bims-mikwok 2024-03-03 papers

bims-mikwok

Biomed News

on Mitochondrial quality control

Issue of 2024‒03‒03
twenty papers selected by
Gavin McStay, Liverpool John Moores University

FBXL4: safeguarding against mitochondrial depletion through suppression of mitophagy.
Aging STINGs: mitophagy at the crossroads of neuroinflammation.
Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress.
Mitophagy protects against silver nanoparticle-induced hepatotoxicity by inhibiting mitochondrial ROS and the NLRP3 inflammasome.
NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP.
[New research direction of organ dysfunction caused by hemorrhagic shock: mechanisms of mitochondrial quality control].
Mitochondria in disease: changes in shapes and dynamics.
Optic atrophy 1 mediates muscle differentiation by promoting a metabolic switch via the supercomplex assembly factor SCAF1.
Reorganization of mitochondria-organelle interactions during postnatal development in skeletal muscle.
SS-31 inhibits mtDNA-cGAS-STING signaling to improve POCD by activating mitophagy in aged mice.
The Janus face of mitophagy in myocardial ischemia/reperfusion injury and recovery.
Mitochondrial stress in the spaceflight environment.
ATF4-dependent increase in mitochondrial-endoplasmic reticulum tethering following OPA1 deletion in skeletal muscle.
Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis.
Sodium butyrate ameliorates high glucose-suppressed neuronal mitophagy by restoring PRKN expression via inhibiting the RELA-HDAC8 complex.
[Role of mitophagy in diabetes mellitus and its complications and traditional Chinese medicine intervention: a review].
Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase.
Role of the mitophagy-apoptosis axis in the pathogenesis of polycystic ovarian syndrome.
Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis.
Chemical inhibition of phosphatidylcholine biogenesis reveals its role in mitochondrial division.

Autophagy. 2024 Feb 29. 1-3

FBXL4: safeguarding against mitochondrial depletion through suppression of mitophagy.

Prajakta Kulkarni, Giang Thanh Nguyen-Dien, Keri-Lyn Kozul, Julia K Pagan.

  Mitophagy is a critical mitochondrial quality control process that selectively removes dysfunctional or excess mitochondria through the autophagy-lysosome system. The process is tightly controlled to ensure cellular and physiological homeostasis. Insufficient mitophagy can result in failure to remove damaged mitochondria and consequent cellular degeneration, but it is equally important to appropriately restrain mitophagy to prevent excessive mitochondrial depletion. Here, we discuss our recent discovery that the SKP1-CUL1-F-box (SCF)-FBXL4 (F-box and leucine-rich repeat protein 4) E3 ubiquitin ligase localizes to the mitochondrial outer membrane, where it constitutively mediates the ubiquitination and degradation of BNIP3L/NIX and BNIP3 mitophagy receptors to suppress mitophagy. The post-translational regulation of BNIP3L and BNIP3 is disrupted in mitochondrial DNA depletion syndrome 13 (MTDPS13), a multi-systemic disorder caused by mutations in the FBXL4 gene and characterized by elevated mitophagy and mitochondrial DNA/mtDNA depletion in patient fibroblasts. Our results demonstrate that mitophagy is not solely stimulated in response to specific conditions but is instead also actively suppressed through the continuous degradation of BNIP3L and BNIP3 mediated by the SCF-FBXL4 ubiquitin ligase. Thus, cellular conditions or signaling events that prevent the FBXL4-mediated turnover of BNIP3L and BNIP3 on specific mitochondria are expected to facilitate their selective removal.

Keywords:  BNIP3; BNIP3L/NIX; FBXL4; MTDPS13; mitophagy; ubiquitin ligase

DOI:  https://doi.org/10.1080/15548627.2024.2318077
Autophagy. 2024 Feb 27.

Aging STINGs: mitophagy at the crossroads of neuroinflammation.

Juan Ignacio Jiménez-Loygorri, Patricia Boya.

  Loss of proteostasis and dysregulated mitochondrial function are part of the traditional hallmarks of aging, and in their last revision impaired macroautophagy and chronic inflammation are also included. Mitophagy is at the intersection of all these processes but whether it undergoes age-associated perturbations was not known. In our recent work, we performed a systematic and systemic analysis of mitolysosome levels in mice and found that, despite the already-known decrease in non-selective macroautophagy, mitophagy remains stable or increases upon aging in all tissues analyzed and is mediated by the PINK1-PRKN-dependent pathway. Further analyses revealed a concomitant increase in mtDNA leakage into the cytosol and activation of the CGAS-STING1 inflammation axis. Notably, both phenomena are also observed in primary fibroblasts from aged human donors. We hypothesized that mitophagy might be selectively upregulated during aging to improve mitochondrial fitness and reduce mtDNA-induced inflammation. Treatment with the mitophagy inducer urolithin A alleviates age-associated neurological decline, including improved synaptic connectivity, cognitive memory and visual function. Supporting our initial hypothesis, urolithin A reduces the levels of cytosolic mtDNA, CGAS-STING1 activation and neuroinflammation. Finally, using an in vitro model of mitochondrial membrane permeabilization we validated that PINK1-PRKN-mediated mitophagy is essential to resolve cytosolic mtDNA-triggered inflammation. These findings open up an integrative approach to tackle aging and increase healthspan via mitophagy induction.

Keywords:  Inflammation; PINK1; Parkin; mitochondria; mtDNA; retina

DOI:  https://doi.org/10.1080/15548627.2024.2322421
Proc Natl Acad Sci U S A. 2024 Mar 05. 121(10): e2313540121

Tom20 gates PINK1 activity and mediates its tethering of the TOM and TIM23 translocases upon mitochondrial stress.

Mohamed A Eldeeb, Andrew N Bayne, Armaan Fallahi, Thomas Goiran, Emma J MacDougall, Andrea Soumbasis, Cornelia E Zorca, Jace-Jones Tabah, Rhalena A Thomas, Nathan Karpilovsky, Meghna Mathur, Thomas M Durcan, Jean-François Trempe, Edward A Fon.

  Mutations in PTEN-induced putative kinase 1 (PINK1) cause autosomal recessive early-onset Parkinson's disease (PD). PINK1 is a Ser/Thr kinase that regulates mitochondrial quality control by triggering mitophagy mediated by the ubiquitin (Ub) ligase Parkin. Upon mitochondrial damage, PINK1 accumulates on the outer mitochondrial membrane forming a high-molecular-weight complex with the translocase of the outer membrane (TOM). PINK1 then phosphorylates Ub, which enables recruitment and activation of Parkin followed by autophagic clearance of the damaged mitochondrion. Thus, Parkin-dependent mitophagy hinges on the stable accumulation of PINK1 on the TOM complex. Yet, the mechanism linking mitochondrial stressors to PINK1 accumulation and whether the translocases of the inner membrane (TIMs) are also involved remain unclear. Herein, we demonstrate that mitochondrial stress induces the formation of a PINK1-TOM-TIM23 supercomplex in human cultured cell lines, dopamine neurons, and midbrain organoids. Moreover, we show that PINK1 is required to stably tether the TOM to TIM23 complexes in response to stress such that the supercomplex fails to accumulate in cells lacking PINK1. This tethering is dependent on an interaction between the PINK1 N-terminal-C-terminal extension module and the cytosolic domain of the Tom20 subunit of the TOM complex, the disruption of which, by either designer or PD-associated PINK1 mutations, inhibits downstream mitophagy. Together, the findings provide key insight into how PINK1 interfaces with the mitochondrial import machinery, with important implications for the mechanisms of mitochondrial quality control and PD pathogenesis.

Keywords:  PINK1; mitochondrial import; mitochondrial quality control; mitophagy; proteolysis

DOI:  https://doi.org/10.1073/pnas.2313540121
Ecotoxicol Environ Saf. 2024 Feb 26. pii: S0147-6513(24)00212-4. [Epub ahead of print]273 116137

Mitophagy protects against silver nanoparticle-induced hepatotoxicity by inhibiting mitochondrial ROS and the NLRP3 inflammasome.

Jiangyan Li, Ming Li, Ruirui Wang, Jiaqi Lan, Lian Yu, Jie Gao, Hezuo Lü, Qiang Fang, Fengchao Wang.

  Silver nanoparticles (AgNPs) have wide clinical applications because of their excellent antibacterial properties; however, they can cause liver inflammation in animals. Macrophages are among the main cells mediating inflammation and are also responsible for the phagocytosis of nanomaterials. The NLRP3 inflammasome is a major mechanism of inflammation, and its activation both induces cytokine release and triggers inflammatory cell death (i.e., pyroptosis). In previous studies, we demonstrated that mitophagy activation plays a protective role against AgNP-induced hepatotoxicity. However, the exact molecular mechanisms underlying these processes are not fully understood. In this study, we demonstrate that AgNP exposure induces NLRP3 inflammasome activation, mitochondrial damage and pyroptosis in vivo and in vitro. NLRP3 silencing or inhibiting mitochondrial reactive oxygen species (ROS) overproduction reduces PINK1-Parkin-mediated mitophagy. Meanwhile, the inhibition of mitophagy ROS production, mitochondrial, NLRP3-mediated inflammation, and pyroptosis in RAW264.7 cells were more pronounced than in the control group. These results suggest that PINK1-Parkin-mediated mitophagy plays a protective role by reducing AgNP-induced mitochondrial ROS and subsequent NLRP3 inflammasome activation.

Keywords:  Mitochondrial reactive oxygen species; Mitophagy; NLRP3 inflammasome; Pyroptosis; Silver nanoparticles

DOI:  https://doi.org/10.1016/j.ecoenv.2024.116137
Cell Rep. 2024 Feb 26. pii: S2211-1247(24)00188-8. [Epub ahead of print]43(3): 113860

NEMF-mediated Listerin-independent mitochondrial translational surveillance by E3 ligase Pirh2 and mitochondrial protease ClpXP.

Liang Lv, Jinyou Mo, Yumin Qing, Shuchao Wang, Leijie Chen, Anna Mei, Ru Xu, Hualin Huang, Jieqiong Tan, Yifu Li, Jia Liu.

  The ribosome-associated protein quality control (RQC) pathway acts as a translational surveillance mechanism to maintain proteostasis. In mammalian cells, the cytoplasmic RQC pathway involves nuclear export mediator factor (NEMF)-dependent recruitment of the E3 ligase Listerin to ubiquitinate ribosome-stalled nascent polypeptides on the lysine residue for degradation. However, the quality control of ribosome-stalled nuclear-encoded mitochondrial nascent polypeptides remains elusive, as these peptides can be partially imported into mitochondria through translocons, restricting accessibility to the lysine by Listerin. Here, we identify a Listerin-independent organelle-specific mitochondrial RQC pathway that acts on NEMF-mediated carboxy-terminal poly-alanine modification. In the pathway, mitochondrial proteins carrying C-end poly-Ala tails are recognized by the cytosolic E3 ligase Pirh2 and the ClpXP protease in the mitochondria, which coordinately clear ribosome-stalled mitochondrial nascent polypeptides. Defects in this elimination pathway result in NEMF-mediated aggregates and mitochondrial integrity failure, thus providing a potential molecular mechanism of the RQC pathway in mitochondrial-associated human diseases.

Keywords:  CP: Microbiology; CP: Molecular biology; ClpXP; Listerin; NEMF; Pirh2; mitochondrion

DOI:  https://doi.org/10.1016/j.celrep.2024.113860
Zhonghua Wei Zhong Bing Ji Jiu Yi Xue. 2024 Jan;36(1): 93-97

[New research direction of organ dysfunction caused by hemorrhagic shock: mechanisms of mitochondrial quality control].

Zheng Zhang, Hongjie Duan, Jiake Chai, Xiaofang Zou, Shaofang Han, Hailiang Bai, Yufang Zhang, Huiting Yun, Ran Sun.

Hemorrhagic shock (HS) is one of the leading causes of death among young adults worldwide. Multiple organ dysfunction in HS is caused by an imbalance between tissue oxygen supply and demand, which is closely related to the poor prognosis of patient. Mitochondrial dysfunction is one of the key mechanisms contributing to multiple organ dysfunction in HS, while mitochondrial quality control regulates mitochondrial function through a series of processes, including mitochondrial biogenesis, mitochondrial dynamics, mitophagy, mitochondrial-derived vesicles, and mitochondrial protein homeostasis. Modulating mitochondrial quality control can improve organ dysfunction. This review aims to summarize the effects of mitochondrial dysfunction on organ function in HS and discuss the potential mechanisms of mitochondrial quality control, providing insights into the injury mechanisms underlying HS and guiding clinical management.

DOI: https://doi.org/10.3760/cma.j.cn121430-20230711-00510
Trends Biochem Sci. 2024 Feb 23. pii: S0968-0004(24)00031-8. [Epub ahead of print]

Mitochondria in disease: changes in shapes and dynamics.

Brenita C Jenkins, Kit Neikirk, Prasanna Katti, Steven M Claypool, Annet Kirabo, Melanie R McReynolds, Antentor Hinton.

  Mitochondrial structure often determines the function of these highly dynamic, multifunctional, eukaryotic organelles, which are essential for maintaining cellular health. The dynamic nature of mitochondria is apparent in descriptions of different mitochondrial shapes [e.g., donuts, megamitochondria (MGs), and nanotunnels] and crista dynamics. This review explores the significance of dynamic alterations in mitochondrial morphology and regulators of mitochondrial and cristae shape. We focus on studies across tissue types and also describe new microscopy techniques for detecting mitochondrial morphologies both in vivo and in vitro that can improve understanding of mitochondrial structure. We highlight the potential therapeutic benefits of regulating mitochondrial morphology and discuss prospective avenues to restore mitochondrial bioenergetics to manage diseases related to mitochondrial dysfunction.

Keywords:  clinical diagnostics; contact sites; cristae dynamics; microscopy; mitochondrial morphology; mitochondrial shapes

DOI:  https://doi.org/10.1016/j.tibs.2024.01.011
iScience. 2024 Mar 15. 27(3): 109164

Optic atrophy 1 mediates muscle differentiation by promoting a metabolic switch via the supercomplex assembly factor SCAF1.

Matthew Triolo, Nicole Baker, Soniya Agarwal, Nikita Larionov, Tina Podinić, Mireille Khacho.

  Myogenic differentiation is integral for the regeneration of skeletal muscle following tissue damage. Though high-energy post-mitotic muscle relies predominantly on mitochondrial respiration, the importance of mitochondrial remodeling in enabling muscle differentiation and the players involved are not fully known. Here we show that the mitochondrial fusion protein OPA1 is essential for muscle differentiation. Our study demonstrates that OPA1 loss or inhibition, through genetic and pharmacological means, abolishes in vivo muscle regeneration and in vitro myotube formation. We show that both the inhibition and genetic deletion of OPA1 prevent the early onset metabolic switch required to drive myoblast differentiation. In addition, we observe an OPA1-dependent upregulation of the supercomplex assembly factor, SCAF1, at the onset of differentiation. Importantly, preventing the upregulation of SCAF1, through OPA1 loss or siRNA-mediated SCAF1 knockdown, impairs metabolic reprogramming and muscle differentiation. These findings reveal the integral role of OPA1 and mitochondrial reprogramming at the onset of myogenic differentiation.

Keywords:  Molecular biology; Physiology

DOI:  https://doi.org/10.1016/j.isci.2024.109164
J Physiol. 2024 Mar 01.

Reorganization of mitochondria-organelle interactions during postnatal development in skeletal muscle.

Yuho Kim, Hailey A Parry, T Bradley Willingham, Greg Alspaugh, Eric Lindberg, Christian A Combs, Jay R Knutson, Christopher K E Bleck, Brian Glancy.

  Skeletal muscle cellular development requires the integrated assembly of mitochondria and other organelles adjacent to the sarcomere in support of muscle contractile performance. However, it remains unclear how interactions among organelles and with the sarcomere relates to the development of muscle cell function. Here, we combine 3D volume electron microscopy, proteomic analyses, and live cell functional imaging to investigate the postnatal reorganization of mitochondria-organelle interactions in skeletal muscle. We show that while mitochondrial networks are disorganized and loosely associated with the contractile apparatus at birth, contact sites among mitochondria, lipid droplets and the sarcoplasmic reticulum are highly abundant in neonatal muscles. The maturation process is characterized by a transition to highly organized mitochondrial networks wrapped tightly around the muscle sarcomere but also to less frequent interactions with both lipid droplets and the sarcoplasmic reticulum. Concomitantly, expression of proteins involved in mitochondria-organelle membrane contact sites decreases during postnatal development in tandem with a decrease in abundance of proteins associated with sarcomere assembly despite an overall increase in contractile protein abundance. Functionally, parallel measures of mitochondrial membrane potential, NADH redox status, and NADH flux within intact cells revealed that mitochondria in adult skeletal muscle fibres maintain a more activated electron transport chain compared with neonatal muscle mitochondria. These data demonstrate a developmental redesign reflecting a shift from muscle cell assembly and frequent inter-organelle communication toward a muscle fibre with mitochondrial structure, interactions, composition and function specialized to support contractile function. KEY POINTS: Mitochondrial network organization is remodelled during skeletal muscle postnatal development. The mitochondrial outer membrane is in frequent contact with other organelles at birth and transitions to more close associations with the contractile apparatus in mature muscles. Mitochondrial energy metabolism becomes more activated during postnatal development. Understanding the developmental redesign process within skeletal muscle cells may help pinpoint specific areas of deficit in muscles with developmental disorders.

Keywords:  3D mitochondrial structure; functional cellular imaging; organelle interactions; postnatal muscle development; volume electron microscopy

DOI:  https://doi.org/10.1113/JP285014
Inflamm Res. 2024 Feb 27.

SS-31 inhibits mtDNA-cGAS-STING signaling to improve POCD by activating mitophagy in aged mice.

Yelong Ji, Yuanyuan Ma, Yimei Ma, Ying Wang, Xining Zhao, Danfeng Jin, Li Xu, Shengjin Ge.

  BACKGROUND: Neuroinflammation is crucial in the development of postoperative cognitive dysfunction (POCD), and microglial activation is an active participant in this process. SS-31, a mitochondrion-targeted antioxidant, is widely regarded as a potential drug for neurodegenerative diseases and inflammatory diseases. In this study, we sought to explore whether SS-31 plays a neuroprotective role and the underlying mechanism.METHODS: Internal fixation of tibial fracture was performed in 18-month-old mice to induce surgery-associated neurocognitive dysfunction. LPS was administrated to BV2 cells to induce neuroinflammation. Neurobehavioral deficits, hippocampal injury, protein expression, mitophagy level and cell state were evaluated after treatment with SS-31, PHB2 siRNA and an STING agonist.
RESULTS: Our study revealed that SS-31 interacted with PHB2 to activate mitophagy and improve neural damage in surgically aged mice, which was attributed to the reduced cGAS-STING pathway and M1 microglial polarization by decreased release of mitochondrial DNA (mtDNA) but not nuclear DNA (nDNA). In vitro, knockdown of PHB2 and an STING agonist abolished the protective effect of SS-31.
CONCLUSIONS: SS-31 conferred neuroprotection against POCD by promoting PHB2-mediated mitophagy activation to inhibit mtDNA release, which in turn suppressed the cGAS-STING pathway and M1 microglial polarization.

Keywords:  Mitophagy; PHB2; POCD; SS-31; cGAS–STING; mtDNA

DOI:  https://doi.org/10.1007/s00011-024-01860-1
Biomed Pharmacother. 2024 Feb 28. pii: S0753-3322(24)00221-X. [Epub ahead of print]173 116337

The Janus face of mitophagy in myocardial ischemia/reperfusion injury and recovery.

Jiaxin Deng, Qian Liu, Linxi Ye, Shuo Wang, Zhenyan Song, Mingyan Zhu, Fangfang Qiang, Yulin Zhou, Zhen Guo, Wei Zhang, Ting Chen.

  In myocardial ischemia/reperfusion injury (MIRI), moderate mitophagy is a protective or adaptive mechanism because of clearing defective mitochondria accumulates during MIRI. However, excessive mitophagy lead to an increase in defective mitochondria and ultimately exacerbate MIRI by causing overproduction or uncontrolled production of mitochondria. Phosphatase and tensin homolog (PTEN)-induced kinase 1 (Pink1), Parkin, FUN14 domain containing 1 (FUNDC1) and B-cell leukemia/lymphoma 2 (BCL-2)/adenovirus E1B19KD interaction protein 3 (BNIP3) are the main mechanistic regulators of mitophagy in MIRI. Pink1 and Parkin are mitochondrial surface proteins involved in the ubiquitin-dependent pathway, while BNIP3 and FUNDC1 are mitochondrial receptor proteins involved in the non-ubiquitin-dependent pathway, which play a crucial role in maintaining mitochondrial homeostasis and mitochondrial quality. These proteins can induce moderate mitophagy or inhibit excessive mitophagy to protect against MIRI but may also trigger excessive mitophagy or insufficient mitophagy, thereby worsening the condition. Understanding the actions of these mitophagy mechanistic proteins may provide valuable insights into the pathological mechanisms underlying MIRI development. Based on the above background, this article reviews the mechanism of mitophagy involved in MIRI through Pink1/Parkin pathway and the receptor mediated pathway led by FUNDC1 and BNIP3, as well as the related drug treatment, aim to provide effective strategies for the prevention and treatment of MIRI.

Keywords:  BNIP3; FUNDC1; Myocardial ischemia/reperfusion injury; Pink1/Parkin; The Janus face of mitophagy

DOI:  https://doi.org/10.1016/j.biopha.2024.116337
Mitochondrion. 2024 Feb 23. pii: S1567-7249(24)00013-8. [Epub ahead of print]76 101855

Mitochondrial stress in the spaceflight environment.

Agata M Rudolf, Wendy R Hood.

  Space is a challenging environment that deregulates individual homeostasis. The main external hazards associated with spaceflight include ionizing space radiation, microgravity, isolation and confinement, distance from Earth, and hostile environment. Characterizing the biological responses to spaceflight environment is essential to validate the health risks, and to develop effective protection strategies. Mitochondria energetics is a key mechanism underpinning many physiological, ecological and evolutionary processes. Moreover, mitochondrial stress can be considered one of the fundamental features of space travel. So, we attempt to synthesize key information regarding the extensive effects of spaceflight on mitochondria. In summary, mitochondria are affected by all of the five main hazards of spaceflight at multiple levels, including their morphology, respiratory function, protein, and genetics, in various tissues and organ systems. We emphasize that investigating mitochondrial biology in spaceflight conditions should become the central focus of research on the impacts of spaceflight on human health, as this approach will help resolve numerous challenges of space health and combat several health disorders associated with mitochondrial dysfunction.

Keywords:  Microgravity; Mitochondria; Oxidative stress; Radiation; Spaceflight

DOI:  https://doi.org/10.1016/j.mito.2024.101855
J Cell Physiol. 2024 Feb 28.

ATF4-dependent increase in mitochondrial-endoplasmic reticulum tethering following OPA1 deletion in skeletal muscle.

Antentor Hinton, Prasanna Katti, Margaret Mungai, Duane D Hall, Olha Koval, Jianqiang Shao, Zer Vue, Edgar Garza Lopez, Rahmati Rostami, Kit Neikirk, Jessica Ponce, Jennifer Streeter, Brandon Schickling, Serif Bacevac, Chad Grueter, Andrea Marshall, Heather K Beasley, Young Do Koo, Sue C Bodine, Nayeli G Reyes Nava, Anita M Quintana, Long-Sheng Song, Isabella M Grumbach, Renata O Pereira, Brian Glancy, E Dale Abel.

  Mitochondria and endoplasmic reticulum (ER) contact sites (MERCs) are protein- and lipid-enriched hubs that mediate interorganellar communication by contributing to the dynamic transfer of Ca2+ , lipid, and other metabolites between these organelles. Defective MERCs are associated with cellular oxidative stress, neurodegenerative disease, and cardiac and skeletal muscle pathology via mechanisms that are poorly understood. We previously demonstrated that skeletal muscle-specific knockdown (KD) of the mitochondrial fusion mediator optic atrophy 1 (OPA1) induced ER stress and correlated with an induction of Mitofusin-2, a known MERC protein. In the present study, we tested the hypothesis that Opa1 downregulation in skeletal muscle cells alters MERC formation by evaluating multiple myocyte systems, including from mice and Drosophila, and in primary myotubes. Our results revealed that OPA1 deficiency induced tighter and more frequent MERCs in concert with a greater abundance of MERC proteins involved in calcium exchange. Additionally, loss of OPA1 increased the expression of activating transcription factor 4 (ATF4), an integrated stress response (ISR) pathway effector. Reducing Atf4 expression prevented the OPA1-loss-induced tightening of MERC structures. OPA1 reduction was associated with decreased mitochondrial and sarcoplasmic reticulum, a specialized form of ER, calcium, which was reversed following ATF4 repression. These data suggest that mitochondrial stress, induced by OPA1 deficiency, regulates skeletal muscle MERC formation in an ATF4-dependent manner.

Keywords:  activating transcription factor 4; endoplasmic reticulum; integrated stress response; interorganelle communication; mitochondria

DOI:  https://doi.org/10.1002/jcp.31204
bioRxiv. 2024 Jan 29. pii: 2024.01.25.577217. [Epub ahead of print]

Genetic and bioinformatic analyses reveal transcriptional networks underlying dual genomic coordination of mitochondrial biogenesis.

Fan Zhang, Annie Lee, Anna Freitas, Jake Herb, Zongheng Wang, Snigdha Gupta, Zhe Chen, Hong Xu.

Mitochondrial genome encodes handful genes of respiratory chain complexes, whereas all the remaining mitochondrial proteins are encoded on the nuclear genome. However, the mechanisms coordinating these two genomes to control mitochondrial biogenesis remain largely unknown. To identify transcription circuits involved in these processes, we performed a candidate RNAi screen in developing eyes that had reduced mitochondrial DNA contents. We reasoned that impaired mitochondrial biogenesis would synergistically interact with mtDNA deficiency in disrupting tissue development. Over 638 transcription factors annotated in the fly genome, we identified 77 transcription factors that may be involved in mitochondrial genome maintenance and gene expression. Additional genetic and genomic analyses revealed that a novel transcription factor, CG1603, and its upstream factor YL-1 are essential for mitochondrial biogenesis. We constructed a regulator network among positive hits using the published CHIP-seq data. The network analysis revealed extensive connections, and complex hierarchical organization underlying the transcription regulation of mitochondrial biogenesis.

DOI: https://doi.org/10.1101/2024.01.25.577217
Autophagy. 2024 Feb 26.

Sodium butyrate ameliorates high glucose-suppressed neuronal mitophagy by restoring PRKN expression via inhibiting the RELA-HDAC8 complex.

Ji Hyeon Cho, Chang Woo Chae, Jae Ryong Lim, Young Hyun Jung, Su Jong Han, Jee Hyeon Yoon, Ji Yong Park, Ho Jae Han.

  Damaged mitochondria accumulation in diabetes is one of the main features that contribute to increased incidence of cognitive impairment by inducing apoptosis. Butyrate is a major metabolite produced by microbiota that has neuroprotective effects by regulating mitochondrial function. However, detailed mechanisms underlying how butyrate can regulate neuronal mitophagy remain unclear. Here, we examined the regulatory effects of sodium butyrate (NaB) on high glucose-induced mitophagy dysregulation, neuronal apoptosis, and cognitive impairment and its underlying mechanisms in human-induced pluripotent stem cell-derived neurons, SH-SY5Ys, and streptozotocin (STZ)-induced diabetic mice. In our results, diabetic mice showed gut-microbiota dysbiosis, especially a decreased number of butyrate-producing bacteria and reduced NaB plasma concentration. NaB ameliorated high glucose-induced neuronal mitochondrial dysfunction by recovering PRKN/Parkin-mediated mitophagy. High glucose-induced reactive oxygen species (ROS) and -inhibited PRKAA/AMPKα stimulated the RELA/p65-HDAC8 complex, which downregulated PRKN protein expression by binding to the PRKN promoter region. NaB restored PRKN expression by blocking RELA nuclear translocation and directly inhibiting HDAC8 in the nucleus. In addition, HDAC8 overexpression inhibited the positive effect of NaB on high glucose-induced mitophagy dysfunction and neuronal apoptosis. Oral administration of NaB improved cognitive impairment in diabetic mice by restoring mitophagy in the hippocampus. Taken together, NaB ameliorates neuronal mitophagy through PRKN restoration by inhibiting RELA-HDAC8 complexes, suggesting that NaB is an important substance for protecting neuronal apoptosis in diabetes-associated cognitive impairment.

Keywords:  Autophagy; Scfas; diabetes; gut-brain axis; mitochondria; neuronal apoptosis

DOI:  https://doi.org/10.1080/15548627.2024.2323785
Zhongguo Zhong Yao Za Zhi. 2024 Jan;49(1): 46-54

[Role of mitophagy in diabetes mellitus and its complications and traditional Chinese medicine intervention: a review].

Li-Hui Fan, Xia Yang, Zhi-Gang Wang.

  Diabetes mellitus(DM) is a chronic endocrine disease characterized by hyperglycemia caused by carbohydrate or lipid metabolism disorders or insulin dysfunction. Hyperglycemia and long-term metabolic disorders in DM can damage tissues and organs throughout the body, leading to serious complications. Mitochondrial autophagy(mitophagy) is an important mitochondrial quality control process in cells and a special autophagy phenomenon, in which damaged or redundant mitochondria can be selectively removed by autophagic lysosome, which is crucial to maintain cell stability and survival under stress. Studies have confirmed that changes in autophagy play a role in the development and control of DM and its complications. Mitophagy has become a research hotspot in recent years and it is closely associated with the pathogenesis of a variety of diseases. Substantial evidence suggests that mitophagy plays a crucial role in regulating the metabolic homeostasis in the case of DM and its complications. Because the destructive great vessel complications and microvascular complications cause increased mortality, blindness, renal failure, and declined quality of life of DM patients, it is urgent to develop targeted therapies to intervene in DM and its complications. Traditional Chinese medicine(TCM), with a multi-component, multi-target, and multi-level action manner, can prevent the development of drug resistance and have significant therapeutic effects in the prevention and treatment of DM and its complications. Therefore, exploring the mechanisms of TCM in regulating mito-phagy may become a new method for treating DM and its complications. With focus on the roles and mechanisms of mitophagy in DM and its complications, this paper summarizes and prospects the research on the treatment of DM and its complications with TCM via re-gulating mitophagy, aiming to provide new ideas for the clinical practice.

Keywords:  diabetes mellitus; diabetic complications; mechanism; mitophagy; traditional Chinese medicine

DOI:  https://doi.org/10.19540/j.cnki.cjcmm.20230809.702
Commun Biol. 2024 Feb 29. 7(1): 245

Parkin inhibits proliferation and migration of bladder cancer via ubiquitinating Catalase.

Renjie Zhang, Wenyu Jiang, Gang Wang, Yi Zhang, Wei Liu, Mingxing Li, Jingtian Yu, Xin Yan, Fenfang Zhou, Wenzhi Du, Kaiyu Qian, Yu Xiao, Tongzu Liu, Lingao Ju, Xinghuan Wang.

PRKN is a key gene involved in mitophagy in Parkinson's disease. However, recent studies have demonstrated that it also plays a role in the development and metastasis of several types of cancers, both in a mitophagy-dependent and mitophagy-independent manner. Despite this, the potential effects and underlying mechanisms of Parkin on bladder cancer (BLCA) remain unknown. Therefore, in this study, we investigated the expression of Parkin in various BLCA cohorts derived from human. Here we show that PRKN expression was low and that PRKN acts as a tumor suppressor by inhibiting the proliferation and migration of BLCA cells in a mitophagy-independent manner. We further identified Catalase as a binding partner and substrate of Parkin, which is an important antioxidant enzyme that regulates intracellular ROS levels during cancer progression. Our data showed that knockdown of CAT led to increased intracellular ROS levels, which suppressed cell proliferation and migration. Conversely, upregulation of Catalase decreased intracellular ROS levels, promoting cell growth and migration. Importantly, we found that Parkin upregulation partially restored these effects. Moreover, we discovered that USP30, a known Parkin substrate, could deubiquitinate and stabilize Catalase. Overall, our study reveals a novel function of Parkin and identifies a potential therapeutic target in BLCA.

DOI: https://doi.org/10.1038/s42003-024-05935-x
J Obstet Gynaecol Res. 2024 Feb 28.

Role of the mitophagy-apoptosis axis in the pathogenesis of polycystic ovarian syndrome.

Hiroshi Kobayashi, Hiroshi Shigetomi, Sho Matsubara, Chiharu Yoshimoto, Shogo Imanaka.

  AIM: Polycystic ovary syndrome (PCOS) is a common endocrine disorder characterized by menstrual irregularities, androgen excess, and polycystic ovarian morphology, but its pathogenesis remains largely unknown. This review focuses on how androgen excess influences the molecular basis of energy metabolism, mitochondrial function, and mitophagy in granulosa cells and oocytes, summarizes our current understanding of the pathogenesis of PCOS, and discuss perspectives on future research directions.METHODS: A search of PubMed and Google Scholar databases were used to identify relevant studies for this narrative literature review.
RESULTS: Female offspring born of pregnant animals exposed to androgens recapitulates the PCOS phenotype. Abnormal mitochondrial morphology, altered expression of genes related to glycolysis, mitochondrial biogenesis, fission/fusion dynamics, and mitophagy have been identified in PCOS patients and androgenic animal models. Androgen excess causes uncoupling of the electron transport chain and depletion of the cellular adenosine 5'-triphosphate pool, indicating further impairment of mitochondrial function. A shift toward mitochondrial fission restores mitochondrial quality control mechanisms. However, prolonged mitochondrial fission disrupts autophagy/mitophagy induction due to loss of compensatory reserve for mitochondrial biogenesis. Disruption of compensatory mechanisms that mediate the quality control switch from mitophagy to apoptosis may cause a disease phenotype. Furthermore, genetic predisposition, altered expression of genes related to glycolysis and oxidative phosphorylation, or a combination of these factors may also contribute to the development of PCOS.
CONCLUSION: In conclusion, fetuses exposed to a hyperandrogenemic intrauterine environment may cause the PCOS phenotype possibly through disruption of the compensatory regulation of the mitophagy-apoptosis axis.

Keywords:  androgen; anti-Müllerian hormone; compensatory mechanism; mitochondrial function; mitophagy; polycystic ovarian syndrome

DOI:  https://doi.org/10.1111/jog.15916
Int J Gen Med. 2024 ;17 639-650

Bioinformatics Analysis and Experimental Validation of Mitochondrial Autophagy Genes in Knee Osteoarthritis.

Kuihan Tang, Li Sun, Long Chen, Xiaobo Feng, Jiarui Wu, Hao Guo, Yong Zheng.

  Background: Mitochondrial autophagy is closely related to the pathogenesis of osteoarthritis, In order to explore the role of mitochondrial autophagy related genes in knee osteoarthritis (KOA) and its molecular mechanism.Methods: KOA-related transcriptome data were extracted from the Gene Expression Omnibus (GEO) database. Differentially expressed mitochondrial autophagy gene (DEMGs) were screened in patients with KOA by differential expression analysis. The STRING website was used to construct a protein-protein interaction (PPI) network among DEMGs. Molecular complex detection (MCODE) method in Cytoscape software was performed to identify hub DEMGs. Support vector machine recursive feature elimination (SVM-RFE) method was used to construct the hub DEMG diagnosis model. Genes with diagnostic value were identified as biomarkers by plotting receiver operating characteristic (ROC) curves and Expression validation. CIBERSORT algorithm was used to calculate the proportion of 22 immune cells in each sample in the GSE114007 dataset. Finally, biomarker expression was verified by qPCR.
Results: A total of 15 DEMGs were obtained and enrichment analyses showed that these DEMG strains were mainly enriched in the mitophagy-animal, shigellosis, autophagy-animal and FoxO signal pathways. The PPI network unveiled 13 DEMGs with interactions. In addition, 8 hub DEMGs (ULK1, CALCOCO2, MAP1LC3B, BNIP3L, GABARAPL1, BNIP3, FKBP8 and FOXO3) were obtained for KOA. And 5 model DEMGs (BNIP3L, BNIP3, MAP1LC3B, ULK1 and FOXO3) were screened. The ROC curves revealed that BNIP3 and FOXO3 has strong diagnostic value in these models of DEMG. Immune-infiltration and correlation analysis showed that BNIP3 and FOXO3 were significantly correlated with three different immune cells, including primary B cells, M0 macrophage and M2 macrophage. The cartilage tissue samples qPCR verification results show that FOXO3 and BNIP3 were all down-regulated in KOA (p < 0.01), and the validation results are consistent with the above analysis.
Conclusion: BNIP3 and FOXO3 have been identified as biomarkers for the diagnosis of KOA, which might supply a new insight for the pathogenesis and treatment of KOA.

Keywords:  Gene Expression Omnibus; bioinformatics analysis; biomarkers; diagnostic; immune infiltration

DOI:  https://doi.org/10.2147/IJGM.S444847
iScience. 2024 Mar 15. 27(3): 109189

Chemical inhibition of phosphatidylcholine biogenesis reveals its role in mitochondrial division.

Hiroya Shiino, Shinya Tashiro, Michiko Hashimoto, Yuki Sakata, Takamitsu Hosoya, Toshiya Endo, Hirotatsu Kojima, Yasushi Tamura.

  Phospholipids are major components of biological membranes and play structural and regulatory roles in various biological processes. To determine the biological significance of phospholipids, the use of chemical inhibitors of phospholipid metabolism offers an effective approach; however, the availability of such compounds is limited. In this study, we performed a chemical-genetic screening using yeast and identified small molecules capable of inhibiting phosphatidylcholine (PC) biogenesis, which we designated PC inhibitors 1, 2, 3, and 4 (PCiB-1, 2, 3, and 4). Biochemical analyses indicated that PCiB-2, 3, and 4 inhibited the phosphatidylethanolamine (PE) methyltransferase activity of Cho2, whereas PCiB-1 may inhibit PE transport from mitochondria to the endoplasmic reticulum (ER). Interestingly, we found that PCiB treatment resulted in mitochondrial fragmentation, which was suppressed by expression of a dominant-negative mutant of the mitochondrial division factor Dnm1. These results provide evidence that normal PC biogenesis is important for the regulation of mitochondrial division.

Keywords:  Biochemistry; Biological sciences; Cell biology

DOI:  https://doi.org/10.1016/j.isci.2024.109189