bims-mitdyn Biomed News
on Mitochondrial dynamics: mechanisms
Issue of 2021–04–25
fiveteen papers selected by
Edmond Chan, Queen’s University, School of Medicine
  1. Mitochondrial NADP(H) generation is essential for proline biosynthesis.
  2. NKX3.1 localization to mitochondria suppresses prostate cancer initiation.
  3. Interleukin-33 regulates metabolic reprogramming of the retinal pigment epithelium in response to immune stressors.
  4. Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
  5. Optic atrophy-associated TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I.
  6. The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs.
  7. VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
  8. SLC22A14 is a mitochondrial riboflavin transporter required for sperm oxidative phosphorylation and male fertility.
  9. SPATA33 functions as a mitophagy receptor in mammalian germline.
  10. Mechanistic connections between mitochondrial biology and regulated cell death.
  11. ALS/FTD mutations in UBQLN2 are linked to mitochondrial dysfunction through loss-of-function in mitochondrial protein import.
  12. MitopatHs: a new logically-framed tool for visualizing multiple mitochondrial pathways.
  13. Assembly and Cryo-EM structure determination of yeast mitochondrial RNA polymerase initiation complex intermediates.
  14. The role of SQSTM1 (p62) in mitochondrial function and clearance in human cortical neurons.
  15. The effect of mitochondrial calcium uniporter and cyclophilin D knockout on resistance of brain mitochondria to Ca2+-induced damage.
  1. Science. 2021 Apr 22. pii: eabd5491. [Epub ahead of print]
    Mitochondrial NADP(H) generation is essential for proline biosynthesis.
    Jiajun Zhu, Simon Schwörer, Mirela Berisa, Yeon Ju Kyung, Keun Woo Ryu, Junmei Yi, Xuejun Jiang, Justin R Cross, Craig B Thompson.
      The coenzyme nicotinamide adenine dinucleotide phosphate (NADP+) and its reduced form (NADPH) regulate reductive metabolism in a subcellularly compartmentalized manner. Mitochondrial NADP(H) production depends on the phosphorylation of NAD(H) by NAD kinase 2 (NADK2). Deletion of NADK2 in human cell lines did not alter mitochondrial folate pathway activity, tricarboxylic acid cycle activity, or mitochondrial oxidative stress, but led to impaired cell proliferation in minimal medium. This growth defect was rescued by proline supplementation. NADK2-mediated mitochondrial NADP(H) generation was required for the reduction of glutamate and hence proline biosynthesis. Furthermore, mitochondrial NADP(H) availability determined the production of collagen proteins by cells of mesenchymal lineage. Thus, a primary function of the mitochondrial NADP(H) pool is to support proline biosynthesis for use in cytosolic protein synthesis.
    DOI:  https://doi.org/10.1126/science.abd5491
  2. Cancer Discov. 2021 Apr 23. pii: candisc.1765.2020. [Epub ahead of print]
    NKX3.1 localization to mitochondria suppresses prostate cancer initiation.
    Alexandros Papachristodoulou, Antonio Rodriguez-Calero, Sukanya Panja, Elizabeth Margolskee, Renu K Virk, Teresa A Milner, Luis Pina Martina, Jaime Y Kim, Matteo Di Bernardo, Alanna B Williams, Elvis A Maliza, Joseph M Caputo, Christopher Haas, Vinson Wang, Guarionex Joel De Castro, Sven Wenske, Hanina Hibshoosh, James M McKiernan, Michael M Shen, Mark A Rubin, Antonina Mitrofanova, Aditya Dutta, Cory Abate-Shen.
      Mitochondria provide the front-line of defense against the tumor-promoting effects of oxidative stress. Here we show that the prostate-specific homeoprotein, NKX3.1, suppresses prostate cancer initiation by protecting mitochondria from oxidative stress. Integrating analyses of genetically-engineered mouse models, human prostate cancer cells, and human prostate cancer organotypic cultures, we find that, in response to oxidative stress, NKX3.1 is imported to mitochondria via the chaperone protein, HSPA9, where it regulates transcription of mitochondrial-encoded electron transport chain (ETC) genes, thereby restoring oxidative phosphorylation and preventing cancer initiation. Germline polymorphisms of NKX3.1 associated with increased cancer risk fail to protect from oxidative stress or suppress tumorigenicity. Low expression levels of NKX3.1 combined with low expression of mitochondrial ETC genes are associated with adverse clinical outcome, whereas high levels of mitochondrial NKX3.1 protein are associated with favorable outcome. This work reveals an extranuclear role for NKX3.1 in suppression of prostate cancer by protecting mitochondrial function.
    DOI:  https://doi.org/10.1158/2159-8290.CD-20-1765
  3. JCI Insight. 2021 Apr 22. pii: 129429. [Epub ahead of print]6(8):
    Interleukin-33 regulates metabolic reprogramming of the retinal pigment epithelium in response to immune stressors.
    Louis M Scott, Emma E Vincent, Natalie Hudson, Chris Neal, Nicholas Jones, Ed Lavelle, Matthew Campbell, Andrew P Halestrap, Andrew D Dick, Sofia Theodoropoulou.
      It remains unresolved how retinal pigment epithelial cell metabolism is regulated following immune activation to maintain retinal homeostasis and retinal function. We exposed retinal pigment epithelium (RPE) to several stress signals, particularly Toll-like receptor stimulation, and uncovered an ability of RPE to adapt their metabolic preference on aerobic glycolysis or oxidative glucose metabolism in response to different immune stimuli. We have identified interleukin-33 (IL-33) as a key metabolic checkpoint that antagonizes the Warburg effect to ensure the functional stability of the RPE. The identification of IL-33 as a key regulator of mitochondrial metabolism suggests roles for the cytokine that go beyond its extracellular "alarmin" activities. IL-33 exerts control over mitochondrial respiration in RPE by facilitating oxidative pyruvate catabolism. We have also revealed that in the absence of IL-33, mitochondrial function declined and resultant bioenergetic switching was aligned with altered mitochondrial morphology. Our data not only shed new light on the molecular pathway of activation of mitochondrial respiration in RPE in response to immune stressors but also uncover a potentially novel role of nuclear intrinsic IL-33 as a metabolic checkpoint regulator.
    Keywords:  Glucose metabolism; Metabolism; Mitochondria; Ophthalmology; Retinopathy
    DOI:  https://doi.org/10.1172/jci.insight.129429
  4. Mol Cell. 2021 Apr 09. pii: S1097-2765(21)00263-X. [Epub ahead of print]
    Structural basis of translation termination, rescue, and recycling in mammalian mitochondria.
    Eva Kummer, Katharina Noel Schubert, Tanja Schoenhut, Alain Scaiola, Nenad Ban.
      The mitochondrial translation system originates from a bacterial ancestor but has substantially diverged in the course of evolution. Here, we use single-particle cryo-electron microscopy (cryo-EM) as a screening tool to identify mitochondrial translation termination mechanisms and to describe them in molecular detail. We show how mitochondrial release factor 1a releases the nascent chain from the ribosome when it encounters the canonical stop codons UAA and UAG. Furthermore, we define how the peptidyl-tRNA hydrolase ICT1 acts as a rescue factor on mitoribosomes that have stalled on truncated messages to recover them for protein synthesis. Finally, we present structural models detailing the process of mitochondrial ribosome recycling to explain how a dedicated elongation factor, mitochondrial EFG2 (mtEFG2), has specialized for cooperation with the mitochondrial ribosome recycling factor to dissociate the mitoribosomal subunits at the end of the translation process.
    Keywords:  ICT1; cryo-EM; mitochondria; mtEFG2; mtRF1a; mtRRF; recycling; ribosome; termination; translation
    DOI:  https://doi.org/10.1016/j.molcel.2021.03.042
  5. Proc Natl Acad Sci U S A. 2021 Apr 27. pii: e2019665118. [Epub ahead of print]118(17):
    Optic atrophy-associated TMEM126A is an assembly factor for the ND4-module of mitochondrial complex I.
    Luke E Formosa, Boris Reljic, Alice J Sharpe, Daniella H Hock, Linden Muellner-Wong, David A Stroud, Michael T Ryan.
      Mitochondrial disease is a debilitating condition with a diverse genetic etiology. Here, we report that TMEM126A, a protein that is mutated in patients with autosomal-recessive optic atrophy, participates directly in the assembly of mitochondrial complex I. Using a combination of genome editing, interaction studies, and quantitative proteomics, we find that loss of TMEM126A results in an isolated complex I deficiency and that TMEM126A interacts with a number of complex I subunits and assembly factors. Pulse-labeling interaction studies reveal that TMEM126A associates with the newly synthesized mitochondrial DNA (mtDNA)-encoded ND4 subunit of complex I. Our findings indicate that TMEM126A is involved in the assembly of the ND4 distal membrane module of complex I. In addition, we find that the function of TMEM126A is distinct from its paralogue TMEM126B, which acts in assembly of the ND2-module of complex I.
    Keywords:  complex I; membrane protein; mitochondria; optic atrophy; oxidative phosphorylation
    DOI:  https://doi.org/10.1073/pnas.2019665118
  6. Proc Natl Acad Sci U S A. 2021 Apr 13. pii: e2009329118. [Epub ahead of print]118(15):
    The pentatricopeptide repeat protein Rmd9 recognizes the dodecameric element in the 3'-UTRs of yeast mitochondrial mRNAs.
    Hauke S Hillen, Dmitriy A Markov, Ireneusz D Wojtas, Katharina B Hofmann, Michael Lidschreiber, Andrew T Cowan, Julia L Jones, Dmitry Temiakov, Patrick Cramer, Michael Anikin.
      Stabilization of messenger RNA is an important step in posttranscriptional gene regulation. In the nucleus and cytoplasm of eukaryotic cells it is generally achieved by 5' capping and 3' polyadenylation, whereas additional mechanisms exist in bacteria and organelles. The mitochondrial mRNAs in the yeast Saccharomyces cerevisiae comprise a dodecamer sequence element that confers RNA stability and 3'-end processing via an unknown mechanism. Here, we isolated the protein that binds the dodecamer and identified it as Rmd9, a factor that is known to stabilize yeast mitochondrial RNA. We show that Rmd9 associates with mRNA around dodecamer elements in vivo and that recombinant Rmd9 specifically binds the element in vitro. The crystal structure of Rmd9 bound to its dodecamer target reveals that Rmd9 belongs to the family of pentatricopeptide (PPR) proteins and uses a previously unobserved mode of specific RNA recognition. Rmd9 protects RNA from degradation by the mitochondrial 3'-exoribonuclease complex mtEXO in vitro, indicating that recognition and binding of the dodecamer element by Rmd9 confers stability to yeast mitochondrial mRNAs.
    Keywords:  PAR-CLIP; PPR proteins; gene expression; mitochondria; protein-RNA complex
    DOI:  https://doi.org/10.1073/pnas.2009329118
  7. J Cell Biol. 2021 May 03. pii: e202010004. [Epub ahead of print]220(5):
    VPS13D bridges the ER to mitochondria and peroxisomes via Miro.
    Andrés Guillén-Samander, Marianna Leonzino, Michael G Hanna, Ni Tang, Hongying Shen, Pietro De Camilli.
      Mitochondria, which are excluded from the secretory pathway, depend on lipid transport proteins for their lipid supply from the ER, where most lipids are synthesized. In yeast, the outer mitochondrial membrane GTPase Gem1 is an accessory factor of ERMES, an ER-mitochondria tethering complex that contains lipid transport domains and that functions, partially redundantly with Vps13, in lipid transfer between the two organelles. In metazoa, where VPS13, but not ERMES, is present, the Gem1 orthologue Miro was linked to mitochondrial dynamics but not to lipid transport. Here we show that Miro, including its peroxisome-enriched splice variant, recruits the lipid transport protein VPS13D, which in turn binds the ER in a VAP-dependent way and thus could provide a lipid conduit between the ER and mitochondria. These findings reveal a so far missing link between function(s) of Gem1/Miro in yeast and higher eukaryotes, where Miro is a Parkin substrate, with potential implications for Parkinson's disease pathogenesis.
    DOI:  https://doi.org/10.1083/jcb.202010004
  8. Cell Rep. 2021 Apr 20. pii: S2211-1247(21)00339-9. [Epub ahead of print]35(3): 109025
    SLC22A14 is a mitochondrial riboflavin transporter required for sperm oxidative phosphorylation and male fertility.
    Wenhua Kuang, Jie Zhang, Zhou Lan, R N V Krishna Deepak, Chao Liu, Zhilong Ma, Lili Cheng, Xinbin Zhao, Xianbin Meng, Weihua Wang, Xueying Wang, Lina Xu, Yupei Jiao, Qi Luo, Ziyi Meng, Kehkooi Kee, Xiaohui Liu, Haiteng Deng, Wei Li, Hao Fan, Ligong Chen.
      Ablation of Slc22a14 causes male infertility in mice, but the underlying mechanisms remain unknown. Here, we show that SLC22A14 is a riboflavin transporter localized at the inner mitochondrial membrane of the spermatozoa mid-piece and show by genetic, biochemical, multi-omic, and nutritional evidence that riboflavin transport deficiency suppresses the oxidative phosphorylation and reprograms spermatozoa energy metabolism by disrupting flavoenzyme functions. Specifically, we find that fatty acid β-oxidation (FAO) is defective with significantly reduced levels of acyl-carnitines and metabolites from the TCA cycle (the citric acid cycle) but accumulated triglycerides and free fatty acids in Slc22a14 knockout spermatozoa. We demonstrate that Slc22a14-mediated FAO is essential for spermatozoa energy generation and motility. Furthermore, sperm from wild-type mice treated with a riboflavin-deficient diet mimics those in Slc22a14 knockout mice, confirming that an altered riboflavin level causes spermatozoa morphological and bioenergetic defects. Beyond substantially advancing our understanding of spermatozoa energy metabolism, our study provides an attractive target for the development of male contraceptives.
    Keywords:  SLC22A14 transporter; energy metabolism; fatty acid β-oxidation; male infertility; riboflavin
    DOI:  https://doi.org/10.1016/j.celrep.2021.109025
  9. Autophagy. 2021 Apr 05. 1-3
    SPATA33 functions as a mitophagy receptor in mammalian germline.
    Xu Xu, Ying Zhang, Hanhua Cheng, Rongjia Zhou.
      Mitophagy is an essential mechanism in maintaining cellular homeostasis, in which damaged and superfluous mitochondria are selectively degraded by the autophagy-lysosome pathway. Our recent study revealed that SPATA33 functions as a novel receptor for mitophagy in the priming of mitochondria for degradation in male germline cells. SPATA33 directly mediates the interaction of the outer mitochondrial membrane protein VDAC2 with the autophagy machinery component ATG16L1 during mitophagy. Upon starvation induction, SPATA33 can promote mitophagy as an autophagy receptor. Thus, SPATA33 confers cargo selectivity during mitophagy in germline cells. These findings provide new insights into selective autophagy and mitochondrial homeostasis.
    Keywords:  Autophagy; SPATA33; mammals; mitochondria; spermatogenesis
    DOI:  https://doi.org/10.1080/15548627.2021.1909836
  10. Dev Cell. 2021 Apr 16. pii: S1534-5807(21)00308-7. [Epub ahead of print]
    Mechanistic connections between mitochondrial biology and regulated cell death.
    Jerry Edward Chipuk, Jarvier N Mohammed, Jesse D Gelles, Yiyang Chen.
      The ancient, dynamic, and multifaceted functions of the mitochondrial network are essential for organismal homeostasis and contribute to numerous human diseases. As central hubs for metabolism, ion transport, and multiple macromolecular synthesis pathways, mitochondria establish and control extensive signaling networks to ensure cellular survival. In this review, we explore how these same mitochondrial functions also participate in the control of regulated cell death (RCD). We discuss the complementary essential mitochondrial functions as compartments that participate in the production and presentation of key molecules and platforms that actively enable, initiate, and execute RCD.
    Keywords:  cell biology; mitochondrial function; programed cell death; regulated cell death; signal transduction; stress signaling
    DOI:  https://doi.org/10.1016/j.devcel.2021.03.033
  11. Hum Mol Genet. 2021 Apr 22. pii: ddab116. [Epub ahead of print]
    ALS/FTD mutations in UBQLN2 are linked to mitochondrial dysfunction through loss-of-function in mitochondrial protein import.
    Brian C Lin, Trong H Phung, Nicole R Higgins, Jessie E Greenslade, Miguel A Prado, Daniel Finley, Mariusz Karbowski, Brian M Polster, Mervyn J Monteiro.
      UBQLN2 mutations cause amyotrophic lateral sclerosis (ALS) with frontotemporal dementia (FTD), but the pathogenic mechanisms by which they cause disease remain unclear. Proteomic profiling identified 'mitochondrial proteins' as comprising the largest category of protein changes in the spinal cord (SC) of the P497S UBQLN2 mouse model of ALS/FTD. Immunoblots confirmed P497S animals have global changes in proteins predictive of a severe decline in mitochondrial health, including oxidative phosphorylation (OXPHOS), mitochondrial protein import, and network dynamics. Functional studies confirmed mitochondria purified from the SC of P497S animals have age-dependent decline in nearly all steps of OXPHOS. Mitochondria cristae deformities were evident in spinal motor neurons of aged P497S animals. Knockout (KO) of UBQLN2 in HeLa cells resulted in changes in mitochondrial proteins and OXPHOS activity similar to those seen in the SC. KO of UBQLN2 also compromised targeting and processing of the mitochondrial import factor, TIMM44, resulting in accumulation in abnormal foci. The functional OXPHOS deficits and TIMM44 targeting defects were rescued by re-expression of WT UBQLN2 but not by ALS/FTD mutant UBQLN2 proteins. In-vitro binding assays revealed ALS/FTD mutant UBQLN2 proteins bind weaker with TIMM44 than WT UBQLN2 protein, suggesting that the loss of UBQLN2 binding may underlie the import and/or delivery defect of TIMM44 to mitochondria. Our studies indicate a potential key pathogenic disturbance in mitochondrial health caused by UBQLN2 mutations.
    DOI:  https://doi.org/10.1093/hmg/ddab116
  12. iScience. 2021 Apr 23. 24(4): 102324
    MitopatHs: a new logically-framed tool for visualizing multiple mitochondrial pathways.
    Saverio Marchi, Marco Zanella, Paolo Pinton, Silvia Crafa, Giovanni Boniolo.
      Mitochondria are key organelles inside the cell that house a wide range of molecular pathways involved in energy metabolism, ions homeostasis, and cell death. Several databases characterize the different mitochondrial aspects and thus support basic and clinical research. Here we present MitopatHs, a web-based data set that allows navigating among the biochemical signaling pathways (PatHs) of human (H) mitochondria (Mito). MitopatHs is designed to visualize and comprehend virtually all types of pathways in two complementary ways: a logical view, where the sequence of biochemical reactions is presented as logical deductions, and an intuitive graphical visualization, which enables the examination and the analysis of each step of the pathway. MitopatHs is a manually curated, open access and collaborative tool, whose goal is to enable the visualization and comprehension of complicated molecular routes in an easy and fast way.
    Keywords:  Cell Biology; Molecular Network; Software
    DOI:  https://doi.org/10.1016/j.isci.2021.102324
  13. STAR Protoc. 2021 Jun 18. 2(2): 100431
    Assembly and Cryo-EM structure determination of yeast mitochondrial RNA polymerase initiation complex intermediates.
    Sergio E Martinez, Anupam Singh, Brent De Wijngaert, Shemaila Sultana, Chhaya Dharia, Hans Vanbuel, Jiayu Shen, Daniel Vasilchuk, Smita S Patel, Kalyan Das.
      In yeast mitochondria, transcription initiation requires assembly of mitochondrial RNA polymerase and transcription initiation factor MTF1 at the DNA promoter initiation site. This protocol describes the purification of the component proteins and assembly of partially melted and fully melted initiation complex states. Both states co-exist in equilibrium in the same sample as seen by cryoelectron microscopy (cryo-EM) and allow elucidation of MTF1's structural roles in controlling the transition into elongation. We further outline how analysis of the complex by light scattering, thermal shift assay, and ultrafiltration assay exhibits reproducible results. For complete details on the use and execution of this protocol, please refer to De Wijngaert et al. (2021).
    Keywords:  Cryo-EM; Protein expression and purification; Structural Biology
    DOI:  https://doi.org/10.1016/j.xpro.2021.100431
  14. Stem Cell Reports. 2021 Apr 13. pii: S2213-6711(21)00161-2. [Epub ahead of print]
    The role of SQSTM1 (p62) in mitochondrial function and clearance in human cortical neurons.
    Anna Poon, Harpreet Saini, Siddharth Sethi, Gregory A O'Sullivan, Hélène Plun-Favreau, Selina Wray, Lee A Dawson, James M McCarthy.
      Sequestosome-1 (SQSTM1/p62) is involved in cellular processes such as autophagy and metabolic reprogramming. Mutations resulting in the loss of function of SQSTM1 lead to neurodegenerative diseases including frontotemporal dementia. The pathogenic mechanism that contributes to SQSTM1-related neurodegeneration has been linked to its role as an autophagy adaptor, but this is poorly understood, and its precise role in mitochondrial function and clearance remains to be clarified. Here, we assessed the importance of SQSTM1 in human induced pluripotent stem cell (iPSC)-derived cortical neurons through the knockout of SQSTM1. We show that SQSTM1 depletion causes altered mitochondrial gene expression and functionality, as well as autophagy flux, in iPSC-derived neurons. However, SQSTM1 is not essential for mitophagy despite having a significant impact on early PINK1-dependent mitophagy processes including PINK1 recruitment and phosphorylation of ubiquitin on depolarized mitochondria. These findings suggest that SQSTM1 is important for mitochondrial function rather than clearance.
    Keywords:  FTD; SQSTM1; iPSC disease modeling; mitochondria
    DOI:  https://doi.org/10.1016/j.stemcr.2021.03.030
  15. J Biol Chem. 2021 Apr 14. pii: S0021-9258(21)00458-0. [Epub ahead of print] 100669
    The effect of mitochondrial calcium uniporter and cyclophilin D knockout on resistance of brain mitochondria to Ca2+-induced damage.
    James Hamilton, Tatiana Brustovetsky, Nickolay Brustovetsky.
      The mitochondrial calcium uniporter (MCU) and cyclophilin D (CyD) are key players in induction of the permeability transition pore (PTP), which leads to mitochondrial depolarization and swelling, the major sings of Ca2+-induced mitochondrial damage. Mitochondrial depolarization inhibits ATP production, whereas swelling results in the release of mitochondrial pro-apoptotic proteins. The extent to which simultaneous deletion of MCU and CyD inhibits PTP induction and prevents damage of brain mitochondria is not clear. Here, we investigated the effects of MCU and CyD deletion on the propensity for PTP induction using mitochondria isolated from the brains of MCU-KO, CyD-KO, and newly created MCU/CyD-double knockout (DKO) mice. Neither deletion of MCU nor of CyD affected respiration or membrane potential in mitochondria isolated from the brains of these mice. Mitochondria from MCU-KO and MCU/CyD-DKO mice displayed reduced Ca2+ uptake and diminished extent of PTP induction. The Ca2+ uptake by mitochondria from CyD-KO mice was increased compared to mitochondria from wild-type mice. Deletion of CyD prevented mitochondrial swelling and resulted in transient depolarization in response to Ca2+, but it did not prevent Ca2+-induced delayed mitochondrial depolarization. Mitochondria from MCU/CyD-DKO mice did not swell in response to Ca2+, but they did exhibit mild sustained depolarization. Dibucaine, an inhibitor of the Ca2+-activated mitochondrial phospholipase A2, attenuated, and bovine serum albumin completely eliminated the sustained depolarization. This suggests the involvement of phospholipase A2 and free fatty acids. Thus, in addition to induction of the classical PTP, alternative deleterious mechanisms may contribute to mitochondrial damage following exposure to elevated Ca2+.
    Keywords:  calcium; cyclophilin D; membrane potential; mitochondria; mitochondrial calcium uniporter; permeability transition pore; respiration
    DOI:  https://doi.org/10.1016/j.jbc.2021.100669
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