scholarly journals GC content elevates mutation and recombination rates in the yeast Saccharomyces cerevisiae

2018 ◽  
Vol 115 (30) ◽  
pp. E7109-E7118 ◽  
Author(s):  
Denis A. Kiktev ◽  
Ziwei Sheng ◽  
Kirill S. Lobachev ◽  
Thomas D. Petes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Polymerase ◽  
Base Composition ◽  
Genome Stability ◽  
Gc Content ◽  
Substantial Effect ◽  
Recombination Rates ◽  
Yeast Saccharomyces Cerevisiae ◽  
Basic Parameters ◽  
Elevated Rate

The chromosomes of many eukaryotes have regions of high GC content interspersed with regions of low GC content. In the yeast Saccharomyces cerevisiae, high-GC regions are often associated with high levels of meiotic recombination. In this study, we constructed URA3 genes that differ substantially in their base composition [URA3-AT (31% GC), URA3-WT (43% GC), and URA3-GC (63% GC)] but encode proteins with the same amino acid sequence. The strain with URA3-GC had an approximately sevenfold elevated rate of ura3 mutations compared with the strains with URA3-WT or URA3-AT. About half of these mutations were single-base substitutions and were dependent on the error-prone DNA polymerase ζ. About 30% were deletions or duplications between short (5–10 base) direct repeats resulting from DNA polymerase slippage. The URA3-GC gene also had elevated rates of meiotic and mitotic recombination relative to the URA3-AT or URA3-WT genes. Thus, base composition has a substantial effect on the basic parameters of genome stability and evolution.

scholarly journals Alterations in the adenine-plus-thymine-rich region of CEN3 affect centromere function in Saccharomyces cerevisiae.

1987 ◽  
Vol 7 (1) ◽  
pp. 68-75 ◽  
Author(s):  
A Gaudet ◽  
M Fitzgerald-Hayes
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Base Composition ◽  
Consensus Sequence ◽  
Fold Increase ◽  
Base Pairs ◽  
Yeast Saccharomyces Cerevisiae ◽  
Core Element ◽  
Sequence Elements ◽  
Dna Elements ◽  
Chromosome Iii

Centromere DNA from 11 of the 16 chromosomes of the yeast Saccharomyces cerevisiae have been analyzed and reveal three sequence elements common to each centromere, referred to as conserved centromere DNA elements (CDE). The adenine-plus-thymine (A + T)-rich central core element, CDE II, is flanked by two short conserved sequences, CDE I (8 base pairs [bp]) and CDE III (25 bp). Although no consensus sequence exists among the different CDE II regions, they do have three common features of sequence organization. First, the CDE II regions are similar in length, ranging from 78 to 86 bp measured from CDE I to the left boundary of CDE III. Second, the base composition is always greater than 90% A + T. Finally, the A and T residues in these segments are often arranged in runs of A and runs of T residues, sometimes with six or seven bases in a stretch. We constructed insertion, deletion, and replacement mutations in the CDE II region of the centromere from chromosome III, CEN3, designed to investigate the length and sequence requirements for function of the CDE II region of the centromere. We analyzed the effect of these altered centromeres on plasmid and chromosome segregation in S. cerevisiae. Our results show that increasing the length of CDE II from 84 to 154 bp causes a 100-fold increase in chromosome nondisjunction. Deletion mutations removing segments of the A + T-rich CDE II DNA also cause aberrant segregation. In some cases partial function could be restored by replacing the deleted DNA with fragments whose primary sequence or base composition is very different from that of the wild-type CDE II DNA. In addition, we found that identical mutations introduced into different positions in CDE II have very similar effects.

scholarly journals Replication slippage between distant short repeats in Saccharomyces cerevisiae depends on the direction of replication and the RAD50 and RAD52 genes.

1995 ◽  
Vol 15 (10) ◽  
pp. 5607-5617 ◽  
Author(s):  
H T Tran ◽  
N P Degtyareva ◽  
N N Koloteva ◽  
A Sugino ◽  
H Masumoto ◽  
...  
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Genome Stability ◽  
Genome Instability ◽  
Temperature Sensitive ◽  
Direct Repeats ◽  
Dna Polymerase Delta ◽  
Dna Double Strand Breaks ◽  
Yeast Saccharomyces Cerevisiae ◽  
Replication Slippage ◽  
Random Sequences

Small direct repeats, which are frequent in all genomes, are a potential source of genome instability. To study the occurrence and genetic control of repeat-associated deletions, we developed a system in the yeast Saccharomyces cerevisiae that was based on small direct repeats separated by either random sequences or inverted repeats. Deletions were examined in the LYS2 gene, using a set of 31- to 156-bp inserts that included inserts with no apparent potential for secondary structure as well as two quasipalindromes. All inserts were flanked by 6- to 9-bp direct repeats of LYS2 sequence, providing an opportunity for Lys+ reversion via precise excision. Reversions could arise by extended deletions involving either direct repeats or random sequences and by -1-or +2-bp frameshift mutations. The deletion breakpoints were always associated with short (3- to 9-bp) perfect or imperfect direct repeats. Compared with the POL+ strain, deletions between small direct repeats were increased as much as 100-fold, and the spectrum was changed in a temperature-sensitive DNA polymerase delta pol3-t mutant, suggesting a role for replication. The type of deletion depended on orientation relative to the origin of replication. On the basis of these results, we propose (i) that extended deletions between small repeats arise by replication slippage and (ii) that the deletions occur primarily in either the leading or lagging strand. The RAD50 and RAD52 genes, which are required for the recombinational repair of many kinds of DNA double-strand breaks, appeared to be required also for the production of up to 90% of the deletions arising between separated repeats in the pol3-t mutant, suggesting a newly identified role for these genes in genome stability and possibly replication.

scholarly journals DNA polymerases δ and λ cooperate in repairing double-strand breaks by microhomology-mediated end-joining in Saccharomyces cerevisiae

2015 ◽  
Vol 112 (50) ◽  
pp. E6907-E6916 ◽  
Author(s):  
Damon Meyer ◽  
Becky Xu Hua Fu ◽  
Wolf-Dietrich Heyer
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Dna Polymerase ◽  
Genome Stability ◽  
Double Strand Breaks ◽  
Dna Polymerase Delta ◽  
Dna Double Strand Breaks ◽  
End Joining ◽  
Strand Breaks ◽  
Repair Efficiency ◽  
Repair Pathways

Maintenance of genome stability is carried out by a suite of DNA repair pathways that ensure the repair of damaged DNA and faithful replication of the genome. Of particular importance are the repair pathways, which respond to DNA double-strand breaks (DSBs), and how the efficiency of repair is influenced by sequence homology. In this study, we developed a genetic assay in diploid Saccharomyces cerevisiae cells to analyze DSBs requiring microhomologies for repair, known as microhomology-mediated end-joining (MMEJ). MMEJ repair efficiency increased concomitant with microhomology length and decreased upon introduction of mismatches. The central proteins in homologous recombination (HR), Rad52 and Rad51, suppressed MMEJ in this system, suggesting a competition between HR and MMEJ for the repair of a DSB. Importantly, we found that DNA polymerase delta (Pol δ) is critical for MMEJ, independent of microhomology length and base-pairing continuity. MMEJ recombinants showed evidence that Pol δ proofreading function is active during MMEJ-mediated DSB repair. Furthermore, mutations in Pol δ and DNA polymerase 4 (Pol λ), the DNA polymerase previously implicated in MMEJ, cause a synergistic decrease in MMEJ repair. Pol λ showed faster kinetics associating with MMEJ substrates following DSB induction than Pol δ. The association of Pol δ depended on RAD1, which encodes the flap endonuclease needed to cleave MMEJ intermediates before DNA synthesis. Moreover, Pol δ recruitment was diminished in cells lacking Pol λ. These data suggest cooperative involvement of both polymerases in MMEJ.

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.

scholarly journals Structure/Function Analysis of the Hif1 Histone Chaperone in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Nora Saud Dannah
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Genome Stability ◽  
Function Analysis ◽  
Molecular Genetic ◽  
Histone Chaperone ◽  
Chromatin Assembly ◽  
Biological Processes ◽  
Genetic Approach ◽  
Yeast Saccharomyces Cerevisiae

Understanding the regulation of chromatin structure is a vital aspect of molecular biology regarding its influences on biological processes such as DNA replication, transcription (gene expression), DNA repair, chromosome segregation and recombination. In the budding yeast Saccharomyces cerevisiae, a histone chaperone called Hif1 has been found in the nuclei as having a functional role in chromatin assembly. Hif1 is a homolog of the human protein NASP that is involved in the maintenance of genome stability. Previously, Hif1 has been shown to physically interact with Hat1, Hat2 and H3/H4 to form the NuB4 complex directly involved in chromatin assembly. A molecular genetic approach was conducted to determine which domain of Hif1 is involved in the interaction with the HAT1 complex.

scholarly journals Structure/Function Analysis of the Hif1 Histone Chaperone in Saccharomyces cerevisiae

2021 ◽  
Author(s):  
Nora Saud Dannah
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromosome Segregation ◽  
Genome Stability ◽  
Function Analysis ◽  
Molecular Genetic ◽  
Histone Chaperone ◽  
Chromatin Assembly ◽  
Biological Processes ◽  
Genetic Approach ◽  
Yeast Saccharomyces Cerevisiae

Understanding the regulation of chromatin structure is a vital aspect of molecular biology regarding its influences on biological processes such as DNA replication, transcription (gene expression), DNA repair, chromosome segregation and recombination. In the budding yeast Saccharomyces cerevisiae, a histone chaperone called Hif1 has been found in the nuclei as having a functional role in chromatin assembly. Hif1 is a homolog of the human protein NASP that is involved in the maintenance of genome stability. Previously, Hif1 has been shown to physically interact with Hat1, Hat2 and H3/H4 to form the NuB4 complex directly involved in chromatin assembly. A molecular genetic approach was conducted to determine which domain of Hif1 is involved in the interaction with the HAT1 complex.

scholarly journals Loss of Rereplication Control in Saccharomyces cerevisiae Results in Extensive DNA Damage

2005 ◽  
Vol 16 (1) ◽  
pp. 421-432 ◽  
Author(s):  
Brian M. Green ◽  
Joachim J. Li
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Cell Cycle ◽  
Dna Damage ◽  
Genome Stability ◽  
Eukaryotic Cell ◽  
Entire Genome ◽  
Yeast Saccharomyces Cerevisiae ◽  
Checkpoint Response ◽  
Checkpoint Protein ◽  
C Terminus

To maintain genome stability, the entire genome of a eukaryotic cell must be replicated once and only once per cell cycle. In many organisms, multiple overlapping mechanisms block rereplication, but the consequences of deregulating these mechanisms are poorly understood. Here, we show that disrupting these controls in the budding yeast Saccharomyces cerevisiae rapidly blocks cell proliferation. Rereplicating cells activate the classical DNA damage-induced checkpoint response, which depends on the BRCA1 C-terminus checkpoint protein Rad9. In contrast, Mrc1, a checkpoint protein required for recognition of replication stress, does not play a role in the response to rereplication. Strikingly, rereplicating cells accumulate subchromosomal DNA breakage products. These rapid and severe consequences suggest that even limited and sporadic rereplication could threaten the genome with significant damage. Hence, even subtle disruptions in the cell cycle regulation of DNA replication may predispose cells to the genomic instability associated with tumorigenesis.

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