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Adaptive Aneuploidy Protects Against Thiol Peroxidase Deficiency by Increasing Respiration Via Key Mitochondrial Proteins

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Adaptive Aneuploidy Protects Against Thiol Peroxidase Deficiency by Increasing Respiration Via Key Mitochondrial Proteins Adaptive aneuploidy protects against thiol peroxidase deficiency by increasing respiration via key mitochondrial proteins Alaattin Kayaa, Maxim V. Gerashchenkoa, Inge Seima, Jean Labarreb, Michel B. Toledanob, and Vadim N. Gladysheva,1 aDivision of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115; and bOxidative Stress and Cancer, Institut de Biologie et Technologie-Saclay, FRE3377 Commisariat à l’Energie Atomique (CEA), Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud, CEA-Saclay, F-91191 Gif Sur Yvette, France Edited by Angelika Amon, Massachusetts Institute of Technology, Cambridge, MA, and approved July 10, 2015 (received for review March 16, 2015) Aerobic respiration is a fundamental energy-generating process; Notable among them are peroxiredoxins (Prxs) and glutathi- however, there is cost associated with living in an oxygen-rich one peroxidases (Gpxs), two families of thiol-specific peroxide environment, because partially reduced oxygen species can damage scavengers (7) collectively known as thiol peroxidases. Prxs and cellular components. Organisms evolved enzymes that alleviate this Gpxs are highly conserved, and many organisms have multiple damage and protect the intracellular milieu, most notably thiol copies of these genes. For example, five Prxs and three Gpxs, peroxidases, which are abundant and conserved enzymes that localized to different cellular compartments, have been identi- mediate hydrogen peroxide signaling and act as the first line of fied in Saccharomyces cerevisiae (8). One of the most deleterious defense against oxidants in nearly all living organisms. Deletion of damage forms inflicted by ROS is DNA damage (9). Many genetic Δ all eight thiol peroxidase genes in yeast ( 8 strain) is not lethal, but disorders as well as different forms of cancer are associated with results in slow growth and a high mutation rate. Here we charac- oxidative stress-induced DNA damage (10, 11). Recent studies terized mechanisms that allow yeast cells to survive under condi- offer direct proof that thiol peroxidases represent the first line of Δ tions of thiol peroxidase deficiency. Two independent 8 strains defense against oxidative stress-induced DNA damage (12, 13). increased mitochondrial content, altered mitochondrial distribution, The observation that compromised function of thiol peroxi- and became dependent on respiration for growth but they were not dases causes the loss of genome stability and a broad spectrum of hypersensitive to H O . In addition, both strains independently ac- 2 2 mutations and chromosomal rearrangements has provided fur- quired a second copy of chromosome XI and increased expression of ther evidence that these enzymes are significant contributors to genes encoded by it. Survival of Δ8 cells was dependent on mito- genome stability (14, 15). Aneuploidy, with its aberrant number chondrial cytochrome-c peroxidase (CCP1)andUTH1, present on chromosome XI. Coexpression of these genes in Δ8cellsledtothe of chromosomes, is also associated with oxidative stress (16); elimination of the extra copy of chromosome XI and improved cell however, a link between thiol peroxidase status and aneuploidy growth, whereas deletion of either gene was lethal. Thus, thiol has not been reported previously. peroxidase deficiency requires dosage compensation of CCP1 and UTH1 via chromosome XI aneuploidy, wherein these proteins sup- Significance port hydroperoxide removal with the reducing equivalents gener- ated by the electron transport chain. To our knowledge, this is the Aneuploidy, a condition of abnormal chromosomal content, first evidence of adaptive aneuploidy counteracting oxidative stress. can support adaptive mechanisms in response to environmen- tal cues but comes at the expense of decreased proliferation thiol peroxidase | oxidative stress | aneuploidy | respiration and dysfunction of cellular processes. Here we show that the gain of an extra copy of chromosome XI in yeast is an adaptive everal fundamental biological processes such as respiration, mechanism to deal with oxidative stress under conditions of Sphotosynthesis, and the immune response, as well as nu- antioxidant deficiency. We narrowed down the effect of merous other cellular processes, lead to the production of partially adaptive aneuploidy to two genes on chromosome XI, which reduced species of molecular oxygen known as reactive oxygen supported increased mitochondrial abundance and respiration, species (ROS) (1, 2). Elevated levels of ROS are often associated which in turn provided reducing equivalents for hydroperoxide with oxidative stress, which manifests as damage to lipids, proteins, removal. Forced expression of these genes eliminated aneu- DNA, metabolites, and other biomolecules (3). However, ROS ploidy, improved cell growth, and was sufficient for protection are not only deleterious factors but may also participate in the against oxidative stress. Thus, aneuploidy can adaptively re- regulation of cellular processes. For example, hydrogen peroxide program cellular metabolism, protecting against oxidative stress by upregulating respiration. (H2O2)-mediated oxidation of cysteine residues is involved in re- dox signaling (4, 5). Therefore, it is important for organisms to Author contributions: A.K. and V.N.G. designed research; A.K., M.V.G., and J.L. performed carefully control redox homeostasis. research; A.K., M.V.G., I.S., M.B.T., and V.N.G. analyzed data; and A.K. and V.N.G. wrote To deal with the dual role of ROS as deleterious or beneficial the paper. species, organisms have evolved several mechanisms. Protectors The authors declare no conflict of interest. from ROS, known as antioxidants, can be categorized as non- This article is a PNAS Direct Submission. enzymatic and enzymatic ROS molecules. The nonenzymatic Data deposition: The genome reads reported in this paper have been deposited in the antioxidants buffer the intracellular milieu against ROS toxic- BioProject database, www.ncbi.nlm.nih.gov/bioproject (accession no. PRJNA287442). ity. For example, ascorbate, tocopherol, flavonoids, alkaloids, Transcriptome (RNA-sequencing) reads and fragments per kilobase of transcript per mil- and carotenoids can scavenge oxygen-derived free radicals, lion mapped read values have been deposited in the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov/geo (accession no. GSE70036). Ribosome profiling (Ribo- whereas glutathione (GSH), a highly abundant tripeptide, sup- sequencing) data have also been deposited in the GEO database (accession no. GSE59573). ports two electron reduction mechanisms (6). Enzyme antioxi- 1To whom correspondence should be addressed. Email: [email protected]. dants include superoxide dismutases (eliminate the superoxide edu. radical) and catalases (eliminate H2O2), as well as many other This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. BIOCHEMISTRY enzymes (6). 1073/pnas.1505315112/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1505315112 PNAS | August 25, 2015 | vol. 112 | no. 34 | 10685–10690 Downloaded by guest on October 2, 2021 Recently, we isolated two independent strains lacking all eight fact that the observed phenotypes appeared in two independent Δ8 thiol peroxidase genes (Δ8 cells) (15). In the current study, we isolates suggest that increased respiration is an adaptive feature of investigated how these cells deal with hydroperoxides. We found Δ8cells. that both Δ8 mutants were strictly dependent on respiration and were characterized by chromosome XI (chr-XI) aneuploidy. Two Chr-XI Aneuploidy in Δ8 Cells. Genomic sequencing of Wt cells genes, CCP1 and UTH1, located on this chromosome were re- revealed uniform coverage of reads across the genome, as ex- Δ sponsible for the whole-chromosome duplication, because they pected; however, both 8 strains had twice as many reads corre- sponding to chr-XI (Fig. 2A). As a control, we sequenced the allowed H2O2 elimination with the reducing equivalents of the electron transport chain (ETC). These two genes were essential genome and analyzed the growth and sensitivity to respiration for these cells, whereas their forced coexpression in Δ8 mutants inhibitors of the Wt-M11 strain, which is characterized by dupli- allowed cells to lose the extra copy of chr-XI and increase their cation of chr-XI and has a complete set of thiol peroxidase genes. B growth. These findings identify a mechanism of adaptive aneu- This strain was not sensitive to inhibitors of respiration (Fig. 1 ), but its genome coverage was identical to that of Δ8 strains (Fig. ploidy, which in turn points to new targets for therapeutic in- A terventions for diseases associated with oxidative stress. 2 ). In contrast, genome sequencing of cells lacking all five Prxs (Δ5 cells) or all three Gpxs (Δ3 cells), which served as the initial Results strains for independent preparation of the two Δ8 isolates, did not A Δ Characterization of Δ8 Strains. Our previous analyses of Δ8 cells show increased chr-XI coverage (Fig. 2 ). Thus, the two 8 revealed that thiol peroxidases are not essential; however, they strains independently acquired a second copy of chr-XI and are surprisingly could withstand several stresses (17). Two inde- characterized by aneuploidy. pendent Δ8isolatesalsomanifestedphenotypessuchasslow Previous studies showed that genes encoded on duplicated chromosomes tend to be more highly expressed (19, 20). Indeed, growth, short lifespan, and decreased colony
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