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Studying the Ballistics of Yeast Mutagenesis

February 6, 2014

Like different fireworks bursting across the sky in distinct patterns, different mutator strains pepper genomes with distinct patterns of mutations. Photo by Marek Skrzypek

Fireworks shells all pretty much look the same from the outside. They definitely all make the same boom when they’re launched. But when they burst in the air, each different kind creates a different shimmering pattern.

It turns out that the same is true for yeast strains carrying mutator alleles.
These are mutant alleles of genes that normally stop mutations from happening. When these genes are disabled, a strain eventually accumulates lots of extra mutations.

Mutator strains tend to look similar from the outside; many are deficient in DNA replication and repair pathways. But, in a new paper in GENETICS, Stirling and coworkers show that like different firework shells, each strain ends up with a distinct pattern of secondary mutations bursting across their respective genomes. Not only is this fascinating information about how yeast maintains its genomic integrity, but it may also provide valuable insights into how cancers progress.

Mutator genes have been found previously using the knockout collection of mutations in nonessential genes. But, not surprisingly, many genes required for genome maintenance are essential to life. So the first step by Stirling and coworkers was to expand the list of mutator genes by screening conditional mutant alleles of essential genes.

Using an assay for mutation frequency that counts canavanine resistance mutations arising in the CAN1 gene, they came up with 47 alleles in 38 essential genes that caused a mutator phenotype.  But this standard assay for mutator phenotype has its limitations: the only mutations that can be detected are those that fall in or near the CAN1 gene, and inactivate it. So that they could look at the full spectrum of mutations arising in the mutator strains, Stirling and coworkers decided to use whole genome sequencing instead to detect them.

The researchers chose 11 mutator alleles of genes representative of different processes such as homologous recombination, oxidative stress tolerance, splicing, transcription, mitochondrial function, telomere capping, and several aspects of DNA replication. They grew these strains for 200 generations and then did whole-genome sequencing of 4 to 6 independent progeny of each to find all the resulting mutations.

Under these conditions, wild-type yeast accumulated 2-4 mutations per genome. In contrast, the mutator strains ended up with 2- to 10-fold more mutations. And most every type was represented: single-nucleotide variants, structural variants (showing altered chromosome structure), copy-number variants (amplification of certain regions or entire chromosomes), and insertions or deletions.

However, while all of the mutator strains had accumulated mutations, the different types of mutation were in different proportions. For example, a mutant in the Replication Factor C subunit gene, rfc2-1, tended to give rise to transition mutations (changing a pyrimidine to a pyrimidine, or a purine to a purine).  The same was true for the telomere-capping protein mutant, stn1-13

But the pol1-ts DNA polymerase mutant instead showed more transversions (changing a purine to a pyrimidine or vice versa). And a deletion of the nonessential RAD52 gene, encoding a recombinase, tended to cause mutations in the transcribed strand of genes, suggesting that transcription-associated recombination was compromised in those cells and this affected DNA repair. 

Positions of the accumulated mutations also differed between strains. The stn1-13 and pol1-ts mutants preferentially accumulated mutations in subtelomeric regions. Some of the alleles gave rise to clusters of mutations, while others did not. And, as has been seen in cancer cells, many of the mutator strains had mutations in regions of the genome that replicate late in DNA replication.

Even though this work generated a huge amount of data (much more than we can discuss here), one conclusion reached by the authors is that even more mutant progeny of mutator strains, arising under a variety of different conditions, need to be analyzed using whole-genome sequencing to give a truly comprehensive picture of the mutational spectrum associated with each allele.

But another conclusion is clear: that different mutator alleles do result in characteristic patterns of mutations. Given that some of these same genes have been found to be mutated in cancer cells, this work may help other scientists predict what mutations a cancer will develop. And that would really give us a bang for our research buck!

by D. Barry Starr, Ph.D., Director of Outreach Activities, Stanford Genetics