bims-mitdyn 2023-07-02 papers

bims-mitdyn

Biomed News

on Mitochondrial dynamics: mechanisms

Issue of 2023–07–02
eleven papers selected by
Edmond Chan, Queen’s University, School of Medicine

Mitochondrial transfer from cancer associated fibroblasts increases migration in aggressive breast cancer.
mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.
Fast fragmenting mitochondria by TORC2.
Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.
Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria.
The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering non-imported proteins.
α-Synuclein Interactions in Mitochondria-ER Contacts: A Possible Role in Parkinson's Disease.
The Endoplasmic Reticulum-Mitochondria Encounter Structure and its Regulatory Proteins.
Molecular Regulations of FUNDC1 at ER-Mitochondria Contacts Under Hypoxic Stress.
Interactome Analysis of the ER Stress Sensor Perk Uncovers Key Components of ER-Mitochondria Contact Sites and Ca2+ Signalling.
35 Years of TFAM Research: Old Protein, New Puzzles.

J Cell Sci. 2023 Jun 26. pii: jcs.260419. [Epub ahead of print]

Mitochondrial transfer from cancer associated fibroblasts increases migration in aggressive breast cancer.

Kayla F Goliwas, Sarah Libring, Emily Berestesky, Shayan Gholizadeh, Samantha C Schwager, Andra R Frost, Thomas R Gaborski, Jian Zhang, Cynthia A Reinhart-King.

  Cancer associated fibroblasts (CAFs) have distinct roles within the tumor microenvironment, which may impact the mode and efficacy of tumor cell migration. CAFs are known to increase invasion of less-aggressive breast cancer cells through matrix remodeling and leader-follower dynamics. Here, we demonstrate that CAFs communicate with breast cancer cells through the formation of contact-dependent tunneling nanotubes (TNTs) that allow for the exchange of cargo between cell types. The transferring of CAF mitochondria is an integral cargo component, and CAF mitochondria are sufficient to increase the 3D migration of cancer cells. This cargo transfer results in an increase in mitochondrial ATP production in cancer cells while having negligible impact on glycolytic ATP production. Manually increasing mitochondrial oxidative phosphorylation (OXPHOS) by providing extra substrates for OXPHOS fails to enhance cancer cell migration unless glycolysis is maintained at a constant level. Together, these data indicate that tumor-stromal crosstalk via TNTs and the associated metabolic symbiosis is a finely controlled mechanism by which tumor cells co-opt their microenvironment to promote cancer progression and may become a potential therapeutic target.

Keywords:  ATP production.; Bioenergetics; CAF; Reverse Warburg effect; Tumor microenvironment; Tumor spheroid; Tunneling nanotube

DOI:  https://doi.org/10.1242/jcs.260419
Nat Cell Biol. 2023 Jun 29.

mTORC2-NDRG1-CDC42 axis couples fasting to mitochondrial fission.

Nuria Martinez-Lopez, Pamela Mattar, Miriam Toledo, Henrietta Bains, Manu Kalyani, Marie Louise Aoun, Mridul Sharma, Laura Beth J McIntire, Leslie Gunther-Cummins, Frank P Macaluso, Jennifer T Aguilan, Simone Sidoli, Mathieu Bourdenx, Rajat Singh.

Fasting triggers diverse physiological adaptations including increases in circulating fatty acids and mitochondrial respiration to facilitate organismal survival. The mechanisms driving mitochondrial adaptations and respiratory sufficiency during fasting remain incompletely understood. Here we show that fasting or lipid availability stimulates mTORC2 activity. Activation of mTORC2 and phosphorylation of its downstream target NDRG1 at serine 336 sustains mitochondrial fission and respiratory sufficiency. Time-lapse imaging shows that NDRG1, but not the phosphorylation-deficient NDRG1Ser336Ala mutant, engages with mitochondria to facilitate fission in control cells, as well as in those lacking DRP1. Using proteomics, a small interfering RNA screen, and epistasis experiments, we show that mTORC2-phosphorylated NDRG1 cooperates with small GTPase CDC42 and effectors and regulators of CDC42 to orchestrate fission. Accordingly, RictorKO, NDRG1Ser336Ala mutants and Cdc42-deficient cells each display mitochondrial phenotypes reminiscent of fission failure. During nutrient surplus, mTOR complexes perform anabolic functions; however, paradoxical reactivation of mTORC2 during fasting unexpectedly drives mitochondrial fission and respiration.

DOI: https://doi.org/10.1038/s41556-023-01163-3
Nat Cell Biol. 2023 Jun 29.

Fast fragmenting mitochondria by TORC2.

Miriam Valera-Alberni, William B Mair.

DOI: https://doi.org/10.1038/s41556-023-01173-1
Nat Genet. 2023 Jun 29.

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.

Caleb A Lareau, Sonia M Dubois, Frank A Buquicchio, Yu-Hsin Hsieh, Kopal Garg, Pauline Kautz, Lena Nitsch, Samantha D Praktiknjo, Patrick Maschmeyer, Jeffrey M Verboon, Jacob C Gutierrez, Yajie Yin, Evgenij Fiskin, Wendy Luo, Eleni P Mimitou, Christoph Muus, Rhea Malhotra, Sumit Parikh, Mark D Fleming, Lena Oevermann, Johannes Schulte, Cornelia Eckert, Anshul Kundaje, Peter Smibert, Santosha A Vardhana, Ansuman T Satpathy, Aviv Regev, Vijay G Sankaran, Suneet Agarwal, Leif S Ludwig.

Pathogenic mutations in mitochondrial DNA (mtDNA) compromise cellular metabolism, contributing to cellular heterogeneity and disease. Diverse mutations are associated with diverse clinical phenotypes, suggesting distinct organ- and cell-type-specific metabolic vulnerabilities. Here we establish a multi-omics approach to quantify deletions in mtDNA alongside cell state features in single cells derived from six patients across the phenotypic spectrum of single large-scale mtDNA deletions (SLSMDs). By profiling 206,663 cells, we reveal the dynamics of pathogenic mtDNA deletion heteroplasmy consistent with purifying selection and distinct metabolic vulnerabilities across T-cell states in vivo and validate these observations in vitro. By extending analyses to hematopoietic and erythroid progenitors, we reveal mtDNA dynamics and cell-type-specific gene regulatory adaptations, demonstrating the context-dependence of perturbing mitochondrial genomic integrity. Collectively, we report pathogenic mtDNA heteroplasmy dynamics of individual blood and immune cells across lineages, demonstrating the power of single-cell multi-omics for revealing fundamental properties of mitochondrial genetics.

DOI: https://doi.org/10.1038/s41588-023-01433-8
Nat Commun. 2023 Jun 30. 14(1): 3882

Targeted cross-linker delivery for the in situ mapping of protein conformations and interactions in mitochondria.

Yuwan Chen, Wen Zhou, Yufei Xia, Weijie Zhang, Qun Zhao, Xinwei Li, Hang Gao, Zhen Liang, Guanghui Ma, Kaiguang Yang, Lihua Zhang, Yukui Zhang.

Current methods for intracellular protein analysis mostly require the separation of specific organelles or changes to the intracellular environment. However, the functions of proteins are determined by their native microenvironment as they usually form complexes with ions, nucleic acids, and other proteins. Here, we show a method for in situ cross-linking and analysis of mitochondrial proteins in living cells. By using the poly(lactic-co-glycolic acid) (PLGA) nanoparticles functionalized with dimethyldioctadecylammonium bromide (DDAB) to deliver protein cross-linkers into mitochondria, we subsequently analyze the cross-linked proteins using mass spectrometry. With this method, we identify a total of 74 pairs of protein-protein interactions that do not exist in the STRING database. Interestingly, our data on mitochondrial respiratory chain proteins ( ~ 94%) are also consistent with the experimental or predicted structural analysis of these proteins. Thus, we provide a promising technology platform for in situ defining protein analysis in cellular organelles under their native microenvironment.

DOI: https://doi.org/10.1038/s41467-023-39485-3
Mol Biol Cell. 2023 Jun 28. mbcE23050205

The unfolded protein response of the endoplasmic reticulum supports mitochondrial biogenesis by buffering non-imported proteins.

Katharina Knöringer, Carina Groh, Lena Krämer, Kevin C Stein, Katja G Hansen, Jannik Zimmermann, Bruce Morgan, Johannes M Herrmann, Judith Frydman, Felix Boos.

Almost all mitochondrial proteins are synthesized in the cytosol and subsequently targeted to mitochondria. The accumulation of non-imported precursor proteins occurring upon mitochondrial dysfunction can challenge cellular protein homeostasis. Here we show that blocking protein translocation into mitochondria results in the accumulation of mitochondrial membrane proteins at the endoplasmic reticulum, thereby triggering the unfolded protein response (UPRER). Moreover, we find that mitochondrial membrane proteins are also routed to the ER under physiological conditions. The level of ER-resident mitochondrial precursors is enhanced by import defects as well as metabolic stimuli that increase the expression of mitochondrial proteins. Under such conditions, the UPRER is crucial to maintain protein homeostasis and cellular fitness. We propose the ER serves as a physiological buffer zone for those mitochondrial precursors that cannot be immediately imported into mitochondria while engaging the UPRER to adjust the ER proteostasis capacity to the extent of precursor accumulation.

DOI: https://doi.org/10.1091/mbc.E23-05-0205
Contact (Thousand Oaks). 2022 Jan-Dec;5:5 25152564221119347

α-Synuclein Interactions in Mitochondria-ER Contacts: A Possible Role in Parkinson's Disease.

Adolfo Garcia Erustes, Gabriel Cicolin Guarache, Erika da Cruz Guedes, Anderson Henrique França Figueredo Leão, Gustavo José da Silva Pereira, Soraya Soubhi Smaili.

  Endoplasmic reticulum-mitochondria contact sites regulate various biological processes, such as mitochondrial dynamics, calcium homeostasis, autophagy and lipid metabolism. Notably, dysfunctions in these contact sites are closely related to neurodegenerative diseases, including Parkinson's disease, Alzheimer's disease and amyotrophic lateral sclerosis. However, details about the role of endoplasmic reticulum-mitochondria contact sites in neurodegenerative diseases remain unknown. In Parkinson's disease, interactions between α-synuclein in the contact sites and components of tether complexes that connect organelles can lead to various dysfunctions, especially with regards to calcium homeostasis. This review will summarize the main tether complexes present in endoplasmic reticulum-mitochondria contact sites, and their roles in calcium homeostasis and trafficking. We will discuss the impact of α-synuclein accumulation, its interaction with tethering complex components and the implications in Parkinson's disease pathology.

Keywords:  Parkinson's disease; calcium; endoplasmic reticulum; mitochondria; mitochondria-ER contact sites; α-synuclein

DOI:  https://doi.org/10.1177/25152564221119347
Contact (Thousand Oaks). 2021 Jan-Dec;4:4 25152564211064491

The Endoplasmic Reticulum-Mitochondria Encounter Structure and its Regulatory Proteins.

Javairia Y Cheema, Jiajia He, Wenfan Wei, Chuanhai Fu.

  In fungi, the endoplasmic reticulum-mitochondria encounter structure (ERMES) is present between the endoplasmic reticulon (ER) and mitochondria to promote the formation of the ER-mitochondria contact sites. Four constitutive components (Mmm1, Mdm12, Mdm34, and Mdm10) assemble to form the ERMES complex while regulator proteins are required for regulating the organization and function of the ERMES complex. Multiple regulator proteins, including Gem1, Lam6, Tom7, and Emr1, of the ERMES complex, have been identified recently. In this review, we discuss the organization of the ERMES complex and the roles of the regulator proteins of the ERMES complex.

Keywords:  ER; ERMES; membrane contact sites; mitochondria

DOI:  https://doi.org/10.1177/25152564211064491
Contact (Thousand Oaks). 2022 Jan-Dec;5:5 25152564221092487

Molecular Regulations of FUNDC1 at ER-Mitochondria Contacts Under Hypoxic Stress.

Yi Zhang, Haixia Zhuang, Hao Liu, Du Feng.

  A recent research paper published in Journal of Cell Biology by Chen and colleagues describes a novel mechanism by which the MAM (Mitochondrial-associated endoplasmic reticulum membrane) protein FUNDC1 (FUN14 domain-containing protein 1) regulates mitochondrial division through altered protein post-translational modifications under hypoxic stress. The authors found that in a hypoxic environment, the endoplasmic reticulum-localized deubiquitinating enzyme USP19 accumulates at the MAM and interacts with the enriched mitochondrial outer membrane protein FUNDC1, which subsequently induces its deubiquitination and promotes the oligomerization and activity of DRP1, and mitochondria eventually divide in the presence of DRP1. This article provides new insights into the regulation of mitochondrial dynamics by FUNDC1 under hypoxic condition.

Keywords:  DRP1; FUNDC1; MAM; Mitochondria; USP19

DOI:  https://doi.org/10.1177/25152564221092487
Contact (Thousand Oaks). 2021 Jan-Dec;4:4 25152564211052392

Interactome Analysis of the ER Stress Sensor Perk Uncovers Key Components of ER-Mitochondria Contact Sites and Ca2+ Signalling.

Maria Livia Sassano, Rita Derua, Etienne Waelkens, Patrizia Agostinis, Alexander R van Vliet.

  We recently reported that the ER stress kinase PERK regulates ER-mitochondria appositions and ER- plasma membrane (ER-PM) contact sites, independent of its canonical role in the unfolded protein response. PERK regulation of ER-PM contacts was revealed by a proximity biotinylation (BioID) approach and involved a dynamic PERK-Filamin A interaction supporting the formation of ER-PM contacts by actin-cytoskeleton remodeling in response to depletion of ER-Ca2+ stores. In this report, we further interrogated the PERK BioID interactome by validating through co-IP experiments the interaction between PERK and two proteins involved in Ca2+ handling and ER-mitochondria contact sites. These included the vesicle associated membrane (VAMP)-associated proteins (VAPA/B) and the main ER Ca2+ pump sarcoplasmic/endoplasmic reticulum Ca ATPase 2 (SERCA2). These data identify new putative PERK interacting proteins with a crucial role in membrane contact sites and Ca2+ signaling further supporting the uncanonical role of PERK in Ca2+ signaling through membrane contact sites (MCSs).

Keywords:  ER stress; cell biology; endoplasmic reticulum; mitochondrial associated membranes (MAM); sarco/endoplasmic reticulum Ca2+-ATPase (SERCA)

DOI:  https://doi.org/10.1177/25152564211052392
Biology (Basel). 2023 Jun 06. pii: 823. [Epub ahead of print]12(6):

35 Years of TFAM Research: Old Protein, New Puzzles.

Natalya Kozhukhar, Mikhail F Alexeyev.

  Transcription Factor A Mitochondrial (TFAM), through its contributions to mtDNA maintenance and expression, is essential for cellular bioenergetics and, therefore, for the very survival of cells. Thirty-five years of research on TFAM structure and function generated a considerable body of experimental evidence, some of which remains to be fully reconciled. Recent advancements allowed an unprecedented glimpse into the structure of TFAM complexed with promoter DNA and TFAM within the open promoter complexes. These novel insights, however, raise new questions about the function of this remarkable protein. In our review, we compile the available literature on TFAM structure and function and provide some critical analysis of the available data.

Keywords:  mitochondria; mitochondrial DNA; mitochondrial DNA repair; mitochondrial DNA replication; mitochondrial DNA transcription; mitochondrial biogenesis; mitochondrial transcription factor A (TFAM)

DOI:  https://doi.org/10.3390/biology12060823