Computationally Driven, Quantitative Experiments Discover Genes Required for Mitochondrial Biogenesis

Abstract

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.

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability ofSaccharomyces cerevisiaeS288C Strains

“…As noted above, it is affected by a plethora of genes (Contamine and Picard 2000;Hess et al 2009). We have identified alleles in three such genes (SAL1, CAT5, and MIP1) that in combination produce a high mtDNA instability in the BY/S288C strain.…”

“…Recently, a computation-based screen for genes that might affect mitochondrial function or transmission identified 100 single-deletion mutant alleles that significantly altered petite frequency relative to the wild-type BY/S288C strain that was used in the analysis (Hess et al 2009). Interestingly, none of the CAT5, MIP1, MKT1, and SAL1 genes was identified in this screen.…”

“…More than 200 genes are required for the faithful maintenance of rho 1 yeast mtDNA (Contamine and Picard 2000;Hess et al 2009). However, only a fraction of these genes are involved in pathways that directly affect mtDNA transactions such as replication, recombination, and repair, as well as mtDNA packaging into nucleoids, nucleoid division, and nucleoid segregation to daughter cells (Contamine and Picard 2000;Chen and Butow 2005).…”

Mitofilin complexes: conserved organizers of mitochondrial membrane architecture

“…Regions with stacked, lamellar cristae are found in Aim5-deficient mitochondria, but less frequently compared to mio10 Δ or fcj1 Δ mutant mitochondria. AIM5 as well as two other genes encoding mitofilin/Fcj1-interacting proteins ( AIM13 and AIM37 ) have originally been identified in S. cerevisiae as genes that are involved in the correct distribution of mitochondria from mother to daughter cells during the budding process (Hess et al , 2009 ). In this genetic screen for altered inheritance of mitochondria (AIM), a direct or indirect role in mitochondrial biogenesis and distribution has been attributed to over 100 different gene products, more than half of which previously had no assigned function.…”

“…The Aim proteins include factors involved in mitochondrial migration, several metabolic pathways, respiratory chain assembly and mitochondrial morphology. Notably, the FCJ1 gene was also identified in the same screen and therefore received the alternative name AIM28 (Hess et al , 2009 ).…”