scholarly journals ROLE OF DNA SEQUENCES IN GENETIC RECOMBINATION IN THE ISO-1-CYTOCHROME c GENE OF YEAST. II. COMPARISON OF MUTANTS ALTERED AT THE SAME AND NEARBY BASE PAIRS

Genetics ◽  
1977 ◽  
Vol 85 (1) ◽  
pp. 1-22
Author(s):  
Carol W Moore ◽  
Fred Sherman
Keyword(s):  
Cytochrome C ◽  
Dna Sequences ◽  
Meiotic Recombination ◽  
Base Pair ◽  
Genetic Recombination ◽  
Initiation Codon ◽  
Recombination Rates ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
X Ray

ABSTRACT X-ray-induced mitotic recombination rates and spontaneous meiotic recombination rates have been determined in two-point crosses of various defined cyc1 mutants of the yeast Saccharomyces cerevisiae. All but one of the 17 cyc1 mutants chosen for this study contained either the addition, deletion or substitution of single base-pairs located within a defined segment of the gene that corresponds to the 11 amino acid residues at the amino terminus of iso-1-cytochrome c; approximately half of these mutants had alterations of the AUG initiation codon, some at the same base pair. Up to 66-fold differences in X-ray-induced recombination rates were observed when the same cyc1 mutant was crossed to cyc1 mutants having different alterations in the AUG initiation codon; over a ten-fold difference was observed in series of homologous crosses involving mutants with different changes at the same base-pair. Recombination rates that were associated with specific cyc1 mutants co-segregated with the particular alleles following meiosis, and comparable recombination patterns were also observed for independently isolated, identical mutations. With the mutants used in this study, the frequencies of meiotic recombination did not differ as markedly, suggesting a dissimilar dependence on specific DNA sequences for these two modes of recombination. These disproportionalities of recombination rates suggest that the nature of the mismatched bases influences the recombination process, but not in a way that can be simply interpreted.

scholarly journals Differential mismatch repair can explain the disproportionalities between physical distances and recombination frequencies of cyc1 mutations in yeast.

Genetics ◽  
1988 ◽  
Vol 119 (1) ◽  
pp. 21-34
Author(s):  
C W Moore ◽  
D M Hampsey ◽  
J F Ernst ◽  
F Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Mismatch Repair ◽  
Meiotic Recombination ◽  
Mitotic Recombination ◽  
The Other ◽  
Recombination Rates ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
X Ray ◽  
Mismatched Base Pair

Abstract Recombination rates have been examined in two-point crosses of various defined cyc1 mutations that cause the loss or nonfunction of iso-1-cytochrome c in the yeast Saccharomyces cerevisiae. Recombinants arising by three different means were investigated, including X-ray induced mitotic recombination, spontaneous mitotic recombination, and meiotic recombination. Heteroallelic diploid strains were derived by crossing cyc1 mutants containing a series of alterations at or near the same site to cyc1 mutants containing alterations at various distances. Marked disproportionalities between physical distances and recombination frequencies were observed with certain cyc1 mutations, indicating that certain mismatched bases can significantly affect recombination. The marker effects were more pronounced when the two mutational sites of the heteroalleles were within about 20 base pairs, but separated by at least 4 base pairs. Two alleles, cyc1-163 and cyc1-166, which arose by G.C----C.G transversions at nucleotide positions 3 and 194, respectively, gave rise to especially high rates of recombination. Other mutations having different substitutions at the same nucleotide positions were not associated with abnormally high recombination frequencies. We suggest that these marker effects are due to the lack of repair of either G/G or C/C mismatched base pairs, while the other mismatched base pair of the heteroallele undergoes substantial repair. Furthermore, we suggest that diminished recombination frequencies are due to the concomitant repair of both mismatches within the same DNA tract.

Highly mutable sites for ICR-170-induced frameshift mutations are associated with potential DNA hairpin structures: studies with SUP4 and other Saccharomyces cerevisiae genes

1986 ◽  
Vol 6 (12) ◽  
pp. 4425-4432
Author(s):  
D M Hampsey ◽  
R A Koski ◽  
F Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Base Pair ◽  
Temporal Stability ◽  
Loop Formation ◽  
Induced Mutations ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Mutagen Specificity ◽  
Hairpin Structures

The majority of the mutations induced by ICR-170 in both the CYC1 gene (J. F. Ernst et al. Genetics 111:233-241, 1985) and the HIS4 gene (L. Mathison and M. R. Culbertson, Mol. Cell. Biol. 5:2247-2256, 1985) of the yeast Saccharomyces cerevisiae were recently shown to be single G . C base-pair insertions at monotonous runs of two or more G . C base pairs. However, not all sites were equally mutable; in both the CYC1 and HIS4 genes there is a single highly mutable site where a G . C base pair is preferentially inserted at a [sequence in text]. Here we report the ICR-170 mutagen specificity at the SUP4-o tyrosine tRNA gene of yeast. Genetic fine structure analysis and representative DNA sequence determination of ICR-170-induced mutations revealed that there is also a single highly mutable site in SUP4-o and that the mutation is a G . C base-pair insertion at a monotonous run of G . C base pairs. Analysis of DNA sequences encompassing the regions of highly mutable sites for all three genes indicated that the mutable sites are at the bases of potential hairpin structures; this type of structure could not be found at any of the other, less mutable G . C runs in SUP4, CYC1, and HIS4. Based on these results and recent information regarding novel DNA structural conformations, we present a mechanism for ICR-170-induced mutagenesis. (i) ICR-170 preferentially binds to DNA in the beta conformation; factors that increase the temporal stability of this structure, such as adjacent stem-and-loop formation, increase the frequency of ICR-170 binding; (ii) the observed mutagen specificity reflects formation of a preferred ICR-170 intercalative geometry at [sequence in text] sites; (iii) during replication or repair, ICR-170 remains associated with the single-stranded template; (iv) stuttering or strand slippage by the polymerization complex as it encounters the mutagen results in nucleotide duplication; (v) subsequent replication or mismatch repair fixes the insertion into the genome. This mechanism accounts for both the IRC-170 mutagenic specificity and the molecular basis of the highly mutable sites in S. cerevisiae.

scholarly journals A DELETION MAP OF cyc1 MUTANTS AND ITS CORRESPONDENCE TO MUTATIONALLY ALTERED ISO-1-CYTOCHROMES c OF YEAST

Genetics ◽  
1975 ◽  
Vol 81 (1) ◽  
pp. 51-73 ◽  
Author(s):  
Fred Sherman ◽  
Mary Jackson ◽  
Susan W Liebman ◽  
Ann Marie Schweingruber ◽  
John W Stewart
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Cytochrome C ◽  
Primary Structure ◽  
Recombination Rates ◽  
Yeast Saccharomyces Cerevisiae ◽  
X Ray ◽  
Cytochromes C ◽  
Adjacent Point

ABSTRACT Mutants arising spontaneously from sporulated cultures of certain strains of yeast, Saccharomyces cerevisiae, contained deletions of the CYC1 gene which controls the primary structure of iso-1-cytochrome c. At least 60 different kinds of deletions were uncovered among the 104 deletions examined and these ranged in length from those encompassing only two adjacent point mutants to those encompassing at least the entire CYC1 gene. X-ray-induced recombination rates of crosses involving these deletions and cyc1 point mutants resulted in the assignment of 211 point mutants to 47 mutational sites and made it possible to unambiguously order 40 of these 47 sites. Except for one mutant, cyc1-15, there was a strict colinear relationship between the deletion map and the positions of 13 sites that were previously determined by amino acid alterations in iso-1-cytochromes c from intragenic revertants.

scholarly journals Single base-pair mutations in centromere element III cause aberrant chromosome segregation in Saccharomyces cerevisiae.

1986 ◽  
Vol 6 (2) ◽  
pp. 530-538 ◽  
Author(s):  
J McGrew ◽  
B Diehl ◽  
M Fitzgerald-Hayes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Dna Sequences ◽  
Base Pair ◽  
Site Directed Mutagenesis ◽  
Chromosome Stability ◽  
Functional Requirements ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Centromere Function

In this paper we show that a 211-base pair segment of CEN3 DNA is sufficient to confer wild-type centromere function in the yeast Saccharomyces cerevisiae. We used site-directed mutagenesis of the 211-base pair fragment to examine the sequence-specific functional requirements of a conserved 11-base pair segment of centromere DNA, element III (5'-TGATTTATCCGAA-3'). Element III is the most highly conserved of the centromeric DNA sequences, differing by only a single adenine X thymine base pair among the four centromere DNAs sequenced thus far. All of the element III sequences contain specific cytosine X guanine base pairs, including a 5'-CCG-3' arrangement, which we targeted for single cytosine-to-thymine mutations by using sodium bisulfite. The effects of element III mutations on plasmid and chromosome segregation were determined by mitotic stability assays. Conversion of CCG to CTG completely abolished centromere function both in plasmids and in chromosome III, whereas conversion of CCG to TCG decreased plasmid and chromosome stability moderately. The other two guanine X cytosine base pairs in element III could be independently converted to adenine X thymine base pairs without affecting plasmid or chromosome stability. We concluded that while some specific nucleotides within the conserved element III sequence are essential for proper centromere function, other conserved nucleotides can be changed.

scholarly journals ROLE OF DNA SEQUENCES IN GENETIC RECOMBINATION IN THE ISO-1-CYTOCHROME c GENE OF YEAST. I. DISCREPANCIES BETWEEN PHYSICAL DISTANCES AND GENETIC DISTANCES DETERMINED BY FIVE MAPPING PROCEDURES

Genetics ◽  
1975 ◽  
Vol 79 (3) ◽  
pp. 397-418
Author(s):  
Carol W Moore ◽  
Fred Sherman
Keyword(s):  
Ultraviolet Light ◽  
Dna Sequences ◽  
Meiotic Recombination ◽  
Genetic Recombination ◽  
Genetic Distances ◽  
Nucleotide Sequences ◽  
X Rays ◽  
Recombination Rates ◽  
Near Ultraviolet ◽  
X Irradiation

ABSTRACT Recombination rates have been examined in two-point crosses of various defined cyc1 mutants using five mapping methods. Nucleotide sequences of mutant codons were identified in previous studies from alterations in functional iso-1-cytochromes c produced by intragenic revertants. Heteroallelic diploids were analyzed for rates of mitotic recombination that occurred spontaneously and that were induced with X-rays, ultraviolet light and the near-ultraviolet light emitted by sunlamps, as well as rates of meiotic recombination that occur after sporulation. Frequencies of both mitotic and meiotic recombination do not necessarily correspond with physical distances separating altered nucleotides. The most extreme discrepancy involved two adjacent intervals of thirteen base pairs which differed approximately thirtyfold in their spontaneous and X-ray-induced recombination rates. Marked disproportions between genetic and physical distances appear to be due to the interaction of the two nucleotide sequences in the heteroallelic combination and not to the sequences of the mutant codons alone. Recombination values that were obtained by all five methods could not be used to establish the correct order of mutant sites. Relationships of the recombination rates for the various pairwise crosses are different after mitosis from those after meiosis, suggesting that these two recombinational processes are to some extent different in their dependence on particular nucleotide configurations. On the other hand, the relationships of the rates induced by UV-, sunlamp- and X-irradiation were identical or very similar. In addition to the intrinsic properties of the alleles affecting frequencies of mitotic and meiotic recombination rates, two- to threefold variations in recombination rates could be attributed to genetic backgrounds.

Single base-pair mutations in centromere element III cause aberrant chromosome segregation in Saccharomyces cerevisiae

1986 ◽  
Vol 6 (2) ◽  
pp. 530-538
Author(s):  
J McGrew ◽  
B Diehl ◽  
M Fitzgerald-Hayes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Dna Sequences ◽  
Base Pair ◽  
Site Directed Mutagenesis ◽  
Chromosome Stability ◽  
Functional Requirements ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Centromere Function

In this paper we show that a 211-base pair segment of CEN3 DNA is sufficient to confer wild-type centromere function in the yeast Saccharomyces cerevisiae. We used site-directed mutagenesis of the 211-base pair fragment to examine the sequence-specific functional requirements of a conserved 11-base pair segment of centromere DNA, element III (5'-TGATTTATCCGAA-3'). Element III is the most highly conserved of the centromeric DNA sequences, differing by only a single adenine X thymine base pair among the four centromere DNAs sequenced thus far. All of the element III sequences contain specific cytosine X guanine base pairs, including a 5'-CCG-3' arrangement, which we targeted for single cytosine-to-thymine mutations by using sodium bisulfite. The effects of element III mutations on plasmid and chromosome segregation were determined by mitotic stability assays. Conversion of CCG to CTG completely abolished centromere function both in plasmids and in chromosome III, whereas conversion of CCG to TCG decreased plasmid and chromosome stability moderately. The other two guanine X cytosine base pairs in element III could be independently converted to adenine X thymine base pairs without affecting plasmid or chromosome stability. We concluded that while some specific nucleotides within the conserved element III sequence are essential for proper centromere function, other conserved nucleotides can be changed.

scholarly journals Highly mutable sites for ICR-170-induced frameshift mutations are associated with potential DNA hairpin structures: studies with SUP4 and other Saccharomyces cerevisiae genes.

1986 ◽  
Vol 6 (12) ◽  
pp. 4425-4432 ◽  
Author(s):  
D M Hampsey ◽  
R A Koski ◽  
F Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Sequences ◽  
Base Pair ◽  
Temporal Stability ◽  
Loop Formation ◽  
Induced Mutations ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Mutagen Specificity ◽  
Hairpin Structures

The majority of the mutations induced by ICR-170 in both the CYC1 gene (J. F. Ernst et al. Genetics 111:233-241, 1985) and the HIS4 gene (L. Mathison and M. R. Culbertson, Mol. Cell. Biol. 5:2247-2256, 1985) of the yeast Saccharomyces cerevisiae were recently shown to be single G . C base-pair insertions at monotonous runs of two or more G . C base pairs. However, not all sites were equally mutable; in both the CYC1 and HIS4 genes there is a single highly mutable site where a G . C base pair is preferentially inserted at a [sequence in text]. Here we report the ICR-170 mutagen specificity at the SUP4-o tyrosine tRNA gene of yeast. Genetic fine structure analysis and representative DNA sequence determination of ICR-170-induced mutations revealed that there is also a single highly mutable site in SUP4-o and that the mutation is a G . C base-pair insertion at a monotonous run of G . C base pairs. Analysis of DNA sequences encompassing the regions of highly mutable sites for all three genes indicated that the mutable sites are at the bases of potential hairpin structures; this type of structure could not be found at any of the other, less mutable G . C runs in SUP4, CYC1, and HIS4. Based on these results and recent information regarding novel DNA structural conformations, we present a mechanism for ICR-170-induced mutagenesis. (i) ICR-170 preferentially binds to DNA in the beta conformation; factors that increase the temporal stability of this structure, such as adjacent stem-and-loop formation, increase the frequency of ICR-170 binding; (ii) the observed mutagen specificity reflects formation of a preferred ICR-170 intercalative geometry at [sequence in text] sites; (iii) during replication or repair, ICR-170 remains associated with the single-stranded template; (iv) stuttering or strand slippage by the polymerization complex as it encounters the mutagen results in nucleotide duplication; (v) subsequent replication or mismatch repair fixes the insertion into the genome. This mechanism accounts for both the IRC-170 mutagenic specificity and the molecular basis of the highly mutable sites in S. cerevisiae.

scholarly journals Theoretical modelling of epigenetically modified DNA sequences

F1000Research ◽  
2015 ◽  
Vol 4 ◽  
pp. 52 ◽  
Author(s):  
Alexandra Teresa Pires Carvalho ◽  
Maria Leonor Gouveia ◽  
Charan Raju Kanna ◽  
Sebastian K. T. S. Wärmländer ◽  
Jamie Platts ◽  
...  
Keyword(s):  
Molecular Mechanics ◽  
Dna Sequences ◽  
Base Pair ◽  
Density Functional ◽  
Epigenetic Modifications ◽  
Theoretical Modelling ◽  
Sugar Phosphate ◽  
Base Pairs ◽  
Phosphate Backbone ◽  
Modified Dna

We report herein a set of calculations designed to examine the effects of epigenetic modifications on the structure of DNA. The incorporation of methyl, hydroxymethyl, formyl and carboxy substituents at the 5-position of cytosine is shown to hardly affect the geometry of CG base pairs, but to result in rather larger changes to hydrogen-bond and stacking binding energies, as predicted by dispersion-corrected density functional theory (DFT) methods. The same modifications within double-stranded GCG and ACA trimers exhibit rather larger structural effects, when including the sugar-phosphate backbone as well as sodium counterions and implicit aqueous solvation. In particular, changes are observed in the buckle and propeller angles within base pairs and the slide and roll values of base pair steps, but these leave the overall helical shape of DNA essentially intact. The structures so obtained are useful as a benchmark of faster methods, including molecular mechanics (MM) and hybrid quantum mechanics/molecular mechanics (QM/MM) methods. We show that previously developed MM parameters satisfactorily reproduce the trimer structures, as do QM/MM calculations which treat bases with dispersion-corrected DFT and the sugar-phosphate backbone with AMBER. The latter are improved by inclusion of all six bases in the QM region, since a truncated model including only the central CG base pair in the QM region is considerably further from the DFT structure. This QM/MM method is then applied to a set of double-stranded DNA heptamers derived from a recent X-ray crystallographic study, whose size puts a DFT study beyond our current computational resources. These data show that still larger structural changes are observed than in base pairs or trimers, leading us to conclude that it is important to model epigenetic modifications within realistic molecular contexts.

scholarly journals DNA SEQUENCES OF FRAMESHIFT AND OTHER MUTATIONS INDUCED BY ICR-170 IN YEAST

Genetics ◽  
1985 ◽  
Vol 111 (2) ◽  
pp. 233-241
Author(s):  
Joachim F Ernst ◽  
D Michael Hampsey ◽  
Fred Sherman
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Amino Acid ◽  
Sequence Analysis ◽  
Genetic Analysis ◽  
Dna Sequences ◽  
Induced Mutations ◽  
Sequence Analyses ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Frameshift Mutations

ABSTRACT ICR-170-induced mutations in the CYC1 gene of the yeast Saccharomyces cerevisiae were investigated by genetic and DNA sequence analyses. Genetic analysis of 33 cyc1 mutations induced by ICR-170 and sequence analysis of eight representatives demonstrated that over one-third were frameshift mutations that occurred at one site corresponding to amino acid positions 29-30, whereas the remaining mutations were distributed more-or-less randomly, and a few of these were not frameshift mutations. The sequence results indicate that ICR-170 primarily induces G·C additions at sites containing monotonous runs of three G·C base pairs. However, some (see PDF) sites within the CYC1 gene were not mutated by ICR-170. Thus, ICR-170 is a relatively specific mutagen that preferentially acts on certain sites with monotonous runs of G·C base pairs.

scholarly journals Localization of DNA sequences involved in dexamethasone-dependent expression of the rat alpha 1-acid glycoprotein gene.

1986 ◽  
Vol 6 (7) ◽  
pp. 2551-2561 ◽  
Author(s):  
H Baumann ◽  
L E Maquat
Keyword(s):  
Glucocorticoid Receptor ◽  
Receptor Binding ◽  
Dna Sequences ◽  
Base Pair ◽  
Binding Sites ◽  
Gene Region ◽  
Start Site ◽  
Base Pairs ◽  
Acid Glycoprotein ◽  
Cat Gene

Synthesis of rat alpha 1-acid glycoprotein (AGP), one of the major inflammation-induced plasma proteins, is positively regulated by dexamethasone. To define the dexamethasone-responsive genetic element, we isolated and tested AGP gene sequences for the ability to confer glucocorticoid induction to the bacterial chloramphenicol acetyltransferase (CAT) gene in L cells. A 141-base-pair region of the AGP gene, including 120 base pairs of DNA upstream from the start site of transcription and 21 base pairs of the 5' untranslated region, was sufficient for maximal CAT gene induction by dexamethasone. To localize more precisely the AGP glucocorticoid-responsive element, parts of this 141-base-pair region were inserted 5' to either an AGP promoter-CAT gene or a human triosephosphate isomerase promoter-CAT gene, both of which lacked a response to the steroid. The AGP gene region between 120 and 42 base pairs upstream from the start site of transcription was found to mediate maximal dexamethasone induction of CAT enzyme levels. This result was unexpected because this region does not contain sequence homologies to known glucocorticoid receptor-binding sites and those AGP gene regions that lay further upstream and were homologous to other glucocorticoid receptor-binding sites were inactive in the CAT assay. The fact that the AGP gene region mediating dexamethasone regulation was distinct from the transcribed region indicates that glucocorticoids increase AGP gene expression primarily at the transcriptional rather than the posttranscriptional level.

Sign in / Sign up

Export Citation Format

Share Document