bims-midmar 2022-03-27 papers

bims-midmar

Biomed News

on Mitochondrial DNA maintenance and replication

Issue of 2022–03–27
twelve papers selected by
Flavia Söllner, Ludwig-Maximilians University

Biallelic Variants in ENDOG Associated with Mitochondrial Myopathy and Multiple mtDNA Deletions.
Mitochondria transplantation between living cells.
Nuclear-Mitochondrial Interactions.
Live cell microscopy of mitochondria-lysosome contact site formation and tethering dynamics.
Peri-operative management of an adult with POLG-related mitochondrial disease.
Preprint Highlight: ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA- dependent STING signaling.
Mitochondrial Sirtuins in Chronic Degenerative Diseases: New Metabolic Targets in Colorectal Cancer.
Parasite Powerhouse: a Review of the Toxoplasma gondii Mitochondrion.
MitoQ Inhibits Human Breast Cancer Cell Migration, Invasion and Clonogenicity.
mtDNA haplogroup A enhances the effect of obesity on the risk of knee OA in a Mexican population.
Community Consensus Guidelines to Support FAIR Data Standards in Clinical Research Studies in Primary Mitochondrial Disease.
Mitochondrion-encoded circular RNAs are widespread and translatable in plants.

Cells. 2022 Mar 12. pii: 974. [Epub ahead of print]11(6):

Biallelic Variants in ENDOG Associated with Mitochondrial Myopathy and Multiple mtDNA Deletions.

Alessia Nasca, Andrea Legati, Megi Meneri, Melisa Emel Ermert, Chiara Frascarelli, Nadia Zanetti, Manuela Garbellini, Giacomo Pietro Comi, Alessia Catania, Costanza Lamperti, Dario Ronchi, Daniele Ghezzi.

  Endonuclease G (ENDOG) is a nuclear-encoded mitochondrial-localized nuclease. Although its precise biological function remains unclear, its proximity to mitochondrial DNA (mtDNA) makes it an excellent candidate to participate in mtDNA replication, metabolism and maintenance. Indeed, several roles for ENDOG have been hypothesized, including maturation of RNA primers during mtDNA replication, splicing of polycistronic transcripts and mtDNA repair. To date, ENDOG has been deemed as a determinant of cardiac hypertrophy, but no pathogenic variants or genetically defined patients linked to this gene have been described. Here, we report biallelic ENDOG variants identified by NGS in a patient with progressive external ophthalmoplegia, mitochondrial myopathy and multiple mtDNA deletions in muscle. The absence of the ENDOG protein in the patient's muscle and fibroblasts indicates that the identified variants are pathogenic. The presence of multiple mtDNA deletions supports the role of ENDOG in mtDNA maintenance; moreover, the patient's clinical presentation is very similar to mitochondrial diseases caused by mutations in other genes involved in mtDNA homeostasis. Although the patient's fibroblasts did not present multiple mtDNA deletions or delay in the replication process, interestingly, we detected an accumulation of low-level heteroplasmy mtDNA point mutations compared with age-matched controls. This may indicate a possible role of ENDOG in mtDNA replication or repair. Our report provides evidence of the association of ENDOG variants with mitochondrial myopathy.

Keywords:  ENDOG; endonuclease G; mitochondrial DNA; mitochondrial myopathy; multiple mtDNA deletions

DOI:  https://doi.org/10.3390/cells11060974
PLoS Biol. 2022 Mar;20(3): e3001576

Mitochondria transplantation between living cells.

Christoph G Gäbelein, Qian Feng, Edin Sarajlic, Tomaso Zambelli, Orane Guillaume-Gentil, Benoît Kornmann, Julia A Vorholt.

Mitochondria and the complex endomembrane system are hallmarks of eukaryotic cells. To date, it has been difficult to manipulate organelle structures within single live cells. We developed a FluidFM-based approach to extract, inject, and transplant organelles from and into living cells with subcellular spatial resolution. The technology combines atomic force microscopy, optical microscopy, and nanofluidics to achieve force and volume control with real-time inspection. We developed dedicated probes that allow minimally invasive entry into cells and optimized fluid flow to extract specific organelles. When extracting single or a defined number of mitochondria, their morphology transforms into a pearls-on-a-string phenotype due to locally applied fluidic forces. We show that the induced transition is calcium independent and results in isolated, intact mitochondria. Upon cell-to-cell transplantation, the transferred mitochondria fuse to the host cells mitochondrial network. Transplantation of healthy and drug-impaired mitochondria into primary keratinocytes allowed monitoring of mitochondrial subpopulation rescue. Fusion with the mitochondrial network of recipient cells occurred 20 minutes after transplantation and continued for over 16 hours. After transfer of mitochondria and cell propagation over generations, donor mitochondrial DNA (mtDNA) was replicated in recipient cells without the need for selection pressure. The approach opens new prospects for the study of organelle physiology and homeostasis, but also for therapy, mechanobiology, and synthetic biology.

DOI: https://doi.org/10.1371/journal.pbio.3001576
Biomolecules. 2022 Mar 10. pii: 427. [Epub ahead of print]12(3):

Nuclear-Mitochondrial Interactions.

Brittni R Walker, Carlos T Moraes.

  Mitochondria, the cell's major energy producers, also act as signaling hubs, interacting with other organelles both directly and indirectly. Despite having its own circular genome, the majority of mitochondrial proteins are encoded by nuclear DNA. To respond to changes in cell physiology, the mitochondria must send signals to the nucleus, which can, in turn, upregulate gene expression to alter metabolism or initiate a stress response. This is known as retrograde signaling. A variety of stimuli and pathways fall under the retrograde signaling umbrella. Mitochondrial dysfunction has already been shown to have severe implications for human health. Disruption of retrograde signaling, whether directly associated with mitochondrial dysfunction or cellular environmental changes, may also contribute to pathological deficits. In this review, we discuss known signaling pathways between the mitochondria and the nucleus, examine the possibility of direct contacts, and identify pathological consequences of an altered relationship.

Keywords:  MAMs; integrated stress response; mitochondria; nucleus; retrograde signaling

DOI:  https://doi.org/10.3390/biom12030427
STAR Protoc. 2022 Jun 17. 3(2): 101262

Live cell microscopy of mitochondria-lysosome contact site formation and tethering dynamics.

Tayler B Belton, Eric D Leisten, Jasmine Cisneros, Yvette C Wong.

  Mitochondria-lysosome contact sites are critical for maintaining cellular homeostasis by regulating mitochondrial and lysosomal network dynamics and mediating metabolite exchange. Here, we present a protocol to quantitatively analyze the formation and tethering duration of mitochondria-lysosome contact sites by using time-lapse live confocal microscopy of LAMP1 and TOMM20. Although this protocol focuses on mammalian HeLa cells, it can be applied to other cell types for further studies on mitochondria-lysosome contact regulation and function, and elucidation of their role in human disorders. For complete details on the use and execution of this protocol, please refer to Wong et al. (2018) and Wong et al. (2019b).

Keywords:  Cell Biology; Cell culture; Microscopy

DOI:  https://doi.org/10.1016/j.xpro.2022.101262
Anaesth Rep. 2022 Jan-Jun;10(1):10(1): e12159

Peri-operative management of an adult with POLG-related mitochondrial disease.

A Valent, L Delorme, E Roland, C Lambe, S Sarnacki, P Cattan, B Plaud.

  POLG-related mitochondrial disease is a rare mitochondrial disorder that is potentially associated with anaesthetic complications such as propofol-related infusion syndrome. A 19-year-old man with mitochondrial DNA deletions and POLG-related disorders presented for an elective robotic Heller-Dor myotomy for the treatment of oesophageal pseudo-achalasia associated with severe gastro-oesophageal reflux. The fasting period was minimised to reduce the risk of metabolic stress. The anaesthetic technique included a rapid sequence induction with propofol and rocuronium, a remifentanil and sevoflurane-based general anaesthesia with multimodal monitoring and peri-operative lactate-free intravenous fluids with added dextrose. The patient did not experience propofol-related infusion syndrome but did have delayed tracheal extubation due to residual neuromuscular blockade requiring a second dose of sugammadex. This report demonstrates the safety of single-use, low-dose propofol in this patient group. Patients with POLG-related mitochondrial disease may be at risk of prolonged neuromuscular blockade, and appropriate dosing of neuromuscular blocking agents with monitoring of neuromuscular blockade is strongly encouraged.

Keywords:  POLG; mitochondrial disease; prolonged NMB risk‐factors; propofol infusion syndrome

DOI:  https://doi.org/10.1002/anr3.12159
Mol Biol Cell. 2022 Apr 01. 33(4): mbcP22021003

Preprint Highlight: ER-lysosome lipid transfer protein VPS13C/PARK23 prevents aberrant mtDNA- dependent STING signaling.

Luis Bonet-Ponce.

DOI: https://doi.org/10.1091/mbc.P22-02-1003
Int J Mol Sci. 2022 Mar 16. pii: 3212. [Epub ahead of print]23(6):

Mitochondrial Sirtuins in Chronic Degenerative Diseases: New Metabolic Targets in Colorectal Cancer.

Antonino Colloca, Anna Balestrieri, Camilla Anastasio, Maria Luisa Balestrieri, Nunzia D'Onofrio.

  Sirtuins (SIRTs) are a family of class III histone deacetylases (HDACs) consisting of seven members, widely expressed in mammals. SIRTs mainly participate in metabolic homeostasis, DNA damage repair, cell survival, and differentiation, as well as other cancer-related biological processes. Growing evidence shows that SIRTs have pivotal roles in chronic degenerative diseases, including colorectal cancer (CRC), the third most frequent malignant disease worldwide. Metabolic alterations are gaining attention in the context of CRC development and progression, with mitochondrion representing a crucial point of complex and intricate molecular mechanisms. Mitochondrial SIRTs, SIRT2, SIRT3, SIRT4 and SIRT5, control mitochondrial homeostasis and dynamics. Here, we provide a comprehensive review on the latest advances on the role of mitochondrial SIRTs in the initiation, promotion and progression of CRC. A deeper understanding of the pathways by which mitochondrial SIRTs control CRC metabolism may provide new molecular targets for future innovative strategies for CRC prevention and therapy.

Keywords:  SIRT2; SIRT3; SIRT4; SIRT5; chronic degenerative diseases; colorectal cancer; metabolism; mitochondria

DOI:  https://doi.org/10.3390/ijms23063212
J Eukaryot Microbiol. 2022 Mar 21. e12906

Parasite Powerhouse: a Review of the Toxoplasma gondii Mitochondrion.

Madelaine M Usey, Diego Huet.

  Toxoplasma gondii is a member of the apicomplexan phylum, a group of single-celled eukaryotic parasites that cause significant human morbidity and mortality around the world. T. gondii harbors two organelles of endosymbiotic origin: a non-photosynthetic plastid, known as the apicoplast, and a single mitochondrion derived from the ancient engulfment of an α-proteobacterium. Due to excitement surrounding the novelty of the apicoplast, the T. gondii mitochondrion was, to a certain extent, overlooked for about two decades. However, recent work has illustrated that the mitochondrion is an essential hub of apicomplexan-specific biology. Development of novel techniques, such as cryo-electron microscopy, complexome profiling, and next-generation sequencing have led to a renaissance in mitochondrial studies. This review will cover what is currently known about key features of the T. gondii mitochondrion, ranging from its genome to protein import machinery and biochemical pathways. Particular focus will be given to mitochondrial features that diverge significantly from the mammalian host, along with discussion of this important organelle as a drug target.

Keywords:  Apicomplexan; biosynthesis; drug target; electron transport chain; metabolism; mitochondrial genome; mitochondrial protein import

DOI:  https://doi.org/10.1111/jeu.12906
Cancers (Basel). 2022 Mar 16. pii: 1516. [Epub ahead of print]14(6):

MitoQ Inhibits Human Breast Cancer Cell Migration, Invasion and Clonogenicity.

Tania Capeloa, Joanna Krzystyniak, Donatienne d'Hose, Amanda Canas Rodriguez, Valery L Payen, Luca X Zampieri, Justine A Van de Velde, Zohra Benyahia, Erica Pranzini, Thibaut Vazeille, Maude Fransolet, Caroline Bouzin, Davide Brusa, Carine Michiels, Bernard Gallez, Michael P Murphy, Paolo E Porporato, Pierre Sonveaux.

  To successfully generate distant metastases, metastatic progenitor cells must simultaneously possess mesenchymal characteristics, resist to anoïkis, migrate and invade directionally, resist to redox and shear stresses in the systemic circulation, and possess stem cell characteristics. These cells primarily originate from metabolically hostile areas of the primary tumor, where oxygen and nutrient deprivation, together with metabolic waste accumulation, exert a strong selection pressure promoting evasion. Here, we followed the hypothesis according to which metastasis as a whole implies the existence of metabolic sensors. Among others, mitochondria are singled out as a major source of superoxide that supports the metastatic phenotype. Molecularly, stressed cancer cells increase mitochondrial superoxide production, which activates the transforming growth factor-β pathway through src directly within mitochondria, ultimately activating focal adhesion kinase Pyk2. The existence of mitochondria-targeted antioxidants constitutes an opportunity to interfere with the metastatic process. Here, using aggressive triple-negative and HER2-positive human breast cancer cell lines as models, we report that MitoQ inhibits all the metastatic traits that we tested in vitro. Compared to other mitochondria-targeted antioxidants, MitoQ already successfully passed Phase I safety clinical trials, which provides an important incentive for future preclinical and clinical evaluations of this drug for the prevention of breast cancer metastasis.

Keywords:  MitoQ; breast cancer; clonogenicity; invasion; metastasis; migration; mitochondria; mitochondria-targeted antioxidant; mitochondrial superoxide; spheroids

DOI:  https://doi.org/10.3390/cancers14061516
Sci Rep. 2022 Mar 25. 12(1): 5173

mtDNA haplogroup A enhances the effect of obesity on the risk of knee OA in a Mexican population.

Paula Ramos-Louro, Rubén Daniel Arellano Pérez Vertti, Alberto López Reyes, Gabriela Angélica Martínez-Nava, Rolando Espinosa, Carlos Pineda, Faviel Francisco González Galarza, Rafael Argüello Astorga, Lizette Sarai Aguilar Muñiz, Fernando Hernández Terán, Nancy Marbella Parra Torres, Alejandro Durán Sotuela, Mercedes Fernández-Moreno, Vanesa Balboa Barreiro, Francisco J Blanco, Ignacio Rego-Pérez.

To evaluate the influence of mitochondrial DNA haplogroups on the risk of knee OA in terms of their interaction with obesity, in a population from Mexico. Samples were obtained from (n = 353) knee OA patients (KL grade ≥ I) and (n = 364) healthy controls (KL grade = 0) from Mexico city and Torreon (Mexico). Both Caucasian and Amerindian mtDNA haplogroups were assigned by single base extension assay. A set of clinical and demographic variables, including obesity status, were considered to perform appropriate statistical approaches, including chi-square contingency tables, regression models and interaction analyses. To ensure the robustness of the predictive model, a statistical cross-validation strategy of B = 1000 iterations was used. All the analyses were performed using boot, GmAMisc and epiR package from R software v4.0.2 and SPSS software v24. The frequency distribution of the mtDNA haplogroups between OA patients and healthy controls for obese and non-obese groups showed the haplogroup A as significantly over-represented in knee OA patients within the obese group (OR 2.23; 95% CI 1.22-4.05; p-value = 0.008). The subsequent logistic regression analysis, including as covariate the interaction between obesity and mtDNA haplogroup A, supported the significant association of this interaction (OR 2.57; 95% CI 1.24-5.32; p-value = 0.011). The statistical cross-validation strategy confirmed the robustness of the regression model. The data presented here indicate a link between obesity in knee OA patients and mtDNA haplogroup A.

DOI: https://doi.org/10.1038/s41598-022-09265-y
Adv Genet (Hoboken). 2022 Mar;pii: 2100047. [Epub ahead of print]3(1):

Community Consensus Guidelines to Support FAIR Data Standards in Clinical Research Studies in Primary Mitochondrial Disease.

Amel Karaa, Laura E MacMullen, John C Campbell, John Christodoulou, Bruce H Cohen, Thomas Klopstock, Yasutoshi Koga, Costanza Lamperti, Rob van Maanen, Robert McFarland, Sumit Parikh, Shamima Rahman, Fernando Scaglia, Alexander V Sherman, Philip Yeske, Marni J Falk.

  Primary mitochondrial diseases (PMD) are genetic disorders with extensive clinical and molecular heterogeneity where therapeutic development efforts have faced multiple challenges. Clinical trial design, outcome measure selection, lack of reliable biomarkers, and deficiencies in long-term natural history data sets remain substantial challenges in the increasingly active PMD therapeutic development space. Developing "FAIR" (findable, accessible, interoperable, reusable) data standards to make data sharable and building a more transparent community data sharing paradigm to access clinical research metadata are the first steps to address these challenges. This collaborative community effort describes the current landscape of PMD clinical research data resources available for sharing, obstacles, and opportunities, including ways to incentivize and encourage data sharing among diverse stakeholders. This work highlights the importance of, and challenges to, developing a unified system that enables clinical research structured data sharing and supports harmonized data deposition standards across clinical consortia and research groups. The goal of these efforts is to improve the efficiency and effectiveness of drug development and improve understanding of the natural history of PMD. This initiative aims to maximize the benefit for PMD patients, research, industry, and other stakeholders while acknowledging challenges related to differing needs and international policies on data privacy, security, management, and oversight.

Keywords:  FAIR standards; clinical trials; data sharing; primary mitochondrial disease; therapeutic developments

DOI:  https://doi.org/10.1002/ggn2.202100047
Plant Physiol. 2022 Mar 24. pii: kiac143. [Epub ahead of print]

Mitochondrion-encoded circular RNAs are widespread and translatable in plants.

Xun Liao, Xiao-Jie Li, Guan-Tao Zheng, Feng-Rui Chang, Lin Fang, Hang Yu, Jun Huang, Ya-Feng Zhang.

Nucleus-encoded circular RNAs (ncircRNAs) have been widely detected in eukaryotes, and most circRNA identification algorithms are designed to identify them. However, using these algorithms, few mitochondrion-encoded circRNAs (mcircRNAs) have been identified in plants, and the role of plant mcircRNAs has not yet been addressed. Here, we developed a circRNA identification algorithm, mitochondrion-encoded circRNA identifier (MeCi), based on common features of plant mitochondrial genomes. We identified 7,524, 9,819, 1,699, 1,821, 1,809, and 5,133 mcircRNAs in maize (Zea mays), Arabidopsis (Arabidopsis thaliana), rice (Oryza sativa), tomato (Solanum lycopersicum), cucumber (Cucumis sativus), and grape (Vitis vinifera), respectively. These mcircRNAs were experimentally validated. Plant mcircRNAs had distinct characteristics from ncircRNAs, and they were more likely to be derived from RNA degradation but not intron backsplicing. Alternative circularization was prevalent in plant mitochondria, and most parental genomic regions hosted multiple mcircRNA isoforms, which have homogenous 5' termini but heterogeneous 3' ends. By analysis of mitopolysome and mitoribosome profiling data, 1,463 mcircRNAs bound to ribosomes were detected in maize and Arabidopsis. Further analysis of mass spectrometry-based proteomics data identified 358 mcircRNA-derived polypeptides. Overall, we developed a computational pipeline that efficiently identifies plant mcircRNAs, and we demonstrated mcircRNAs are widespread and translated in plants.

DOI: https://doi.org/10.1093/plphys/kiac143