Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation
- University of Gothenburg, Sweden
- Sun Yat-sen University Cancer Center, China
- Norwegian University of Life Sciences, Norway
- University of Gothenburg, Spain
- Chalmers University of Technology, Sweden
- Université Côte d'Azur, CNRS, INSERM, IRCAN, France
Abstract
Deletion of mitochondrial DNA in eukaryotes is currently attributed to rare accidental events associated with mitochondrial replication or repair of double-strand breaks. We report the discovery that yeast cells arrest harmful intramitochondrial superoxide production by shutting down respiration through genetically controlled deletion of mitochondrial oxidative phosphorylation genes. We show that this process critically involves the antioxidant enzyme superoxide dismutase 2 and two-way mitochondrial-nuclear communication through Rtg2 and Rtg3. While mitochondrial DNA homeostasis is rapidly restored after cessation of a short-term superoxide stress, long-term stress causes maladaptive persistence of the deletion process, leading to complete annihilation of the cellular pool of intact mitochondrial genomes and irrevocable loss of respiratory ability. This shows that oxidative stress-induced mitochondrial impairment may be under strict regulatory control. If the results extend to human cells, the results may prove to be of etiological as well as therapeutic importance with regard to age-related mitochondrial impairment and disease.
Data availability
Sequence data that support the findings of this study have been deposited in Sequencing Read Archive (SRA) with the accession codes PRJNA622836.The growth phenotyping code can be found at https://github.com/Scan-o-Matic/scanomatic.git, the simulation code at https://github.com/HelstVadsom/GenomeAdaptation.git and the imaging code at https://github.com/CamachoDejay/SStenberg_3Dyeast_tools.The authors declare that all other data supporting the findings of this study are available within the paper as Supplemental Information Data S1-S30, which can be previewed at https://data.mendeley.com/datasets/mvx7t7rw2d/draft?a=95381e47-dc80-47af-85ab-e0478912a209.
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Chronic superoxide distress causes irreversible loss of mtDNA segmentsNCBI BioProject, PRJNA622836.
Article and author information
Author details
Carles González Peña
Funding
Vetenskapsrådet (2014-6547)
- Jonas Warringer
Agence Nationale de la Recherche (ANR-13-BSV6-0006-01)
- Gianni Liti
Agence Nationale de la Recherche (ANR-15-IDEX-01)
- Gianni Liti
Agence Nationale de la Recherche (ANR-16-CE12-0019)
- Gianni Liti
Agence Nationale de la Recherche (ANR-18-CE12-0004)
- Gianni Liti
Human Frontiers Science Program (LT000182/2019-L)
- Johan Hallin
Vetenskapsrådet (2014-4605)
- Jonas Warringer
Vetenskapsrådet (2015-05427)
- Mikael Molin
Vetenskapsrådet (2018-03638)
- Mikael Molin
Vetenskapsrådet (2018-03453)
- Johanna L Höög
Cancerfonden (2017-778)
- Mikael Molin
Norges Forskningsråd (178901/V30)
- Stig W Omholt
Norges Forskningsråd (222364/F20)
- Stig W Omholt
Agence Nationale de la Recherche (ANR-11-LABX-0028-01)
- Gianni Liti
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Stenberg et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Genetically controlled mtDNA deletions prevent ROS damage by arresting oxidative phosphorylation
eLife 11:e76095.
https://doi.org/10.7554/eLife.76095
Further reading
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- Cell Biology
Distal appendages are nine-fold symmetric blade-like structures attached to the distal end of the mother centriole. These structures are critical for formation of the primary cilium, by regulating at least four critical steps: ciliary vesicle recruitment, recruitment and initiation of intraflagellar transport (IFT), and removal of CP110. While specific proteins that localize to the distal appendages have been identified, how exactly each protein functions to achieve the multiple roles of the distal appendages is poorly understood. Here we comprehensively analyze known and newly discovered distal appendage proteins (CEP83, SCLT1, CEP164, TTBK2, FBF1, CEP89, KIZ, ANKRD26, PIDD1, LRRC45, NCS1, CEP15) for their precise localization, order of recruitment, and their roles in each step of cilia formation. Using CRISPR-Cas9 knockouts, we show that the order of the recruitment of the distal appendage proteins is highly interconnected and a more complex hierarchy. Our analysis highlights two protein modules, CEP83-SCLT1 and CEP164-TTBK2, as critical for structural assembly of distal appendages. Functional assays revealed that CEP89 selectively functions in RAB34+ ciliary vesicle recruitment, while deletion of the integral components, CEP83-SCLT1-CEP164-TTBK2, severely compromised all four steps of cilium formation. Collectively, our analyses provide a more comprehensive view of the organization and the function of the distal appendage, paving the way for molecular understanding of ciliary assembly.
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- Cell Biology
The primary cilium is a microtubule-based organelle that cycles through assembly and disassembly. In many cell types, formation of the cilium is initiated by recruitment of ciliary vesicles to the distal appendage of the mother centriole. However, the distal appendage mechanism that directly captures ciliary vesicles is yet to be identified. In an accompanying paper, we show that the distal appendage protein, CEP89, is important for the ciliary vesicle recruitment, but not for other steps of cilium formation (Tomoharu Kanie, Love, Fisher, Gustavsson, & Jackson, 2023). The lack of a membrane binding motif in CEP89 suggests that it may indirectly recruit ciliary vesicles via another binding partner. Here, we identify Neuronal Calcium Sensor-1 (NCS1) as a stoichiometric interactor of CEP89. NCS1 localizes to the position between CEP89 and a ciliary vesicle marker, RAB34, at the distal appendage. This localization was completely abolished in CEP89 knockouts, suggesting that CEP89 recruits NCS1 to the distal appendage. Similarly to CEP89 knockouts, ciliary vesicle recruitment as well as subsequent cilium formation was perturbed in NCS1 knockout cells. The ability of NCS1 to recruit the ciliary vesicle is dependent on its myristoylation motif and NCS1 knockout cells expressing a myristoylation defective mutant failed to rescue the vesicle recruitment defect despite localizing properly to the centriole. In sum, our analysis reveals the first known mechanism for how the distal appendage recruits the ciliary vesicles.
