sequence of the wild-type dnaK gene of E. coli B differed from that of E. coli K-12 in 15 bp, none of which altered the amino acid sequence. Two temperature-sensitive dnaK mutations were examined by cloning and sequence analyses. Results showed that one dnaK mutation, dnaK7(Ts), was a one-base substitution of T for C at nucleotide position 448 in the open reading frame yielding an amber nonsense codon. The other mutation, dnaK756(Ts), consisted of base substitutions (A for G) at three nucleotide positions, 95, 1364, and 1403, in the open reading frame resulting in an aspartic acid codon in place of a glycine codon.

Amino Acid Sequence↗