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A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex.

ABSTRACT: Unlike many other organisms, the yeast Saccharomyces cerevisiae can tolerate the loss of mitochondrial DNA (mtDNA). Although a few proteins have been identified that are required for yeast cell viability without mtDNA, the mechanism of mtDNA-independent growth is not completely understood. To probe the relationship between the mitochondrial genome and cell viability, we conducted a microarray-based, genomewide screen for mitochondrial DNA-dependent yeast mutants. Among the several genes that we discovered is MGR1, which encodes a novel subunit of the i-AAA protease complex located in the mitochondrial inner membrane. mgr1Delta mutants retain some i-AAA protease activity, yet mitochondria lacking Mgr1p contain a misassembled i-AAA protease and are defective for turnover of mitochondrial inner membrane proteins. Our results highlight the importance of the i-AAA complex and proteolysis at the inner membrane in cells lacking mitochondrial DNA.

SUBMITTER: Dunn CD

PROVIDER: S-EPMC1345660 | biostudies-literature | 2006 Jan

REPOSITORIES: biostudies-literature

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A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex.

Dunn Cory D CD Lee Marina S MS Spencer Forrest A FA Jensen Robert E RE

Molecular biology of the cell 20051102 1

Unlike many other organisms, the yeast Saccharomyces cerevisiae can tolerate the loss of mitochondrial DNA (mtDNA). Although a few proteins have been identified that are required for yeast cell viability without mtDNA, the mechanism of mtDNA-independent growth is not completely understood. To probe the relationship between the mitochondrial genome and cell viability, we conducted a microarray-based, genomewide screen for mitochondrial DNA-dependent yeast mutants. Among the several genes that we ...[more]

PMID: 16267274

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Project description:BackgroundMitochondrial respiration is central to cellular and organismal health in eukaryotes. In baker's yeast, however, respiration is dispensable under fermentation conditions. Because yeast are tolerant of this mitochondrial dysfunction, yeast are widely used by biologists as a model organism to ask a variety of questions about the integrity of mitochondrial respiration. Fortunately, baker's yeast also display a visually identifiable Petite colony phenotype that indicates when cells are incapable of respiration. Petite colonies are smaller than their Grande (wild-type) counterparts, and their frequency can be used to infer the integrity of mitochondrial respiration in populations of cells. Unfortunately, the computation of Petite colony frequencies currently relies on laborious manual colony counting methods which limit both experimental throughput and reproducibility.ResultsTo address these problems, we introduce a deep learning enabled tool, petiteFinder, that increases the throughput of the Petite frequency assay. This automated computer vision tool detects Grande and Petite colonies and computes Petite colony frequencies from scanned images of Petri dishes. It achieves accuracy comparable to human annotation but at up to 100 times the speed and outperforms semi-supervised Grande/Petite colony classification approaches. Combined with the detailed experimental protocols we provide, we believe this study can serve as a foundation to standardize this assay. Finally, we comment on how Petite colony detection as a computer vision problem highlights ongoing difficulties with small object detection in existing object detection architectures.ConclusionColony detection with petiteFinder results in high accuracy Petite and Grande detection in images in a completely automated fashion. It addresses issues in scalability and reproducibility of the Petite colony assay which currently relies on manual colony counting. By constructing this tool and providing details of experimental conditions, we hope this study will enable larger-scale experiments that rely on Petite colony frequencies to infer mitochondrial function in yeast.

Dataset Information

A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex.

Publications

A genomewide screen for petite-negative yeast strains yields a new subunit of the i-AAA protease complex.

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