bims-mitdyn 2022-02-06 papers

bims-mitdyn

Biomed News

on Mitochondrial dynamics: mechanisms

Issue of 2022–02–06
eleven papers selected by
Edmond Chan, Queen’s University, School of Medicine

The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice.
Drp1 regulates transcription of ribosomal protein genes in embryonic hearts.
Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.
The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.
MRP5 and MRP9 play a concerted role in male reproduction and mitochondrial function.
Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains.
TAZ links exercise to mitochondrial biogenesis via mitochondrial transcription factor A.
Protection of Quiescence and Longevity of IgG Memory B Cells by Mitochondrial Autophagy.
Protocols for analyzing metabolic derangements caused by increased NADH/NAD+ ratio in cell lines and in mice.
Perinatal versus adult loss of ULK1 and ULK2 distinctly influences cardiac autophagy and function.
The importance of mitochondrial quality control for maintaining skeletal muscle function across healthspan.

Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2120476119. [Epub ahead of print]119(6):

The cardiac-enriched microprotein mitolamban regulates mitochondrial respiratory complex assembly and function in mice.

Catherine A Makarewich, Amir Z Munir, Svetlana Bezprozvannaya, Aaron M Gibson, Soo Young Kim, Misty S Martin-Sandoval, Thomas P Mathews, Luke I Szweda, Rhonda Bassel-Duby, Eric N Olson.

  Emerging evidence indicates that a subset of RNA molecules annotated as noncoding contain short open reading frames that code for small functional proteins called microproteins, which have largely been overlooked due to their small size. To search for cardiac-expressed microproteins, we used a comparative genomics approach and identified mitolamban (Mtlbn) as a highly conserved 47-amino acid transmembrane protein that is abundantly expressed in the heart. Mtlbn localizes specifically to the inner mitochondrial membrane where it interacts with subunits of complex III of the electron transport chain and with mitochondrial respiratory supercomplexes. Genetic deletion of Mtlbn in mice altered complex III assembly dynamics and reduced complex III activity. Unbiased metabolomic analysis of heart tissue from Mtlbn knockout mice further revealed an altered metabolite profile consistent with deficiencies in complex III activity. Cardiac-specific Mtlbn overexpression in transgenic (TG) mice induced cardiomyopathy with histological, biochemical, and ultrastructural pathologic features that contributed to premature death. Metabolomic analysis and biochemical studies indicated that hearts from Mtlbn TG mice exhibited increased oxidative stress and mitochondrial dysfunction. These findings reveal Mtlbn as a cardiac-expressed inner mitochondrial membrane microprotein that contributes to mitochondrial electron transport chain activity through direct association with complex III and the regulation of its assembly and function.

Keywords:  cardiac; microprotein; mitochondria; oxidative phosphorylation

DOI:  https://doi.org/10.1073/pnas.2120476119
J Cell Sci. 2022 Jan 31. pii: jcs.258956. [Epub ahead of print]

Drp1 regulates transcription of ribosomal protein genes in embryonic hearts.

Qiancong Zhao, Shun Yan, Jin Lu, Danitra J Parker, Huiying Wu, Qianchuang Sun, David K Crossman, Shanrun Liu, Qin Wang, Hiromi Sesaki, Kasturi Mitra, Kexiang Liu, Kai Jiao.

  Mitochondrial dysfunction causes severe congenital cardiac abnormalities and prenatal/neonatal lethality. The lack of sufficient knowledge regarding how mitochondrial abnormalities affect cardiogenesis poses a major barrier for the development of clinical applications that target mitochondrial deficiency induced inborn cardiomyopathies. Mitochondrial morphology, which is regulated by fission and fusion, plays a key role in determining mitochondrial activity. Dnm1l encodes a dynamin-related GTPase, Drp1, which is required for mitochondrial fission. To investigate the role of Drp1 on cardiogenesis during the embryonic metabolic shift period, we specifically inactivated Dnm1l in second heart field-derived structures. Mutant cardiomyocytes in the right ventricle (RV) displayed severe defects in mitochondrial morphology, ultrastructure, and activity. These defects caused increased cell death, decreased cell survival, disorganized cardiomyocytes, and embryonic lethality. Through characterizing this model, we reveal a novel AMPK-SIRT7-GABPB axis that relays the reduced cellular energy level to decreased transcription of ribosomal protein genes in cardiomyocytes. We therefore provide the first mouse genetic evidence to suggest that Drp1 is essential for RV development. Our research provides further mechanistic insight regarding how mitochondrial dysfunction causes pathological molecular and cellular alterations during cardiogenesis.

Keywords:  Drp1; Heart development; RP gene transcription

DOI:  https://doi.org/10.1242/jcs.258956
Nat Commun. 2022 Feb 03. 13(1): 651

Mitochondrial protein import determines lifespan through metabolic reprogramming and de novo serine biosynthesis.

Eirini Lionaki, Ilias Gkikas, Ioanna Daskalaki, Maria-Konstantina Ioannidi, Maria I Klapa, Nektarios Tavernarakis.

Sustained mitochondrial fitness relies on coordinated biogenesis and clearance. Both processes are regulated by constant targeting of proteins into the organelle. Thus, mitochondrial protein import sets the pace for mitochondrial abundance and function. However, our understanding of mitochondrial protein translocation as a regulator of longevity remains enigmatic. Here, we targeted the main protein import translocases and assessed their contribution to mitochondrial abundance and organismal physiology. We find that reduction in cellular mitochondrial load through mitochondrial protein import system suppression, referred to as MitoMISS, elicits a distinct longevity paradigm. We show that MitoMISS triggers the mitochondrial unfolded protein response, orchestrating an adaptive reprogramming of metabolism. Glycolysis and de novo serine biosynthesis are causatively linked to longevity, whilst mitochondrial chaperone induction is dispensable for lifespan extension. Our findings extent the pro-longevity role of UPRmt and provide insight, relevant to the metabolic alterations that promote or undermine survival and longevity.

DOI: https://doi.org/10.1038/s41467-022-28272-1
Mol Cell. 2022 Jan 28. pii: S1097-2765(22)00008-9. [Epub ahead of print]

The interplay between BAX and BAK tunes apoptotic pore growth to control mitochondrial-DNA-mediated inflammation.

Katia Cosentino, Vanessa Hertlein, Andreas Jenner, Timo Dellmann, Milos Gojkovic, Aida Peña-Blanco, Shashank Dadsena, Noel Wajngarten, John S H Danial, Jervis Vermal Thevathasan, Markus Mund, Jonas Ries, Ana J Garcia-Saez.

  BAX and BAK are key apoptosis regulators that mediate the decisive step of mitochondrial outer membrane permeabilization. However, the mechanism by which they assemble the apoptotic pore remains obscure. Here, we report that BAX and BAK present distinct oligomerization properties, with BAK organizing into smaller structures with faster kinetics than BAX. BAK recruits and accelerates BAX assembly into oligomers that continue to grow during apoptosis. As a result, BAX and BAK regulate each other as they co-assemble into the same apoptotic pores, which we visualize. The relative availability of BAX and BAK molecules thereby determines the growth rate of the apoptotic pore and the relative kinetics by which mitochondrial contents, most notably mtDNA, are released. This feature of BAX and BAK results in distinct activation kinetics of the cGAS/STING pathway with implications for mtDNA-mediated paracrine inflammatory signaling.

Keywords:  AFM; BAK; BAX; BCL-2; inflammatory cell death; membrane pore; mitochondria; pore-forming protein; single-molecule imaging; super-resolution microscopy

DOI:  https://doi.org/10.1016/j.molcel.2022.01.008
Proc Natl Acad Sci U S A. 2022 Feb 08. pii: e2111617119. [Epub ahead of print]119(6):

MRP5 and MRP9 play a concerted role in male reproduction and mitochondrial function.

Ian G Chambers, Praveen Kumar, Jens Lichtenberg, Pengcheng Wang, Jianshi Yu, John D Phillips, Maureen A Kane, David Bodine, Iqbal Hamza.

  Multidrug Resistance Proteins (MRPs) are transporters that play critical roles in cancer even though the physiological substrates of these enigmatic transporters are poorly elucidated. In Caenorhabditis elegans, MRP5/ABCC5 is an essential heme exporter because mrp-5 mutants are unviable due to their inability to export heme from the intestine to extraintestinal tissues. Heme supplementation restores viability of these mutants but fails to restore male reproductive deficits. Correspondingly, cell biological studies show that MRP5 regulates heme levels in the mammalian secretory pathway even though MRP5 knockout (KO) mice do not show reproductive phenotypes. The closest homolog of MRP5 is MRP9/ABCC12, which is absent in C. elegans, raising the possibility that MRP9 may genetically compensate for MRP5. Here, we show that MRP5 and MRP9 double KO (DKO) mice are viable but reveal significant male reproductive deficits. Although MRP9 is highly expressed in sperm, MRP9 KO mice show reproductive phenotypes only when MRP5 is absent. Both ABCC transporters localize to mitochondrial-associated membranes, dynamic scaffolds that associate the mitochondria and endoplasmic reticulum. Consequently, DKO mice reveal abnormal sperm mitochondria with reduced mitochondrial membrane potential and fertilization rates. Metabolomics show striking differences in metabolite profiles in the DKO testes, and RNA sequencing shows significant alterations in genes related to mitochondrial function and retinoic acid metabolism. Targeted functional metabolomics reveal lower retinoic acid levels in the DKO testes and higher levels of triglycerides in the mitochondria. These findings establish a model in which MRP5 and MRP9 play a concerted role in regulating male reproductive functions and mitochondrial sufficiency.

Keywords:  fertility; heme; mitochondria; multidrug resistance proteins; reproduction

DOI:  https://doi.org/10.1073/pnas.2111617119
iScience. 2022 Feb 18. 25(2): 103734

Multi-omics analysis identifies essential regulators of mitochondrial stress response in two wild-type C. elegans strains.

Arwen W Gao, Gaby El Alam, Amélia Lalou, Terytty Yang Li, Marte Molenaars, Yunyun Zhu, Katherine A Overmyer, Evgenia Shishkova, Kevin Hof, Maroun Bou Sleiman, Riekelt H Houtkooper, Joshua J Coon, Johan Auwerx.

  The mitochondrial unfolded protein response (UPRmt) is a promising pharmacological target for aging and age-related diseases. However, the integrative analysis of the impact of UPRmt activation on different signaling layers in animals with different genetic backgrounds is lacking. Here, we applied systems approaches to investigate the effect of UPRmt induced by doxycycline (Dox) on transcriptome, proteome, and lipidome in two genetically divergent worm strains, named N2 and CB4856. From the integrated omics datasets, we found that Dox prolongs lifespan of both worm strains through shared and strain-specific mechanisms. Specifically, Dox strongly impacts mitochondria, upregulates defense response, and lipid metabolism, while decreasing triglycerides. We further validated that lipid genes acs-2/20 and fat-7/6 were required for Dox-induced UPRmt and longevity in N2 and CB4856 worms, respectively. Our data have translational value as they indicate that the beneficial effects of Dox-induced UPRmt on lifespan are consistent across different genetic backgrounds through different regulators.

Keywords:  Chronobiology; Proteomics; Transcriptomics

DOI:  https://doi.org/10.1016/j.isci.2022.103734
Nat Commun. 2022 Feb 03. 13(1): 653

TAZ links exercise to mitochondrial biogenesis via mitochondrial transcription factor A.

Jun-Ha Hwang, Kyung Min Kim, Ho Taek Oh, Gi Don Yoo, Mi Gyeong Jeong, Hyun Lee, Joori Park, Kwon Jeong, Yoon Ki Kim, Young-Gyu Ko, Eun Sook Hwang, Jeong-Ho Hong.

Mitochondria are energy-generating organelles and mitochondrial biogenesis is stimulated to meet energy requirements in response to extracellular stimuli, including exercise. However, the mechanisms underlying mitochondrial biogenesis remain unknown. Here, we demonstrate that transcriptional coactivator with PDZ-binding motif (TAZ) stimulates mitochondrial biogenesis in skeletal muscle. In muscle-specific TAZ-knockout (mKO) mice, mitochondrial biogenesis, respiratory metabolism, and exercise ability were decreased compared to wild-type mice. Mechanistically, TAZ stimulates the translation of mitochondrial transcription factor A via Ras homolog enriched in brain (Rheb)/Rheb like 1 (Rhebl1)-mTOR axis. TAZ stimulates Rhebl1 expression via TEA domain family transcription factor. Rhebl1 introduction by adeno-associated virus or mTOR activation recovered mitochondrial biogenesis in mKO muscle. Physiologically, mKO mice did not stimulate exercise-induced mitochondrial biogenesis. Collectively, our results suggested that TAZ is a novel stimulator for mitochondrial biogenesis and exercise-induced muscle adaptation.

DOI: https://doi.org/10.1038/s41467-022-28247-2
J Immunol. 2022 Jan 31. pii: ji2100969. [Epub ahead of print]

Protection of Quiescence and Longevity of IgG Memory B Cells by Mitochondrial Autophagy.

Srikanth Kodali, Min Li, Marietta M Budai, Min Chen, Jin Wang.

The development of long-lived immune memory cells against pathogens is critical for the success of vaccines to establish protection against future infections. However, the mechanisms governing the long-term survival of immune memory cells remain to be elucidated. In this article, we show that the maintenance mitochondrial homeostasis by autophagy is critical for restricting metabolic functions to protect IgG memory B cell survival. Knockout of mitochondrial autophagy genes, Nix and Bnip3, leads to mitochondrial accumulation and increases in oxidative phosphorylation and fatty acid synthesis, resulting in the loss of IgG+ memory B cells in mice. Inhibiting fatty acid synthesis or silencing necroptosis gene Ripk3 rescued Nix-/-Bnip3-/- IgG memory B cells, indicating that mitochondrial autophagy is important for limiting metabolic functions to prevent cell death. Our results suggest a critical role for mitochondrial autophagy in the maintenance of immunological memory by protecting the metabolic quiescence and longevity of memory B cells.

DOI: https://doi.org/10.4049/jimmunol.2100969
STAR Protoc. 2022 Mar 18. 3(1): 101120

Protocols for analyzing metabolic derangements caused by increased NADH/NAD+ ratio in cell lines and in mice.

Shanshan Liu, Yan Ma, Hui Jiang.

  Mitochondrial electron transport chain (ETC) dysfunction elevates the NADH/NAD+ ratio to cause metabolic derangements. Here we describe a protocol to measure the NADH/NAD+ ratio and analyze the rewiring of glucose metabolism using [4-2H]-glucose, [3-2H]-glucose, and [U-13C]-glucose in ETC-inhibited human cancer cells. We also describe a protocol to analyze the NADH/NAD+ ratio-sensitive metabolites in mouse plasma and mouse liver following phenformin treatment. These protocols comprehensively analyze the metabolic derangements resulting from increased NADH/NAD+ ratio in in vitro and in vivo models. For complete details on the use and execution of this profile, please refer to Liu et al. (2021).

Keywords:  Cell Biology; Cell culture; Cell-based Assays; Mass Spectrometry; Metabolism; Model Organisms

DOI:  https://doi.org/10.1016/j.xpro.2021.101120
Autophagy. 2022 Feb 01. 1-17

Perinatal versus adult loss of ULK1 and ULK2 distinctly influences cardiac autophagy and function.

Matthew P Harris, Quan J Zhang, Cole T Cochran, Jessica Ponce, Sean Alexander, Ana Kronemberger, Jordan D Fuqua, Yuan Zhang, Ranan Fattal, Tyler Harper, Matthew L Murry, Chad E Grueter, E Dale Abel, Vitor A Lira.

  Impairments in macroautophagy/autophagy, which degrades dysfunctional organelles as well as long-lived and aggregate proteins, are associated with several cardiomyopathies; however, the regulation of cardiac autophagy remains insufficiently understood. In this regard, ULK1 and ULK2 are thought to play primarily redundant roles in autophagy initiation, but whether their function is developmentally determined, potentially having an impact on cardiac integrity and function remains unknown. Here, we demonstrate that perinatal loss of ULK1 or ULK2 in cardiomyocytes (cU1-KO and cU2-KO mice, respectively) enhances basal autophagy without altering autophagy machinery content while preserving cardiac function. This increased basal autophagy is dependent on the remaining ULK protein given that perinatal loss of both ULK1 and ULK2 in cU1/2-DKO mice impaired autophagy causing age-related cardiomyopathy and reduced survival. Conversely, adult loss of cardiac ULK1, but not of ULK2 (i.e., icU1-KO and icU2-KO mice, respectively), led to a rapidly developing cardiomyopathy, heart failure and early death. icU1-KO mice had impaired autophagy with robust deficits in mitochondrial respiration and ATP synthesis. Trehalose ameliorated autophagy impairments in icU1-KO hearts but did not delay cardiac dysfunction suggesting that ULK1 plays other critical, autophagy-independent, functions in the adult heart. Collectively, these results indicate that cardiac ULK1 and ULK2 are functionally redundant in the developing heart, while ULK1 assumes a more unique, prominent role in the adult heart.Abbreviations: ATG4: autophagy related 4, cysteine peptidase; ATG5: autophagy related 5; ATG7: autophagy related 7; ATG9: autophagy related 9; ATG13: autophagy related 13; CYCS: Cytochrome C; DNM1L, dynamin 1-like; MAP1LC3A: microtubule-associated protein 1 light chain 3 alpha; MAP1LC3B: microtubule-associated protein 1 light chain 3 beta; MFN1: mitofusin 1; MFN2: mitofusin 2; MT-CO1: mitochondrially encoded cytochrome c oxidase I; MYH: myosin, heavy polypeptide; NBR1: NBR1 autophagy cargo receptor; NDUFA9: NADH:ubiquinone oxidoreductase subunit A9; OPA1: OPA1, mitochondrial dynamin like GTPase; PPARGC1A, peroxisome proliferator activated receptor, gamma, coactivator 1 alpha; SDHA: succinate dehydrogenase complex, subunit A, flavoprotein (Fp); SQSTM1: sequestosome 1; ULK1: unc-51 like kinase 1; ULK2: unc-51 like kinase 2; UQCRC1: ubiquinol-cytochrome c reductase core protein 1.

Keywords:  Age-related cardiomyopathy; MAP1LC3; NBR1; SQSTM1; dilated cardiomyopathy; heart failure; mitochondria; mitophagy

DOI:  https://doi.org/10.1080/15548627.2021.2022289
Am J Physiol Cell Physiol. 2022 Feb 02.

The importance of mitochondrial quality control for maintaining skeletal muscle function across healthspan.

James Sligar, Danielle A Debruin, Nicholas J Saner, Ashleigh M Philp, Andrew Philp.

  As the principal energy-producing organelles of the cell, mitochondria support numerous biological processes related to metabolism, growth and regeneration in skeletal muscle. Deterioration in skeletal muscle functional capacity with age is thought to be driven in part by a reduction in skeletal muscle oxidative capacity and reduced fatigue resistance. Underlying this maladaptive response is the development of mitochondrial dysfunction caused by alterations in mitochondrial quality control (MQC), a term encompassing processes of mitochondrial synthesis (biogenesis), remodelling (dynamics) and degradation (mitophagy). Knowledge regarding the role and regulation of MQC in skeletal muscle and the influence of ageing in this process have rapidly advanced in the last decade. Given the emerging link between ageing and MQC, therapeutic approaches to manipulate MQC to prevent mitochondrial dysfuntion during ageing hold tremendous therapeutic potential.

Keywords:  biogenesis; metabolism; mitochondria; mitophagy; skeletal muscle

DOI:  https://doi.org/10.1152/ajpcell.00388.2021