A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

Abstract

In eukaryotic cells, the production of cellular energy requires close interplay between nuclear and mitochondrial genomes. The mitochondrial genome is essential in that it encodes several genes involved in oxidative phosphorylation. Each cell contains several mitochondrial genome copies and mitochondrial DNA recombination is a widespread process occurring in plants, fungi, protists, and invertebrates. Saccharomyces cerevisiae has proved to be an excellent model to dissect mitochondrial biology. Several studies have focused on DNA recombination in this organelle, yet mostly relied on reporter genes or artificial systems. However, no complete mitochondrial recombination map has been released for any eukaryote so far. In the present work, we sequenced pools of diploids originating from a cross between two different S. cerevisiae strains to detect recombination events. This strategy allowed us to generate the first genome-wide map of recombination for yeast mitochondrial DNA. We demonstrated that recombination events are enriched in specific hotspots preferentially localized in non-protein-coding regions. Additionally, comparison of the recombination profiles of two different crosses showed that the genetic background affects hotspot localization and recombination rates. Finally, to gain insights into the mechanisms involved in mitochondrial recombination, we assessed the impact of individual depletion of four genes previously associated with this process. Deletion of NTG1 and MGT1 did not substantially influence the recombination landscape, alluding to the potential presence of additional regulatory factors. Our findings also revealed the loss of large mitochondrial DNA regions in the absence of MHR1, suggesting a pivotal role for Mhr1 in mitochondrial genome maintenance during mating. This study provides a comprehensive overview of mitochondrial DNA recombination in yeast and thus paves the way for future mechanistic studies of mitochondrial recombination and genome maintenance.

Genome Diversity and Evolution in the Budding Yeasts (Saccharomycotina)

“…In this species, the mitochondrial genome consists of a few dozens of copies of a ∼80-kb circular mtDNA molecule containing, in addition to the above, long AT-rich intergenic regions including short GC-rich palindromes. They recombine between themselves (Dujon et al 1974; Fritsch et al 2014). Today, the evolution of the mitochondrial genomes of Saccharomycotina is illustrated by the complete mtDNA sequences of >80 different species (reviewed in Freel et al 2015) and it shows a remarkable consistency with the four subdivisions deduced from nuclear genomes (above).…”

Mitochondria-encoded genes contribute to the evolution of heat and cold tolerance amongSaccharomycesspecies

“…mtDNA was enriched following a protocol adapted from Fritsch et al (2014) and Wolters et al (2015). 50ml YPEG (1% yeast extract, 2% peptone, 2% ethanol, 2% glycerol) medium was inoculated with overnight YPD starter cultures, shaken at 300rpm at 23°C.…”

Discordant evolution of mitochondrial and nuclear yeast genomes at population level

“…Recombination can occur between yeast mitochondria during the transient heteroplasmic phase following the mating. However the two parental organelles are kept physically separated and can only be in contact and recombine on a limited interaction surface (Fritsch et al 2014). The S288C laboratory genetic background contains approximately 20 copies of mitochondrial genomes and 5% of non-essential genes are required for mtDNA maintenance (Puddu et al 2019).…”