bims-mecmid 2021-09-05 papers

bims-mecmid

Biomed News

on Membrane communication in mitochondrial dynamics

Issue of 2021–09–05
thirteen papers selected by
Mauricio Cardenas Rodriguez, University of Padova

Aim32 is a dual-localized 2Fe-2S mitochondrial protein that functions in redox quality control.
Mitofusin 2 Deficiency Causes Pro-Inflammatory Effects in Human Primary Macrophages.
The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging.
Short-form OPA1 is a molecular chaperone in mitochondrial intermembrane space.
Protocol for assessing real-time changes in mitochondrial morphology, fission and fusion events in live cells using confocal microscopy.
Essential role for paxillin tyrosine phosphorylation in LPS-induced mitochondrial fission, ROS generation and lung endothelial barrier loss.
Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.
Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs.
Potential biomarkers and targets of mitochondrial dynamics.
In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography.
Cell reprogramming shapes the mitochondrial DNA landscape.
Mitochondrial Fragmentation Triggers Ineffective Hematopoiesis in Myelodysplastic Syndromes.
Leigh Syndrome: A Tale of Two Genomes.

J Biol Chem. 2021 Aug 27. pii: S0021-9258(21)00936-4. [Epub ahead of print] 101135

Aim32 is a dual-localized 2Fe-2S mitochondrial protein that functions in redox quality control.

Danyun Zhang, Owen R Dailey, Daniel J Simon, Kamilah Roca-Datzer, Yasaman Jami-Alahmadi, Mikayla S Hennen, James A Wolfschlegel, Carla M Koehler, Deepa V Dabir.

  Yeast is a facultative anaerobe and uses diverse electron acceptors to maintain redox-regulated import of cysteine-rich precursors via the mitochondrial intermembrane space assembly (MIA) pathway. With the growing diversity of substrates utilizing the MIA pathway, understanding the capacity of the intermembrane space (IMS) to handle different types of stress is crucial. We used mass spectrometry to identify additional proteins that interacted with the sulfhydryl oxidase Erv1 of the MIA pathway. Aim32, a thioredoxin-like [2Fe-2S] ferredoxin protein, was identified as an Erv1 binding protein. Detailed localization studies showed that Aim32 resided in both the mitochondrial matrix and IMS. Aim32 interacted with additional proteins including redox protein Osm1 and protein import components Tim17, Tim23, and Tim22. Deletion of Aim32 or mutation of conserved cysteine residues that coordinate the Fe-S center in Aim32 resulted in an increased accumulation of proteins with aberrant disulfide linkages. In addition, the steady-state level of assembled TIM22, TIM23, and Oxa1 protein import complexes was decreased. Aim32 also bound to several mitochondrial proteins under nonreducing conditions, suggesting a function in maintaining the redox status of proteins by potentially targeting cysteine residues that may be sensitive to oxidation. Finally, Aim32 was essential for growth in conditions of stress such as elevated temperature and hydroxyurea (HU), and under anaerobic conditions. These studies suggest that the Fe-S protein Aim32 has a potential role in general redox homeostasis in the matrix and IMS. Thus, Aim32 may be poised as a sensor or regulator in quality control for a broad range of mitochondrial proteins.

Keywords:  disulfide; mitochondria; mitochondrial transport; protein import; redox regulation; thiol; thioredoxin

DOI:  https://doi.org/10.1016/j.jbc.2021.101135
Front Immunol. 2021 ;12 723683

Mitofusin 2 Deficiency Causes Pro-Inflammatory Effects in Human Primary Macrophages.

Vera Khodzhaeva, Yannick Schreiber, Gerd Geisslinger, Ralf P Brandes, Bernhard Brüne, Dmitry Namgaladze.

  Mitofusin 2 (MFN2) is a mitochondrial outer membrane GTPase, which modulates mitochondrial fusion and affects the interaction between endoplasmic reticulum and mitochondria. Here, we explored how MFN2 influences mitochondrial functions and inflammatory responses towards zymosan in primary human macrophages. A knockdown of MFN2 by small interfering RNA decreased mitochondrial respiration without attenuating mitochondrial membrane potential and reduced interactions between endoplasmic reticulum and mitochondria. A MFN2 deficiency potentiated zymosan-elicited inflammatory responses of human primary macrophages, such as expression and secretion of pro-inflammatory cytokines interleukin-1β, -6, -8 and tumor necrosis factor α, as well as induction of cyclooxygenase 2 and prostaglandin E2 synthesis. MFN2 silencing also increased zymosan-induced nuclear factor kappa-light-chain-enhancer of activated B cells and mitogen-activated protein kinases inflammatory signal transduction, without affecting mitochondrial reactive oxygen species production. Mechanistic studies revealed that MFN2 deficiency enhanced the toll-like receptor 2-dependent branch of zymosan-triggered responses upstream of inhibitor of κB kinase. This was associated with elevated, cytosolic expression of interleukin-1 receptor-associated kinase 4 in MFN2-deficient cells. Our data suggest pro-inflammatory effects of MFN2 deficiency in human macrophages.

Keywords:  endoplasmic reticulum ; inflammation; macrophages; mitochondria; mitochondrial dynamics; zymosan

DOI:  https://doi.org/10.3389/fimmu.2021.723683
Elife. 2021 09 01. pii: e63453. [Epub ahead of print]10

The mitochondrial permeability transition pore activates the mitochondrial unfolded protein response and promotes aging.

Suzanne Angeli, Anna Foulger, Manish Chamoli, Tanuja Harshani Peiris, Akos Gerencser, Azar Asadi Shahmirzadi, Julie Andersen, Gordon Lithgow.

  Mitochondrial activity determines aging rate and the onset of chronic diseases. The mitochondrial permeability transition pore (mPTP) is a pathological pore in the inner mitochondrial membrane thought to be composed of the F-ATP synthase (complex V). OSCP, a subunit of F-ATP synthase, helps protect against mPTP formation. How the destabilization of OSCP may contribute to aging, however, is unclear. We have found that loss OSCP in the nematode Caenorhabditis elegans initiates the mPTP and shortens lifespan specifically during adulthood, in part via initiation of the mitochondrial unfolded protein response (UPRmt). Pharmacological or genetic inhibition of the mPTP inhibits the UPRmt and restores normal lifespan. Loss of the putative pore-forming component of F-ATP synthase extends adult lifespan, suggesting that the mPTP normally promotes aging. Our findings reveal how an mPTP/UPRmt nexus may contribute to aging and age-related diseases and how inhibition of the UPRmt may be protective under certain conditions.

Keywords:  C. elegans; F-ATP synthase; aging; c-subunit; cell biology; mitochondrial permeability transition pore; mitochondrial unfolded protein response; oscp/atp-3

DOI:  https://doi.org/10.7554/eLife.63453
Sci China Life Sci. 2021 Aug 31.

Short-form OPA1 is a molecular chaperone in mitochondrial intermembrane space.

Deyang Yao, Yukun Li, Sheng Zeng, Zhifan Li, Zahir Shah, Bigui Song, Jinglei Liu, Yi Wu, Liang Yang, Qi Long, Wenqian Wang, Zhijuan Hu, Haite Tang, Xingguo Liu.

  Mitochondria, double-membrane organelles, are known to participate in a variety of metabolic and signal transduction pathways. The intermembrane space (IMS) of mitochondria is proposed to subject to multiple damages emanating from the respiratory chain. The optic atrophy 1 (OPA1), an important protein for mitochondrial fusion, is cleaved into soluble short-form (S-OPA1) under stresses. Here we report that S-OPA1 could function as a molecular chaperone in IMS. We purified the S-OPA1 (amino acid sequence after OPA1 isoform 5 S1 site) protein and showed it protected substrate proteins from thermally and chemically induced aggregation and strengthened the thermotolerance of Escherichia coli (E. coli). We also showed that S-OPA1 conferred thermotolerance on IMS proteins, e.g., neurolysin. The chaperone activity of S-OPA1 may be required for maintaining IMS homeostasis in mitochondria.

Keywords:  OPA1; chaperone; heat shock; mitochondria; mitochondrial homeostasis

DOI:  https://doi.org/10.1007/s11427-021-1962-0
STAR Protoc. 2021 Sep 17. 2(3): 100767

Protocol for assessing real-time changes in mitochondrial morphology, fission and fusion events in live cells using confocal microscopy.

Irene Bertolini, Frederick Keeney, Dario C Altieri.

  Changes in mitochondrial size, shape, and subcellular position, a process collectively known as mitochondrial dynamics, are exploited for various cancer traits. Modulation of subcellular mitochondrial trafficking and accumulation at the cortical cytoskeleton has been linked to the machinery of cell movements, fueling cell invasion and metastatic spreading. Here, we detail a technique to track changes in mitochondrial volume using a commercial CellLight™ Mitochondria-RFP/GFP reporter and live confocal microscopy. This allows a real-time study of mitochondrial dynamics in live cells. For complete details on the use and execution of this protocol, please refer to Bertolini et al. (2020).

Keywords:  Cancer; Microscopy; Molecular/Chemical Probes

DOI:  https://doi.org/10.1016/j.xpro.2021.100767
Sci Rep. 2021 Sep 02. 11(1): 17546

Essential role for paxillin tyrosine phosphorylation in LPS-induced mitochondrial fission, ROS generation and lung endothelial barrier loss.

Panfeng Fu, Yulia Epshtein, Ramaswamy Ramchandran, Joseph B Mascarenhas, Anne E Cress, Jeffrey Jacobson, Joe G N Garcia, Viswanathan Natarajan.

We have shown that both reactive oxygen species (ROS) and paxillin tyrosine phosphorylation regulate LPS-induced human lung endothelial permeability. Mitochondrial ROS (mtROS) is known to increase endothelial cell (EC) permeability which requires dynamic change in mitochondrial morphology, events that are likely to be regulated by paxillin. Here, we investigated the role of paxillin and its tyrosine phosphorylation in regulating LPS-induced mitochondrial dynamics, mtROS production and human lung microvascular EC (HLMVEC) dysfunction. LPS, in a time-dependent manner, induced higher levels of ROS generation in the mitochondria compared to cytoplasm or nucleus. Down-regulation of paxillin expression with siRNA or ecto-expression of paxillin Y31F or Y118F mutant plasmids attenuated LPS-induced mtROS in HLMVECs. Pre-treatment with MitoTEMPO, a scavenger of mtROS, attenuated LPS-induced mtROS, endothelial permeability and VE-cadherin phosphorylation. Further, LPS-induced mitochondrial fission in HLMVECs was attenuated by both a paxillin siRNA, and paxillin Y31F/Y118F mutant. LPS stimulated phosphorylation of dynamin-related protein (DRP1) at S616, which was also attenuated by paxillin siRNA, and paxillinY31/Y118 mutants. Inhibition of DRP1 phosphorylation by P110 attenuated LPS-induced mtROS and endothelial permeability. LPS challenge of HLMVECs enhanced interaction between paxillin, ERK, and DRP1, and inhibition of ERK1/2 activation with PD98059 blocked mitochondrial fission. Taken together, these results suggest a key role for paxillin tyrosine phosphorylation in LPS-induced mitochondrial fission, mtROS generation and EC barrier dysfunction.

DOI: https://doi.org/10.1038/s41598-021-97006-y
J Cell Biol. 2021 Nov 01. pii: e202104073. [Epub ahead of print]220(11):

Vps13D functions in a Pink1-dependent and Parkin-independent mitophagy pathway.

James L Shen, Tina M Fortier, Ruoxi Wang, Eric H Baehrecke.

Defects in autophagy cause problems in metabolism, development, and disease. The autophagic clearance of mitochondria, mitophagy, is impaired by the loss of Vps13D. Here, we discover that Vps13D regulates mitophagy in a pathway that depends on the core autophagy machinery by regulating Atg8a and ubiquitin localization. This process is Pink1 dependent, with loss of pink1 having similar autophagy and mitochondrial defects as loss of vps13d. The role of Pink1 has largely been studied in tandem with Park/Parkin, an E3 ubiquitin ligase that is widely considered to be crucial in Pink1-dependent mitophagy. Surprisingly, we find that loss of park does not exhibit the same autophagy and mitochondrial deficiencies as vps13d and pink1 mutant cells and contributes to mitochondrial clearance through a pathway that is parallel to vps13d. These findings provide a Park-independent pathway for Pink1-regulated mitophagy and help to explain how Vps13D regulates autophagy and mitochondrial morphology and contributes to neurodegenerative diseases.

DOI: https://doi.org/10.1083/jcb.202104073
Proc Natl Acad Sci U S A. 2021 Sep 07. pii: e2104219118. [Epub ahead of print]118(36):

Calmodulin extracts the Ras family protein RalA from lipid bilayers by engagement with two membrane-targeting motifs.

Samuel G Chamberlain, Andrea Gohlke, Arooj Shafiq, Iolo J Squires, Darerca Owen, Helen R Mott.

  RalA is a small GTPase and a member of the Ras family. This molecular switch is activated downstream of Ras and is widely implicated in tumor formation and growth. Previous work has shown that the ubiquitous Ca2+-sensor calmodulin (CaM) binds to small GTPases such as RalA and K-Ras4B, but a lack of structural information has obscured the functional consequences of these interactions. Here, we have investigated the binding of CaM to RalA and found that CaM interacts exclusively with the C terminus of RalA, which is lipidated with a prenyl group in vivo to aid membrane attachment. Biophysical and structural analyses show that the two RalA membrane-targeting motifs (the prenyl anchor and the polybasic motif) are engaged by distinct lobes of CaM and that CaM binding leads to removal of RalA from its membrane environment. The structure of this complex, along with a biophysical investigation into membrane removal, provides a framework with which to understand how CaM regulates the function of RalA and sheds light on the interaction of CaM with other small GTPases, including K-Ras4B.

Keywords:  K-Ras; Ral; calmodulin; membrane; nuclear magnetic resonance

DOI:  https://doi.org/10.1073/pnas.2104219118
Clin Transl Med. 2021 Aug;11(8): e529

Potential biomarkers and targets of mitochondrial dynamics.

Liyang Li, Ruixue Qi, Linlin Zhang, Yuexin Yu, Jiayun Hou, Yutong Gu, Dongli Song, Xiangdong Wang.

  Mitochondrial dysfunction contributes to the imbalance of cellular homeostasis and the development of diseases, which is regulated by mitochondria-associated factors. The present review aims to explore the process of the mitochondrial quality control system as a new source of the potential diagnostic biomarkers and/or therapeutic targets for diseases, including mitophagy, mitochondrial dynamics, interactions between mitochondria and other organelles (lipid droplets, endoplasmic reticulum, endosomes, and lysosomes), as well as the regulation and posttranscriptional modifications of mitochondrial DNA/RNA (mtDNA/mtRNA). The direct and indirect influencing factors were especially illustrated in understanding the interactions among regulators of mitochondrial dynamics. In addition, mtDNA/mtRNAs and proteomic profiles of mitochondria in various lung diseases were also discussed as an example. Thus, alternations of mitochondria-associated regulators can be a new category of biomarkers and targets for disease diagnosis and therapy.

Keywords:  lung diseases; mitochondria; mitochondrial dynamics; mtDNA

DOI:  https://doi.org/10.1002/ctm2.529
Elife. 2021 Sep 01. pii: e73099. [Epub ahead of print]10

In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography.

Mohammed Kaplan, Georges Chreifi, Lauren Ann Metskas, Janine Liedtke, Cecily R Wood, Catherine M Oikonomou, William J Nicolas, Poorna Subramanian, Lori A Zacharoff, Yuhang Wang, Yi-Wei Chang, Morgan Beeby, Megan Dobro, Yongtao Zhu, Mark McBride, Ariane Briegel, Carrie Shaffer, Grant J Jensen.

  The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~ 90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: 1) tubes with a uniform diameter (with or without an internal scaffold), 2) tubes with irregular diameter, 3) tubes with a vesicular dilation at their tip, 4) pearling tubes, 5) connected chains of vesicles (with or without neck-like connectors), 6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.

Keywords:  infectious disease; microbiology

DOI:  https://doi.org/10.7554/eLife.73099
Nat Commun. 2021 Sep 02. 12(1): 5241

Cell reprogramming shapes the mitochondrial DNA landscape.

Wei Wei, Daniel J Gaffney, Patrick F Chinnery.

Individual induced pluripotent stem cells (iPSCs) show considerable phenotypic heterogeneity, but the reasons for this are not fully understood. Comprehensively analysing the mitochondrial genome (mtDNA) in 146 iPSC and fibroblast lines from 151 donors, we show that most age-related fibroblast mtDNA mutations are lost during reprogramming. However, iPSC-specific mutations are seen in 76.6% (108/141) of iPSC lines at a mutation rate of 8.62 × 10-5/base pair. The mutations observed in iPSC lines affect a higher proportion of mtDNA molecules, favouring non-synonymous protein-coding and tRNA variants, including known disease-causing mutations. Analysing 11,538 single cells shows stable heteroplasmy in sub-clones derived from the original donor during differentiation, with mtDNA variants influencing the expression of key genes involved in mitochondrial metabolism and epidermal cell differentiation. Thus, the dynamic mtDNA landscape contributes to the heterogeneity of human iPSCs and should be considered when using reprogrammed cells experimentally or as a therapy.

DOI: https://doi.org/10.1038/s41467-021-25482-x
Cancer Discov. 2021 Aug 30. pii: candisc.0032.2021. [Epub ahead of print]

Mitochondrial Fragmentation Triggers Ineffective Hematopoiesis in Myelodysplastic Syndromes.

Yasushige Aoyagi, Yoshihiro Hayashi, Yuka Harada, Kwangmin Choi, Natsumi Matsunuma, Daichi Sadato, Yuki Maemoto, Akihiro Ito, Shigeru Yanagi, Daniel T Starczynowski, Hironori Harada.

Ineffective hematopoiesis is a fundamental process leading to the pathogenesis of myelodysplastic syndromes (MDS). However, the pathobiological mediators of ineffective hematopoiesis in MDS remain unclear. Here, we demonstrated that overwhelming mitochondrial fragmentation in mutant hematopoietic stem cells and progenitors (HSC/Ps) triggers ineffective hematopoiesis in MDS. Mouse modeling of CBL exon-deletion with RUNX1 mutants, previously unreported co-mutations in MDS patients, recapitulated not only clinically relevant MDS phenotypes but also a distinct MDS-related gene signature. Mechanistically, dynamin-related protein 1 (DRP1)-dependent excessive mitochondrial fragmentation in HSC/Ps led to excessive ROS production, induced inflammatory signaling activation, and promoted subsequent dysplasia formation and impairment of granulopoiesis. Mitochondrial fragmentation was generally observed in patients with MDS. Pharmacological inhibition of DRP1 attenuated mitochondrial fragmentation and rescued ineffective hematopoiesis phenotypes in MDS mice. These findings provide mechanistic insights into ineffective hematopoiesis and indicate that dysregulated mitochondrial dynamics could be a therapeutic target for bone marrow failure in MDS.

DOI: https://doi.org/10.1158/2159-8290.CD-21-0032
Front Physiol. 2021 ;12 693734

Leigh Syndrome: A Tale of Two Genomes.

Ajibola B Bakare, Edward J Lesnefsky, Shilpa Iyer.

  Leigh syndrome is a rare, complex, and incurable early onset (typically infant or early childhood) mitochondrial disorder with both phenotypic and genetic heterogeneity. The heterogeneous nature of this disorder, based in part on the complexity of mitochondrial genetics, and the significant interactions between the nuclear and mitochondrial genomes has made it particularly challenging to research and develop therapies. This review article discusses some of the advances that have been made in the field to date. While the prognosis is poor with no current substantial treatment options, multiple studies are underway to understand the etiology, pathogenesis, and pathophysiology of Leigh syndrome. With advances in available research tools leading to a better understanding of the mitochondria in health and disease, there is hope for novel treatment options in the future.

Keywords:  Leigh syndrome; mitochondria; mitochondrial DNA; mitochondrial genetics; respiratory chain complex

DOI:  https://doi.org/10.3389/fphys.2021.693734