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  • 1
    Electronic Resource
    Electronic Resource
    The DNA secondary structure of the Bacillus subtilis genome (2003)
    Oxford, UK : Blackwell Publishing Ltd
    FEMS microbiology letters 218 (2003), S. 0 
    Details
    ISSN: 1574-6968
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Biology
    Notes: The entire genomic DNA sequence of the Gram-positive bacterium Bacillus subtilis reported in the SubtiList database has been subjected in this work to a complete bioinformatic analysis of the potential formation of secondary DNA structures such as hairpins and bending. The most significant of these structures have been mapped with respect to their genomic location and compared to those structures already known to have a physiological role, such as the rho-independent transcription terminators. The distribution of these structures along the bacterial chromosome shows two major features: (i) the concentration of the most curved DNA in the intergenic regions rather than within the ORFs, and (ii) a decreasing gradient of large hairpins from the origin towards the ter C end of chromosomal DNA replication. Given the increasing biological relevance of secondary DNA structures, these findings should facilitate further studies on the evolution, dynamics and expression of the genetic information stored in bacterial genomes.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1111/j.1574-6968.2003.tb11493.x
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  • 2
    Electronic Resource
    Electronic Resource
    Introduction of nonselectible 2μ plasmid into [cir°] cells of the yeast S. cerevisiae by DNA transformation and in vivo site-specific resolution (1989)
    Springer
    Current genetics 15 (1989), S. 83-90 
    Details
    ISSN: 1432-0983
    Keywords: DNA transformation ; Saccharomyces cerevisiae ; Site-specific recombination ; 2μ DNA plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The 2μ DNA plasmid of the yeast Saccharomyces cerevisiae does not confer any known selectable phenotype to the host cell carrying it. Selection of cells transformed with purified 2μ DNA therefore cannot be achieved, and the intracellular presence of 2μ can only be assessed by molecular analysis of the DNA complement. In addition, 2μ alone does not replicate in bacterial hosts, thus rendering its amplification by conventional methods impossible. We have isolated a shuttle plasmid, pBH-2L, generated by in vivo sites-pecific recombination between the endogenous 2μ DNA plasmid and pRL, a pBR322 derivative containing the yeast LEU2 gene and one 2μ repeat sequence associated with the origin of replication. This new shuttle plasmid has the property, when transformed into yeast, of undergoing site-specific recombinational resolution between its two direct repeat sequences. This releases 2μ plasmid and pRL as individual molecules. The latter can undergo progressive mitotic loss during growth in nonselective medium, ultimately leaving leucine auxotrophic transformants that contain only 2μ DNA plasmid. This system can be utilized to introduce 2μ DNA alone into cells lacking it, thereby providing a novel means to study the biology and the molecular genetics of the plasmid and its potential practical applications as a vector.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00435453
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  • 3
    Electronic Resource
    Electronic Resource
    High frequency FLP-independent homologous DNA recombination of 2 μ plasmid in the yeast Saccharomyces cerevisiae (1988)
    Springer
    Current genetics 14 (1988), S. 191-199 
    Details
    ISSN: 1432-0983
    Keywords: Saccharomyces cerevisiae ; Site specific recombination ; 2 μ DNA plasmid
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary The purpose of this work is to identify and quantitate in vivo 2 μ plasmid FLP-independent recombination in yeast, using a nonselective assay system for rapid detection of phenotypic expression of the recombination events. A tester plasmid was constructed such that in vivo recombination between 2 μ direct repeat sequences produces the resolution of the plasmid into two circular DNA molecules. This recombinational event is detected as a phenotypic shift from red to white colonies, due to the mitotic loss of the plasmid portion containing the yeast ADE8 gene in a recipient ade1 ade2 ade8 genetic background. In the absence of the 2 μ FLP recombinase and/or its target DNA sequence, recombination is not abolished but rather continues at a high frequency of about 17%. This suggests that the FLP-independent events are mediated by the chromosomally-encoded general homologous recombination system. We therefore conclude that the totality of 2 μ DNA recombination events occurring in FLP+ cells is the contribution of both FLP-mediated and FLP-independent events.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00376739
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  • 4
    Electronic Resource
    Electronic Resource
    Recombinators, recombinases and recombination genes of yeasts (1994)
    Springer
    Current genetics 25 (1994), S. 1-11 
    Details
    ISSN: 1432-0983
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00712959
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  • 5
    Electronic Resource
    Electronic Resource
    Simultaneous detection of changes in chromosome number, gene conversion and intergenic recombination during mitosis of Saccharomyces cerevisiae: spontaneous and ultraviolet light induced events (1982)
    Springer
    Current genetics 6 (1982), S. 5-11 
    Details
    ISSN: 1432-0983
    Keywords: Chromosomal loss ; Mitotic nondisjunction ; Gene conversion ; Mitotic recombination ; Ultraviolet light
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Summary We have employed a hyperhaploid strain of Saccharomyces cerevisiae disomic for chromosome VII to monitor spontaneous and ultraviolet light induced restitution of haploidy (chromosomal loss and/or nondisjunction), mitotic gene conversion and mitotic intergenic recombination. The disomic chromosomal pair incorporates six heterozygous markers, including cyh2 r, distributed on both sides of the centromere. Cycloheximide resistant segregants of spontaneous origin were analyzed to calculate the spontaneous mitotic rates of restitution of haploidy, intergenic recombination and gene conversion that result in expression of the cyh2 r mutation. Restitution of haploidy was found to be the most common source of spontaneously arising cycloheximide resistant segregants. In contrast, those induced by ultraviolet light resulted most frequently from gene conversion of CYH2 s to cyh2 r. The chromosome VII hyperhaploid system provides a sensitive method to detect the aneugenic and recombinagenic effects of suspect chemical and physical agents.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00397633
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  • 6
    Electronic Resource
    Electronic Resource
    Nonrandomly-associated forward mutation and mitotic recombination yield yeast diploids homozygous for recessive mutations (1994)
    Springer
    Current genetics 26 (1994), S. 302-307 
    Details
    ISSN: 1432-0983
    Keywords: S. cerevisiae ; Spontaneous mutation ; Mitotic segregation ; Loss of heterozygosity ; Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract We have employed the analysis of spontaneous forward mutations that confer the ability to utilize L-α-aminoadipate as a nitrogen source (α-Aa+) to discern the events that contribute to mitotic segregation of spontaneous recessive mutations by diploid cells. α-Aa- diploid cells yield α-Aa+ mutants at a rate of 7.8±3.6×10-9. As in haploid strains, approximately 97% (30/31) of α-Aa+ mutants are spontaneous lys2-x recessive mutations. α-Aa+ mutants of diploid cells reflect mostly the fate of LYS2/lys2-x heterozygotes that arise by mutation within LYS2/LYS2 populations at a rate of 1.2±0.4×10-6. Mitotic recombination occurs in nonrandom association with forward mutation of LYS2 at a rate of 1.3±0.6×10-3. This mitotic recombination rate is tenfold higher than that of a control LYS2/lys2-1 diploid. Mitotic segregation within LYS2/lys2-x subpopulations yields primarily lys2-x/lys2-x diploids and a minority of lys2-x aneuploids. Fifteen percent of lys2-x/lys2-x diploids appear to have arisen by gene conversion of LYS2 to lys2-x; 85% of lys2-x/lys2-x diploids appear to have arisen by mitotic recombination in the CENII-LYS2 interval. lys2-1/lys2-1 mitotic segregants of a control LYS2/lys2-1 diploid consist similarly of 18% of lys2-1/lys2-1 diploids that appear to have arisen by gene conversion of LYS2 to lys2-1 and 82% of lys2-1/lys2-1 diploids that appear to have arisen by mitotic recombination in the CENII-LYS2 interval. The methods described can be used to simultaneously monitor the effects of yeast gene mutations and carcinogens on the principal parameters affecting the genomic stability of diploid mitotic cells: mutation, gene conversion, intergenic recombination, and chromosomal loss or rearrangement.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00310493
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  • 7
    Electronic Resource
    Electronic Resource
    Diploid yeast cells yield homozygous spontaneous mutations (1993)
    Springer
    Current genetics 23 (1993), S. 430-434 
    Details
    ISSN: 1432-0983
    Keywords: S. cerevisiae ; Mutational homozygosis ; Loss of heterozygosity ; Mutation ; Recombination
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract A leucine-requiring hybrid of Saccharomyces cerevisiae, homoallelic at the LEU1 locus (leu1–12/leu1–12) and heterozygous for three chromosome-VII genetic markers distal to the LEU1 locus, was employed to inquire: (1) whether spontaneous gene mutation and mitotic segregation of heterozygous markers occur in positive nonrandom association and (2) whether homozygous LEU1/LEU1 mutant diploids are generated. The results demonstrate that gene mutation of leu1–12 to LEU1 and mitotic segregation of heterozygous chromosome-VII markers occur in strong positive nonrandom association, suggesting that the stimulatory DNA lesion is both mutagenic and recombinogenic. In addition, genetic analysis of diploid Leu+ revertants revealed that approximately 3% of mutations of leu1–12 to LEU1 result in LEU1/LEU1 homozygotes. Red-white sectored Leu+ colonies exhibit genotypes that implicate postreplicational chromatid breakage and exchange near the site of leu1–12 reversion, chromosome loss, and subsequent restitution of diploidy, in the sequence of events leading to mutational homozygosis. By analogy, diploid cell populations can yield variants homozygous for novel recessive gene mutations at biologically significant rates. Mutational homozygosis may be relevant to both carcinogenesis and the evolution of asexual diploid organisms.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00312630
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  • 8
    Electronic Resource
    Electronic Resource
    The genomic instability of yeast cdc6-1/cdc6-1 mutants involves chromosome structure and recombination (1995)
    Springer
    Molecular genetics and genomics 249 (1995), S. 8-18 
    Details
    ISSN: 1617-4623
    Keywords: Yeast CDC6 gene ; Genomic instability ; DNA recombination ; Chromosomal rearrangement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology
    Notes: Abstract When diploid cells of Saccharomyces cerevisiae homozygous for the temperature-sensitive cell division cycle mutation cdc6-1 are grown at a semipermissive temperature they exhibit elevated genomic instability, as indicated by enhanced mitotic gene conversion, mitotic intergenic recombination, chromosomal loss, chromosomal gain, and chromosomal rearrangements. Employing quantitative Southern analysis of chromosomes separated by transverse alternating field gel electrophoresis (TAFE), we have demonstrated that 2N-1 cells monosomic for chromosome VII, owing to the cdc6-1 defect, show slow growth and subsequently yield 2N variants that grow at a normal rate in association with restitution of disomy for chromosome VII. Analysis of TAFE gels also demonstrates that cdc6-1/cdc6-1 diploids give rise to aberrant chromosomes of novel lengths. We propose an explanation for the genomic instability induced by the cdc6-1 mutation, which suggests that hyper-recombination, chromosomal loss, chromosomal gain and chromosomal rearrangements reflect aberrant mitotic division by cdc6-1/cdc6-1 cells containing chromosomes that have not replicated fully.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1007/BF00290230
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  • 9
    Electronic Resource
    Electronic Resource
    VII. Yeast sequencing reports. The sequence of an 11·1 kb fragment on the left arm of Saccharomyces cerevisiae chromosome VII reveals six open reading frames including NSP49, KEM1 and four putative new genes (1995)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 11 (1995), S. 1187-1194 
    Details
    ISSN: 0749-503X
    Keywords: genome sequencing ; Saccharomyces cerevisiae ; chromosome VII ; KEM1 ; NSP49 ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We report the sequence of an 11·1 kb fragment located on the left arm of chromosome VII of Saccharomyces cerevisiae. By sequence analysis we have detected six open reading frames (ORFs) longer than 300 bp, which cover 87% of the entire sequence. ORF G1645 is 100% identical to the KEM1 gene, also identified as DST2, XRN1, SEP1 and RAR5, while G1648 is 100% identical to the NSP49 or NUP49 gene. ORF G1642 shares some identity with a hypothetical protein of Caenorhabditis elegans, while the other four ORFs show no significant homology to known proteins. The sequence has been submitted to the EMBL data library under Accession Number X84705.
    Additional Material: 4 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/yea.320111209
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  • 10
    Electronic Resource
    Electronic Resource
    Specificity of DNA uptake during whole cell transformation of S. cerevisiae (1987)
    New York, NY [u.a.] : Wiley-Blackwell
    Yeast 3 (1987), S. 131-137 
    Details
    ISSN: 0749-503X
    Keywords: Transformation ; Saccharomyces ; plasmid ; DNA uptake ; Life and Medical Sciences ; Genetics
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Biology
    Notes: We have studied the mechanism of DNA transformation of whole yeast cells in Saccharomyces cerevisiae with particular emphasis on the role of the cell wall complex in DNA uptake. Two new aspects of the process have been investigated in order to evaluated its specificity. Such aspects are: (i) effect of monovalent vs. divalent cations during incubation with the transforming DNA and (ii) timing of DNA adsorption and uptake. We found that the specificity for cation requirement is a strain-dependent characteristic influenced by the presence of transforming DNA in the cell suspension. This finding is supported by reports from several laboratories that some yeast strains show mutually exclusive transformability with monovalent vs. divalent cations. While irreversible adsorption of plasmid DNA molecules is induced by both heat shock and polyethylene-glycol(PEG), DNA uptake seems to occur only after the removal of PEG. In the course of this study we have developed a new, alternative method of whole cell DNA transformation with CaCl2 able to transform strains that do not respond to other methods.
    Additional Material: 3 Ill.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1002/yea.320030209
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