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Benedicto AM, Lucantoni F, Fuster-Martínez I, Diaz-Pozo P, Dorcaratto D, Muñoz-Forner E, Victor VM, Esplugues JV, Blas-García A, Apostolova N. Interference with mitochondrial function as part of the antifibrogenic effect of Rilpivirine: A step towards novel targets in hepatic stellate cell activation. Biomed Pharmacother 2024; 178:117206. [PMID: 39079261 DOI: 10.1016/j.biopha.2024.117206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 07/15/2024] [Accepted: 07/23/2024] [Indexed: 08/25/2024] Open
Abstract
Activated hepatic stellate cells (aHSCs), the main perpetrators of liver fibrosis, are a promising therapeutic target in the treatment of chronic liver disease. During liver injury, HSCs transcend from a quiescent to a fibrotic phenotype, a process which involves major metabolic reprogramming with altered mitochondrial function. The antiretroviral drug Rilpivirine (RPV) has demonstrated a hepatoprotective and specifically antifibrotic effect in several animal models of chronic liver injury, as well as in vitro. Herein, we use HSCs activated with the profibrogenic cytokine TGF-β to explore whether mitochondrial function is implicated in this effect. The mitochondrial bioenergetic profile, morphology and dynamics of TGF-β-treated cells (48 h) were altered and these effects were prevented by co-treatment with clinically relevant concentrations of RPV. A MitoStress Test (Seahorse Analyzer) revealed that TGF-β increased both oxygen consumption rate (basal respiration, maximal respiration and spare respiratory capacity) and extracellular acidification rate (indicative of increased glycolysis). Cells exposed to TGF-β also displayed diminished mitochondrial membrane potential and enhanced mitochondrial fission. All of these effects were rescued with RPV. RNA sequencing analysis of cells exposed to TGF-β revealed the presence of 338 differentially expressed genes that encode mitochondrial proteins (mito-DEGs), of which 139 and 199 were significantly up- and down-regulated (adjusted p<0.05). This alteration in 15 (10.79 %) and 31 (22.03 %) of the up-regulated and 16 (8.04 %) and 49 (24.62 %) of the down-regulated mitoDEGs was prevented with co-exposure to RPV 4μM or 8μM, respectively. In conclusion, alterations in mitochondrial function are implicated in the antifibrogenic action of RPV, pointing to potential novel antifibrotic targets.
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Affiliation(s)
- Ana M Benedicto
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain
| | - Federico Lucantoni
- Laboratory of Cellular Stress and Cell Death Pathways, Centro de Investigación Príncipe Felipe (CIPF), Valencia, Spain
| | - Isabel Fuster-Martínez
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain
| | | | - Dimitri Dorcaratto
- Unidad de Cirugía Hepato-Bilio-Pancreática, Hospital Clínico Universitario, Valencia, Spain; INCLIVA (Instituto de Investigación Sanitaria), Valencia, Spain
| | - Elena Muñoz-Forner
- Unidad de Cirugía Hepato-Bilio-Pancreática, Hospital Clínico Universitario, Valencia, Spain; INCLIVA (Instituto de Investigación Sanitaria), Valencia, Spain
| | - Victor M Victor
- FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain; INCLIVA (Instituto de Investigación Sanitaria), Valencia, Spain; Departamento de Fisiología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Valencia, Spain
| | - Juan V Esplugues
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain; CIBERehd (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Valencia, Spain
| | - Ana Blas-García
- FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain; Departamento de Fisiología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; CIBERehd (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Valencia, Spain
| | - Nadezda Apostolova
- Departamento de Farmacología, Facultad de Medicina, Universidad de Valencia, Valencia, Spain; FISABIO-Hospital Universitario Dr. Peset, Valencia, Spain; CIBERehd (Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas), Valencia, Spain.
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2
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Bennett GM, Kwak Y, Maynard R. Endosymbioses Have Shaped the Evolution of Biological Diversity and Complexity Time and Time Again. Genome Biol Evol 2024; 16:evae112. [PMID: 38813885 PMCID: PMC11154151 DOI: 10.1093/gbe/evae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 05/17/2024] [Accepted: 05/17/2024] [Indexed: 05/31/2024] Open
Abstract
Life on Earth comprises prokaryotes and a broad assemblage of endosymbioses. The pages of Molecular Biology and Evolution and Genome Biology and Evolution have provided an essential window into how these endosymbiotic interactions have evolved and shaped biological diversity. Here, we provide a current perspective on this knowledge by drawing on decades of revelatory research published in Molecular Biology and Evolution and Genome Biology and Evolution, and insights from the field at large. The accumulated work illustrates how endosymbioses provide hosts with novel phenotypes that allow them to transition between adaptive landscapes to access environmental resources. Such endosymbiotic relationships have shaped and reshaped life on Earth. The early serial establishment of mitochondria and chloroplasts through endosymbioses permitted massive upscaling of cellular energetics, multicellularity, and terrestrial planetary greening. These endosymbioses are also the foundation upon which all later ones are built, including everything from land-plant endosymbioses with fungi and bacteria to nutritional endosymbioses found in invertebrate animals. Common evolutionary mechanisms have shaped this broad range of interactions. Endosymbionts generally experience adaptive and stochastic genome streamlining, the extent of which depends on several key factors (e.g. mode of transmission). Hosts, in contrast, adapt complex mechanisms of resource exchange, cellular integration and regulation, and genetic support mechanisms to prop up degraded symbionts. However, there are significant differences between endosymbiotic interactions not only in how partners have evolved with each other but also in the scope of their influence on biological diversity. These differences are important considerations for predicting how endosymbioses will persist and adapt to a changing planet.
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Affiliation(s)
- Gordon M Bennett
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Younghwan Kwak
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
- National Science Foundation Biological Integration Institute—INSITE, University of California, Merced, CA, USA
| | - Reo Maynard
- Department of Life and Environmental Sciences, University of California, Merced, CA, USA
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3
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Keeling PJ, Mtawali M, Trznadel M, Livingston SJ, Wakeman KC. Parallel functional reduction in the mitochondria of apicomplexan parasites. Eur J Protistol 2024; 94:126065. [PMID: 38492251 DOI: 10.1016/j.ejop.2024.126065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/21/2024] [Accepted: 02/22/2024] [Indexed: 03/18/2024]
Abstract
Extreme functional reduction of mitochondria has taken place in parallel in many distantly related lineages of eukaryotes, leading to a number of recurring metabolic states with variously lost electron transport chain (ETC) complexes, loss of the tricarboxylic acid (TCA) cycle, and/or loss of the mitochondrial genome. The resulting mitochondria-related organelles (MROs) are generally structurally reduced and in the most extreme cases barely recognizable features of the cell with no role in energy metabolism whatsoever (e.g., mitosomes, which generally only make iron-sulfur clusters). Recently, a wide diversity of MROs were discovered to be hiding in plain sight: in gregarine apicomplexans. This diverse group of invertebrate parasites has been known and observed for centuries, but until recent applications of culture-free genomics, their mitochondria were unremarkable. The genomics, however, showed that mitochondrial function has reduced in parallel in multiple gregarine lineages to several different endpoints, including the most reduced mitosomes. Here we review this remarkable case of parallel evolution of MROs, and some of the interesting questions this work raises.
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Affiliation(s)
- Patrick J Keeling
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada.
| | - Mahara Mtawali
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Morelia Trznadel
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Samuel J Livingston
- Department of Botany, University of British Columbia, 3156-6270 University Blvd., Vancouver V6T 1Z4, BC, Canada
| | - Kevin C Wakeman
- Institute for the Advancement of Higher Education, Hokkaido University, Sapporo 060-0810, Hokkaido, Japan
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4
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Zhou QY, Ren C, Li JY, Wang L, Duan Y, Yao RQ, Tian YP, Yao YM. The crosstalk between mitochondrial quality control and metal-dependent cell death. Cell Death Dis 2024; 15:299. [PMID: 38678018 PMCID: PMC11055915 DOI: 10.1038/s41419-024-06691-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/29/2024]
Abstract
Mitochondria are the centers of energy and material metabolism, and they also serve as the storage and dispatch hubs of metal ions. Damage to mitochondrial structure and function can cause abnormal levels and distribution of metal ions, leading to cell dysfunction and even death. For a long time, mitochondrial quality control pathways such as mitochondrial dynamics and mitophagy have been considered to inhibit metal-induced cell death. However, with the discovery of new metal-dependent cell death including ferroptosis and cuproptosis, increasing evidence shows that there is a complex relationship between mitochondrial quality control and metal-dependent cell death. This article reviews the latest research results and mechanisms of crosstalk between mitochondrial quality control and metal-dependent cell death in recent years, as well as their involvement in neurodegenerative diseases, tumors and other diseases, in order to provide new ideas for the research and treatment of related diseases.
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Affiliation(s)
- Qi-Yuan Zhou
- Department of Emergency, the Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Chao Ren
- Department of Pulmonary and Critical Care Medicine, Beijing Chaoyang Hospital, Capital Medical University, Beijing, 100020, China
| | - Jing-Yan Li
- Department of Emergency, the Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China
| | - Lu Wang
- Department of Critical Care Medicine, the First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China
| | - Yu Duan
- Department of Critical Care Medicine, Affiliated Chenzhou Hospital (the First People's Hospital of Chenzhou), Southern Medical University, Chenzhou, 423000, China
| | - Ren-Qi Yao
- Department of General Surgery, the First Medical Center of Chinese PLA General Hospital, Beijing, 100853, China.
- Medical Innovation Research Division, Translational Medicine Research Center and the Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100853, China.
| | - Ying-Ping Tian
- Department of Emergency, the Second Hospital of Hebei Medical University, Shijiazhuang, 050000, China.
| | - Yong-Ming Yao
- Medical Innovation Research Division, Translational Medicine Research Center and the Fourth Medical Center of Chinese PLA General Hospital, Beijing, 100853, China.
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5
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Horten P, Song K, Garlich J, Hardt R, Colina-Tenorio L, Horvath SE, Schulte U, Fakler B, van der Laan M, Becker T, Stuart RA, Pfanner N, Rampelt H. Identification of MIMAS, a multifunctional mega-assembly integrating metabolic and respiratory biogenesis factors of mitochondria. Cell Rep 2024; 43:113772. [PMID: 38393949 PMCID: PMC11010658 DOI: 10.1016/j.celrep.2024.113772] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/03/2024] [Accepted: 01/24/2024] [Indexed: 02/25/2024] Open
Abstract
The mitochondrial inner membrane plays central roles in bioenergetics and metabolism and contains several established membrane protein complexes. Here, we report the identification of a mega-complex of the inner membrane, termed mitochondrial multifunctional assembly (MIMAS). Its large size of 3 MDa explains why MIMAS has escaped detection in the analysis of mitochondria so far. MIMAS combines proteins of diverse functions from respiratory chain assembly to metabolite transport, dehydrogenases, and lipid biosynthesis but not the large established supercomplexes of the respiratory chain, ATP synthase, or prohibitin scaffold. MIMAS integrity depends on the non-bilayer phospholipid phosphatidylethanolamine, in contrast to respiratory supercomplexes whose stability depends on cardiolipin. Our findings suggest that MIMAS forms a protein-lipid mega-assembly in the mitochondrial inner membrane that integrates respiratory biogenesis and metabolic processes in a multifunctional platform.
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Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Kuo Song
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Joshua Garlich
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Robert Hardt
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Susanne E Horvath
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany
| | - Uwe Schulte
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Bernd Fakler
- Institute of Physiology, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Martin van der Laan
- Medical Biochemistry and Molecular Biology, Center for Molecular Signaling, PZMS, Faculty of Medicine, Saarland University, 66421 Homburg, Germany
| | - Thomas Becker
- Institute of Biochemistry and Molecular Biology, Faculty of Medicine, University of Bonn, 53115 Bonn, Germany
| | - Rosemary A Stuart
- Department of Biological Sciences, Marquette University, Milwaukee, WI 53233, USA
| | - Nikolaus Pfanner
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany; BIOSS Centre for Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany.
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6
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Shi X, DeCiucis M, Grabinska KA, Kanyo J, Liu A, Lam TT, Shen H. Dual regulation of SLC25A39 by AFG3L2 and iron controls mitochondrial glutathione homeostasis. Mol Cell 2024; 84:802-810.e6. [PMID: 38157846 PMCID: PMC10922821 DOI: 10.1016/j.molcel.2023.12.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/02/2023] [Accepted: 12/08/2023] [Indexed: 01/03/2024]
Abstract
Organelle transporters define metabolic compartmentalization, and how this metabolite transport process can be modulated is poorly explored. Here, we discovered that human SLC25A39, a mitochondrial transporter critical for mitochondrial glutathione uptake, is a short-lived protein under dual regulation at the protein level. Co-immunoprecipitation mass spectrometry and CRISPR knockout (KO) in mammalian cells identified that mitochondrial m-AAA protease AFG3L2 is responsible for degrading SLC25A39 through the matrix loop 1. SLC25A39 senses mitochondrial iron-sulfur cluster using four matrix cysteine residues and inhibits its degradation. SLC25A39 protein regulation is robust in developing and mature neurons. This dual transporter regulation, by protein quality control and metabolic sensing, allows modulating mitochondrial glutathione level in response to iron homeostasis, opening avenues for exploring regulation of metabolic compartmentalization. Neuronal SLC25A39 regulation connects mitochondrial protein quality control, glutathione, and iron homeostasis, which were previously unrelated biochemical features in neurodegeneration.
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Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Marisa DeCiucis
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Kariona A Grabinska
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Jean Kanyo
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT, USA
| | - Adam Liu
- Amity High School, Woodbridge, CT, USA
| | - Tukiet T Lam
- Keck MS & Proteomics Resource, Yale School of Medicine, New Haven, CT, USA; Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA; Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
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7
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Zhu X, Oldfather LE, Cobine PA. Metal Uptake by Mitochondrial Carrier Family Proteins Using Lactococcus lactis. Methods Mol Biol 2024; 2839:99-110. [PMID: 39008250 DOI: 10.1007/978-1-0716-4043-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Metal ion homeostasis in mitochondria is essential to maintaining proper cellular physiology. However, the ability of metals to bind off target or form complexes with multiple metabolites presents major challenges to understanding the mechanisms that govern this homeostasis. Adding further to the complexity, some of the major mitochondrial transporters have shown substrate promiscuity. In many cases, mitochondrial metals are found in the matrix compartment that is surrounded by the impermeable inner membrane. Four major classes of transporters facilitate the movement of solute across the inner membrane. These are mitochondrial carrier family, ATP-binding cassette transporters, mitochondrial pyruvate carriers, and sideroflexins. For iron, the matrix is the site of iron-sulfur clusters and heme synthesis and therefore transport must occur in a coordinated fashion with the cellular needs for these critical cofactors. Iron could be transported in numerous forms as it has been shown to form complexes with abundant metabolites such as citrate, nucleotides, or glutathione. Here, we describe assays to study iron (or any metal) transport by mitochondrial carrier family proteins expressed in Lactococcus lactis using a nisin-controlled expression system.
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Affiliation(s)
- Xinyu Zhu
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Laura E Oldfather
- Department of Biological Sciences, Auburn University, Auburn, AL, USA
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.
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8
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Byrne KL, Szeligowski RV, Shen H. Phylogenetic Analysis Guides Transporter Protein Deorphanization: A Case Study of the SLC25 Family of Mitochondrial Metabolite Transporters. Biomolecules 2023; 13:1314. [PMID: 37759714 PMCID: PMC10526428 DOI: 10.3390/biom13091314] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 08/13/2023] [Accepted: 08/14/2023] [Indexed: 09/29/2023] Open
Abstract
Homology search and phylogenetic analysis have commonly been used to annotate gene function, although they are prone to error. We hypothesize that the power of homology search in functional annotation depends on the coupling of sequence variation to functional diversification, and we herein focus on the SoLute Carrier (SLC25) family of mitochondrial metabolite transporters to survey this coupling in a family-wide manner. The SLC25 family is the largest family of mitochondrial metabolite transporters in eukaryotes that translocate ligands of different chemical properties, ranging from nucleotides, amino acids, carboxylic acids and cofactors, presenting adequate experimentally validated functional diversification in ligand transport. Here, we combine phylogenetic analysis to profile SLC25 transporters across common eukaryotic model organisms, from Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Danio rerio, to Homo sapiens, and assess their sequence adaptations to the transported ligands within individual subfamilies. Using several recently studied and poorly characterized SLC25 transporters, we discuss the potentials and limitations of phylogenetic analysis in guiding functional characterization.
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Affiliation(s)
- Katie L. Byrne
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT 06510, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT 06516, USA
- Yale College, New Haven, CT 06511, USA
| | - Richard V. Szeligowski
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT 06510, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT 06516, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT 06510, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT 06516, USA
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9
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Nishi K, Yoshii A, Abell L, Zhou B, Frausto R, Ritterhoff J, McMillen TS, Sweet I, Wang Y, Gao C, Tian R. Branched-chain keto acids inhibit mitochondrial pyruvate carrier and suppress gluconeogenesis in hepatocytes. Cell Rep 2023; 42:112641. [PMID: 37310861 PMCID: PMC10592489 DOI: 10.1016/j.celrep.2023.112641] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/06/2023] [Accepted: 05/29/2023] [Indexed: 06/15/2023] Open
Abstract
Branched-chain amino acid (BCAA) metabolism is linked to glucose homeostasis, but the underlying signaling mechanisms are unclear. We find that gluconeogenesis is reduced in mice deficient of Ppm1k, a positive regulator of BCAA catabolism, which protects against obesity-induced glucose intolerance. Accumulation of branched-chain keto acids (BCKAs) inhibits glucose production in hepatocytes. BCKAs suppress liver mitochondrial pyruvate carrier (MPC) activity and pyruvate-supported respiration. Pyruvate-supported gluconeogenesis is selectively suppressed in Ppm1k-deficient mice and can be restored with pharmacological activation of BCKA catabolism by BT2. Finally, hepatocytes lack branched-chain aminotransferase that alleviates BCKA accumulation via reversible conversion between BCAAs and BCKAs. This renders liver MPC most susceptible to circulating BCKA levels hence a sensor of BCAA catabolism.
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Affiliation(s)
- Kiyoto Nishi
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Department of Pharmacology, Shiga University of Medical Science, Otsu, Shiga 520-2182, Japan
| | - Akira Yoshii
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Lauren Abell
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Bo Zhou
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Ricardo Frausto
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Julia Ritterhoff
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Timothy S McMillen
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA
| | - Ian Sweet
- University of Washington Medicine Diabetes Institute, University of Washington, 750 Republican Street, Seattle, WA 98109, USA
| | - Yibin Wang
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Signature Program in Cardiovascular and Metabolic Diseases, Duke-NUS School of Medicine, Singapore, Singapore
| | - Chen Gao
- Department of Anesthesiology, Cardiovascular Research Laboratories, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Pharmacology and Systems Physiology, University of Cincinnati, College of Medicine, Cincinnati, OH 45267-0575, USA.
| | - Rong Tian
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
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10
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Yook JS, Taxin ZH, Yuan B, Oikawa S, Auger C, Mutlu B, Puigserver P, Hui S, Kajimura S. The SLC25A47 locus controls gluconeogenesis and energy expenditure. Proc Natl Acad Sci U S A 2023; 120:e2216810120. [PMID: 36812201 PMCID: PMC9992842 DOI: 10.1073/pnas.2216810120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 01/12/2023] [Indexed: 02/24/2023] Open
Abstract
Mitochondria provide essential metabolites and adenosine triphosphate (ATP) for the regulation of energy homeostasis. For instance, liver mitochondria are a vital source of gluconeogenic precursors under a fasted state. However, the regulatory mechanisms at the level of mitochondrial membrane transport are not fully understood. Here, we report that a liver-specific mitochondrial inner-membrane carrier SLC25A47 is required for hepatic gluconeogenesis and energy homeostasis. Genome-wide association studies found significant associations between SLC25A47 and fasting glucose, HbA1c, and cholesterol levels in humans. In mice, we demonstrated that liver-specific depletion of SLC25A47 impaired hepatic gluconeogenesis selectively from lactate, while significantly enhancing whole-body energy expenditure and the hepatic expression of FGF21. These metabolic changes were not a consequence of general liver dysfunction because acute SLC25A47 depletion in adult mice was sufficient to enhance hepatic FGF21 production, pyruvate tolerance, and insulin tolerance independent of liver damage and mitochondrial dysfunction. Mechanistically, SLC25A47 depletion leads to impaired hepatic pyruvate flux and malate accumulation in the mitochondria, thereby restricting hepatic gluconeogenesis. Together, the present study identified a crucial node in the liver mitochondria that regulates fasting-induced gluconeogenesis and energy homeostasis.
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Affiliation(s)
- Jin-Seon Yook
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Zachary H. Taxin
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Bo Yuan
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Satoshi Oikawa
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Christopher Auger
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
| | - Beste Mutlu
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA02115
| | - Pere Puigserver
- Department of Cell Biology, Harvard Medical School, Boston, MA02115
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA02115
| | - Sheng Hui
- Department of Molecular Metabolism, Harvard T. H. Chan School of Public Health, Boston, MA02115
| | - Shingo Kajimura
- Division of Endocrinology, Diabetes and Metabolism, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA02115
- HHMI, Chevy Chase, MD20815
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11
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Mohareer K, Banerjee S. Mycobacterial infection alters host mitochondrial activity. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2023. [DOI: 10.1016/bs.ircmb.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
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12
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Uszczynska-Ratajczak B, Sugunan S, Kwiatkowska M, Migdal M, Carbonell-Sala S, Sokol A, Winata CL, Chacinska A. Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafish. Life Sci Alliance 2022; 6:6/1/e202201514. [PMID: 36283702 PMCID: PMC9595208 DOI: 10.26508/lsa.202201514] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022] Open
Abstract
Most mitochondrial proteins are encoded by nuclear genes, synthetized in the cytosol and targeted into the organelle. To characterize the spatial organization of mitochondrial gene products in zebrafish (Danio rerio), we sequenced RNA from different cellular fractions. Our results confirmed the presence of nuclear-encoded mRNAs in the mitochondrial fraction, which in unperturbed conditions, are mainly transcripts encoding large proteins with specific properties, like transmembrane domains. To further explore the principles of mitochondrial protein compartmentalization in zebrafish, we quantified the transcriptomic changes for each subcellular fraction triggered by the chchd4a -/- mutation, causing the disorders in the mitochondrial protein import. Our results indicate that the proteostatic stress further restricts the population of transcripts on the mitochondrial surface, allowing only the largest and the most evolutionary conserved proteins to be synthetized there. We also show that many nuclear-encoded mitochondrial transcripts translated by the cytosolic ribosomes stay resistant to the global translation shutdown. Thus, vertebrates, in contrast to yeast, are not likely to use localized translation to facilitate synthesis of mitochondrial proteins under proteostatic stress conditions.
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Affiliation(s)
- Barbara Uszczynska-Ratajczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland .,Centre of New Technologies, University of Warsaw, Warsaw, Poland
| | - Sreedevi Sugunan
- ReMedy International Research Agenda Unit, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Monika Kwiatkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland,Centre of New Technologies, University of Warsaw, Warsaw, Poland,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Migdal
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Silvia Carbonell-Sala
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Anna Sokol
- Department of Developmental Genetics, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany,Biomolecular Mass Spectrometry, Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | - Cecilia L Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Agnieszka Chacinska
- ReMedy International Research Agenda Unit, IMol Polish Academy of Sciences, Warsaw, Poland
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13
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Zhao X, Chen J, Yin S, Shi J, Zheng M, He C, Meng H, Han Y, Han J, Guo J, Yuan Z, Wang Y. The expression of cuproptosis-related genes in hepatocellular carcinoma and their relationships with prognosis. Front Oncol 2022; 12:992468. [PMID: 36313717 PMCID: PMC9614267 DOI: 10.3389/fonc.2022.992468] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 09/22/2022] [Indexed: 11/22/2022] Open
Abstract
Background The mechanism of cuproptosis has recently been reported in lipoylated proteins of the tricarboxylic acid (TCA) cycle. Besides, the role of copper was previously recognized in cancer progression. We evaluated the prognostic value of cuproptosis-related gene expression in hepatocellular carcinoma (HCC). Methods Remarkable genes were selected both in differential expression analysis and Kaplan-Meier survival analysis from ninety-six cuproptosis-related genes using The Cancer Genome Atlas (TCGA) database. The relationships between clinical characteristics and gene expression were performed with Wilcoxon signed-rank test, Kruskal-Wallis test, and logistic regression. Clinicopathologic factors correlated with overall survival in HCCs conducting univariate and multivariate Cox regression analysis. Gene Expression Profiling Interactive Analysis 2 (GEPIA2) and Human Protein Atlas (HPA) databases were utilized to verify the results. Furthermore, Gene Set Enrichment Analysis (GSEA) identified the potential key pathways that dominate cuproptosis in HCC. Results Elevated ATP7A, SLC25A3, SCO2, COA6, TMEM199, ATP6AP1, LIPT1, DLAT, PDHA1, MTF1, ACP1, FDX2, NUBP2, CIAPIN1, ISCA2 and NDOR1 expression, as well as declined AOC1, FDX1, MT-CO1, and ACO1 expression were significantly emerged in HCC tumor tissues and were significantly associated with HCCs poor survival. The expressions of screened cuproptosis-related genes were prominently related to clinical features. GSEA analysis reported many key signaling pathways (such as natural killer cell mediated cytotoxicity, TCA cycle, glutathione metabolism, ATP-binding cassette (ABC) transporters, Notch signaling pathway, ErbB signaling pathway, and metabolism of xenobiotics by cytochrome p450) were differentially enriched in HCCs with varying degrees of cuproptosis-related genes expression. Conclusions The twenty cuproptosis-related genes might be utilized as new candidate prognostic biomarkers for HCC.
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Affiliation(s)
- Xueying Zhao
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Jin Chen
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Shangqi Yin
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingren Shi
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Mei Zheng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Chaonan He
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Huan Meng
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Ying Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jinyu Han
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Jingjing Guo
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
| | - Zhengrong Yuan
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Zhengrong Yuan, ; Yajie Wang,
| | - Yajie Wang
- Department of Clinical Laboratory, Beijing Ditan Hospital, Capital Medical University, Beijing, China
- *Correspondence: Zhengrong Yuan, ; Yajie Wang,
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14
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Jain A, Zoncu R. Organelle transporters and inter-organelle communication as drivers of metabolic regulation and cellular homeostasis. Mol Metab 2022; 60:101481. [PMID: 35342037 PMCID: PMC9043965 DOI: 10.1016/j.molmet.2022.101481] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/14/2022] [Accepted: 03/21/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Spatial compartmentalization of metabolic pathways within membrane-separated organelles is key to the ability of eukaryotic cells to precisely regulate their biochemical functions. Membrane-bound organelles such as mitochondria, endoplasmic reticulum (ER) and lysosomes enable the concentration of metabolic precursors within optimized chemical environments, greatly accelerating the efficiency of both anabolic and catabolic reactions, enabling division of labor and optimal utilization of resources. However, metabolic compartmentalization also poses a challenge to cells because it creates spatial discontinuities that must be bridged for reaction cascades to be connected and completed. To do so, cells employ different methods to coordinate metabolic fluxes occurring in different organelles, such as membrane-localized transporters to facilitate regulated metabolite exchange between mitochondria and lysosomes, non-vesicular transport pathways via physical contact sites connecting the ER with both mitochondria and lysosomes, as well as localized regulatory signaling processes that coordinately regulate the activity of all these organelles. SCOPE OF REVIEW This review covers how cells use membrane transporters, membrane contact sites, and localized signaling pathways to mediate inter-organelle communication and coordinate metabolism. We also describe how disruption of inter-organelle communication is an emerging driver in a multitude of diseases, from cancer to neurodegeneration. MAJOR CONCLUSIONS Effective communication among organelles is essential to cellular health and function. Identifying the major molecular players involved in mediating metabolic coordination between organelles will further our understanding of cellular metabolism in health and lead us to design better therapeutics against dysregulated metabolism in disease.
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Affiliation(s)
- Aakriti Jain
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Roberto Zoncu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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15
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Medlock AE, Hixon JC, Bhuiyan T, Cobine PA. Prime Real Estate: Metals, Cofactors and MICOS. Front Cell Dev Biol 2022; 10:892325. [PMID: 35669513 PMCID: PMC9163361 DOI: 10.3389/fcell.2022.892325] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 05/02/2022] [Indexed: 12/23/2022] Open
Abstract
Metals are key elements for the survival and normal development of humans but can also be toxic to cells when mishandled. In fact, even mild disruption of metal homeostasis causes a wide array of disorders. Many of the metals essential to normal physiology are required in mitochondria for enzymatic activities and for the formation of essential cofactors. Copper is required as a cofactor in the terminal electron transport chain complex cytochrome c oxidase, iron is required for the for the formation of iron-sulfur (Fe-S) clusters and heme, manganese is required for the prevention of oxidative stress production, and these are only a few examples of the critical roles that mitochondrial metals play. Even though the targets of these metals are known, we are still identifying transporters, investigating the roles of known transporters, and defining regulators of the transport process. Mitochondria are dynamic organelles whose content, structure and localization within the cell vary in different tissues and organisms. Our knowledge of the impact that alterations in mitochondrial physiology have on metal content and utilization in these organelles is very limited. The rates of fission and fusion, the ultrastructure of the organelle, and rates of mitophagy can all affect metal homeostasis and cofactor assembly. This review will focus of the emerging areas of overlap between metal homeostasis, cofactor assembly and the mitochondrial contact site and cristae organizing system (MICOS) that mediates multiple aspects of mitochondrial physiology. Importantly the MICOS complexes may allow for localization and organization of complexes not only involved in cristae formation and contact between the inner and outer mitochondrial membranes but also acts as hub for metal-related proteins to work in concert in cofactor assembly and homeostasis.
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Affiliation(s)
- Amy E. Medlock
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
- Augusta University/University of Georgia Medical Partnership, University of Georgia, Athens, GA, United States
| | - J. Catrice Hixon
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
| | - Tawhid Bhuiyan
- Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA, United States
| | - Paul A. Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, United States
- *Correspondence: Paul A. Cobine,
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16
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Shi X, Reinstadler B, Shah H, To TL, Byrne K, Summer L, Calvo SE, Goldberger O, Doench JG, Mootha VK, Shen H. Combinatorial GxGxE CRISPR screen identifies SLC25A39 in mitochondrial glutathione transport linking iron homeostasis to OXPHOS. Nat Commun 2022; 13:2483. [PMID: 35513392 PMCID: PMC9072411 DOI: 10.1038/s41467-022-30126-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 04/18/2022] [Indexed: 12/18/2022] Open
Abstract
The SLC25 carrier family consists of 53 transporters that shuttle nutrients and co-factors across mitochondrial membranes. The family is highly redundant and their transport activities coupled to metabolic state. Here, we use a pooled, dual CRISPR screening strategy that knocks out pairs of transporters in four metabolic states - glucose, galactose, OXPHOS inhibition, and absence of pyruvate - designed to unmask the inter-dependence of these genes. In total, we screen 63 genes in four metabolic states, corresponding to 2016 single and pair-wise genetic perturbations. We recover 19 gene-by-environment (GxE) interactions and 9 gene-by-gene (GxG) interactions. One GxE interaction hit illustrates that the fitness defect in the mitochondrial folate carrier (SLC25A32) KO cells is genetically buffered in galactose due to a lack of substrate in de novo purine biosynthesis. GxG analysis highlights a buffering interaction between the iron transporter SLC25A37 (A37) and the poorly characterized SLC25A39 (A39). Mitochondrial metabolite profiling, organelle transport assays, and structure-guided mutagenesis identify A39 as critical for mitochondrial glutathione (GSH) import. Functional studies reveal that A39-mediated glutathione homeostasis and A37-mediated mitochondrial iron uptake operate jointly to support mitochondrial OXPHOS. Our work underscores the value of studying family-wide genetic interactions across different metabolic environments.
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Affiliation(s)
- Xiaojian Shi
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Bryn Reinstadler
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hardik Shah
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Tsz-Leung To
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Katie Byrne
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Luanna Summer
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA
| | - Sarah E Calvo
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Olga Goldberger
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | | | - Vamsi K Mootha
- Howard Hughes Medical Institute and Department of Molecular Biology, Massachusetts General Hospital, Boston, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
- Broad Institute, Cambridge, MA, USA
| | - Hongying Shen
- Cellular and Molecular Physiology Department, Yale School of Medicine, New Haven, CT, USA.
- Systems Biology Institute, Yale West Campus, West Haven, CT, USA.
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17
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Gao LF, Zhong Y, Long T, Wang X, Zhu JX, Wang XY, Hu ZY, Li ZG. Tumor bud-derived CCL5 recruits fibroblasts and promotes colorectal cancer progression via CCR5-SLC25A24 signaling. J Exp Clin Cancer Res 2022; 41:81. [PMID: 35241150 PMCID: PMC8892738 DOI: 10.1186/s13046-022-02300-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 12/17/2022] Open
Abstract
Background Tumor budding is included in the routine diagnosis of colorectal cancer (CRC) and is considered a tumor prognostic factor independent of TNM staging. This study aimed to identify the fibroblast-mediated effect of tumor bud-derived C–C chemokine ligand 5 (CCL5) on the tumor microenvironment (TME). Methods Recruitment assays and a human cytokine array were used to detect the main cytokines that CRC tumor buds secrete to recruit fibroblasts. siRNA transfection and inhibitor treatment were used to investigate the role of fibroblast CCL5 receptors in fibroblast recruitment. Subsequently, transcriptome sequencing was performed to explore the molecular changes occurring in fibroblasts upon stimulation with CCL5. Finally, clinical specimens and orthotopic xenograft mouse models were studied to explore the contribution of CCL5 to angiogenesis and collagen synthesis. Results Hematoxylin–eosin staining and immunochemistry revealed a higher number of fibroblasts at the invasive front of CRC tissue showing tumor budding than at sites without tumor budding. In vitro experiments demonstrated that CCL5 derived from tumor buds could recruit fibroblasts by acting on the CCR5 receptors on fibroblasts. Tumor bud-derived CCL5 could also positively regulate solute carrier family 25 member 24 (SLC25A24) expression in fibroblasts, potentially activating pAkt-pmTOR signaling. Moreover, CCL5 could increase the number of α-SMAhigh CD90high FAPlow fibroblasts and thus promote tumor angiogenesis by enhancing VEGFA expression and making fibroblasts transdifferentiate into vascular endothelial cells. Finally, the results also showed that CCL5 could promote collagen synthesis through fibroblasts, thus contributing to tumor progression. Conclusions At the invasive front of CRC, tumor bud-derived CCL5 can recruit fibroblasts via CCR5-SLC25A24 signaling, further promoting angiogenesis and collagen synthesis via recruited fibroblasts, and eventually create a tumor-promoting microenvironment. Therefore, CCL5 may serve as a potential diagnostic marker and therapeutic target for tumor budding in CRC. Supplementary Information The online version contains supplementary material available at 10.1186/s13046-022-02300-w.
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Affiliation(s)
- Ling-Fang Gao
- Department of Pathology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518101, Guangdong, China.,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Yan Zhong
- Department of Pathology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518101, Guangdong, China
| | - Ting Long
- Department of Pathology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518101, Guangdong, China
| | - Xia Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Jia-Xian Zhu
- Department of Pathology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518101, Guangdong, China
| | - Xiao-Yan Wang
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zhi-Yan Hu
- Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.,Department of Pathology, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, Guangdong, China
| | - Zu-Guo Li
- Department of Pathology, Shenzhen Hospital, Southern Medical University, Shenzhen, 518101, Guangdong, China. .,Department of Pathology, School of Basic Medical Sciences, Southern Medical University, Guangzhou, 510515, Guangdong, China.
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18
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Wynne ME, Lane AR, Singleton KS, Zlatic SA, Gokhale A, Werner E, Duong D, Kwong JQ, Crocker AJ, Faundez V. Heterogeneous Expression of Nuclear Encoded Mitochondrial Genes Distinguishes Inhibitory and Excitatory Neurons. eNeuro 2021; 8:ENEURO.0232-21.2021. [PMID: 34312306 PMCID: PMC8387155 DOI: 10.1523/eneuro.0232-21.2021] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 06/25/2021] [Accepted: 07/17/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondrial composition varies by organ and their constituent cell types. This mitochondrial diversity likely determines variations in mitochondrial function. However, the heterogeneity of mitochondria in the brain remains underexplored despite the large diversity of cell types in neuronal tissue. Here, we used molecular systems biology tools to address whether mitochondrial composition varies by brain region and neuronal cell type in mice. We reasoned that proteomics and transcriptomics of microdissected brain regions combined with analysis of single-cell mRNA sequencing (scRNAseq) could reveal the extent of mitochondrial compositional diversity. We selected nuclear encoded gene products forming complexes of fixed stoichiometry, such as the respiratory chain complexes and the mitochondrial ribosome, as well as molecules likely to perform their function as monomers, such as the family of SLC25 transporters. We found that the proteome encompassing these nuclear-encoded mitochondrial genes and obtained from microdissected brain tissue segregated the hippocampus, striatum, and cortex from each other. Nuclear-encoded mitochondrial transcripts could only segregate cell types and brain regions when the analysis was performed at the single-cell level. In fact, single-cell mitochondrial transcriptomes were able to distinguish glutamatergic and distinct types of GABAergic neurons from one another. Within these cell categories, unique SLC25A transporters were able to identify distinct cell subpopulations. Our results demonstrate heterogeneous mitochondrial composition across brain regions and cell types. We postulate that mitochondrial heterogeneity influences regional and cell type-specific mechanisms in health and disease.
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Affiliation(s)
- Meghan E Wynne
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Alicia R Lane
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | | | | | - Avanti Gokhale
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Erica Werner
- Department of Cell Biology, Emory University, Atlanta, GA 30322
| | - Duc Duong
- Department of Biochemistry, Emory University, Atlanta, GA 30322
| | | | - Amanda J Crocker
- Program in Neuroscience, Middlebury College, Middlebury, VT 05753
| | - Victor Faundez
- Department of Cell Biology, Emory University, Atlanta, GA 30322
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19
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Encarnación-Rosado J, Kimmelman AC. Harnessing metabolic dependencies in pancreatic cancers. Nat Rev Gastroenterol Hepatol 2021; 18:482-492. [PMID: 33742165 PMCID: PMC8249349 DOI: 10.1038/s41575-021-00431-7] [Citation(s) in RCA: 92] [Impact Index Per Article: 30.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/16/2021] [Indexed: 02/07/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive disease with a 5-year survival rate of <10%. The tumour microenvironment (TME) of PDAC is characterized by excessive fibrosis and deposition of extracellular matrix, termed desmoplasia. This unique TME leads to high interstitial pressure, vascular collapse and low nutrient and oxygen diffusion. Together, these factors contribute to the unique biology and therapeutic resistance of this deadly tumour. To thrive in this hostile environment, PDAC cells adapt by using non-canonical metabolic pathways and rely on metabolic scavenging pathways such as autophagy and macropinocytosis. Here, we review the metabolic pathways that PDAC use to support their growth in the setting of an austere TME. Understanding how PDAC tumours rewire their metabolism and use scavenging pathways under environmental stressors might enable the identification of novel therapeutic approaches.
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Affiliation(s)
| | - Alec C Kimmelman
- Perlmutter Cancer Center, New York University School of Medicine, New York, NY, USA.
- Department of Radiation Oncology, New York University School of Medicine, New York, NY, USA.
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20
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Noterman MF, Chaubey K, Lin-Rahardja K, Rajadhyaksha AM, Pieper AA, Taylor EB. Dual-process brain mitochondria isolation preserves function and clarifies protein composition. Proc Natl Acad Sci U S A 2021; 118:e2019046118. [PMID: 33836587 PMCID: PMC7980376 DOI: 10.1073/pnas.2019046118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The brain requires continuously high energy production to maintain ion gradients and normal function. Mitochondria critically undergird brain energetics, and mitochondrial abnormalities feature prominently in neuropsychiatric disease. However, many unique aspects of brain mitochondria composition and function are poorly understood. Developing improved neuroprotective therapeutics thus requires more comprehensively understanding brain mitochondria, including accurately delineating protein composition and channel-transporter functional networks. However, obtaining pure mitochondria from the brain is especially challenging due to its distinctive lipid and cell structure properties. As a result, conflicting reports on protein localization to brain mitochondria abound. Here we illustrate this problem with the neuropsychiatric disease-associated L-type calcium channel Cav1.2α1 subunit previously observed in crude mitochondria. We applied a dual-process approach to obtain functionally intact versus compositionally pure brain mitochondria. One branch utilizes discontinuous density gradient centrifugation to isolate semipure mitochondria suitable for functional assays but unsuitable for protein localization because of endoplasmic reticulum (ER) contamination. The other branch utilizes self-forming density gradient ultracentrifugation to remove ER and yield ultrapure mitochondria that are suitable for investigating protein localization but functionally compromised. Through this process, we evaluated brain mitochondria protein content and observed the absence of Cav1.2α1 and other previously reported mitochondrial proteins, including the NMDA receptor, ryanodine receptor 1, monocarboxylate transporter 1, excitatory amino acid transporter 1, and glyceraldehyde 3-phosphate dehydrogenase. Conversely, we confirmed mitochondrial localization of several plasma membrane proteins previously reported to also localize to mitochondria. We expect this dual-process isolation procedure will enhance understanding of brain mitochondria in both health and disease.
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Affiliation(s)
- Maria F Noterman
- Interdisciplinary Graduate Program in Neuroscience, University of Iowa, Iowa City, IA 52242
| | - Kalyani Chaubey
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106
| | - Kristi Lin-Rahardja
- Department of Systems Biology and Bioinformatics, Case Western Reserve University, Cleveland, OH 44106
| | - Anjali M Rajadhyaksha
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY 10065
- Pediatric Neurology, Pediatrics, Weill Cornell Medicine of Cornell University, New York, NY 10065
| | - Andrew A Pieper
- Harrington Discovery Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106;
- Department of Psychiatry, Case Western Reserve University, Cleveland, OH 44106
- Weill Cornell Autism Research Program, Weill Cornell Medicine of Cornell University, New York, NY 10065
- Geriatric Research Education and Clinical Centers, Louis Stokes Cleveland VA Medical Center, Cleveland, OH 44106
- Department of Neuroscience, School of Medicine, Case Western Reserve University, Cleveland, OH 44106
| | - Eric B Taylor
- Department of Molecular Physiology and Biophysics, Carver College of Medicine, University of Iowa, Iowa City, IA 52242;
- Pappajohn Biomedical Institute, University of Iowa, Iowa City, IA 52242
- Fraternal Order of Eagles Diabetes Research Center, University of Iowa, Iowa City, IA 52242
- Holden Comprehensive Cancer Center, University of Iowa, Iowa City, IA 52242
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242
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21
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Zhu X, Boulet A, Buckley KM, Phillips CB, Gammon MG, Oldfather LE, Moore SA, Leary SC, Cobine PA. Mitochondrial copper and phosphate transporter specificity was defined early in the evolution of eukaryotes. eLife 2021; 10:64690. [PMID: 33591272 PMCID: PMC7924939 DOI: 10.7554/elife.64690] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/15/2021] [Indexed: 12/21/2022] Open
Abstract
The mitochondrial carrier family protein SLC25A3 transports both copper and phosphate in mammals, yet in Saccharomyces cerevisiae the transport of these substrates is partitioned across two paralogs: PIC2 and MIR1. To understand the ancestral state of copper and phosphate transport in mitochondria, we explored the evolutionary relationships of PIC2 and MIR1 orthologs across the eukaryotic tree of life. Phylogenetic analyses revealed that PIC2-like and MIR1-like orthologs are present in all major eukaryotic supergroups, indicating an ancient gene duplication created these paralogs. To link this phylogenetic signal to protein function, we used structural modeling and site-directed mutagenesis to identify residues involved in copper and phosphate transport. Based on these analyses, we generated an L175A variant of mouse SLC25A3 that retains the ability to transport copper but not phosphate. This work highlights the utility of using an evolutionary framework to uncover amino acids involved in substrate recognition by mitochondrial carrier family proteins.
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Affiliation(s)
- Xinyu Zhu
- Department of Biological Sciences, Auburn University, Auburn, United States
| | - Aren Boulet
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | | | - Casey B Phillips
- Department of Biological Sciences, Auburn University, Auburn, United States
| | - Micah G Gammon
- Department of Biological Sciences, Auburn University, Auburn, United States
| | - Laura E Oldfather
- Department of Biological Sciences, Auburn University, Auburn, United States
| | - Stanley A Moore
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Scot C Leary
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, Canada
| | - Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, United States
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Hewton KG, Johal AS, Parker SJ. Transporters at the Interface between Cytosolic and Mitochondrial Amino Acid Metabolism. Metabolites 2021; 11:metabo11020112. [PMID: 33669382 PMCID: PMC7920303 DOI: 10.3390/metabo11020112] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Mitochondria are central organelles that coordinate a vast array of metabolic and biologic functions important for cellular health. Amino acids are intricately linked to the bioenergetic, biosynthetic, and homeostatic function of the mitochondrion and require specific transporters to facilitate their import, export, and exchange across the inner mitochondrial membrane. Here we review key cellular metabolic outputs of eukaryotic mitochondrial amino acid metabolism and discuss both known and unknown transporters involved. Furthermore, we discuss how utilization of compartmentalized amino acid metabolism functions in disease and physiological contexts. We examine how improved methods to study mitochondrial metabolism, define organelle metabolite composition, and visualize cellular gradients allow for a more comprehensive understanding of how transporters facilitate compartmentalized metabolism.
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Affiliation(s)
- Keeley G. Hewton
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
| | - Amritpal S. Johal
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
| | - Seth J. Parker
- Department of Biochemistry & Molecular Biology, University of British Columbia, Vancouver, BC V6T 1Z4, Canada; (K.G.H.); (A.S.J.)
- British Columbia Children’s Hospital Research Institute, Vancouver, BC V6H 0B3, Canada
- Correspondence: ; Tel.: +1-604-875-3121
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23
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Cobine PA, Moore SA, Leary SC. Getting out what you put in: Copper in mitochondria and its impacts on human disease. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118867. [PMID: 32979421 DOI: 10.1016/j.bbamcr.2020.118867] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 08/22/2020] [Accepted: 09/15/2020] [Indexed: 12/19/2022]
Abstract
Mitochondria accumulate copper in their matrix for the eventual maturation of the cuproenzymes cytochrome c oxidase and superoxide dismutase. Transport into the matrix is achieved by mitochondrial carrier family (MCF) proteins. The major copper transporting MCF described to date in yeast is Pic2, which imports the metal ion into the matrix. Pic2 is one of ~30 MCFs that move numerous metabolites, nucleotides and co-factors across the inner membrane for use in the matrix. Genetic and biochemical experiments showed that Pic2 is required for cytochrome c oxidase activity under copper stress, and that it is capable of transporting ionic and complexed forms of copper. The Pic2 ortholog SLC25A3, one of 53 mammalian MCFs, functions as both a copper and a phosphate transporter. Depletion of SLC25A3 results in decreased accumulation of copper in the matrix, a cytochrome c oxidase defect and a modulation of cytosolic superoxide dismutase abundance. The regulatory roles for copper and cuproproteins resident to the mitochondrion continue to expand beyond the organelle. Mitochondrial copper chaperones have been linked to the modulation of cellular copper uptake and export and the facilitation of inter-organ communication. Recently, a role for matrix copper has also been proposed in a novel cell death pathway termed cuproptosis. This review will detail our understanding of the maturation of mitochondrial copper enzymes, the roles of mitochondrial signals in regulating cellular copper content, the proposed mechanisms of copper transport into the organelle and explore the evolutionary origins of copper homeostasis pathways.
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Affiliation(s)
- Paul A Cobine
- Department of Biological Sciences, Auburn University, Auburn, AL, USA.
| | - Stanley A Moore
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Scot C Leary
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK, Canada.
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Horten P, Colina-Tenorio L, Rampelt H. Biogenesis of Mitochondrial Metabolite Carriers. Biomolecules 2020; 10:E1008. [PMID: 32645990 PMCID: PMC7408425 DOI: 10.3390/biom10071008] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/02/2020] [Accepted: 07/03/2020] [Indexed: 12/28/2022] Open
Abstract
: Metabolite carriers of the mitochondrial inner membrane are crucial for cellular physiology since mitochondria contribute essential metabolic reactions and synthesize the majority of the cellular ATP. Like almost all mitochondrial proteins, carriers have to be imported into mitochondria from the cytosol. Carrier precursors utilize a specialized translocation pathway dedicated to the biogenesis of carriers and related proteins, the carrier translocase of the inner membrane (TIM22) pathway. After recognition and import through the mitochondrial outer membrane via the translocase of the outer membrane (TOM) complex, carrier precursors are ushered through the intermembrane space by hexameric TIM chaperones and ultimately integrated into the inner membrane by the TIM22 carrier translocase. Recent advances have shed light on the mechanisms of TOM translocase and TIM chaperone function, uncovered an unexpected versatility of the machineries, and revealed novel components and functional crosstalk of the human TIM22 translocase.
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Affiliation(s)
- Patrick Horten
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- Faculty of Biology, University of Freiburg, 79104 Freiburg, Germany
| | - Lilia Colina-Tenorio
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
| | - Heike Rampelt
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, 79104 Freiburg, Germany; (P.H.); (L.C.-T.)
- CIBSS Centre for Integrative Biological Signalling Studies, University of Freiburg, 79104 Freiburg, Germany
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25
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Cunningham CN, Rutter J. 20,000 picometers under the OMM: diving into the vastness of mitochondrial metabolite transport. EMBO Rep 2020; 21:e50071. [PMID: 32329174 DOI: 10.15252/embr.202050071] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/17/2020] [Accepted: 03/27/2020] [Indexed: 12/14/2022] Open
Abstract
The metabolic compartmentalization enabled by mitochondria is key feature of many cellular processes such as energy conversion to ATP production, redox balance, and the biosynthesis of heme, urea, nucleotides, lipids, and others. For a majority of these functions, metabolites need to be transported across the impermeable inner mitochondrial membrane by dedicated carrier proteins. Here, we examine the substrates, structural features, and human health implications of four mitochondrial metabolite carrier families: the SLC25A family, the mitochondrial ABCB transporters, the mitochondrial pyruvate carrier (MPC), and the sideroflexin proteins.
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Affiliation(s)
- Corey N Cunningham
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Jared Rutter
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, USA.,Howard Hughes Medical Institute, University of Utah School of Medicine, Salt Lake City, UT, USA
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