Visualization of Mitochondria in Budding Yeast

Analyzing membrane dynamics with live cell fluorescence microscopy with a focus on yeast mitochondria

With the availability of increasing numbers of fluorescent protein variants and state-of-the-art imaging techniques, live cell microscopy has become a standard procedure in modern cell biology. Fluorescent markers are used to visualize the dynamic processes that take place in living cells, including the behavior of membrane-bound organelles. Here, we provide two examples of how we analyze the membrane dynamics of mitochondria in living yeast cells using wide field and confocal microscopy: (1) Long-term observation of mitochondrial shape changes using mitochondria-targeted fluorescent proteins and (2) monitoring the behavior of individual mitochondria using a mitochondria-targeted version of a photoconvertible fluorescent protein.

Mitochondrial DNA heteroplasmy in Candida glabrata after mitochondrial transformation

Genetic manipulation of mitochondrial DNA (mtDNA) is the most direct method for investigating mtDNA, but until now, this has been achieved only in the diploid yeast Saccharomyces cerevisiae. In this study, the ATP6 gene on mtDNA of the haploid yeast Candida glabrata (Torulopsis glabrata) was deleted by biolistic transformation of DNA fragments with a recoded ARG8(m) mitochondrial genetic marker, flanked by homologous arms to the ATP6 gene. Transformants were identified by arginine prototrophy. However, in the transformants, the original mtDNA was not lost spontaneously, even under arginine selective pressure. Moreover, the mtDNA transformants selectively lost the transformed mtDNA under aerobic conditions. The mtDNA heteroplasmy in the transformants was characterized by PCR, quantitative PCR, and Southern blotting, showing that the heteroplasmy was relatively stable in the absence of arginine. Aerobic conditions facilitated the loss of the original mtDNA, and anaerobic conditions favored loss of the transformed mtDNA. Moreover, detailed investigations showed that increases in reactive oxygen species in mitochondria lacking ATP6, along with their equal cell division, played important roles in determining the dynamics of heteroplasmy. Based on our analysis of mtDNA heteroplasmy in C. glabrata, we were able to generate homoplasmic Deltaatp6 mtDNA strains.

Microtubule-dependent spatial organization of mitochondria in fission yeast

The microtubule cytoskeleton has an important role in the control of mitochondrial distribution in higher eukaryotes. In humans, defects in axonal mitochondrial transport are linked to neurodegenerative diseases. This chapter highlights fission yeast Schizosaccharomyces pombe as a powerful genetic model system for the study of microtubule-dependent mitochondrial movement, dynamics and inheritance.

Mitochondrial dysfunction leads to nuclear genome instability via an iron-sulfur cluster defect

Mutations and deletions in the mitochondrial genome (mtDNA), as well as instability of the nuclear genome, are involved in multiple human diseases. Here, we report that in Saccharomyces cerevisiae, loss of mtDNA leads to nuclear genome instability, through a process of cell-cycle arrest and selection we define as a cellular crisis. This crisis is not mediated by the absence of respiration, but instead correlates with a reduction in the mitochondrial membrane potential. Analysis of cells undergoing this crisis identified a defect in iron-sulfur cluster (ISC) biogenesis, which requires normal mitochondrial function. We found that downregulation of nonmitochondrial ISC protein biogenesis was sufficient to cause increased genomic instability in cells with intact mitochondrial function. These results suggest mitochondrial dysfunction stimulates nuclear genome instability by inhibiting the production of ISC-containing protein(s), which are required for maintenance of nuclear genome integrity. For a video summary of this article, see the PaperFlick file available with the online Supplemental Data.

Computationally driven, quantitative experiments discover genes required for mitochondrial biogenesis

Mitochondria are central to many cellular processes including respiration, ion homeostasis, and apoptosis. Using computational predictions combined with traditional quantitative experiments, we have identified 100 proteins whose deficiency alters mitochondrial biogenesis and inheritance in Saccharomyces cerevisiae. In addition, we used computational predictions to perform targeted double-mutant analysis detecting another nine genes with synthetic defects in mitochondrial biogenesis. This represents an increase of about 25% over previously known participants. Nearly half of these newly characterized proteins are conserved in mammals, including several orthologs known to be involved in human disease. Mutations in many of these genes demonstrate statistically significant mitochondrial transmission phenotypes more subtle than could be detected by traditional genetic screens or high-throughput techniques, and 47 have not been previously localized to mitochondria. We further characterized a subset of these genes using growth profiling and dual immunofluorescence, which identified genes specifically required for aerobic respiration and an uncharacterized cytoplasmic protein required for normal mitochondrial motility. Our results demonstrate that by leveraging computational analysis to direct quantitative experimental assays, we have characterized mutants with subtle mitochondrial defects whose phenotypes were undetected by high-throughput methods.

Mitochondria are the proverbial powerhouses of the cell, running the fundamental biochemical processes that produce energy from nutrients using oxygen. These processes are conserved in all eukaryotes, from humans to model organisms such as baker's yeast. In humans, mitochondrial dysfunction plays a role in a variety of diseases, including diabetes, neuromuscular disorders, and aging. In order to better understand fundamental mitochondrial biology, we studied genes involved in mitochondrial biogenesis in the yeast S. cerevisiae, discovering over 100 proteins with novel roles in this process. These experiments assigned function to 5% of the genes whose function was not known. In order to achieve this rapid rate of discovery, we developed a system incorporating highly quantitative experimental assays and an integrated, iterative process of computational protein function prediction. Beginning from relatively little prior knowledge, we found that computational predictions achieved about 60% accuracy and rapidly guided our laboratory work towards hundreds of promising candidate genes. Thus, in addition to providing a more thorough understanding of mitochondrial biology, this study establishes a framework for successfully integrating computation and experimentation to drive biological discovery. A companion manuscript, published in PLoS Computational Biology (doi:10.1371/journal.pcbi.1000322), discusses observations and conclusions important for the computational community.