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At least 343 records · Page 19Linked to original sources

Genetic control of capsid length in bacteriophage T4: DNA sequence analysis of petite and petite/giant mutants.

The T4 gene 23 product (gp23) encodes the major structural protein of the mature capsid. Mutations in this gene have been described which disrupt the normal length-determining mechanism (A.H. Doermann, F.A. Eiserling, and L. Boehner, J. Virol. 12:374-385, 1973). Mutants which produce high levels of petite and giant phage (ptg) are restricted to three tight clusters in gene 23 (A.H. Doermann, A. Pao, and P. Jackson, J. Virol. 61:2823-2827, 1987). Twenty-six of these ptg mutations were cloned, and their DNA sequence alterations were determined. Each member of this set of ptg mutants arose from a single mutation, and the set defined 10 different sites at which ptg mutations can occur in gene 23. Two petite (pt) mutations in gene 23 (pt21-34 and ptE920g), which produce high frequencies of petite particles but no giants, were also sequenced. Both pt21-34 and ptE920g were shown to include multiple mutations. The phenotypes attributed to both pt and ptg mutations are discussed relative to the mechanism of capsid morphogenesis. A site-directed mutation (SD-1E) was created at the ptgNg191 site, and its phenotypic consequences were examined. Plaque morphology revertants arising from a gene 23 mutant derivative of pt21-34 and from SD-1E were isolated. A preliminary mapping of the mutation(s) responsible for their revertant phenotypes suggested that both intra- and extragenic suppressors of the petite phenotype can be isolated by this method.

Amino Acid Sequence↗

Mitochondrial DNA sequence analysis of the masu salmon--phylogeny in the genus Oncorhynchus.

We determined 2162-bp sequences from the mitochondrial genome of the masu salmon Oncorhynchus masou masou, chum salmon Oncorhynchus keta, and Atlantic salmon Salmo salar by using polymerase chain reactions. These DNA sequences span from the 3' region of the gene for ATPase subunit 6 to the 5' region of the gene for NADH dehydrogenase subunit 4L. With the aid of the sequence data from other Pacific salmonid species (Thomas and Beckenbach, 1989, J. Mol. Evol. 29: 233-245), the evolutionary distances among the masu salmon and other species in the genus Oncorhynchus were calculated. These evolutionary distances were then used to construct a neighbor-joining tree. Further, a maximum parsimony tree was constructed. The evolutionary trees that were obtained suggest that masu salmon first diverged from the common ancestor of the genus Oncorhynchus.

Animals↗

DNA sequence analysis of newly formed telomeres in yeast.

A plasmid can be maintained in linear form in baker's yeast if it bears telomeric sequences at each end. Linear plasmids bearing cloned telomeric C4A4 repeats at one end (test end) and a natural DNA terminus with approximately 300 bps of C4A2 repeats at the other or control end were introduced by transformation into yeast. Test-end termini of 28 to 112 bps supported telomere formation. During telomere formation, C4A2 repeats were often transferred to test-end termini. To determine in greater detail the fate of test-end sequences on these plasmids after propagation in yeast, test-end telomeres were subcloned into E. coli and sequenced. DNA sequencing established a number of points about the molecular events involved in telomere formation in yeast. The results suggest that there are at least two mechanisms for telomere formation in yeast. One is mediated by a recombination event that requires neither a long stretch of homology nor the RAD52 gene product. The other mechanism is by addition of C1-3A repeats to the termini of linear DNA molecules. The telomeric sequence required to support C1-3A addition need not be at the very end of a molecule for telomere formation.

Base Sequence↗

Cloning, DNA sequence analysis, and expression in Escherichia coli of the gene for mandelate racemase from Pseudomonas putida.

The gene for mandelate racemase (EC 5.1.2.2) from Pseudomonas putida (ATCC 12633) was cloned in Pseudomonas aeruginosa (ATCC 15692). The selection for the cloned gene was based upon the inability of P. aeruginosa to grow on (R)-mandelate as sole carbon source by virtue of the absence of mandelate racemase in its mandelate pathway. Fragments of P. putida DNA obtained by digestion of chromosomal DNA with Sau3A were ligated into the BamHI site of the Gram-negative vector pKT230 and transformed into the P. aeruginosa host. A transformant able to utilize (R)-mandelate as sole carbon source was characterized, and the plasmid was found to contain approximately five kilobase pairs of P. putida DNA. Subcloning of this DNA revealed the position of the gene for the racemase within the cloned DNA from P. putida. The dideoxy-DNA sequencing procedure was used to determine the sequence of the gene and its translated sequence. The amino acid sequence and molecular weight for mandelate racemase deduced from the gene sequence (38 570) are in excellent agreement with amino acid composition and molecular weight data for the polypeptide recently determined with enzyme isolated from P. putida; these recent determinations of the polypeptide molecular weight differ significantly from the originally reported value of 69,500 [Fee, Judith A., Hegeman, G.D., & Kenyon, G.L. (1974) Biochemistry 13,2528], which was used to demonstrate that alpha-phenylglycidate, an active site directed irreversible inhibitor, binds to the enzyme with a stoichiometry of 1:1.(ABSTRACT TRUNCATED AT 250 WORDS)

Amino Acid Sequence↗

DNA sequence analysis of the KM19 locus linked to cystic fibrosis. Design of new oligonucleotides to remove non-specific PCR products.

The PstI polymorphism detected by probe KM19 is a highly informative marker in linkage disequilibrium with the cystic fibrosis locus and has been used extensively for prenatal diagnosis. The currently available primers used for polymerase chain reaction- (PCR-) based analysis of this locus have been shown to produce spurious amplification products. In this report, we describe the sequence of the KM19 locus and the major contaminating PCR product. We have used this information to design a more specific amplification procedure for analysis of the KM19 locus.

Base Sequence↗

DNA sequence analysis of spontaneous mutations at a LacZ transgene integrated on the mouse X chromosome.

Transgenic mice with integrated shuttle vectors containing the LacZ mutational target gene were used to study spontaneous mutational events in vivo. The transgenic mouse strain used carries the LacZ transgene on the X chromosome and was previously found to be characterized by approximately 25-fold higher spontaneous mutation frequency in liver and brain compared with at least three other transgenic mouse strains. To determine the nature of in vivo spontaneous mutational events, 35 mutant LacZ genes isolated from liver and brain of mice from strain 35.5 were analyzed at the DNA sequence level. The results obtained indicate that single base-pair changes were predominant in both liver and brain. However, in liver the majority of mutations were transitions whereas in brain transversions were predominantly observed. Six mutants appeared to contain multiple dispersed mutations, separated by as much as 44 bp. Mutations were generally located within a 500 bp region encoding the active site of the beta-galactosidase protein. Our results indicate that spontaneous mutations at the LacZ transgene are tissue specific and dependent on the chromosomal position of the LacZ transgene.

Animals↗

Recombination in adenovirus: DNA sequence analysis of crossover sites in intertypic recombinants.

The nucleotide sequence of the adenovirus type 5 genome has been determined for a 620-bp region that spans the C terminus of the pVI gene and the N terminus of the hexon gene, and compared to the adenovirus type 2 DNA sequence: 25 base changes have been identified, most of which do not lead to alterations in the amino acid sequence and regulatory signals in the region. Crossover sites in three intertypic recombinants have been previously located in this region of the genome by fine restriction mapping. A sequence determination for the three recombinants, and the four ts mutants used in generating the ts+ recombinants, was carried out. The crossovers were in each case located in a small region of complete sequence homology (from 45 to 156 nucleotides long) flanked on either side by sequences derived from each parent. These structures are compatible with a reciprocal crossing over model of generalised recombination, where a recombinant joint has resolved in a region of high DNA homology. For the recombinants considered here, this region abutts onto a neighbouring region of much lower sequence homology, and it is possible that the position of the crossover is determined at least in part by the termination of branch migration at a heterologous boundary.

Adenoviruses, Human↗

Mitochondrial DNA sequence analysis of the cytochrome oxidase subunit II gene from Podospora anserina. A group IA intron with a putative alternative splice site.

A 5 kb region of the 95 kb mitochondrial genome of Podospora anserina race s has been mapped and sequenced (1 kb = 10(3) base-pairs). This DNA region is continuous with the sequence for the ND4L and ND5 gene complex in the accompanying paper. We show that this sequence contains the gene for cytochrome oxidase subunit II (COII). This gene is 4 kb in length and is interrupted by a subgroup IB intron (1267 base-pairs (bp) in length) and a subgroup IA intron (1992 bp in length). This group IA intron has a long open reading frame (ORF; 472 amino acid residues) discontinuous with the upstream exon sequence. A putative alternative splice site is present, which brings the ORF into phase with the 5' exon sequence. The 5'- and 3'-flanking regions of the COII gene contain G + C-rich palindromic sequences that resemble similar sequences flanking many Neurospora crassa mitochondrial genes.

Amino Acid Sequence↗

DNA sequence analysis of mutagenicity and site specificity of ethyl methanesulfonate in Uvr+ and UvrB- strains of Escherichia coli.

EMS-induced mutations within a 180 base pair region of the lacI gene of E. coli were cloned and sequenced. In total, 105 and 79 EMS-induced mutations from a Uvr+ and a UvrB- strain, respectively, were sequenced. The specificity of EMS-induced mutagenesis was very similar in the two strains; G:C----A:T transitions accounted for all but three of the mutants. The overall frequency of induced mutation was fivefold higher in the UvrB- strain compared to the Uvr+ strain. This demonstrates, at the DNA sequence level, that the presumed premutagenic lesion, O6-ethylguanine, is subject to repair by the uvrABC excision repair system of E. coli. An analysis of mutation frequencies with respect to neighboring base sequence, in the two strains, shows that O6-ethylguanine lesions adjacent to A:T base pairs present better targets for the excision repair machinery than those not adjacent to A:T base pairs.

Base Sequence↗

Cloning and DNA sequence analysis of the glucose oxidase gene from Aspergillus niger NRRL-3.

A cDNA library from Aspergillus niger strain NRRL-3 enriched in sequences glucose oxidase was constructed. An 800 bp cDNA clone isolated from this library was used to screen 12,000 recombinant phages from an EMBL3 genomic library. A 15 kbp DNA segment isolated from this library contained the 1815 bp structural gene for glucose oxidase as well as a short 5'- and a longer 3'-noncoding region. The deduced protein sequence was verified by partial peptide sequencing.

Amino Acid Sequence↗

Cloning and DNA sequence analysis of the cDNA for the precursor of porcine follicle stimulating hormone (FSH) beta subunit.

A cDNA library of porcine anterior pituitary was constructed in an expression vector lambda gt11. The cDNAs encoding the porcine follicle stimulating hormone (pFSH) beta subunit were obtained using anti-human FSH beta antiserum or synthetic oligonucleotide. The nucleotide sequence of the pFSH beta subunit cDNA clone (929 base) has been determined. The cDNA contained a part of the signal sequence (six amino acids) and the whole amino acid sequence of the mature molecule (109 amino acids). The predicted protein sequence was different from that of the amino acid sequence analysis in ten residues and had an extended carboxyl terminus. Northern analysis showed that the length of the pFSH greater than subunit mRNA was about 1.8 kb.

Amino Acid Sequence↗

An editing environment for DNA sequence analysis and annotation (extended abstract).

This paper presents a computer system for analyzing and annotating large-scale genomic sequences. The core of the system is a multiple-gene structure identification program, which predicts the most "probable" gene structures based on the given evidence, including pattern recognition, EST and protein homology information. A graphics-based user interface provides an environment which allows the user to interactively control the evidence to be used in the gene identification process. To overcome the computational bottleneck in the database similarity search used in the gene identification process, we have developed an effective way to partition a database into a set of sub-databases of "related" sequences, and reduced the search problem on a large database to a signature identification problem and a search problem on a much smaller sub-database. This reduces the number of sequences to be searched from N to O ([square root of] N) on average, and hence greatly reduces the search time, where N is the number of sequences in the original database. The system provides the user with the ability to facilitate and modify the analysis and modeling in real time.

Base Sequence↗

Cloning and DNA sequence analysis of the cDNA for the precursor of porcine luteinizing hormone (LH) beta subunit.

The cDNAs encoding the porcine luteinizing hormone (LH) beta subunit (pLH beta) were isolated from a cDNA library of porcine anterior pituitary constructed in an expression vector lambda gt11 using anti-pituitary glycoprotein hormone antisera. The nucleotide sequence of pLH beta subunit cDNA clone (543 bases) was determined. The cDNA encodes a signal sequence (20 amino acids) and a further 121 amino acids corresponding to the mature LH beta molecule. The predicted protein sequence differs from that determined by direct peptide sequencing at 6 residues and additionally shows an extended carboxyl terminus. The 5' untranslated sequence shows a low homology and is extremely long when compared with other mammalian LH beta subunit cDNAs. Northern analysis showed that the length of the pLH beta subunit mRNA is about 0.85 kb.

Amino Acid Sequence↗

Definition of a new HLA-B7 subtype (B*0704) by isoelectric focusing, family studies and DNA sequence analysis.

During screening of potential bone marrow donors, a previously undescribed banding position for the serologically defined HLA-B7 antigen was identified in three unrelated families using one dimensional isoelectric focusing and class I specific Western blot analysis. The isoelectric point of the new variant is more acidic than the two HLA-B7 variants that had been defined before. In each family the new B7 variant was found linked to HLA-A2 and -Cw7. Cloning and sequencing of full-length clones of complementary DNA showed that the new allele (B*0704) differs from B*0702, the common allele encoding HLA-B7, by three nucleotide substitutions within the codon for residue 156 of the mature heavy chain. As a result of these differences amino acid 156 is changed from arginine to aspartic acid, a difference consistent with the isoelectric points. The group of three nucleotide substitutions that distinguish B*0704 from B*0702 is present in other HLA-B alleles.

Alleles↗