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A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, Devay RM, Lackner LL, Westermann B, Schuldiner M, Weissman JS, Nunnari J - J. Cell Biol. (2011)

Bottom Line: The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components.We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology.We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.

ABSTRACT
To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

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Generation of the MITO-MAP. (A) Manually defined functional annotations for genes included in the MITO-MAP are summarized in pie charts: 592 genes whose products are predicted to localize to the mitochondria, 437 genes whose products are predicted to localize to the early secretory pathway (ESP), and 529 other genes. Localization groups were based on systematic results with GFP-tagged proteins and GO Slim component annotations. (B) Scatter plot of all full biological replicate genetic interaction score (S-score) measurements for double mutants generated from each of the two possible query-array parent strain combinations. The Pearson correlation for these replicates was 0.65.
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fig1: Generation of the MITO-MAP. (A) Manually defined functional annotations for genes included in the MITO-MAP are summarized in pie charts: 592 genes whose products are predicted to localize to the mitochondria, 437 genes whose products are predicted to localize to the early secretory pathway (ESP), and 529 other genes. Localization groups were based on systematic results with GFP-tagged proteins and GO Slim component annotations. (B) Scatter plot of all full biological replicate genetic interaction score (S-score) measurements for double mutants generated from each of the two possible query-array parent strain combinations. The Pearson correlation for these replicates was 0.65.

Mentions: We measured 616,270 distinct genetic pairwise interactions encompassing a total of 1,482 genes (Tables S1 and S2 and Java Treeview supplemental files). This included 592 genes encoding proteins reported to localize to mitochondria (based largely on proteomic and GFP-localization studies) and 437 genes encoding proteins annotated as acting in the early secretory pathway (Fig. 1 A; Huh et al., 2003; Sickmann et al., 2003). Additionally, we included representative subsets of proteins from a wide range of cellular activities including chromatin, metabolic activities, transcription, translation, cytoskeleton, and signal transduction. The large majority (1,265) of the strains we examined involved complete deletion of nonessential components. We also included compromised (decreased abundance by mRNA perturbation [DAmP] alleles of 217 essential proteins in which the 3′ untranslated region has been deleted, leading to decreased expression levels of the otherwise intact proteins; Schuldiner et al., 2005; Breslow et al., 2008; Table S2). All pairwise mutants were made using the synthetic genetic array marker system developed by C. Boone and others that allows massively parallel, plate-based selection of haploid double mutant products after mating and sporulation (Tong et al., 2001; Schuldiner et al., 2005, 2006). Growth of the double mutants was estimated by automated colony size measurements, which were then used to determine genetic interaction values based on deviations between the observed growth of the double mutant and the value predicted by the growth phenotypes of the two single mutants, assuming the proteins were of unrelated function (Collins et al., 2006, 2010).


A mitochondrial-focused genetic interaction map reveals a scaffold-like complex required for inner membrane organization in mitochondria.

Hoppins S, Collins SR, Cassidy-Stone A, Hummel E, Devay RM, Lackner LL, Westermann B, Schuldiner M, Weissman JS, Nunnari J - J. Cell Biol. (2011)

Generation of the MITO-MAP. (A) Manually defined functional annotations for genes included in the MITO-MAP are summarized in pie charts: 592 genes whose products are predicted to localize to the mitochondria, 437 genes whose products are predicted to localize to the early secretory pathway (ESP), and 529 other genes. Localization groups were based on systematic results with GFP-tagged proteins and GO Slim component annotations. (B) Scatter plot of all full biological replicate genetic interaction score (S-score) measurements for double mutants generated from each of the two possible query-array parent strain combinations. The Pearson correlation for these replicates was 0.65.
© Copyright Policy - openaccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3198156&req=5

fig1: Generation of the MITO-MAP. (A) Manually defined functional annotations for genes included in the MITO-MAP are summarized in pie charts: 592 genes whose products are predicted to localize to the mitochondria, 437 genes whose products are predicted to localize to the early secretory pathway (ESP), and 529 other genes. Localization groups were based on systematic results with GFP-tagged proteins and GO Slim component annotations. (B) Scatter plot of all full biological replicate genetic interaction score (S-score) measurements for double mutants generated from each of the two possible query-array parent strain combinations. The Pearson correlation for these replicates was 0.65.
Mentions: We measured 616,270 distinct genetic pairwise interactions encompassing a total of 1,482 genes (Tables S1 and S2 and Java Treeview supplemental files). This included 592 genes encoding proteins reported to localize to mitochondria (based largely on proteomic and GFP-localization studies) and 437 genes encoding proteins annotated as acting in the early secretory pathway (Fig. 1 A; Huh et al., 2003; Sickmann et al., 2003). Additionally, we included representative subsets of proteins from a wide range of cellular activities including chromatin, metabolic activities, transcription, translation, cytoskeleton, and signal transduction. The large majority (1,265) of the strains we examined involved complete deletion of nonessential components. We also included compromised (decreased abundance by mRNA perturbation [DAmP] alleles of 217 essential proteins in which the 3′ untranslated region has been deleted, leading to decreased expression levels of the otherwise intact proteins; Schuldiner et al., 2005; Breslow et al., 2008; Table S2). All pairwise mutants were made using the synthetic genetic array marker system developed by C. Boone and others that allows massively parallel, plate-based selection of haploid double mutant products after mating and sporulation (Tong et al., 2001; Schuldiner et al., 2005, 2006). Growth of the double mutants was estimated by automated colony size measurements, which were then used to determine genetic interaction values based on deviations between the observed growth of the double mutant and the value predicted by the growth phenotypes of the two single mutants, assuming the proteins were of unrelated function (Collins et al., 2006, 2010).

Bottom Line: The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components.We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology.We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biology, University of California, Davis, Davis, CA 95616, USA.

ABSTRACT
To broadly explore mitochondrial structure and function as well as the communication of mitochondria with other cellular pathways, we constructed a quantitative, high-density genetic interaction map (the MITO-MAP) in Saccharomyces cerevisiae. The MITO-MAP provides a comprehensive view of mitochondrial function including insights into the activity of uncharacterized mitochondrial proteins and the functional connection between mitochondria and the ER. The MITO-MAP also reveals a large inner membrane-associated complex, which we term MitOS for mitochondrial organizing structure, comprised of Fcj1/Mitofilin, a conserved inner membrane protein, and five additional components. MitOS physically and functionally interacts with both outer and inner membrane components and localizes to extended structures that wrap around the inner membrane. We show that MitOS acts in concert with ATP synthase dimers to organize the inner membrane and promote normal mitochondrial morphology. We propose that MitOS acts as a conserved mitochondrial skeletal structure that differentiates regions of the inner membrane to establish the normal internal architecture of mitochondria.

Show MeSH
Related in: MedlinePlus