The genetic basis of mutation rate variation in yeast

AbstractMutations are the root source of genetic variation and underlie the process of evolution. Although the rates at which mutations occur vary considerably between species, little is known about differences within species, or the genetic and molecular basis of these differences. Here we leveraged the power of the yeast Saccharomyces cerevisiae as a model system to uncover natural genetic variants that underlie variation in mutation rate. We developed a high-throughput fluctuation assay and used it to quantify mutation rates in natural yeast isolates and in 1040 segregant progeny from a cross between BY, a lab strain, and RM, a wine strain. We observed that mutation rate varies among yeast strains and is highly heritable (H2=0.46). We performed linkage mapping in the segregants and identified four quantitative trait loci (QTLs) underlying mutation rate variation in the cross. We fine-mapped two QTLs to the underlying causal genes, RAD5 and MKT1, that contribute to mutation rate variation. These genes also underlie sensitivity to the DNA damaging agents 4NQO and MMS, suggesting a connection between spontaneous mutation rate and mutagen sensitivity.

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Faculty Opinions recommendation of Yeast Spontaneous Mutation Rate and Spectrum Vary with Environment.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.735675749.793561451 ◽

2019 ◽

Author(s):

Norman Johnson

Keyword(s):

Mutation Rate ◽

Spontaneous Mutation ◽

Spontaneous Mutation Rate

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Gonad Temperature and Spontaneous Mutation-rate in Man

Nature ◽

10.1038/1801433a0 ◽

1957 ◽

Vol 180 (4599) ◽

pp. 1433-1434 ◽

Cited By ~ 31

Author(s):

LARS EHEENBERG ◽

GÜNTER VON EHRENSTEIN ◽

ARNE HEDGRAN

Keyword(s):

Mutation Rate ◽

Spontaneous Mutation ◽

Spontaneous Mutation Rate

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Scope of action of the immunoglobulin mutator system

Genome ◽

10.1139/g89-022 ◽

1989 ◽

Vol 31 (1) ◽

pp. 118-121 ◽

Cited By ~ 2

Author(s):

Matthias R. Wabl ◽

Hans-Martin Jäck ◽

R. C. von Borstel ◽

Charles M. Steinberg

Keyword(s):

B Cell ◽

Mutation Rate ◽

Heavy Chain ◽

B Lymphocyte ◽

Somatic Hypermutation ◽

Spontaneous Mutation ◽

Cell Lineage ◽

Variable Region ◽

High Rate ◽

Spontaneous Mutation Rate

The authors have developed a method to measure the rate of spontaneous mutations taking place in IgH, the gene encoding the immunoglobulin heavy chain. When an amber chain-termination codon mutates to a sense codon, translation of the polypeptide chain will be completed, and mutant cells producing the heavy chain can be detected with a fluorescent labelled antibody. The protocol used is the compartmentalization test which minimizes any effect of selection. In subclones of the pre-B lymphocyte line 18–81, the spontaneous mutation rate in the part of IgH encoding the variable region is somewhat greater than 10−5 mutations per base pair per generation. This supports the hypothesis that hypermutation is not dependent on cell stimulation by an antigen. In a hybrid between a cell of this line and a myeloma (which represents the terminal stage of the B-cell lineage), the mutation rate was too low to be determined by this test, less than 10−9. When the same loss to gain procedure system was used with an opal chain-terminating codon in the part of IgH encoding the constant region (Cμ), a high rate of reversion by deletion was found. Long (more than one exon) and short (less than one exon) deletions occurred at rates of 1.7 × 10−5 and 1.4 × 10−7 per generation, respectively. It is thought that the high rate of deletion is not related to somatic hypermutation but rather to DNA rearrangement during the heavy-chain class switch, which is occurring in these pre-B cell lines. The point mutation rate was too low to be detected above the background of deletion mutants, less than 5 × 10−8. The immunoglobulin mutator system works weakly, if at all, on two other, nonimmunoglobulin, genes tested: B2m (β2 microglobulin) and the gene for ouabain resistance.Key words: pre-B lymphocyte, B lymphocyte, spontaneous mutation rate, compartmentalization test, deletion mutation, hypermutation.

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Mutation avoidance and DNA repair proficiency in Ustilago maydis are differentially lost with progressive truncation of the REC1 gene product.

Molecular and Cellular Biology ◽

10.1128/mcb.15.10.5329 ◽

1995 ◽

Vol 15 (10) ◽

pp. 5329-5338 ◽

Cited By ~ 15

Author(s):

K Onel ◽

M P Thelen ◽

D O Ferguson ◽

R L Bennett ◽

W K Holloman

Keyword(s):

Amino Acid ◽

Mutation Rate ◽

Spontaneous Mutation ◽

Ustilago Maydis ◽

Radiation Sensitivity ◽

Open Reading Frame ◽

Exonuclease Activity ◽

Amino Acid Residues ◽

Spontaneous Mutation Rate ◽

Reading Frame

The REC1 gene of Ustilago maydis has an uninterrupted open reading frame, predicted from the genomic sequence to encode a protein of 522 amino acid residues. Nevertheless, an intron is present, and functional activity of the gene in mitotic cells requires an RNA processing event to remove the intron. This results in a change in reading frame and production of a protein of 463 amino acid residues. The 3'-->5' exonuclease activity of proteins derived from the REC1 genomic open reading frame, the intronless open reading frame, and several mutants was investigated. The mutants included a series of deletions constructed by removing restriction fragments at the 3' end of the cloned REC1 gene and a set of mutant alleles previously isolated in screens for radiation sensitivity. All of these proteins were overproduced in Escherichia coli as N-terminal polyhistidine-tagged fusions that were subsequently purified by immobilized metal affinity chromatography and assayed for 3'-->5' exonuclease activity. The results indicated that elimination of the C-terminal third of the protein did not result in a serious reduction in 3'-->5' exonuclease activity, but deletion into the midsection caused a severe loss of activity. The biological activity of the rec1-1 allele, which encodes a truncated polypeptide with full 3'-->5' exonuclease activity, and the rec1-5 allele, which encodes a more severely truncated polypeptide with no exonuclease activity, was investigated. The two mutants were equally sensitive to the lethal effect of UV light, but the spontaneous mutation rate was elevated 10-fold over the wild-type rate in the rec1-1 mutant and 100-fold in the rec1-5 mutant. The elevated spontaneous mutation rate correlated with the ablation of exonuclease activity, but the radiation sensitivity did not. These results indicate that the C-terminal portion of the Rec1 protein is not essential for exonuclease activity but is crucial in the role of REC1 in DNA damage repair.

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Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

Nature Communications ◽

10.1038/s41467-020-15185-0 ◽

2020 ◽

Vol 11 (1) ◽

Author(s):

Cai Li ◽

Nicholas M. Luscombe

Keyword(s):

Human Genome ◽

Mutation Rate ◽

Germline Mutation ◽

Nucleosome Positioning ◽

Rate Variation ◽

Mutation Rate Variation

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First Estimation of the Spontaneous Mutation Rate in Diatoms

Genome Biology and Evolution ◽

10.1093/gbe/evz130 ◽

2019 ◽

Vol 11 (7) ◽

pp. 1829-1837 ◽

Cited By ~ 11

Author(s):

Marc Krasovec ◽

Sophie Sanchez-Brosseau ◽

Gwenael Piganeau

Keyword(s):

Mutation Rate ◽

Spontaneous Mutation ◽

Mutation Accumulation ◽

Mutation Rates ◽

Model Organisms ◽

Base Substitution ◽

Unicellular Eukaryote ◽

Fundamental Parameter ◽

Secondary Endosymbiosis ◽

Spontaneous Mutation Rate

Abstract Mutations are the origin of genetic diversity, and the mutation rate is a fundamental parameter to understand all aspects of molecular evolution. The combination of mutation–accumulation experiments and high-throughput sequencing enabled the estimation of mutation rates in most model organisms, but several major eukaryotic lineages remain unexplored. Here, we report the first estimation of the spontaneous mutation rate in a model unicellular eukaryote from the Stramenopile kingdom, the diatom Phaeodactylum tricornutum (strain RCC2967). We sequenced 36 mutation accumulation lines for an average of 181 generations per line and identified 156 de novo mutations. The base substitution mutation rate per site per generation is μbs = 4.77 × 10−10 and the insertion–deletion mutation rate is μid = 1.58 × 10−11. The mutation rate varies as a function of the nucleotide context and is biased toward an excess of mutations from GC to AT, consistent with previous observations in other species. Interestingly, the mutation rates between the genomes of organelles and the nucleus differ, with a significantly higher mutation rate in the mitochondria. This confirms previous claims based on indirect estimations of the mutation rate in mitochondria of photosynthetic eukaryotes that acquired their plastid through a secondary endosymbiosis. This novel estimate enables us to infer the effective population size of P. tricornutum to be Ne∼8.72 × 106.

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Functional Analysis of the NucS/EndoMS of the Hyperthermophilic Archaeon Sulfolobus islandicus REY15A

Frontiers in Microbiology ◽

10.3389/fmicb.2020.607431 ◽

2020 ◽

Vol 11 ◽

Author(s):

Sohail Ahmad ◽

Qihong Huang ◽

Jinfeng Ni ◽

Yuanxi Xiao ◽

Yunfeng Yang ◽

...

Keyword(s):

Mismatch Repair ◽

Mutation Rate ◽

Spontaneous Mutation ◽

Repair Pathway ◽

Wild Type ◽

Spontaneous Mutation Rate ◽

Hyperthermophilic Archaeon ◽

Cleavage Activity ◽

Sulfolobus Islandicus ◽

Mismatch Repair Pathway

EndoMS is a recently identified mismatch specific endonuclease in Thermococcales of Archaea and Mycobacteria of Bacteria. The homologs of EndoMS are conserved in Archaea and Actinobacteria, where classic MutS-MutL-mediated DNA mismatch repair pathway is absent or non-functional. Here, we report a study on the in vitro mismatch cleavage activity and in vivo function of an EndoMS homolog (SisEndoMS) from Sulfolobus islandicus REY15A, the model archaeon belonging to Crenarchaeota. SisEndoMS is highly active on duplex DNA containing G/T, G/G, and T/T mismatches. Interestingly, the cleavage activity of SisEndoMS is stimulated by the heterotrimeric PCNAs, and when Mn2+ was used as the co-factor instead of Mg2+, SisEndoMS was also active on DNA substrates containing C/T or A/G mismatches, suggesting that the endonuclease activity can be regulated by ion co-factors and accessory proteins. We compared the spontaneous mutation rate of the wild type strain REY15A and ∆endoMS by counter selection against 5-fluoroorotic acid (5-FOA). The endoMS knockout mutant had much higher spontaneous mutation rate (5.06 × 10−3) than that of the wild type (4.6 × 10−6). A mutation accumulation analysis also showed that the deletion mutant had a higher mutation occurrence than the wild type, with transition mutation being the dominant, suggesting that SisEndoMS is responsible for mutation avoidance in this hyperthermophilic archaeon. Overexpression of the wild type SisEndoMS in S. islandicus resulted in retarded growth and abnormal cell morphology, similar to strains overexpressing Hje and Hjc, the Holliday junction endonucleases. Transcriptomic analysis revealed that SisEndoMS overexpression led to upregulation of distinct gene including the CRISPR-Cas IIIB system, methyltransferases, and glycosyltransferases, which are mainly localized to specific regions in the chromosome. Collectively, our results support that EndoMS proteins represent a noncanonical DNA repair pathway in Archaea. The mechanism of the mismatch repair pathway in Sulfolobus which have a single chromosome is discussed.

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