Slow Growth and Increased Spontaneous Mutation Frequency in Respiratory Deficientafo1- Yeast Suppressed by a Dominant Mutation inATP3

Abstract

A yeast deletion mutation in the nuclear-encoded gene, AFO1, which codes for a mitochondrial ribosomal protein, led to slow growth on glucose, the inability to grow on glycerol or ethanol, and loss of mitochondrial DNA and respiration. We noticed that afo1-yeast readily obtains secondary mutations that suppress aspects of this phenotype, including its growth defect. We characterized and identified a dominant missense suppressor mutation in the ATP3 gene. Comparing isogenic slowly growing rho-zero and rapidly growing suppressed afo1- strains under carefully controlled fermentation conditions showed that energy charge was not significantly different between strains and was not causal for the observed growth properties. Surprisingly, in a wild-type background, the dominant suppressor allele of ATP3 still allowed respiratory growth but increased the petite frequency. Similarly, a slow-growing respiratory deficient afo1-strain displayed an about twofold increase in spontaneous frequency of point mutations (comparable to the rho-zero strain) while the suppressed strain showed mutation frequency comparable to the repiratory-competent WT strain. We conclude, that phenotypes that result from afo1- are mostly explained by rapidly emerging mutations that compensate for the slow growth that typically follows respiratory deficiency.

Mapping mitonuclear epistasis using a novel recombinant yeast population

“…We expect this to be a general trend. Dominant mutations that suppressed the low growth phenotype of strains with mitochondrial ribosomal protein defects also led to higher petite frequencies [88].…”

Spontaneous Mutation Rates and Spectra of Respiratory-Deficient Yeast

“…In our previous paper, we described that deletion of the MRPL25 gene (also known as AFO1 ; located on chromosome VII), which encodes the large subunit of mitochondrial ribosomes, can result in mtDNA loss and reveal the petite phenotype. The growth defects of the mrpl25Δ mutant can be rapidly rescued by acquiring the atp3 G348T suppressor mutation [ 18 ]. The energy charge and ATPase activity were almost the same between the mrpl25Δ mutant and the mrpl25Δ atp3 G348T double mutant, indicating that these factors are not causal for growth restoration [ 18 ].…”

“…The growth defects of the mrpl25Δ mutant can be rapidly rescued by acquiring the atp3 G348T suppressor mutation [ 18 ]. The energy charge and ATPase activity were almost the same between the mrpl25Δ mutant and the mrpl25Δ atp3 G348T double mutant, indicating that these factors are not causal for growth restoration [ 18 ]. Instead, using mutation accumulation experiments, we observed an elevated SNV rate in the mrpl25Δ strain, suggesting the potential occurrence of genome instability [ 18 ].…”

“…The energy charge and ATPase activity were almost the same between the mrpl25Δ mutant and the mrpl25Δ atp3 G348T double mutant, indicating that these factors are not causal for growth restoration [ 18 ]. Instead, using mutation accumulation experiments, we observed an elevated SNV rate in the mrpl25Δ strain, suggesting the potential occurrence of genome instability [ 18 ]. However, the genome-wide mutation landscape and mutational signatures of the mrpl25Δ strain remain to be characterized for a better understanding of its genome instability.…”

“…However, the genome-wide mutation landscape and mutational signatures of the mrpl25Δ strain remain to be characterized for a better understanding of its genome instability. In this study, we analyzed the whole genome sequencing data from our previous mutation accumulation lines (MALs) [ 18 ], including the MALs of yeast strains with different presence–absence combinations of the mrpl25Δ and atp3 G348T mutations as well as the wildtype and rho0 (cytoplasmic petite) control strains, to systematically characterize their respective mutation landscapes. We compared their mutation rates and spectra in terms of SNVs, INDELs, segmental and chromosomal copy number variants (CNVs and aneuploidies, respectively) and found both shared and background-specific mutational patterns for strains with respiratory dysfunction.…”