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DNA sequence analysis of a 10.4 kbp region on the right arm of yeast chromosome XVI positions GPH1 and SGV1 adjacent to KRE6, and identifies two novel tRNA genes.

Determination of DNA sequence in the KRE6 region of the Saccharomyces cerevisiae genome completes a 10.4 kbp section on the extreme right arm of chromosome XVI. This segment contains two additional genes, GHP1 and SGV1 (Hwang et al., 1989; Irei et al., 1991) previously assigned physically to chromosome XVI, as well as a new tRNA(Gly) gene, and a novel tRNA(Ala) gene which is flanked by a sigma element.

Chromosome Mapping↗

Zymomonas mobilis squalene-hopene cyclase gene (shc): cloning, DNA sequence analysis, and expression in Escherichia coli.

Using a DNA probe from the gene encoding squalene-hopene cyclase (SHC, EC 5.4.99.-) from the Gram-positive bacterium Alicyclobacillus acidocaldarius, we have cloned a 4.3 kb HindIII fragment of chromosomal DNA from Zymomonas mobilis. An open reading frame of 1977 bp was detected that could encode a protein of 658 amino acids with a calculated molecular mass of 74077 Da. Under the control of lac or tac promoters, this gene, shc, was expressed in Escherichia coli K12 strains and its product had squalene-hopene cyclase activity. Sequence alignments with the A. acidocaldarius SHC, the lanosterol cyclase of the yeast Candida albicans, and the cycloartenol synthase of the plant Arabidopsis thaliana revealed six highly conserved regions (mainly in the C-terminal part) of the proteins. These regions contained the core motif Gln-X-X-X-Gly-X-Trp.

Amino Acid Sequence↗

16S ribosomal DNA sequence analysis distinguishes biotypes of Streptococcus bovis: Streptococcus bovis Biotype II/2 is a separate genospecies and the predominant clinical isolate in adult males.

We characterized 22 human clinical strains of Streptococcus bovis by genotypic (16S rRNA gene sequence analysis [MicroSeq]; Applied Biosystems, Foster City, Calif.) and phenotypic (API 20 Strep and Rapid ID32 Strep systems (bioMerieux Vitek, Hazelton, Mo.) methods. The strains, isolated from blood, cerebrospinal fluid (CSF), and urine, formed two distinct 16S ribosomal DNA sequence clusters. Three strains which were associated with endocarditis urinary tract infection (UTI), and sepsis clustered with the S. bovis type strain ATCC 33317 (cluster 1); other closely related type strains were S. equinus and S. infantarius. Nineteen strains clustered at a distance of about 2.5% dissimilarity to the S. bovis type strain (cluster 2) and were associated with central nervous system (CNS) disease in addition to endocarditis, UTI, and sepsis. All strains were distinct from S. gallolyticus. Within cluster 2, a single strain grouped with ATCC strain 43143 (cluster 2a) and may be phenotypically distinct. All the other strains formed a second subgroup (cluster 2b) that was biochemically similar to S. bovis biotype II/2 (mannitol negative and beta galactosidase, alpha galactosidase, beta glucuronidase, and trehalose positive). The API 20 Strep system identified isolates of cluster 2b as S. bovis biotype II/2, those of cluster 1 as S. bovis biotype II/1, and that of cluster 2a as S. bovis biotype I. There was an excellent correlation of biotype and genotype: S. bovis biotype II/2 isolates form a separate genospecies distinct from the S. bovis, S. gallolyticus, and S. infantarius type strains and are the most common isolates in adult males.

Adult↗

DNA sequence analysis of the type-common glycoprotein-D genes of herpes simplex virus types 1 and 2.

The DNA sequences for the coding and flanking regions of the type-common glycoprotein-D (gD) genes of herpes simplex virus (HSV) types 1 and 2 have been determined. The resultant protein sequences are approximately 80% homologous. Both gD proteins are 393 amino acids long and both have maintained three identical potential glycosylation sites. Amino acid changes are found throughout the proteins, with the majority of changes located in the amino and carboxyl/termini. Most of the amino acid differences were found to be conservative. Hydropathy analysis, which determines hydrophobic and hydrophilic regions, reveals a remarkable structural similarity between the proteins. Examination of 5' flanking sequences demonstrates extensive DNA sequence homology adjacent to the start of gD gene transcription. In addition, another homologous noncoding region was found 3' to the gD gene. This second homologous sequence is 5' to a 1.6-kb transcription unit.

Amino Acid Sequence↗

Location by DNA sequence analysis of cop mutations affecting the number of plasmid copies of prophage P1.

The DNA sequence of six P1 cop mutants, which are altered in the control of copy number of the plasmid prophage, was compared to that of P1 wild type. Each cop mutant differs from the wild type by a single base substitution. All of these substitutions are located within a 400 base pair region of P1 DNA that also encodes rep, a gene whose product is required for P1 replication.

Amino Acid Sequence↗

Prediction of function in DNA sequence analysis.

Recognition of function of newly sequenced DNA fragments is an important area of computational molecular biology. Here we present an extensive review of methods for prediction of functional sites, tRNA, and protein-coding genes and discuss possible further directions of research in this area.

Algorithms↗

Microcomputer programs for back translation of protein to DNA sequences and analysis of ambiguous DNA sequences.

Three computer programs are described which may be used to translate a DNA sequence into a protein sequence, back translate the protein sequence into an ambiguous DNA sequence, and then do pattern searching in the ambiguous sequence. The programs are written in the C programming language, have been compiled to run on a microcomputer under the CP/M 80 operating system, and may be copied in binary format through a modem. They are also to become available for the IBM/PC.

Amino Acid Sequence↗

RNA splicing in yeast mitochondria: DNA sequence analysis of mit- mutants deficient in the excision of introns aI1 and aI2 of the gene for subunit I of cytochrome c oxidase.

We have characterized two yeast mutants deficient in the splicing of transcripts of the mitochondrial gene for cytochrome c oxidase subunit I (coxI). Both map to the first intron (aI1). RNA blot analysis shows that in addition to a reduced (mutant M15-190) or blocked (mutant M12-193) excision of the mutated intron aI1, the mutants are unable to excise the adjacent aI2 intron, the reading frame of which displays an amino acid sequence similarity to aI1. Splicing of the downstream introns is not affected, however. Sequence analysis of the first mutant DNA (M12-193) reveals a premature termination of the intron-encoded open reading frame, followed by two alterations at a short distance downstream. The other (M15-190) contains 11 separate changes. Although these occur in the intron reading frame, their main effect on RNA splicing may be exerted through the disturbance of intron secondary structure proposed for the 5' end of several group II introns. The implications of these findings in relation to maturase function and structure of intron aI1 are discussed.

Base Sequence↗

A DNA sequence analysis program for the Apple Macintosh.

This paper describes a new set of programs for analyzing DNA sequences using the Apple Macintosh computer, a computer ideally suited for this kind of analysis. Because of the Macintosh interface and the availability of high quality software-only speech synthesis, these programs are truly easy to use. Instead of typing in commands, the user directs the program by making selections with the mouse, thereby eliminating most typographical and syntax errors. Output options are selected by "pressing buttons" and then clicking "OK" with the mouse. DNA sequences are confirmed by having the program speak them. The high resolution graphics on the Macintosh not only allow for explanatory diagrams to be used to aid in deciding on input parameters, but can be used to produce slides for presentations and figures for papers. Because of the clipboard and the ability of the Macintosh to readily share data among different applications, data can be saved for use directly in word processing documents (e.g. manuscripts).

Animals↗

A convenient and adaptable package of DNA sequence analysis programs for microcomputers.

We describe a package of DNA data handling and analysis programs designed for microcomputers. The package is convenient for immediate use by persons with little or no computer experience, and has been optimized by trial in our group for a year. By typing a single command, the user enters a system which asks questions or gives instructions in English. The system will enter, alter, and manage sequence files or a restriction enzyme library. It generates the reverse complement, translates, calculates codon usage, finds restriction sites, finds homologies with various degrees of mismatch, and graphs amino acid composition or base frequencies. A number of options for data handling and printing can be used to produce figures for publication. The package will be available in ANSI Standard FORTRAN for use with virtually any FORTRAN compiler.

Amino Acid Sequence↗

Molecular phylogeny of grey mullets based on mitochondrial DNA sequence analysis: evidence of a differential rate of evolution at the intrafamily level.

The phylogeny of the grey mullets is considered problematic both at the intra- and interfamily level. Such a difficulty arises from the highly homogeneous morphology displayed by this group of fish and, consequently, from the paucity of the key morphological characters suitable to address their phylogeny and evolution. In the present work, we have approached the phylogenetic and evolutionary relationships of seven species of Mugilidae, six of which from the Mediterranean Sea, on the basis of the DNA sequences of two mitochondrial genes (cytochrome b and 12S rRNA). Despite the morphological homogeneity exhibited by the taxa considered, the two species of the genus Mugil (M. cephalus and M. curema) showed a remarkable genetic divergence compared to all the other members of the family. The relative rate test revealed a significantly higher rate of evolution along the Mugil lineage.

Animals↗

Ribosomal DNA sequence analysis shows that the basidiomycete C30 belongs to the genus Trametes.

The basidiomycete C30 was considered as an isolate of a population of Marasmius quercophilus collected on evergreen oak litter from the Mediterranean forest. Recent phenotypic studies have clearly shown that it differs from newly characterized M. quercophilus isolates. Subsequent analysis of laccase genes revealed that C30 sequences are similar to laccase encoding sequences from organisms belonging to the polyporoid clade. Comparison of sequences of the C30 ITS regions, including 5.8S rDNA, with those found in databanks confirmed that C30 is not a Marasmius. Finally, 25S rDNA analysis revealed that C30 is closely related to the Coriolaceae and, in particular, to Trametes trogii.

Basidiomycota↗

DNA sequence analysis of spontaneous and gamma-radiation (anoxic)-induced lacId mutations in Escherichia coli umuC122::Tn5: differential requirement for umuC at G.C vs. A.T sites and for the production of transversions vs. transitions.

Escherichia coli umuC122::Tn5 cells were gamma-irradiated (137Cs, 750 Gy, under N2), and lac-constitutive mutants were produced at 36% of the wild-type level (the umuC strain was not deficient in spontaneous mutagenesis, and the mutational spectrum determined by sequencing 263 spontaneous lacId mutations was very similar to that for the wild-type strain). The specific nature of the umuC strain's partial radiation mutability was determined by sequencing 325 radiation-induced lacId mutations. The yields of radiation-induced mutation classes in the umuC strain (as a percentage of the wild-type yield) were: 80% for A.T-->G.C transitions, 70% for multi-base additions, 60% for single-base deletions, 53% for A.T-->C.G transversions, 36% for G.C-->A.T transitions, 25% for multi-base deletions, 21% for A.T-->T.A transversions, 11% for G.C-->C.G transversions, 9% for G.C-->T.A transversions, and 0% for multiple mutations. Based on these deficiencies and other factors, it is concluded that the umuC strain is near-normal for A.T-->G.C. transitions, single-base deletions and possibly A.T-->C.G transversions; is generally deficient for mutagenesis at G.C sites and for transversions, and is grossly deficient in multiple mutations. Damage at G.C sites seems more difficult for translesion DNA synthesis to bypass than damage at A.T sites, and especially when trying to produce a transversion. The yield of G.C-->A.T transitions in the umuC strain (36% of the wild-type level) argues that abasic sites are involved in no more than 64% of gamma-radiation-induced base substitutions in the wild-type strain. Altogether, these data suggest that the UmuC and UmuD' proteins facilitate, rather than being absolutely required for, translesion DNA synthesis; with the degree of facilitation being dependent both on the nature of the noncoding DNA damage, i.e., at G.C vs. A.T sites, and on the nature of the misincorporated base, i.e., whether it induces transversions or transitions.

Bacterial Proteins↗

Identification of Candida dubliniensis, based on ribosomal DNA sequence analysis.

Differentiation of Candida albicans and the recently described C. dubliniensis has proven difficult due to the high degree of phenotypic similarity of these species. The present study examines sequence variations in the ribosomal DNA (rDNA) intergenic transcribed spacer (ITS) regions of C. albicans (n = 5) and C. dubliniensis (n = 7) strains, with a view to identifying sequence differences that would enable consistent differentiation of these two species by restriction fragment length polymorphism (RFLP) analysis. The ITS1 and ITS2 regions, together with the entire 5.8S rRNA gene of the strains, were amplified by the polymerase chain reaction (PCR), using primers ITS1 and ITS4, PCR products from both C. albicans and C. dubliniensis were of similar size (around 540 bp); however, sequence analysis revealed over 20 consistent base differences between the products of the two species. On the basis of sequence variation, the restriction enzyme MspA1 I was selected and used to differentiate the PCR products of C. albicans and C. dubliniensis by RFLP analysis. MspA1 I yielded two discernible fragments from C. albicans PCR products, whilst those from C. dubliniensis appeared undigested, thereby providing an approach to differentiate the two species.

Candida↗

[p53 gene mutation determined by single-strand conformational polymorphism and DNA sequencing analysis in pleomorphic adenoma of salivary gland].

OBJECTIVE: To detect p53 exon 6 mutation pattern in pleomorphic adenoma of salivary gland. METHODS: Single-strand conformational polymorphism (SSCP) and DNA sequecing were used. RESULTS: SSCP analysis showed that 6 of 11 cases with SSCP positive were exon 6 abnormal. Comparison of the SSCP results with DNA sequecing, 4 cases with p53 exon 6 mutations were SSCP positive. Mutation pattern included base substitution (point mutation, G-->T, T-->G) and frame-shift mutation (base insertion and base loss). CONCLUSION: Poly-codon and poly-pattern mutations appeared in p53 exon 6. PCR-SSCP was a convenient method to detecte gene mutation.

Adenoma, Pleomorphic↗

Visual Cloning 2000: a DNA sequence analysis program.

VC2000 is a recommendable, easy-to-use and affordable program suited particularly to plot maps of both plasmids and linear DNA fragments for the documentation of cloning procedures. It comes with basic tools for sequence analysis that assist this major utility. A special feature of the program is the integration of web-based tools, providing additional analytical power and flexibility. In this way the user is supplied with the latest versions of these applications.

Cloning, Molecular↗

gm: a practical tool for automating DNA sequence analysis.

The gm (gene modeler) program automates the identification of candidate genes in anonymous, genomic DNA sequence data. gm accepts sequence data, organism-specific consensus matrices and codon asymmetry tables, and a set of parameters as input; it returns a set of models describing the structures of candidate genes in the sequence and a corresponding set of predicted amino acid sequences as output, gm is implemented in C, and has been tested on Sun, VAX, Sequent, MIPS and Cray computers. It is capable of analyzing sequences of several kilobases containing multi-exon genes in less than 1 min execution time on a Sun 4/60.

Algorithms↗

Osteonectin promoter. DNA sequence analysis and S1 endonuclease site potentially associated with transcriptional control in bone cells.

To understand the basis of osteonectin (SPARC) transcriptional regulation, we have isolated a bovine genomic clone (lambda Og15) encoding exon 1 and 15 kilobase pairs (kb) of flanking DNA. Direct RNA sequencing of the 5' end of the osteonectin message showed it contained a sequence identical to that of a 2.4-kb EcoRI-BamHI fragment located midway in the clone lambda Og15. The results indicate exon 1 is located 10 kb away from exon 2 in the bovine genome. The DNA sequence unit CCTG is repeated five times in exon 1 which is composed exclusively of untranslated sequence. Sequence analysis of the 5'-flanking DNA revealed the presence of many regulatory motifs including a "GC" box with four overlapping SP1 consensus sequences. Immediately downstream from the GC box is a 72-base pair purine-rich stretch composed primarily of direct repeats of the sequence motifs GGGGA and GGA (GAGA box). Digestion of the flanking DNA in vitro with S1 endonuclease showed a site for the enzyme at position -55 which is just 3' to the GAGA box. Chimeric chloramphenicol acetyltransferase constructs were prepared containing the S1-sensitive site and showed substantial transcriptional activity in UMR-106 and fetal and adult human bone cells which are known to be high producers of the protein. The results indicate a potential regulatory activity of the S1 site in osteonectin gene activation.

Animals↗