bims-mikwok 2022-10-30 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2022‒10‒30
eight papers selected by
Avinash N. Mukkala, University of Toronto

Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS.
Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.
Mitochondria dysfunction and impaired response to oxidative stress promotes proteostasis disruption in aged human cells.
Structural studies of human fission protein FIS1 reveal a dynamic region important for GTPase DRP1 recruitment and mitochondrial fission.
Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin.
PINK1-PRKN mediated mitophagy: differences between in vitro and in vivo models.
Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.
The mechanisms and roles of selective autophagy in mammals.

Cell Mol Life Sci. 2022 Oct 25. 79(11): 565

Basal Gp78-dependent mitophagy promotes mitochondrial health and limits mitochondrial ROS.

Parsa Alan, Kurt R Vandevoorde, Bharat Joshi, Ben Cardoen, Guang Gao, Yahya Mohammadzadeh, Ghassan Hamarneh, Ivan R Nabi.

  Mitochondria are major sources of cytotoxic reactive oxygen species (ROS), such as superoxide and hydrogen peroxide, that when uncontrolled contribute to cancer progression. Maintaining a finely tuned, healthy mitochondrial population is essential for cellular homeostasis and survival. Mitophagy, the selective elimination of mitochondria by autophagy, monitors and maintains mitochondrial health and integrity, eliminating damaged ROS-producing mitochondria. However, mechanisms underlying mitophagic control of mitochondrial homeostasis under basal conditions remain poorly understood. E3 ubiquitin ligase Gp78 is an endoplasmic reticulum membrane protein that induces mitochondrial fission and mitophagy of depolarized mitochondria. Here, we report that CRISPR/Cas9 knockout of Gp78 in HT-1080 fibrosarcoma cells increased mitochondrial volume, elevated ROS production and rendered cells resistant to carbonyl cyanide m-chlorophenyl hydrazone (CCCP)-induced mitophagy. These effects were phenocopied by knockdown of the essential autophagy protein ATG5 in wild-type HT-1080 cells. Use of the mito-Keima mitophagy probe confirmed that Gp78 promoted both basal and damage-induced mitophagy. Application of a spot detection algorithm (SPECHT) to GFP-mRFP tandem fluorescent-tagged LC3 (tfLC3)-positive autophagosomes reported elevated autophagosomal maturation in wild-type HT-1080 cells relative to Gp78 knockout cells, predominantly in proximity to mitochondria. Mitophagy inhibition by either Gp78 knockout or ATG5 knockdown reduced mitochondrial potential and increased mitochondrial ROS. Live cell analysis of tfLC3 in HT-1080 cells showed the preferential association of autophagosomes with mitochondria of reduced potential. Xenograft tumors of HT-1080 knockout cells show increased labeling for mitochondria and the cell proliferation marker Ki67 and reduced labeling for the TUNEL cell death reporter. Basal Gp78-dependent mitophagic flux is, therefore, selectively associated with reduced potential mitochondria promoting maintenance of a healthy mitochondrial population, limiting ROS production and tumor cell proliferation.

Keywords:  GFP-mRFP tandem fluorescent-tagged LC3; Gp78 ubiquitin ligase; Mitochondria; Mitophagy; Reactive oxygen species; SPECHT; Spot detection

DOI:  https://doi.org/10.1007/s00018-022-04585-8
Cell Mol Life Sci. 2022 Oct 29. 79(11): 574

Mitochondrial proteotoxicity: implications and ubiquitin-dependent quality control mechanisms.

Mariusz Karbowski, Yumiko Oshima, Nicolas Verhoeven.

  Through their role in energy generation and regulation of several vital pathways, including apoptosis and inflammation, mitochondria are critical for the life of eukaryotic organisms. Mitochondrial dysfunction is a major problem implicated in the etiology of many pathologies, including neurodegenerative diseases, such as Parkinson's disease (PD), Alzheimer's disease (AD), Huntington's disease (HD), and amyotrophic lateral sclerosis (ALS), diabetes, cardiovascular diseases, and many others. Proteotoxic stress, here defined as a reduction in bioenergetic activity induced by the accumulation of aberrant proteins in the mitochondria, is likely to be implicated in disease-linked mitochondrial and cellular decline. Various quality control pathways, such as mitochondrial unfolded protein response (mtUPR), the ubiquitin (Ub)-dependent degradation of aberrant mitochondrial proteins, and mitochondria-specific autophagy (mitophagy), respond to proteotoxic stress and eliminate defective proteins or dysfunctional mitochondria. This work provides a concise review of mechanisms by which disease-linked aberrant proteins affect mitochondrial function and an overview of mitochondrial quality control pathways that counteract mitochondrial proteotoxicity. We focus on mitochondrial quality control mechanisms relying on the Ub-mediated protein degradation, such as mitochondria-specific autophagy and the mitochondrial arm of the Ub proteasome system (UPS). We highlight the importance of a widening perspective of how these pathways protect mitochondria from proteotoxic stress to better understand mitochondrial proteotoxicity in overlapping pathophysiological pathways. Implications of these mechanisms in disease development are also briefly summarized.

Keywords:  Mitochondria; Mitophagy; Proteotoxicity; Quality control; Ubiquitin

DOI:  https://doi.org/10.1007/s00018-022-04604-8
Mitochondrion. 2022 Oct 20. pii: S1567-7249(22)00086-1. [Epub ahead of print]

Mitochondria dysfunction and impaired response to oxidative stress promotes proteostasis disruption in aged human cells.

Diogo Trigo, André Nadais, Ana Carvalho, Bárbara Morgado, Francisco Santos, Sandrina Pereira, Odete A B da Cruz E Silva.

The plastic architecture of the mitochondrial network and its dynamic structure play crucial roles ensuring that varying energetic demands are rapidly met. Given the brain's high energy demand, mitochondria play a particularly critical role in neuronal and axonal energy homeostasis With ageing physiological properties of the organism deteriorate, and are associated with loss of cellular homeostasis, accumulation of dysfunctional organelles and damaged macromolecules. Thus, mitochondrial loss of efficiency is likely to be both a cause and a consequence of ageing. Additionally distinct cellular events can contribute to oxidative stress, disruption of metabolism and mitochondria homeostasis, resulting in neuropathology. However, although the correlation between ageing and mitochondria disfunction is well established, the response to oxidative stress, particularly proteostasis, remains to be fully elucidated. The work here described explores the degradation of mitochondria oxidative stress-response mechanisms with ageing in human cells, addressing the physiological effects on proteostasis, focused on its role in differentiating between healthy and pathological ageing. Increased protein aggregation appears to be tightly related to impairment of ageing mitochondria response to oxidative stress, and antioxidative agents are shown to have a progressive protective effect with age; cells from old individuals show higher susceptibility to oxidative stress, in terms of protein aggregation, cell viability, or mitochondria homeostasis. These results support the antioxidant properties of flavonoids as a good therapeutic strategy for age-related diseases. Given their protective effect, this family of compounds can be of strategic therapeutic value for protein-aggregation related diseases.

DOI: https://doi.org/10.1016/j.mito.2022.10.002
J Biol Chem. 2022 Oct 19. pii: S0021-9258(22)01063-8. [Epub ahead of print] 102620

Structural studies of human fission protein FIS1 reveal a dynamic region important for GTPase DRP1 recruitment and mitochondrial fission.

John M Egner, Kelsey A Nolden, Megan C Harwig, Ryan P Bonate, Jaime De Anda, Maxx H Tessmer, Elizabeth L Noey, Ugochukwu K Ihenacho, Ziwen Liu, Francis C Peterson, Gerard C L Wong, Michael E Widlansky, R Blake Hill.

  Fission protein 1 (FIS1) and dynamin-related protein 1 (DRP1) were initially described as being evolutionarily conserved for mitochondrial fission, yet in humans the role of FIS1 in this process is unclear and disputed by many. In budding yeast where Fis1p helps to recruit the DRP1 ortholog from the cytoplasm to mitochondria for fission, an N-terminal "arm" of Fis1p is required for function. The yeast Fis1p arm interacts intramolecularly with a conserved tetratricopeptide repeat (TPR) core and governs in vitro interactions with yeast DRP1. In human FIS1, NMR and X-ray structures show different arm conformations, but its importance for human DRP1 recruitment is unknown. Here, we use MD simulations and comparisons to experimental NMR chemical shifts to show the human FIS1 arm can adopt an intramolecular conformation akin to that observed with yeast Fis1p. This finding is further supported through intrinsic tryptophan fluorescence and NMR experiments on human FIS1 with and without the arm. Using NMR, we observed the human FIS1 arm is also sensitive to environmental changes. We reveal the importance of these findings in cellular studies where removal of the FIS1 arm reduces DRP1 recruitment and mitochondrial fission similar to the yeast system. Moreover, we determined that expression of mitophagy adaptor TBC1D15 can partially rescue arm-less FIS1 in a manner reminiscent of expression of the adaptor Mdv1p in yeast. These findings point to conserved features of FIS1 important for its activity in mitochondrial morphology. More generally, other TPR-containing proteins are flanked by disordered arms/tails, suggesting possible common regulatory mechanisms.

Keywords:  fission; intrinsic disordered region; mitochondria; molecular dynamics; nuclear magnetic resonance (NMR); protein dynamics; protein structure; tetratricopeptide repeat (TPR)

DOI:  https://doi.org/10.1016/j.jbc.2022.102620
Int J Mol Sci. 2022 Oct 11. pii: 12105. [Epub ahead of print]23(20):

Targeting Deubiquitinating Enzymes (DUBs) That Regulate Mitophagy via Direct or Indirect Interaction with Parkin.

Eliona Tsefou, Robin Ketteler.

  The quality control of mitochondria is critical for the survival of cells, and defects in the pathways required for this quality control can lead to severe disease. A key quality control mechanism in cells is mitophagy, which functions to remove damaged mitochondria under conditions of various stresses. Defective mitophagy can lead to a number of diseases including neurodegeneration. It has been proposed that an enhancement of mitophagy can improve cell survival, enhance neuronal function in neurodegeneration and extend health and lifespans. In this review, we highlight the role of deubiquitinating enzymes (DUBs) in the regulation of mitophagy. We summarise the current knowledge on DUBs that regulate mitophagy as drug targets and provide a list of small molecule inhibitors that are valuable tools for the further development of therapeutic strategies targeting the mitophagy pathway in neurodegeneration.

Keywords:  DUB inhibitors; Parkin; Parkinson disease; deubiquitinating enzymes; mitophagy

DOI:  https://doi.org/10.3390/ijms232012105
Autophagy. 2022 Oct 25.

PINK1-PRKN mediated mitophagy: differences between in vitro and in vivo models.

Rui Han, Yanting Liu, Shihua Li, Xiao-Jiang Li, Weili Yang.

  Mitophagy is a key intracellular process that selectively removes damaged mitochondria to prevent their accumulation that can cause neuronal degeneration. During mitophagy, PINK1 (PTEN induced kinase 1), a serine/threonine kinase, works with PRKN/parkin, an E3 ubiquitin ligase, to target damaged mitochondria to the lysosome for degradation. Mutations in the PINK1 and PRKN genes cause early-onset Parkinson disease that is also associated with mitochondrial dysfunction. There are a large number of reports indicating the critical role of PINK1 in mitophagy. However, most of these findings were obtained from in vitro experiments with exogenous PINK1 expression and acute damage of mitochondria by toxins. Recent studies using novel animal models suggest that PINK1-PRKN can also function independent of mitochondria. In this review, we highlight the major differences between in vitro and in vivo models for investigating PINK1 and discuss the potential mechanisms underlying these differences with the aim of understanding how PINK1 functions under different circumstances.

Keywords:  Mitochondria dysfunction; PINK1; PRKN; Parkinson disease; mitophagy

DOI:  https://doi.org/10.1080/15548627.2022.2139080
EMBO J. 2022 Oct 24. e111239

Hypoxia promotes osteogenesis by facilitating acetyl-CoA-mediated mitochondrial-nuclear communication.

Andromachi Pouikli, Monika Maleszewska, Swati Parekh, Ming Yang, Chrysa Nikopoulou, Juan Jose Bonfiglio, Constantine Mylonas, Tonantzi Sandoval, Anna-Lena Schumacher, Yvonne Hinze, Ivan Matic, Christian Frezza, Peter Tessarz.

  Bone-derived mesenchymal stem cells (MSCs) reside in a hypoxic niche that maintains their differentiation potential. While hypoxia (low oxygen concentration) was reported to critically support stem cell function and osteogenesis, the molecular events triggering changes in stem cell fate decisions in response to normoxia (high oxygen concentration) remain elusive. Here, we study the impact of normoxia on mitochondrial-nuclear communication during stem cell differentiation. We show that normoxia-cultured murine MSCs undergo profound transcriptional alterations which cause irreversible osteogenesis defects. Mechanistically, high oxygen promotes chromatin compaction and histone hypo-acetylation, particularly on promoters and enhancers of osteogenic genes. Although normoxia induces metabolic rewiring resulting in elevated acetyl-CoA levels, histone hypo-acetylation occurs due to the trapping of acetyl-CoA inside mitochondria owing to decreased citrate carrier (CiC) activity. Restoring the cytosolic acetyl-CoA pool remodels the chromatin landscape and rescues the osteogenic defects. Collectively, our results demonstrate that the metabolism-chromatin-osteogenesis axis is perturbed upon exposure to high oxygen levels and identifies CiC as a novel, oxygen-sensitive regulator of the MSC function.

Keywords:  histone acetylation; hypoxia; mesenchymal stem cells; metabolism; osteogenesis

DOI:  https://doi.org/10.15252/embj.2022111239
Nat Rev Mol Cell Biol. 2022 Oct 27.

The mechanisms and roles of selective autophagy in mammals.

Jose Norberto S Vargas, Maho Hamasaki, Tsuyoshi Kawabata, Richard J Youle, Tamotsu Yoshimori.

Autophagy is a process that targets various intracellular elements for degradation. Autophagy can be non-selective - associated with the indiscriminate engulfment of cytosolic components - occurring in response to nutrient starvation and is commonly referred to as bulk autophagy. By contrast, selective autophagy degrades specific targets, such as damaged organelles (mitophagy, lysophagy, ER-phagy, ribophagy), aggregated proteins (aggrephagy) or invading bacteria (xenophagy), thereby being importantly involved in cellular quality control. Hence, not surprisingly, aberrant selective autophagy has been associated with various human pathologies, prominently including neurodegeneration and infection. In recent years, considerable progress has been made in understanding mechanisms governing selective cargo engulfment in mammals, including the identification of ubiquitin-dependent selective autophagy receptors such as p62, NBR1, OPTN and NDP52, which can bind cargo and ubiquitin simultaneously to initiate pathways leading to autophagy initiation and membrane recruitment. This progress opens the prospects for enhancing selective autophagy pathways to boost cellular quality control capabilities and alleviate pathology.

DOI: https://doi.org/10.1038/s41580-022-00542-2