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1.
Int J Biol Sci ; 20(7): 2576-2591, 2024.
Article En | MEDLINE | ID: mdl-38725862

We showed that microtubule-associated tumor suppressor gene (MTUS1/ATIP) downregulation correlated with poor survival in head and neck squamous cell carcinoma (HNSCC) patients and that MTUS1/ATIP1 was the most abundant isoform in HNSCC tissue. However, the location and function of MTUS1/ATIP1 have remain unclear. In this study, we confirmed that MTUS1/ATIP1 inhibited proliferation, growth and metastasis in HNSCC in cell- and patient-derived xenograft models in vitro and in vivo. MTUS1/ATIP1 localized in the outer mitochondrial membrane, influence the morphology, movement and metabolism of mitochondria and stimulated oxidative stress in HNSCC cells by directly interacting with MFN2. MTUS1/ATIP1 activated ROS, recruiting Bax to mitochondria, facilitating cytochrome c release to the cytosol to activate caspase-3, and inducing GSDME-dependent pyroptotic death in HNSCC cells. Our findings showed that MTUS1/ATIP1 localized in the outer mitochondrial membrane in HNSCC cells and mediated anticancer effects through ROS-induced pyroptosis, which may provide a novel therapeutic strategy for HNSCC treatment.


Head and Neck Neoplasms , Mitochondria , Pyroptosis , Reactive Oxygen Species , Squamous Cell Carcinoma of Head and Neck , Humans , Reactive Oxygen Species/metabolism , Head and Neck Neoplasms/metabolism , Head and Neck Neoplasms/pathology , Head and Neck Neoplasms/genetics , Animals , Cell Line, Tumor , Mitochondria/metabolism , Squamous Cell Carcinoma of Head and Neck/metabolism , Squamous Cell Carcinoma of Head and Neck/pathology , Squamous Cell Carcinoma of Head and Neck/genetics , Mice , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Carcinoma, Squamous Cell/genetics , Mice, Nude , Tumor Suppressor Proteins/metabolism , Tumor Suppressor Proteins/genetics , Mitochondrial Membranes/metabolism , Cell Proliferation
2.
Nat Commun ; 15(1): 3793, 2024 May 07.
Article En | MEDLINE | ID: mdl-38714822

Across the cell cycle, mitochondrial dynamics are regulated by a cycling wave of actin polymerization/depolymerization. In metaphase, this wave induces actin comet tails on mitochondria that propel these organelles to drive spatial mixing, resulting in their equitable inheritance by daughter cells. In contrast, during interphase the cycling actin wave promotes localized mitochondrial fission. Here, we identify the F-actin nucleator/elongator FMNL1 as a positive regulator of the wave. FMNL1-depleted cells exhibit decreased mitochondrial polarization, decreased mitochondrial oxygen consumption, and increased production of reactive oxygen species. Accompanying these changes is a loss of hetero-fusion of wave-fragmented mitochondria. Thus, we propose that the interphase actin wave maintains mitochondrial homeostasis by promoting mitochondrial content mixing. Finally, we investigate the mechanistic basis for the observation that the wave drives mitochondrial motility in metaphase but mitochondrial fission in interphase. Our data indicate that when the force of actin polymerization is resisted by mitochondrial tethering to microtubules, as in interphase, fission results.


Actins , Homeostasis , Interphase , Mitochondria , Mitochondrial Dynamics , Actins/metabolism , Mitochondria/metabolism , Humans , Formins/metabolism , Reactive Oxygen Species/metabolism , HeLa Cells , Microtubules/metabolism , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Animals
3.
Proc Natl Acad Sci U S A ; 121(21): e2400740121, 2024 May 21.
Article En | MEDLINE | ID: mdl-38743629

The biogenesis of iron-sulfur (Fe/S) proteins entails the synthesis and trafficking of Fe/S clusters, followed by their insertion into target apoproteins. In eukaryotes, the multiple steps of biogenesis are accomplished by complex protein machineries in both mitochondria and cytosol. The underlying biochemical pathways have been elucidated over the past decades, yet the mechanisms of cytosolic [2Fe-2S] protein assembly have remained ill-defined. Similarly, the precise site of glutathione (GSH) requirement in cytosolic and nuclear Fe/S protein biogenesis is unclear, as is the molecular role of the GSH-dependent cytosolic monothiol glutaredoxins (cGrxs). Here, we investigated these questions in human and yeast cells by various in vivo approaches. [2Fe-2S] cluster assembly of cytosolic target apoproteins required the mitochondrial ISC machinery, the mitochondrial transporter Atm1/ABCB7 and GSH, yet occurred independently of both the CIA system and cGrxs. This mechanism was strikingly different from the ISC-, Atm1/ABCB7-, GSH-, and CIA-dependent assembly of cytosolic-nuclear [4Fe-4S] proteins. One notable exception to this cytosolic [2Fe-2S] protein maturation pathway defined here was yeast Apd1 which used the CIA system via binding to the CIA targeting complex through its C-terminal tryptophan. cGrxs, although attributed as [2Fe-2S] cluster chaperones or trafficking proteins, were not essential in vivo for delivering [2Fe-2S] clusters to either CIA components or target apoproteins. Finally, the most critical GSH requirement was assigned to Atm1-dependent export, i.e. a step before GSH-dependent cGrxs function. Our findings extend the general model of eukaryotic Fe/S protein biogenesis by adding the molecular requirements for cytosolic [2Fe-2S] protein maturation.


Cytosol , Glutaredoxins , Glutathione , Iron-Sulfur Proteins , Mitochondria , Saccharomyces cerevisiae Proteins , Saccharomyces cerevisiae , Cytosol/metabolism , Iron-Sulfur Proteins/metabolism , Humans , Saccharomyces cerevisiae/metabolism , Saccharomyces cerevisiae Proteins/metabolism , Saccharomyces cerevisiae Proteins/genetics , Glutathione/metabolism , Mitochondria/metabolism , Glutaredoxins/metabolism , Glutaredoxins/genetics , ATP-Binding Cassette Transporters/metabolism , Mitochondrial Proteins/metabolism
4.
Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi ; 40(4): 311-318, 2024 Apr.
Article Zh | MEDLINE | ID: mdl-38710515

Objective To investigate the effects of mitochondrial transcription factor A (TFAM) on mitochondrial function, autophagy, proliferation, invasion, and migration in cervical cancer HeLa cells and osteosarcoma U2OS cells. Methods TFAM small-interfering RNA (si-TFAM) was transfected to HeLa and U2OS cells for downregulating TFAM expression. Mito-Tracker Red CMXRos staining combined with laser confocal microscopy was used to detect mitochondrial membrane potential (MMP). MitoSOXTM Red labeling was used to test mitochondrial reactive oxygen species (mtROS) levels. The expression of mitochondrial DNA (mtDNA) was detected by real-time quantitative PCR. Changes in the number of autophagosomes were detected by immunofluorescence cytochemistry. Western blot analysis was used to detect the expressions of TFAM, autophagy microtubule associated protein 1 light chain 3A/B (LC3A/B), autophagy associated protein 2A (ATG2A), ATG2B, ATG9A, zinc finger transcription factor Snail, matrix metalloproteinase 2 (MMP2) and MMP9. CCK-8 assay and plate clony formation assay were used to detect cell proliferation, while TranswellTM assay and scratch healing assay were used to detect changes in cell invasion and migration. Results The downregulation of TFAM expression resulted in a decrease in MMP and mtDNA copy number, but an increase in mtROS production. The protein content of LC3A/B decreased significantly compared to the control group and the number of autophagosomes in the cytoplasm decreased significantly. The expressions of ATG2B and ATG9A in the early stage of autophagy were significantly reduced. The expressions of Snail, MMP2 and MMP9 proteins in HeLa and U2OS cells were also decreased. The proliferation, invasion and migration ability of HeLa and U2OS cells were inhibited after being interfered with TFAM expression. Conclusion Downregulation of TFAM expression inhibits mitochondrial function, delays autophagy process and reduces the proliferation, invasion and migration ability of cervical cancer cells and osteosarcoma cells.


Autophagy , Cell Movement , Cell Proliferation , DNA-Binding Proteins , Mitochondrial Proteins , Neoplasm Invasiveness , Osteosarcoma , Transcription Factors , Uterine Cervical Neoplasms , Humans , Cell Movement/genetics , Osteosarcoma/genetics , Osteosarcoma/pathology , Osteosarcoma/metabolism , Cell Proliferation/genetics , Transcription Factors/genetics , Transcription Factors/metabolism , Autophagy/genetics , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Female , Uterine Cervical Neoplasms/genetics , Uterine Cervical Neoplasms/pathology , Uterine Cervical Neoplasms/metabolism , Cell Line, Tumor , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Membrane Potential, Mitochondrial/genetics , Reactive Oxygen Species/metabolism , Matrix Metalloproteinase 2/metabolism , Matrix Metalloproteinase 2/genetics , Mitochondria/metabolism , Mitochondria/genetics , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , HeLa Cells , Matrix Metalloproteinase 9/metabolism , Matrix Metalloproteinase 9/genetics
5.
J Biosci ; 492024.
Article En | MEDLINE | ID: mdl-38726824

Mitochondrial alternative oxidase (AOX) is an important protein that can help in regulating reactive oxygen species and nitric oxide in plants. The role of AOX in regulation of nitro-oxidative stress in chickpea is not known. Using germinating chickpea as a model system, we investigated the role of AOX in nitro-oxidative stress tolerance. NaCl treatment was used as an inducer of nitro-oxidative stress. Treatment of germinating seeds with 150 mM NaCl led to reduced germination and radicle growth. The AOX inhibitor SHAM caused further inhibition of germination, and the AOX inducer pyruvate improved growth of the radicle under NaCl stress. Isolated mitochondria from germinated seeds under salt stress not only increased AOX capacity but also enhanced AOX protein expression. Measurement of superoxide levels revealed that AOX inhibition by SHAM can enhance superoxide levels, whereas the AOX inducer pyruvate reduced superoxide levels. Measurement of NO by gas phase chemiluminescence revealed enhanced NO generation in response to NaCl treatment. Upon NaCl treatment there was enhanced tyrosine nitration, which is an indicator of nitrosative stress response. Taken together, our results revealed that AOX induced under salinity stress in germinating chickpea can help in mitigating nitro-oxidative stress, thereby improving germination.


Cicer , Germination , Mitochondria , Mitochondrial Proteins , Nitric Oxide , Oxidative Stress , Oxidoreductases , Plant Proteins , Superoxides , Cicer/growth & development , Cicer/drug effects , Cicer/metabolism , Plant Proteins/metabolism , Germination/drug effects , Mitochondrial Proteins/metabolism , Mitochondria/metabolism , Mitochondria/drug effects , Oxidative Stress/drug effects , Nitric Oxide/metabolism , Oxidoreductases/metabolism , Superoxides/metabolism , Seeds/growth & development , Seeds/drug effects , Seeds/metabolism , Reactive Oxygen Species/metabolism , Sodium Chloride/pharmacology , Gene Expression Regulation, Plant/drug effects , Pyruvic Acid/metabolism
6.
Mol Biol Rep ; 51(1): 642, 2024 May 10.
Article En | MEDLINE | ID: mdl-38727866

BACKGROUND: The mitochondrial carrier homolog 2 (MTCH2) is a mitochondrial outer membrane protein regulating mitochondrial metabolism and functions in lipid homeostasis and apoptosis. Experimental data on the interaction of MTCH2 with viral proteins in virus-infected cells are very limited. Here, the interaction of MTCH2 with PA subunit of influenza A virus RdRp and its effects on viral replication was investigated. METHODS: The human MTCH2 protein was identified as the influenza A virus PA-related cellular factor with the Y2H assay. The interaction between GST.MTCH2 and PA protein co-expressed in transfected HEK293 cells was evaluated by GST-pull down. The effect of MTCH2 on virus replication was determined by quantification of viral transcript and/or viral proteins in the cells transfected with MTCH2-encoding plasmid or MTCH2-siRNA. An interaction model of MTCH2 and PA was predicted with protein modeling/docking algorithms. RESULTS: It was observed that PA and GST.MTCH2 proteins expressed in HEK293 cells were co-precipitated by glutathione-agarose beads. The influenza A virus replication was stimulated in HeLa cells whose MTCH2 expression was suppressed with specific siRNA, whereas the increase of MTCH2 in transiently transfected HEK293 cells inhibited viral RdRp activity. The results of a Y2H assay and protein-protein docking analysis suggested that the amino terminal part of the viral PA (nPA) can bind to the cytoplasmic domain comprising amino acid residues 253 to 282 of the MTCH2. CONCLUSION: It is suggested that the host mitochondrial MTCH2 protein is probably involved in the interaction with the viral polymerase protein PA to cause negative regulatory effect on influenza A virus replication in infected cells.


Influenza A virus , Virus Replication , Humans , Virus Replication/genetics , HEK293 Cells , Influenza A virus/physiology , Influenza A virus/genetics , HeLa Cells , Down-Regulation , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/genetics , Protein Binding , Mitochondria/metabolism , RNA-Dependent RNA Polymerase/metabolism , RNA-Dependent RNA Polymerase/genetics
7.
Hepatol Commun ; 8(5)2024 May 01.
Article En | MEDLINE | ID: mdl-38696369

BACKGROUND: Human genetic studies have identified several mitochondrial amidoxime-reducing component 1 (MTARC1) variants as protective against metabolic dysfunction-associated steatotic liver disease. The MTARC1 variants are associated with decreased plasma lipids and liver enzymes and reduced liver-related mortality. However, the role of mARC1 in fatty liver disease is still unclear. METHODS: Given that mARC1 is mainly expressed in hepatocytes, we developed an N-acetylgalactosamine-conjugated mouse Mtarc1 siRNA, applying it in multiple in vivo models to investigate the role of mARC1 using multiomic techniques. RESULTS: In ob/ob mice, knockdown of Mtarc1 in mouse hepatocytes resulted in decreased serum liver enzymes, LDL-cholesterol, and liver triglycerides. Reduction of mARC1 also reduced liver weight, improved lipid profiles, and attenuated liver pathological changes in 2 diet-induced metabolic dysfunction-associated steatohepatitis mouse models. A comprehensive analysis of mARC1-deficient liver from a metabolic dysfunction-associated steatohepatitis mouse model by metabolomics, proteomics, and lipidomics showed that Mtarc1 knockdown partially restored metabolites and lipids altered by diet. CONCLUSIONS: Taken together, reducing mARC1 expression in hepatocytes protects against metabolic dysfunction-associated steatohepatitis in multiple murine models, suggesting a potential therapeutic approach for this chronic liver disease.


Disease Models, Animal , Gene Knockdown Techniques , Hepatocytes , Animals , Mice , Hepatocytes/metabolism , Liver/metabolism , Male , RNA, Small Interfering/genetics , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Non-alcoholic Fatty Liver Disease/genetics , Non-alcoholic Fatty Liver Disease/metabolism , Non-alcoholic Fatty Liver Disease/prevention & control , Mice, Inbred C57BL
8.
Life Sci Alliance ; 7(7)2024 Jul.
Article En | MEDLINE | ID: mdl-38697845

Defective mitophagy in renal tubular epithelial cells is one of the main drivers of renal fibrosis in diabetic kidney disease. Our gene sequencing data showed the expression of PINK1 and BNIP3, two key molecules of mitophagy, was decreased in renal tissues of VDR-knockout mice. Herein, streptozotocin (STZ) was used to induce renal interstitial fibrosis in mice. VDR deficiency exacerbated STZ-induced renal impairment and defective mitophagy. Paricalcitol (pari, a VDR agonist) and the tubular epithelial cell-specific overexpression of VDR restored the expression of PINK1 and BNIP3 in the renal cortex and attenuated STZ-induced kidney fibrosis and mitochondrial dysfunction. In HK-2 cells under high glucose conditions, an increased level of α-SMA, COL1, and FN and a decreased expression of PINK1 and BNIP3 with severe mitochondrial damage were observed, and these alterations could be largely reversed by pari treatment. ChIP-qPCR and luciferase reporter assays showed VDR could positively regulate the transcription of Pink1 and Bnip3 genes. These findings reveal that VDR could restore mitophagy defects and attenuate STZ-induced fibrosis in diabetic mice through regulation of PINK1 and BNIP3.


Diabetes Mellitus, Experimental , Diabetic Nephropathies , Ergocalciferols , Membrane Proteins , Mice, Knockout , Mitophagy , Protein Kinases , Receptors, Calcitriol , Streptozocin , Animals , Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Experimental/genetics , Mice , Membrane Proteins/metabolism , Membrane Proteins/genetics , Receptors, Calcitriol/metabolism , Receptors, Calcitriol/genetics , Mitophagy/genetics , Mitophagy/drug effects , Protein Kinases/metabolism , Protein Kinases/genetics , Humans , Diabetic Nephropathies/metabolism , Diabetic Nephropathies/genetics , Male , Mitochondria/metabolism , Mitochondria/drug effects , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Fibrosis , Kidney Tubules/metabolism , Kidney Tubules/pathology , Proto-Oncogene Proteins/metabolism , Proto-Oncogene Proteins/genetics , Mice, Inbred C57BL , Epithelial Cells/metabolism , Epithelial Cells/drug effects , Cell Line , Gene Expression Regulation/drug effects
9.
J Cell Mol Med ; 28(9): e18293, 2024 May.
Article En | MEDLINE | ID: mdl-38722298

Charcot-Marie-Tooth type 2A (CMT2A) is an inherited sensorimotor neuropathy associated with mutations within the Mitofusin 2 (MFN2) gene. These mutations impair normal mitochondrial functioning via different mechanisms, disturbing the equilibrium between mitochondrial fusion and fission, of mitophagy and mitochondrial axonal transport. Although CMT2A disease causes a significant disability, no resolutive treatment for CMT2A patients to date. In this context, reliable experimental models are essential to precisely dissect the molecular mechanisms of disease and to devise effective therapeutic strategies. The most commonly used models are either in vitro or in vivo, and among the latter murine models are by far the most versatile and popular. Here, we critically revised the most relevant literature focused on the experimental models, providing an update on the mammalian models of CMT2A developed to date. We highlighted the different phenotypic, histopathological and molecular characteristics, and their use in translational studies for bringing potential therapies from the bench to the bedside. In addition, we discussed limitations of these models and perspectives for future improvement.


Charcot-Marie-Tooth Disease , Disease Models, Animal , Charcot-Marie-Tooth Disease/genetics , Charcot-Marie-Tooth Disease/pathology , Charcot-Marie-Tooth Disease/therapy , Charcot-Marie-Tooth Disease/metabolism , Animals , Humans , Mutation , Mitochondria/metabolism , Mitochondria/genetics , Mitochondria/pathology , GTP Phosphohydrolases/genetics , GTP Phosphohydrolases/metabolism , Mice , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Mitochondrial Dynamics/genetics
10.
J Mol Biol ; 436(10): 168559, 2024 May 15.
Article En | MEDLINE | ID: mdl-38580077

Upstream open reading frames (uORFs) are cis-acting elements that can dynamically regulate the translation of downstream ORFs by suppressing downstream translation under basal conditions and, in some cases, increasing downstream translation under stress conditions. Computational and empirical methods have identified uORFs in the 5'-UTRs of approximately half of all mouse and human transcripts, making uORFs one of the largest regulatory elements known. Because the prevailing dogma was that eukaryotic mRNAs produce a single functional protein, the peptides and small proteins, or microproteins, encoded by uORFs were rarely studied. We hypothesized that a uORF in the SLC35A4 mRNA is producing a functional microprotein (SLC35A4-MP) because of its conserved amino acid sequence. Through a series of biochemical and cellular experiments, we find that the 103-amino acid SLC35A4-MP is a single-pass transmembrane inner mitochondrial membrane (IMM) microprotein. The IMM contains the protein machinery crucial for cellular respiration and ATP generation, and loss of function studies with SLC35A4-MP significantly diminish maximal cellular respiration, indicating a vital role for this microprotein in cellular metabolism. The findings add SLC35A4-MP to the growing list of functional microproteins and, more generally, indicate that uORFs that encode conserved microproteins are an untapped reservoir of functional microproteins.


Mitochondrial Membranes , Open Reading Frames , Open Reading Frames/genetics , Humans , Mitochondrial Membranes/metabolism , Animals , Mice , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Amino Acid Sequence , RNA, Messenger/genetics , RNA, Messenger/metabolism , 5' Untranslated Regions/genetics , Protein Biosynthesis , Mitochondria/metabolism , Mitochondria/genetics
11.
Int Immunopharmacol ; 133: 112012, 2024 May 30.
Article En | MEDLINE | ID: mdl-38657501

Alveolar macrophages (AMs) seed in lung during embryogenesis and become mature in perinatal period. Establishment of acclimatization to environmental challenges is important, whereas the detailed mechanisms that drive metabolic adaptation of AMs remains to be elucidated. Here, we showed that energy metabolism of AMs was transformed from glycolysis prenatally to oxidative phosphorylation (OXPHOS) postnatally accompanied by up-regulated expression of mitochondrial transcription factor A (TFAM). TFAM deficiency disturbed mitochondrial stability and decreased OXPHOS, which finally impaired AM maintenance and function, but not AM embryonic development. Mechanistically, Tfam-deletion resulted in impaired mitochondrial respiration and decreased ATP production, which triggered endoplasmic reticulum (ER) stress to cause B cell lymphoma 2 ovarian killer (BOK) accumulation and abnormal distribution of intracellular Ca2+, eventually led to induce AM apoptotic death. Thus, our data illustrated mitochondrial-dependent OXPHOS played a key role in orchestrating AM postnatal metabolic adaptation.


Lung , Macrophages, Alveolar , Mitochondria , Oxidative Phosphorylation , Animals , Macrophages, Alveolar/metabolism , Mitochondria/metabolism , Mice , Lung/metabolism , Adaptation, Physiological , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Transcription Factors/metabolism , Transcription Factors/genetics , Endoplasmic Reticulum Stress , Mice, Knockout , Apoptosis , Mice, Inbred C57BL , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Female , Glycolysis , Adenosine Triphosphate/metabolism , High Mobility Group Proteins
12.
Mitochondrion ; 76: 101877, 2024 May.
Article En | MEDLINE | ID: mdl-38599304

Mitochondrial Ca2+ uptake is essential in regulating bioenergetics, cell death, and cytosolic Ca2+ transients. Mitochondrial Calcium Uniporter (MCU) mediates the mitochondrial Ca2+ uptake. Though MCU regulation by MICUs is unequivocally established, there needs to be more knowledge of whether divalent cations regulate MCU. Here, we set out to understand the mitochondrial matrix Mg2+-dependent regulation of MCU activity. We showed that decreased matrix [Mg2+] is associated with increased MCU activity and significantly prompted mitochondrial permeability transition pore opening. Our findings support the critical role of mMg2+ in regulating MCU activity.


Calcium Channels , Calcium , Magnesium , Mitochondria , Calcium/metabolism , Magnesium/metabolism , Calcium Channels/metabolism , Mitochondria/metabolism , Humans , Cell Survival , Mitochondrial Proteins/metabolism
13.
Int J Biol Macromol ; 267(Pt 1): 131455, 2024 May.
Article En | MEDLINE | ID: mdl-38588835

The analysis of cryo-electron tomography images of human and rat mitochondria revealed that the mitochondrial matrix is at least as crowded as the cytosol. To mitigate the crowding effects, metabolite transport in the mitochondria primarily occurs through the intermembrane space, which is significantly less crowded. The scientific literature largely ignores how enzyme systems and metabolite transport are organized in the crowded environment of the mitochondrial matrix. Under crowded conditions, multivalent interactions carried out by disordered protein regions (IDRs), may become extremely important. We analyzed the human mitochondrial proteome to determine the presence and physiological significance of IDRs. Despite mitochondrial proteins being generally more ordered than cytosolic or overall proteome proteins, disordered regions plays a significant role in certain mitochondrial compartments and processes. Even in highly ordered enzyme systems, there are proteins with long IDRs. Some IDRs act as binding elements between highly ordered subunits, while the roles of others are not yet established. Mitochondrial systems, like their bacterial ancestors, rely less on IDRs and more on RNA for LLPS compartmentalization. More evolutionarily advanced subsystems that enable mitochondria-cell interactions contain more IDRs. The study highlights the crucial and often overlooked role played by IDRs and non-coding RNAs in mitochondrial organization.


Intrinsically Disordered Proteins , Mitochondria , Intrinsically Disordered Proteins/metabolism , Intrinsically Disordered Proteins/chemistry , Intrinsically Disordered Proteins/genetics , Mitochondria/metabolism , Humans , Animals , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/chemistry , Mitochondrial Proteins/genetics , RNA/metabolism , Proteome/metabolism , Rats
14.
Nat Commun ; 15(1): 3290, 2024 Apr 17.
Article En | MEDLINE | ID: mdl-38632225

The functions of cellular organelles and sub-compartments depend on their protein content, which can be characterized by spatial proteomics approaches. However, many spatial proteomics methods are limited in their ability to resolve organellar sub-compartments, profile multiple sub-compartments in parallel, and/or characterize membrane-associated proteomes. Here, we develop a cross-link assisted spatial proteomics (CLASP) strategy that addresses these shortcomings. Using human mitochondria as a model system, we show that CLASP can elucidate spatial proteomes of all mitochondrial sub-compartments and provide topological insight into the mitochondrial membrane proteome. Biochemical and imaging-based follow-up studies confirm that CLASP allows discovering mitochondria-associated proteins and revising previous protein sub-compartment localization and membrane topology data. We also validate the CLASP concept in synaptic vesicles, demonstrating its applicability to different sub-cellular compartments. This study extends the scope of cross-linking mass spectrometry beyond protein structure and interaction analysis towards spatial proteomics, and establishes a method for concomitant profiling of sub-organelle and membrane proteomes.


Membrane Proteins , Proteome , Humans , Proteome/metabolism , Membrane Proteins/metabolism , Proteomics/methods , Organelles/metabolism , Mitochondria/metabolism , Mitochondrial Proteins/metabolism
15.
Plant Cell Physiol ; 65(4): 576-589, 2024 May 14.
Article En | MEDLINE | ID: mdl-38591870

In the last years, plant organelles have emerged as central coordinators of responses to internal and external stimuli, which can induce stress. Mitochondria play a fundamental role as stress sensors being part of a complex communication network between the organelles and the nucleus. Among the different environmental stresses, salt stress poses a significant challenge and requires efficient signaling and protective mechanisms. By using the why2 T-DNA insertion mutant and a novel knock-out mutant prepared by CRISPR/Cas9-mediated genome editing, this study revealed that WHIRLY2 is crucial for protecting mitochondrial DNA (mtDNA) integrity during salt stress. Loss-of-function mutants show an enhanced sensitivity to salt stress. The disruption of WHIRLY2 causes the impairment of mtDNA repair that results in the accumulation of aberrant recombination products, coinciding with severe alterations in nucleoid integrity and overall mitochondria morphology besides a compromised redox-dependent response and misregulation of antioxidant enzymes. The results of this study revealed that WHIRLY2-mediated structural features in mitochondria (nucleoid compactness and cristae) are important for an effective response to salt stress.


Arabidopsis Proteins , Arabidopsis , DNA, Mitochondrial , Mitochondria , Salt Stress , Arabidopsis/genetics , Arabidopsis/physiology , Arabidopsis/metabolism , Arabidopsis/drug effects , Arabidopsis Proteins/metabolism , Arabidopsis Proteins/genetics , Salt Stress/genetics , Mitochondria/metabolism , Mitochondria/drug effects , DNA, Mitochondrial/genetics , DNA, Mitochondrial/metabolism , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Gene Expression Regulation, Plant , CRISPR-Cas Systems
16.
Methods Mol Biol ; 2757: 239-257, 2024.
Article En | MEDLINE | ID: mdl-38668970

Mitochondrial proteomes have been experimentally characterized for only a handful of animal species. However, the increasing availability of genomic and transcriptomic data allows one to infer mitochondrial proteins using computational tools. MitoPredictor is a novel random forest classifier, which utilizes orthology search, mitochondrial targeting signal (MTS) identification, and protein domain content to infer mitochondrial proteins in animals. MitoPredictor's output also includes an easy-to-use R Shiny applet for the visualization and analysis of the results. In this article, we provide a guide for predicting and analyzing the mitochondrial proteome of the ctenophore Mnemiopsis leidyi using MitoPredictor.


Ctenophora , Mitochondrial Proteins , Proteome , Animals , Ctenophora/metabolism , Ctenophora/genetics , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , Computational Biology/methods , Mitochondria/metabolism , Proteomics/methods , Software
17.
Pharmacol Res ; 203: 107164, 2024 May.
Article En | MEDLINE | ID: mdl-38569981

The impact of mitochondrial dysfunction on the pathogenesis of cardiovascular disease is increasing. However, the precise underlying mechanism remains unclear. Mitochondria produce cellular energy through oxidative phosphorylation while regulating calcium homeostasis, cellular respiration, and the production of biosynthetic chemicals. Nevertheless, problems related to cardiac energy metabolism, defective mitochondrial proteins, mitophagy, and structural changes in mitochondrial membranes can cause cardiovascular diseases via mitochondrial dysfunction. Mitofilin is a critical inner mitochondrial membrane protein that maintains cristae structure and facilitates protein transport while linking the inner mitochondrial membrane, outer mitochondrial membrane, and mitochondrial DNA transcription. Researchers believe that mitofilin may be a therapeutic target for treating cardiovascular diseases, particularly cardiac mitochondrial dysfunctions. In this review, we highlight current findings regarding the role of mitofilin in the pathogenesis of cardiovascular diseases and potential therapeutic compounds targeting mitofilin.


Cardiovascular Diseases , Mitochondrial Proteins , Muscle Proteins , Humans , Animals , Cardiovascular Diseases/metabolism , Cardiovascular Diseases/drug therapy , Muscle Proteins/metabolism , Muscle Proteins/genetics , Mitochondrial Proteins/metabolism , Mitochondria, Heart/metabolism , Mitochondria, Heart/drug effects
18.
Life Sci Alliance ; 7(7)2024 Jul.
Article En | MEDLINE | ID: mdl-38664021

Mitochondrial transcription factor A, TFAM, is essential for mitochondrial function. We examined the effects of overexpressing the TFAM gene in mice. Two types of transgenic mice were created: TFAM heterozygous (TFAM Tg) and homozygous (TFAM Tg/Tg) mice. TFAM Tg/Tg mice were smaller and leaner notably with longer lifespans. In skeletal muscle, TFAM overexpression changed gene and protein expression in mitochondrial respiratory chain complexes, with down-regulation in complexes 1, 3, and 4 and up-regulation in complexes 2 and 5. The iMPAQT analysis combined with metabolomics was able to clearly separate the metabolomic features of the three types of mice, with increased degradation of fatty acids and branched-chain amino acids and decreased glycolysis in homozygotes. Consistent with these observations, comprehensive gene expression analysis revealed signs of mitochondrial stress, with elevation of genes associated with the integrated and mitochondrial stress responses, including Atf4, Fgf21, and Gdf15. These found that mitohormesis develops and metabolic shifts in skeletal muscle occur as an adaptive strategy.


DNA-Binding Proteins , High Mobility Group Proteins , Longevity , Mice, Transgenic , Mitochondrial Proteins , Muscle, Skeletal , Transcription Factors , Animals , Mice , Muscle, Skeletal/metabolism , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Transcription Factors/genetics , Transcription Factors/metabolism , Longevity/genetics , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Mitochondria/metabolism , Mitochondria/genetics , Male , Metabolomics/methods , Growth Differentiation Factor 15/genetics , Growth Differentiation Factor 15/metabolism , Gene Expression Regulation
19.
Neurobiol Dis ; 195: 106498, 2024 Jun 01.
Article En | MEDLINE | ID: mdl-38583639

CHCHD10-related disease causes a spectrum of clinical presentations including mitochondrial myopathy, cardiomyopathy, amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). We generated a knock-in mouse model bearing the p.Ser59Leu (S59L) CHCHD10 variant. Chchd10S59L/+ mice have been shown to phenotypically replicate the disorders observed in patients: myopathy with mtDNA instability, cardiomyopathy and typical ALS features (protein aggregation, neuromuscular junction degeneration and spinal motor neuron loss). Here, we conducted a comprehensive behavioral, electrophysiological and neuropathological assessment of Chchd10S59L/+ mice. These animals show impaired learning and memory capacities with reduced long-term potentiation (LTP) measured at the Perforant Pathway-Dentate Gyrus (PP-DG) synapses. In the hippocampus of Chchd10S59L/+ mice, neuropathological studies show the involvement of protein aggregates, activation of the integrated stress response (ISR) and neuroinflammation in the degenerative process. These findings contribute to decipher mechanisms associated with CHCHD10 variants linking mitochondrial dysfunction and neuronal death. They also validate the Chchd10S59L/+ mice as a relevant model for FTD, which can be used for preclinical studies to test new therapeutic strategies for this devastating disease.


Disease Models, Animal , Frontotemporal Dementia , Mitochondrial Proteins , Animals , Frontotemporal Dementia/pathology , Frontotemporal Dementia/genetics , Mice , Mitochondrial Proteins/genetics , Mitochondrial Proteins/metabolism , Mice, Transgenic , Behavior, Animal/physiology , Male , Long-Term Potentiation/physiology , Mice, Inbred C57BL , Hippocampus/pathology , Hippocampus/metabolism
20.
Life Sci Alliance ; 7(7)2024 Jul.
Article En | MEDLINE | ID: mdl-38664022

Neural stem cells (NSCs) reside in discrete regions of the adult mammalian brain where they can differentiate into neurons, astrocytes, and oligodendrocytes. Several studies suggest that mitochondria have a major role in regulating NSC fate. Here, we evaluated mitochondrial properties throughout NSC differentiation and in lineage-specific cells. For this, we used the neurosphere assay model to isolate, expand, and differentiate mouse subventricular zone postnatal NSCs. We found that the levels of proteins involved in mitochondrial fusion (Mitofusin [Mfn] 1 and Mfn 2) increased, whereas proteins involved in fission (dynamin-related protein 1 [DRP1]) decreased along differentiation. Importantly, changes in mitochondrial dynamics correlated with distinct patterns of mitochondrial morphology in each lineage. Particularly, we found that the number of branched and unbranched mitochondria increased during astroglial and neuronal differentiation, whereas the area occupied by mitochondrial structures significantly reduced with oligodendrocyte maturation. In addition, comparing the three lineages, neurons revealed to be the most energetically flexible, whereas astrocytes presented the highest ATP content. Our work identified putative mitochondrial targets to enhance lineage-directed differentiation of mouse subventricular zone-derived NSCs.


Astrocytes , Cell Differentiation , Cell Lineage , Dynamins , Mitochondria , Mitochondrial Dynamics , Neural Stem Cells , Neurons , Oligodendroglia , Animals , Neural Stem Cells/metabolism , Neural Stem Cells/cytology , Mitochondria/metabolism , Mice , Cell Differentiation/genetics , Cell Lineage/genetics , Astrocytes/metabolism , Astrocytes/cytology , Oligodendroglia/metabolism , Oligodendroglia/cytology , Neurons/metabolism , Neurons/cytology , Cells, Cultured , Mitochondrial Proteins/metabolism , Mitochondrial Proteins/genetics , GTP Phosphohydrolases/metabolism , GTP Phosphohydrolases/genetics , Neurogenesis , Lateral Ventricles/cytology , Lateral Ventricles/metabolism
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