bims-celmim Biomed News
on Cellular and mitochondrial metabolism
Issue of 2024‒11‒10
fiveteen papers selected by
Marc Segarra Mondejar
  1. Mitochondrial elongation impairs breast cancer metastasis.
  2. Analysis of mitochondrial biogenesis regulation by oxidative stress.
  3. Cellular ATP demand creates metabolically distinct subpopulations of mitochondria.
  4. Analysis of protein trafficking between mitochondria and the endoplasmic reticulum by fluorescence microscopy.
  5. Regulation of leukemogenesis via redox metabolism.
  6. Ca2+ tunneling architecture and function are important for secretion.
  7. Analysis of protein-protein interaction of the mitochondrial translocase at work by using technically effective BPA photo-crosslinking method.
  8. Approaches for the analysis of redox-dependent protein import into mitochondria of mammalian cells.
  9. Activation of lysosomal Ca2+ channels mitigates mitochondrial damage and oxidative stress.
  10. Analysis of mitochondrial translocases TOM and TIM by the patch-clamping technique.
  11. Cancer Metabolism: Historical Landmarks, New Concepts, and Opportunities.
  12. Endoplasmic reticulum stress-mediated autophagy in cancer and its interaction with apoptosis and ferroptosis.
  13. Homeostasis control in health and disease by the unfolded protein response.
  14. Autophagy as a critical driver of metabolic adaptation, therapeutic resistance, and immune evasion of cancer.
  15. Does a transmembrane sodium gradient control membrane potential in mammalian mitochondria?
  1. Sci Adv. 2024 Nov 08. 10(45): eadm8212
    Mitochondrial elongation impairs breast cancer metastasis.
    Lucía Minarrieta, Matthew G Annis, Yannick Audet-Delage, Hellen Kuasne, Alain Pacis, Catherine St-Louis, Alexander Nowakowski, Marco Biondini, Mireille Khacho, Morag Park, Peter M Siegel, Julie St-Pierre.
      Mitochondrial dynamics orchestrate many essential cellular functions, including metabolism, which is instrumental in promoting cancer growth and metastatic progression. However, how mitochondrial dynamics influences metastatic progression remains poorly understood. Here, we show that breast cancer cells with low metastatic potential exhibit a more fused mitochondrial network compared to highly metastatic cells. To study the impact of mitochondrial dynamics on metastasis, we promoted mitochondrial elongation in metastatic breast cancer cells by individual genetic deletion of three key regulators of mitochondrial fission (Drp1, Fis1, Mff) or by pharmacological intervention with leflunomide. Omics analyses revealed that mitochondrial elongation causes substantial alterations in metabolic pathways and processes related to cell adhesion. In vivo, enhanced mitochondrial elongation by loss of mitochondrial fission mediators or treatment with leflunomide notably reduced metastasis formation. Furthermore, the transcriptomic signature associated with elongated mitochondria correlated with improved clinical outcome in patients with breast cancer. Overall, our findings highlight mitochondrial dynamics as a potential therapeutic target in breast cancer.
    DOI:  https://doi.org/10.1126/sciadv.adm8212
  2. Methods Enzymol. 2024 ;pii: S0076-6879(24)00405-1. [Epub ahead of print]707 519-539
    Analysis of mitochondrial biogenesis regulation by oxidative stress.
    Dheeraj Pathak, Thanuja Krishnamoorthy, Naresh Babu V Sepuri.
      Of all the causes of metabolic and neurological disorders, oxidative stress distinguishes itself by its sweeping effect on the dynamic cellular redox homeostasis and, in its wake, exposing the vulnerabilities of the protein machinery of the cell. High levels of Reactive Oxygen Species (ROS) that mitochondria produce during ATP synthesis can damage mtDNA, lipids, and essential mitochondrial proteins. ROS majorly oxidizes cysteine and methionine amino acids in peptides, which can lead to protein unfolding or misfolding of proteins, which ultimately can have a toll on their function. As mitochondrial biogenesis relies on the continuous import of nuclear-encoded proteins into mitochondria mediated by mitochondrial protein import complexes, oxidative stress triggered by mitochondria can rapidly and detrimentally affect mitochondrial biogenesis and homeostasis. Functional Mge1 is a homodimer and acts as a cochaperone and a nucleotide exchange factor of mitochondrial heat shock protein 70 (mHsp70), crucial for mitochondrial protein import. Oxidative stress like ROS, oxidizes Met 155 in Mge1, compromising its ability to dimerize and interact with mHsp70. The cell employs Methionine sulphoxide reductase 2 (Mxr2), a member of the methionine sulphoxide reductase family, to reduce oxidized Met 155 and thereby restore the essential function of Mge1. Oxidation of methionine as a regulated post-translational modification has been gaining traction. Future high throughput studies that can scan the entire mitochondrial proteome to interrogate methionine oxidation and reversal may increase the repertoire of mitochondrial proteins undergoing regulated oxidation and reduction. In this chapter, we describe the methods followed in our laboratory to study the oxidation of Mge1 and its reduction by Mxr2 in vitro.
    Keywords:  Cross linking; Methionine oxidation; Methionine sulfoixde reductase 2; Mge1; Mitochondria; Reactive Oxygen Species
    DOI:  https://doi.org/10.1016/bs.mie.2024.07.060
  3. Nature. 2024 Nov 06.
    Cellular ATP demand creates metabolically distinct subpopulations of mitochondria.
    Keun Woo Ryu, Tak Shun Fung, Daphne C Baker, Michelle Saoi, Jinsung Park, Christopher A Febres-Aldana, Rania G Aly, Ruobing Cui, Anurag Sharma, Yi Fu, Olivia L Jones, Xin Cai, H Amalia Pasolli, Justin R Cross, Charles M Rudin, Craig B Thompson.
      Mitochondria serve a crucial role in cell growth and proliferation by supporting both ATP synthesis and the production of macromolecular precursors. Whereas oxidative phosphorylation (OXPHOS) depends mainly on the oxidation of intermediates from the tricarboxylic acid cycle, the mitochondrial production of proline and ornithine relies on reductive synthesis1. How these competing metabolic pathways take place in the same organelle is not clear. Here we show that when cellular dependence on OXPHOS increases, pyrroline-5-carboxylate synthase (P5CS)-the rate-limiting enzyme in the reductive synthesis of proline and ornithine-becomes sequestered in a subset of mitochondria that lack cristae and ATP synthase. This sequestration is driven by both the intrinsic ability of P5CS to form filaments and the mitochondrial fusion and fission cycle. Disruption of mitochondrial dynamics, by impeding mitofusin-mediated fusion or dynamin-like-protein-1-mediated fission, impairs the separation of P5CS-containing mitochondria from mitochondria that are enriched in cristae and ATP synthase. Failure to segregate these metabolic pathways through mitochondrial fusion and fission results in cells either sacrificing the capacity for OXPHOS while sustaining the reductive synthesis of proline, or foregoing proline synthesis while preserving adaptive OXPHOS. These findings provide evidence of the key role of mitochondrial fission and fusion in maintaining both oxidative and reductive biosyntheses in response to changing nutrient availability and bioenergetic demand.
    DOI:  https://doi.org/10.1038/s41586-024-08146-w
  4. Methods Enzymol. 2024 ;pii: S0076-6879(24)00381-1. [Epub ahead of print]707 153-171
    Analysis of protein trafficking between mitochondria and the endoplasmic reticulum by fluorescence microscopy.
    Shunsuke Matsumoto, Suzuka Ono, Toshiya Endo.
      Precise protein localization is essential for normal cellular functions. However, recent studies have revealed that protein targeting is error-prone, and tail-anchored proteins mistargeted to mitochondria are transferred to the endoplasmic reticulum (ER) by an ATPase Msp1 (yeast)/ATAD1 (human) in the mitochondrial outer membrane for further quality examination in the ER to determine their fate, degradation or re-targeting. Analysis of the inter-organelle transfer of proteins requires a combination of time-lapse fluorescence microscopy and a system to achieve regulation of the protein levels of both transfer substrates and factors regulating the transfer in a coordinated manner at precise timing. This can be achieved by using a promoter switch for expression and acute depletion of involved factors through the degron-based proteasome system. In this chapter, we will describe methods to analyze inter-organelle protein transfer by fluorescence microscope within living yeast cells, by using the example of Msp1-mediated transfer of mistargeted proteins from mitochondria to the ER.
    Keywords:  AID degradation system; Endoplasmic reticulum; Fluorescence microscope; GET system; Inter-organelle protein transfer; Mitochondria; Msp1; Tail-anchored protein
    DOI:  https://doi.org/10.1016/bs.mie.2024.07.041
  5. Trends Cell Biol. 2024 Nov;pii: S0962-8924(23)00205-2. [Epub ahead of print]34(11): 928-941
    Regulation of leukemogenesis via redox metabolism.
    Zhuo Zhang, Chiqi Chen, Xie Li, Junke Zheng, Yuzheng Zhao.
      Redox metabolism plays a central role in the cellular metabolism network, involves catabolic and anabolic reactions of diverse biomass, and determines the redox state of cells. It can be quantitatively and conveniently measured in living cells and organisms with genetically encoded fluorescent sensors, providing novel insights that cannot be readily acquired via conventional metabolic assays. Here, we review the recent progress on the regulation of leukemogenesis via redox metabolism, especially redox biosensor-based findings. In general, low reactive oxygen species levels and high reductive capacity promote leukemogenesis and chemotherapy resistance in leukemia cells, and acute leukemia cells rewire metabolism of glucose, fatty acids, and some amino acids, together with oxidative phosphorylation, to fuel energy production, support biomass-related synthesis, and survive oxidative stress. In summary, redox metabolism is a potential target for the development of novel therapies for leukemia or beneficial dietary regimens for patients with refractory and relapsed leukemia.
    Keywords:  genetically encoded redox sensors; leukemia; leukemia-initiating cells; real-time monitoring; redox metabolism
    DOI:  https://doi.org/10.1016/j.tcb.2023.10.001
  6. J Cell Biol. 2025 Jan 06. pii: e202402107. [Epub ahead of print]224(1):
    Ca2+ tunneling architecture and function are important for secretion.
    Raphael J Courjaret, Larry E Wagner, Rahaf R Ammouri, David I Yule, Khaled Machaca.
      Ca2+ tunneling requires both store-operated Ca2+ entry (SOCE) and Ca2+ release from the endoplasmic reticulum (ER). Tunneling expands the SOCE microdomain through Ca2+ uptake by SERCA into the ER lumen where it diffuses and is released via IP3 receptors. In this study, using high-resolution imaging, we outline the spatial remodeling of the tunneling machinery (IP3R1; SERCA; PMCA; and Ano1 as an effector) relative to STIM1 in response to store depletion. We show that these modulators redistribute to distinct subdomains laterally at the plasma membrane (PM) and axially within the cortical ER. To functionally define the role of Ca2+ tunneling, we engineered a Ca2+ tunneling attenuator (CaTAr) that blocks tunneling without affecting Ca2+ release or SOCE. CaTAr inhibits Cl- secretion in sweat gland cells and reduces sweating in vivo in mice, showing that Ca2+ tunneling is important physiologically. Collectively our findings argue that Ca2+ tunneling is a fundamental Ca2+ signaling modality.
    DOI:  https://doi.org/10.1083/jcb.202402107
  7. Methods Enzymol. 2024 ;pii: S0076-6879(24)00407-5. [Epub ahead of print]707 237-256
    Analysis of protein-protein interaction of the mitochondrial translocase at work by using technically effective BPA photo-crosslinking method.
    Edward Germany, Takuya Shiota.
      The BPA photo-crosslinking method exploits the property of p-benzoyl-L-phenylalanine (pBpa), an amino acid containing a photoreactive side chain, and allows for the crosslinking with nearby proteins upon Ultraviolet irradiation. This feature enables the capture of two proteins within a close proximity with high spatial resolution at the level of amino acid residues. In this chapter, we introduce an example of the employment of the BPA photo-crosslinking method to the Translocase of the Outer Mitochondrial membrane complex of mitochondria in Saccharomyces cerevisiae as a model protein translocase. Here in, we provide three procedures (i) the introduction of pBpa into proteins of interest in living yeast cells by in vivo suppressor tRNA system; (ii) analysis of in vivo subunit-subunit interactions intra-complex; and (iii) analysis of translocase channel-substrate interactions in organello. The use of in vivo and in organello crosslinking tools enable the robust analysis of translocases in a near-to physiological condition.
    Keywords:  Mitochondrial protein import; Photo-crosslink; Protein-protein interaction; TOM complex; Tom40; Unnatural amino acid
    DOI:  https://doi.org/10.1016/bs.mie.2024.07.062
  8. Methods Enzymol. 2024 ;pii: S0076-6879(24)00367-7. [Epub ahead of print]707 637-671
    Approaches for the analysis of redox-dependent protein import into mitochondria of mammalian cells.
    Julia Racho, Jan Riemer.
      Oxidation of cysteine residues in proteins can take place as part of an enzymatic reaction cycle, during oxidative protein folding or as a consequence of redox signalling or oxidative stress. Following changes in protein thiol redox states allows to investigate the mechanisms underlying thiol-disulphide redox processes. In this book chapter, we provide information and protocols on different methods for redox state determination with a focus on these processes in the context of oxidation-dependent protein import into the mitochondrial intermembrane space. These methods include assessing the cysteine redox state of mature proteins, methods to investigate oxidative protein folding in radioactive pulse chase assays and methods to follow specifically the formation of oxidative folding intermediates between oxidoreductases and substrates.
    Keywords:  ALR; MIA40; disulphide bond formation; import; mitochondria; oxidative protein folding; redox
    DOI:  https://doi.org/10.1016/bs.mie.2024.07.031
  9. J Cell Biol. 2025 Jan 06. pii: e202403104. [Epub ahead of print]224(1):
    Activation of lysosomal Ca2+ channels mitigates mitochondrial damage and oxidative stress.
    Xinghua Feng, Weijie Cai, Qian Li, Liding Zhao, Yaping Meng, Haoxing Xu.
      Elevated levels of plasma-free fatty acids and oxidative stress have been identified as putative primary pathogenic factors in endothelial dysfunction etiology, though their roles are unclear. In human endothelial cells, we found that saturated fatty acids (SFAs)-including the plasma-predominant palmitic acid (PA)-cause mitochondrial fragmentation and elevation of intracellular reactive oxygen species (ROS) levels. TRPML1 is a lysosomal ROS-sensitive Ca2+ channel that regulates lysosomal trafficking and biogenesis. Small-molecule agonists of TRPML1 prevented PA-induced mitochondrial damage and ROS elevation through activation of transcriptional factor EB (TFEB), which boosts lysosome biogenesis and mitophagy. Whereas genetically silencing TRPML1 abolished the protective effects of TRPML1 agonism, TRPML1 overexpression conferred a full resistance to PA-induced oxidative damage. Pharmacologically activating the TRPML1-TFEB pathway was sufficient to restore mitochondrial and redox homeostasis in SFA-damaged endothelial cells. The present results suggest that lysosome activation represents a viable strategy for alleviating oxidative damage, a common pathogenic mechanism of metabolic and age-related diseases.
    DOI:  https://doi.org/10.1083/jcb.202403104
  10. Methods Enzymol. 2024 ;pii: S0076-6879(24)00398-7. [Epub ahead of print]707 329-366
    Analysis of mitochondrial translocases TOM and TIM by the patch-clamping technique.
    María Luisa Campo.
      Mitochondrial protein import and sorting relies on sophisticated molecular machineries or translocases, of which channels are integral. Channels are built upon membrane proteins whose functions are driven by conformational changes. This implies that structural and functional information need to be integrated to gain a deep understanding of their dynamic behavior. Patch-clamp approaches are well suited for this purpose. This chapter provides a detailed description and practical guidance for applying the patch-clamp methodology to the electrophysiological characterization of mitochondrial protein import. Implementing the technique to intact mitochondria, mitoplasts, and reconstituted proteoliposomes, combined with genetically modified yeast strains, expands the scope of these studies. Focused on the TOM, TIM23, and TIM22 translocases, an analysis of the patch-clamp contribution to the field is outlined.
    Keywords:  Mitochondria; Mitochondrial protein import; Patch-clamp; Protein import channels; TIM22 translocase; TIM23 translocase; TOM translocase
    DOI:  https://doi.org/10.1016/bs.mie.2024.07.053
  11. Cold Spring Harb Perspect Med. 2024 Nov 05. pii: a041814. [Epub ahead of print]
    Cancer Metabolism: Historical Landmarks, New Concepts, and Opportunities.
    Navdeep S Chandel, Karen H Vousden, Ralph J DeBerardinis.
      Cancer cells undergo changes in metabolism that distinguish them from non-malignant tissue. These may provide a growth advantage by promoting oncogenic signaling and redirecting intermediates to anabolic pathways that provide building blocks for new cellular components. Cancer metabolism is far from uniform, however, and recent work has shed light on its heterogenity within and between tumors. This work is also revealing how cancer metabolism adapts to the tumor microenvironment, as well as ways in which we may capitalize on metabolic changes in cancer cells to create new therapies.
    DOI:  https://doi.org/10.1101/cshperspect.a041814
  12. Biochim Biophys Acta Mol Cell Res. 2024 Oct 26. pii: S0167-4889(24)00212-X. [Epub ahead of print] 119869
    Endoplasmic reticulum stress-mediated autophagy in cancer and its interaction with apoptosis and ferroptosis.
    Qiang Ma, Haitang Liao, Shuang Liu, He Huang, Arul Goel, Pedram Torabian, Chakrabhavi Dhananjaya Mohan, Chenyang Duan.
      The endoplasmic reticulum (ER) is a dynamic organelle that is a site of the synthesis of proteins and lipids and contributes to the regulation of proteostasis, lipid metabolism, redox balance, and calcium storage/-dependent signaling events. The disruption of ER homeostasis due to the accumulation of misfolded proteins in the ER causes ER stress which activates the unfolded protein response (UPR) system through the activation of IRE1, PERK, and ATF6. Activation of UPR is observed in various cancers and the tumor cells effectively utilize the UPR system to overcome ER stress. Also, ER stress and autophagy are the stress response mechanisms that operate together to maintain cellular homeostasis. In cancers, ER stress-mediated autophagy can function as either pro-survival or pro-death in a context-dependent manner. ER stress-mediated autophagy can have crosstalk with other types of cell death pathways including apoptosis and ferroptosis. In this article, we have reviewed the role of ER stress in the regulation of autophagy-mediated tumorigenesis and its interactions with other cell death mechanisms such as apoptosis and ferroptosis. We have also comprehensively discussed the effect of ER stress-mediated autophagy on cancer progression and chemotherapeutic resistance.
    Keywords:  Autophagy; Cancer; Cell death; Endoplasmic reticulum stress; Ferroptosis
    DOI:  https://doi.org/10.1016/j.bbamcr.2024.119869
  13. Nat Rev Mol Cell Biol. 2024 Nov 05.
    Homeostasis control in health and disease by the unfolded protein response.
    Diego Acosta-Alvear, Jonathan M Harnoss, Peter Walter, Avi Ashkenazi.
      Cells rely on the endoplasmic reticulum (ER) to fold and assemble newly synthesized transmembrane and secretory proteins - essential for cellular structure-function and for both intracellular and intercellular communication. To ensure the operative fidelity of the ER, eukaryotic cells leverage the unfolded protein response (UPR) - a stress-sensing and signalling network that maintains homeostasis by rebalancing the biosynthetic capacity of the ER according to need. The metazoan UPR can also redirect signalling from cytoprotective adaptation to programmed cell death if homeostasis restoration fails. As such, the UPR benefits multicellular organisms by preserving optimally functioning cells while removing damaged ones. Nevertheless, dysregulation of the UPR can be harmful. In this Review, we discuss the UPR and its regulatory processes as a paradigm in health and disease. We highlight important recent advances in molecular and mechanistic understanding of the UPR that enable greater precision in designing and developing innovative strategies to harness its potential for therapeutic gain. We underscore the rheostatic character of the UPR, its contextual nature and critical open questions for its further elucidation.
    DOI:  https://doi.org/10.1038/s41580-024-00794-0
  14. Curr Opin Biotechnol. 2023 Oct 27. pii: S0958-1669(23)00122-2. [Epub ahead of print]84 103012
    Autophagy as a critical driver of metabolic adaptation, therapeutic resistance, and immune evasion of cancer.
    Keisuke Yamamoto, Dosuke Iwadate, Eri Naito, Keisuke Tateishi, Mitsuhiro Fujishiro.
      Autophagy is a well-conserved intracellular degradation pathway. Besides its physiological role in normal cells, autophagy is activated in various cancer types and protects cancer cells from stresses such as nutrient deprivation, therapeutic insults, and antitumor immunity. Autophagy in cancer cells as well as normal cells in the host supports tumor metabolism, allowing for tumor growth under a nutrient-limited tumor microenvironment. Autophagy also protects cancer cells from treatments such as radiation therapy, cytotoxic chemotherapy, and targeted therapy. Though the roles of autophagy in antitumor immunity are complex and highly context-dependent, accumulating evidence now supports the role of autophagy in mediating immunotherapy resistance. Based on these preclinical findings, multiple clinical trials are currently ongoing to test the therapeutic efficacy of autophagy inhibition in cancer. Here, we review recent findings on the tumor-promoting roles of autophagy in cancer and discuss advances in therapeutic approaches that target autophagy in cancer.
    DOI:  https://doi.org/10.1016/j.copbio.2023.103012
  15. Cell Calcium. 2024 Oct 23. pii: S0143-4160(24)00120-9. [Epub ahead of print]124 102962
    Does a transmembrane sodium gradient control membrane potential in mammalian mitochondria?
    David G Nicholls.
      In a recent publication, Hernansanz-Agusti̒n et al. propose that a sodium gradient across the inner mitochondrial membrane, generated by a Na+/H+ activity integral to Complex I can account for half of the mitochondrial membrane potential. This conflicts with conventional electrophysiological and chemiosmotic understanding.
    Keywords:  Calcium signaling; Goldman equation; Membrane potential; Mitochondria; Sodium proton exchange
    DOI:  https://doi.org/10.1016/j.ceca.2024.102962
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