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Shapiro IM, Risbud MV, Landis WJ. Toward understanding the cellular control of vertebrate mineralization: The potential role of mitochondria. Bone 2024; 185:117112. [PMID: 38697384 PMCID: PMC11251007 DOI: 10.1016/j.bone.2024.117112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 04/17/2024] [Accepted: 04/29/2024] [Indexed: 05/05/2024]
Abstract
This review examines the possible role of mitochondria in maintaining calcium and phosphate ion homeostasis and participating in the mineralization of bone, cartilage and other vertebrate hard tissues. The paper builds on the known structural features of mitochondria and the documented observations in these tissues that the organelles contain calcium phosphate granules. Such deposits in mitochondria putatively form to buffer excessively high cytosolic calcium ion concentrations and prevent metabolic deficits and even cell death. While mitochondria protect cytosolic enzyme systems through this buffering capacity, the accumulation of calcium ions by mitochondria promotes the activity of enzymes of the tricarboxylic acid (TCA/Krebs) cycle, increases oxidative phosphorylation and ATP synthesis, and leads to changes in intramitochondrial pH. These pH alterations influence ion solubility and possibly the transitions and composition in the mineral phase structure of the granules. Based on these considerations, mitochondria are proposed to support the mineralization process by providing a mobile store of calcium and phosphate ions, in smaller cluster or larger granule form, while maintaining critical cellular activities. The rise in the mitochondrial calcium level also increases the generation of citrate and other TCA cycle intermediates that contribute to cell function and the development of extracellular mineral. This paper suggests that another key role of the mitochondrion, along with the effects just noted, is to supply phosphate ions, derived from the breakdown of ATP, to endolysosomes and autophagic vesicles originating in the endoplasmic reticulum and Golgi and at the plasma membrane. These many separate but interdependent mitochondrial functions emphasize the critical importance of this organelle in the cellular control of vertebrate mineralization.
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Affiliation(s)
- Irving M Shapiro
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States of America.
| | - Makarand V Risbud
- Department of Orthopaedic Surgery, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, United States of America
| | - William J Landis
- Department of Preventive and Restorative Dental Sciences, School of Dentistry, University of California at San Francisco, San Francisco, CA, United States of America
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2
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Gao Q, Ma Y, Shao T, Tao X, Yang X, Li S, Gu J, Yu Z. Development and Validation of Diagnostic Models for Transcriptomic Signature Genes for Multiple Tissues in Osteoarthritis. J Inflamm Res 2024; 17:5113-5127. [PMID: 39099665 PMCID: PMC11298182 DOI: 10.2147/jir.s472118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 07/20/2024] [Indexed: 08/06/2024] Open
Abstract
Background Progress in research on expression profiles in osteoarthritis (OA) has been limited to individual tissues within the joint, such as the synovium, cartilage, or meniscus. This study aimed to comprehensively analyze the common gene expression characteristics of various structures in OA and construct a diagnostic model. Methods Three datasets were selected: synovium, meniscus, and knee joint cartilage. Modular clustering and differential analysis of genes were used for further functional analyses and the construction of protein networks. Signature genes with the highest diagnostic potential were identified and verified using external gene datasets. The expression of these genes was validated in clinical samples by Real-time (RT)-qPCR and immunohistochemistry (IHC) staining. This study investigated the status of immune cells in OA by examining their infiltration. Results The merged OA dataset included 438 DEGs clustered into seven modules using WGCNA. The intersection of these DEGs with WGCNA modules identified 190 genes. Using Least Absolute Shrinkage and Selection Operator (LASSO) and Random Forest algorithms, nine signature genes were identified (CDADC1, PPFIBP1, ENO2, NOM1, SLC25A14, METTL2A, LINC01089, L3HYPDH, NPHP3), each demonstrating substantial diagnostic potential (areas under the curve from 0.701 to 0.925). Furthermore, dysregulation of various immune cells has also been observed. Conclusion CDADC1, PPFIBP1, ENO2, NOM1, SLC25A14, METTL2A, LINC01089, L3HYPDH, NPHP3 demonstrated significant diagnostic efficacy in OA and are involved in immune cell infiltration.
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Affiliation(s)
- Qichang Gao
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Yiming Ma
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Tuo Shao
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Xiaoxuan Tao
- Department of Radiotherapy, The 3st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Xiansheng Yang
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Song Li
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Jiaao Gu
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
| | - Zhange Yu
- Department of Spinal Surgery, The 1st Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People’s Republic of China
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3
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Caggiano EG, Taniguchi CM. UCP2 and pancreatic cancer: conscious uncoupling for therapeutic effect. Cancer Metastasis Rev 2024; 43:777-794. [PMID: 38194152 PMCID: PMC11156755 DOI: 10.1007/s10555-023-10157-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/13/2023] [Indexed: 01/10/2024]
Abstract
Pancreatic cancer has an exaggerated dependence on mitochondrial metabolism, but methods to specifically target the mitochondria without off target effects in normal tissues that rely on these organelles is a significant challenge. The mitochondrial uncoupling protein 2 (UCP2) has potential as a cancer-specific drug target, and thus, we will review the known biology of UCP2 and discuss its potential role in the pathobiology and future therapy of pancreatic cancer.
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Affiliation(s)
- Emily G Caggiano
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
- The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
| | - Cullen M Taniguchi
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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4
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Wang N, Peng YJ, Kang W, Hildreth M, Prabhakar NR, Nanduri J. Transcriptomic Analysis of Postnatal Rat Carotid Body Development. Genes (Basel) 2024; 15:302. [PMID: 38540361 PMCID: PMC10970570 DOI: 10.3390/genes15030302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 06/14/2024] Open
Abstract
The carotid body (CB), located bilaterally at the carotid artery bifurcations, is the primary sensory organ for monitoring arterial blood O2 levels. Carotid bodies are immature at birth, exhibiting low sensitivity to hypoxia, and become more sensitive with maturation during the first few weeks of neonatal life. To understand the molecular basis for the postnatal developmental hypoxic responses of CB, we isolated CBs from 5-day and 21-day-old Sprague-Dawley rats and performed RNA sequencing, which allows comprehensive analysis of gene expression. Differentially expressed genes (DEGs) were generated using Edge R, while functional enrichment analysis was performed using gene-set enrichment analysis (GSEA). Analysis of RNA-Seq data showed 2604 DEGs of the total 12,696 genes shared between neonates and adults. Of the 2604 DEGs, 924 genes were upregulated, and 1680 genes were downregulated. Further analysis showed that genes related to oxidative phosphorylation (Ox/phos) and hypoxia-signaling pathways were significantly upregulated in neonatal CBs compared to adult CBs, suggesting a possible link to differential developmental hypoxic responses seen in CB. Genes related to cytokine signaling (INFγ and TNFα) and transcription factors (CREB and NFΚB) mediated pathways were enriched in adult CBs, suggesting that expression of these pathways may be linked to developmental regulation. The RNA-Seq results were verified by analyzing mRNA changes in selected genes by qRT-PCR. Our results of enrichment analysis of biological pathways offer valuable insight into CB hypoxic sensing responses related to the development process.
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Affiliation(s)
- Ning Wang
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Ying-Jie Peng
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Wenjun Kang
- Center for Research Informatics, The University of Chicago, Chicago, IL 60637, USA
| | - Matthew Hildreth
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Nanduri R. Prabhakar
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
| | - Jayasri Nanduri
- Institute for Integrative Physiology and Center for Systems Biology of O2 Sensing, The University of Chicago, Chicago, IL 60637, USA
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De Leonardis F, Ahmed A, Vozza A, Capobianco L, Riley CL, Barile SN, Di Molfetta D, Tiziani S, DiGiovanni J, Palmieri L, Dolce V, Fiermonte G. Human mitochondrial uncoupling protein 3 functions as a metabolite transporter. FEBS Lett 2024; 598:338-346. [PMID: 38058167 PMCID: PMC10922436 DOI: 10.1002/1873-3468.14784] [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: 11/05/2023] [Revised: 11/22/2023] [Accepted: 11/24/2023] [Indexed: 12/08/2023]
Abstract
Since its discovery, a major debate about mitochondrial uncoupling protein 3 (UCP3) has been whether its metabolic actions result primarily from mitochondrial inner membrane proton transport, a process that decreases respiratory efficiency and ATP synthesis. However, UCP3 expression and activity are induced by conditions that would seem at odds with inefficient 'uncoupled' respiration, including fasting and exercise. Here, we demonstrate that the bacterially expressed human UCP3, reconstituted into liposomes, catalyses a strict exchange of aspartate, malate, sulphate and phosphate. The R282Q mutation abolishes the transport activity of the protein. Although the substrate specificity and inhibitor sensitivity of UCP3 display similarity with that of its close homolog UCP2, the two proteins significantly differ in their transport mode and kinetic constants.
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Affiliation(s)
- Francesco De Leonardis
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Amer Ahmed
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Angelo Vozza
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Christopher L. Riley
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Simona Nicole Barile
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Daria Di Molfetta
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Stefano Tiziani
- Department of Nutritional Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - John DiGiovanni
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Austin, TX. USA
| | - Luigi Palmieri
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Rende, Italy
| | - Giuseppe Fiermonte
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
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Kreiter J, Tyschuk T, Pohl EE. Uncoupling Protein 3 Catalyzes the Exchange of C4 Metabolites Similar to UCP2. Biomolecules 2023; 14:21. [PMID: 38254621 PMCID: PMC10813146 DOI: 10.3390/biom14010021] [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: 09/29/2023] [Revised: 12/14/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024] Open
Abstract
Uncoupling protein 3 (UCP3) belongs to the mitochondrial carrier protein superfamily SLC25 and is abundant in brown adipose tissue (BAT), the heart, and muscles. The expression of UCP3 in tissues mainly dependent on fatty acid oxidation suggests its involvement in cellular metabolism and has drawn attention to its possible transport function beyond the transport of protons in the presence of fatty acids. Based on the high homology between UCP2 and UCP3, we hypothesized that UCP3 transports C4 metabolites similar to UCP2. To test this, we measured the transport of substrates against phosphate (32Pi) in proteoliposomes reconstituted with recombinant murine UCP3 (mUCP3). We found that mUCP3 mainly transports aspartate and sulfate but also malate, malonate, oxaloacetate, and succinate. The transport rates calculated from the exchange of 32Pi against extraliposomal aspartate and sulfate were 23.9 ± 5.8 and 17.5 ± 5.1 µmol/min/mg, respectively. Using site-directed mutagenesis, we revealed that mutation of R84 resulted in impaired aspartate/phosphate exchange, demonstrating its critical role in substrate transport. The difference in substrate preference between mUCP2 and mUCP3 may be explained by their different tissue expression patterns and biological functions in these tissues.
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Affiliation(s)
| | | | - Elena E. Pohl
- Institute of Physiology, Pathophysiology and Biophysics, University of Veterinary Medicine, 1210 Vienna, Austria; (J.K.); (T.T.)
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7
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Holeček M. Aspartic Acid in Health and Disease. Nutrients 2023; 15:4023. [PMID: 37764806 PMCID: PMC10536334 DOI: 10.3390/nu15184023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/12/2023] [Accepted: 09/15/2023] [Indexed: 09/29/2023] Open
Abstract
Aspartic acid exists in L- and D-isoforms (L-Asp and D-Asp). Most L-Asp is synthesized by mitochondrial aspartate aminotransferase from oxaloacetate and glutamate acquired by glutamine deamidation, particularly in the liver and tumor cells, and transamination of branched-chain amino acids (BCAAs), particularly in muscles. The main source of D-Asp is the racemization of L-Asp. L-Asp transported via aspartate-glutamate carrier to the cytosol is used in protein and nucleotide synthesis, gluconeogenesis, urea, and purine-nucleotide cycles, and neurotransmission and via the malate-aspartate shuttle maintains NADH delivery to mitochondria and redox balance. L-Asp released from neurons connects with the glutamate-glutamine cycle and ensures glycolysis and ammonia detoxification in astrocytes. D-Asp has a role in brain development and hypothalamus regulation. The hereditary disorders in L-Asp metabolism include citrullinemia, asparagine synthetase deficiency, Canavan disease, and dicarboxylic aminoaciduria. L-Asp plays a role in the pathogenesis of psychiatric and neurologic disorders and alterations in BCAA levels in diabetes and hyperammonemia. Further research is needed to examine the targeting of L-Asp metabolism as a strategy to fight cancer, the use of L-Asp as a dietary supplement, and the risks of increased L-Asp consumption. The role of D-Asp in the brain warrants studies on its therapeutic potential in psychiatric and neurologic disorders.
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Affiliation(s)
- Milan Holeček
- Department of Physiology, Faculty of Medicine in Hradec Králové, Charles University, Šimkova 870, 500 03 Hradec Králové, Czech Republic
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8
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Wu C, Song Y, Yu Y, Xu Q, Cui X, Wang Y, Wu J, Gu HF. Single-Cell Transcriptional Landscape Reveals the Regulatory Network and Its Heterogeneity of Renal Mitochondrial Damages in Diabetic Kidney Disease. Int J Mol Sci 2023; 24:13502. [PMID: 37686311 PMCID: PMC10487965 DOI: 10.3390/ijms241713502] [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: 08/05/2023] [Revised: 08/26/2023] [Accepted: 08/28/2023] [Indexed: 09/10/2023] Open
Abstract
Diabetic kidney disease (DKD) is one of the common chronic microvascular complications of diabetes in which mitochondrial disorder plays an important role in its pathogenesis. The current study delved into the single-cell level transcriptome heterogeneity of mitochondrial homeostasis in db/db mice, an animal model for study of type 2 diabetes and DKD, with single-cell RNA sequencing (scRNA-Seq) and bulk RNA-seq analyses. From the comprehensive dataset comprising 13 meticulously captured and authenticated renal cell types, an unsupervised cluster analysis of mitochondria-related genes within the descending loop of Henle, collecting duct principal cell, endothelial, B cells and macrophage, showed that they had two types of cell subsets, i.e., health-dominant and DKD-dominant clusters. Pseudotime analysis, cell communication and transcription factors forecast resulted in identification of the hub differentially expressed genes between these two clusters and unveiled that the hierarchical regulatory network of receptor-TF-target genes was triggered by mitochondrial degeneration. Furthermore, the collecting duct principal cells were found to be regulated by the decline of Fzd7, which contributed to the impaired cellular proliferation and development, apoptosis and inactive cell cycle, as well as diminished capacity for material transport. Thereby, both scRNA-Seq and bulk RNA-Seq data from the current study elucidate the heterogeneity of mitochondrial disorders among distinct cell types, particularly in the collecting duct principal cells and B cells during the DKD progression and drug administration, which provide novel insights for better understanding the pathogenesis of DKD.
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Affiliation(s)
- Chenhua Wu
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
- Laboratory of Minigene Pharmacy, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Yuhui Song
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
| | - Yihong Yu
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
- Laboratory of Minigene Pharmacy, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Qing Xu
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
| | - Xu Cui
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
| | - Yurong Wang
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
| | - Jie Wu
- Laboratory of Minigene Pharmacy, School of Life Science and Technology, China Pharmaceutical University, Nanjing 211198, China
| | - Harvest F. Gu
- Laboratory of Molecular Medicine, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China; (C.W.); (Y.S.); (Y.Y.); (Q.X.); (X.C.); (Y.W.)
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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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Antos-Krzeminska N, Kicinska A, Nowak W, Jarmuszkiewicz W. Acanthamoeba castellanii Uncoupling Protein: A Complete Sequence, Activity, and Role in Response to Oxidative Stress. Int J Mol Sci 2023; 24:12501. [PMID: 37569876 PMCID: PMC10419851 DOI: 10.3390/ijms241512501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 08/01/2023] [Accepted: 08/04/2023] [Indexed: 08/13/2023] Open
Abstract
Uncoupling proteins (UCPs) are mitochondrial inner membrane transporters that mediate free-fatty-acid-induced, purine-nucleotide-inhibited proton leak into the mitochondrial matrix, thereby uncoupling respiratory substrate oxidation from ATP synthesis. The aim of this study was to provide functional evidence that the putative Acucp gene of the free-living protozoan amoeba, A. castellanii, encodes the mitochondrial protein with uncoupling activity characteristic of UCPs and to investigate its role during oxidative stress. We report the sequencing and cloning of a complete Acucp coding sequence, its phylogenetic analysis, and the heterologous expression of AcUCP in the S. cerevisiae strain InvSc1. Measurements of mitochondrial respiratory activity and membrane potential indicate that the heterologous expression of AcUCP causes AcUCP-mediated uncoupling activity. In addition, in a model of oxidative stress with increased reactive oxygen species levels (superoxide dismutase 1 knockout yeasts), AcUCP expression strongly promotes cell survival and growth. The level of superoxide anion radicals is greatly reduced in the ΔSOD1 strain expressing AcUCP. These results suggest that AcUCP targeted to yeast mitochondria causes uncoupling and may act as an antioxidant system. Phylogenetic analysis shows that the A. castellanii UCP diverges very early from other UCPs, but clearly locates within the UCP subfamily rather than among other mitochondrial anion carrier proteins.
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Affiliation(s)
- Nina Antos-Krzeminska
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
| | - Anna Kicinska
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
| | - Witold Nowak
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland;
| | - Wieslawa Jarmuszkiewicz
- Department of Bioenergetics, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznanskiego 6, 61-614 Poznan, Poland; (A.K.); (W.J.)
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11
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Gorgoglione R, Seccia R, Ahmed A, Vozza A, Capobianco L, Lodi A, Marra F, Paradies E, Palmieri L, Coppola V, Dolce V, Fiermonte G. Generation of a Yeast Cell Model Potentially Useful to Identify the Mammalian Mitochondrial N-Acetylglutamate Transporter. Biomolecules 2023; 13:biom13050808. [PMID: 37238678 DOI: 10.3390/biom13050808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
The human mitochondrial carrier family (MCF) consists of 53 members. Approximately one-fifth of them are still orphans of a function. Most mitochondrial transporters have been functionally characterized by reconstituting the bacterially expressed protein into liposomes and transport assays with radiolabeled compounds. The efficacy of this experimental approach is constrained to the commercial availability of the radiolabeled substrate to be used in the transport assays. A striking example is that of N-acetylglutamate (NAG), an essential regulator of the carbamoyl synthetase I activity and the entire urea cycle. Mammals cannot modulate mitochondrial NAG synthesis but can regulate the levels of NAG in the matrix by exporting it to the cytosol, where it is degraded. The mitochondrial NAG transporter is still unknown. Here, we report the generation of a yeast cell model suitable for identifying the putative mammalian mitochondrial NAG transporter. In yeast, the arginine biosynthesis starts in the mitochondria from NAG which is converted to ornithine that, once transported into cytosol, is metabolized to arginine. The deletion of ARG8 makes yeast cells unable to grow in the absence of arginine since they cannot synthetize ornithine but can still produce NAG. To make yeast cells dependent on a mitochondrial NAG exporter, we moved most of the yeast mitochondrial biosynthetic pathway to the cytosol by expressing four E. coli enzymes, argB-E, able to convert cytosolic NAG to ornithine. Although argB-E rescued the arginine auxotrophy of arg8∆ strain very poorly, the expression of the bacterial NAG synthase (argA), which would mimic the function of a putative NAG transporter increasing the cytosolic levels of NAG, fully rescued the growth defect of arg8∆ strain in the absence of arginine, demonstrating the potential suitability of the model generated.
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Affiliation(s)
- Ruggiero Gorgoglione
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Roberta Seccia
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Amer Ahmed
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Angelo Vozza
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy
| | - Alessia Lodi
- Department of Nutritional Sciences, College of Natural Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Dell Pediatric Research Institute, Dell Medical School, The University of Texas at Austin, Austin, TX 78723, USA
| | - Federica Marra
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Eleonora Paradies
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70125 Bari, Italy
| | - Luigi Palmieri
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, College of Medicine, The Ohio State University and Arthur G. James Comprehensive Cancer Center, Columbus, OH 43210, USA
| | - Vincenza Dolce
- Department of Pharmacy, Health and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy
| | - Giuseppe Fiermonte
- Department of Bioscience, Biotechnology and Environment, University of Bari, 70125 Bari, Italy
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12
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Citrate Regulates the Saccharomyces cerevisiae Mitochondrial GDP/GTP Carrier (Ggc1p) by Triggering Unidirectional Transport of GTP. J Fungi (Basel) 2022; 8:jof8080795. [PMID: 36012783 PMCID: PMC9410265 DOI: 10.3390/jof8080795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/27/2022] [Accepted: 07/27/2022] [Indexed: 02/01/2023] Open
Abstract
The yeast mitochondrial transport of GTP and GDP is mediated by Ggc1p, a member of the mitochondrial carrier family. The physiological role of Ggc1p in S. cerevisiae is probably to transport GTP into mitochondria in exchange for GDP generated in the matrix. ggc1Δ cells exhibit lower levels of GTP and increased levels of GDP in mitochondria, are unable to grow on nonfermentable substrates and lose mtDNA. Because in yeast, succinyl-CoA ligase produces ATP instead of GTP, and the mitochondrial nucleoside diphosphate kinase is localized in the intermembrane space, Ggc1p is the only supplier of mitochondrial GTP required for the maturation of proteins containing Fe-S clusters, such as aconitase [4Fe-4S] and ferredoxin [2Fe-2S]. In this work, it was demonstrated that citrate is a regulator of purified and reconstituted Ggc1p by trans-activating unidirectional transport of GTP across the proteoliposomal membrane. It was also shown that the binding site of Ggc1p for citrate is different from the binding site for the substrate GTP. It is proposed that the citrate-induced GTP uniport (CIGU) mediated by Ggc1p is involved in the homeostasis of the guanine nucleotide pool in the mitochondrial matrix.
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13
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Du X, He X, Liu Q, Liu Q, Di R, Chu M. Identification of photoperiod-induced specific miRNAs in the adrenal glands of Sunite sheep (Ovis aries). Front Vet Sci 2022; 9:888207. [PMID: 35937294 PMCID: PMC9354845 DOI: 10.3389/fvets.2022.888207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 07/05/2022] [Indexed: 11/18/2022] Open
Abstract
In seasonal estrus, it is well known that melatonin-regulated biorhythm plays a key role. Some studies indicate that the adrenal gland plays an important role in reproduction in mammals, but the molecular mechanism is not clear. This study used an artificially controlled light photoperiod model, combined with RNA-seq technology and bioinformatics analysis, to analyze the messenger RNA (mRNA) and microRNA (miRNA) of ewe (Sunite) adrenal glands under different photoperiod treatments. After identification, the key candidate genes GRHL2, CENPF, FGF16 and SLC25A30 that photoperiod affects reproduction were confirmed. The miRNAs (oar-miR-544-3p, oar-miR-411b-5p, oar-miR-376e-3p, oar-miR-376d, oar-miR-376b-3p, oar-miR-376a-3p) were specifically expressed in the adrenal gland. The candidate mRNA-miRNA pairs (e.g., SLC25A30 coagulated by novel miRNA554, novel miRNA555 and novel miRNA559) may affect seasonal estrus. In summary, we constructed relation network of the mRNAs and miRNAs of sheep adrenal glands using RNA sequencing and bioinformatics analysis, thereby, providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep.
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Affiliation(s)
- Xiaolong Du
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Qingqing Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Qiuyue Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
| | - Mingxing Chu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences of Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Mingxing Chu
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14
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Palmieri F, Monné M, Fiermonte G, Palmieri L. Mitochondrial transport and metabolism of the vitamin B-derived cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD + , and related diseases: A review. IUBMB Life 2022; 74:592-617. [PMID: 35304818 PMCID: PMC9311062 DOI: 10.1002/iub.2612] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 02/17/2022] [Accepted: 02/18/2022] [Indexed: 01/19/2023]
Abstract
Multiple mitochondrial matrix enzymes playing key roles in metabolism require cofactors for their action. Due to the high impermeability of the mitochondrial inner membrane, these cofactors need to be synthesized within the mitochondria or be imported, themselves or one of their precursors, into the organelles. Transporters belonging to the protein family of mitochondrial carriers have been identified to transport the coenzymes: thiamine pyrophosphate, coenzyme A, FAD and NAD+ , which are all structurally similar to nucleotides and derived from different B-vitamins. These mitochondrial cofactors bind more or less tightly to their enzymes and, after having been involved in a specific reaction step, are regenerated, spontaneously or by other enzymes, to return to their active form, ready for the next catalysis round. Disease-causing mutations in the mitochondrial cofactor carrier genes compromise not only the transport reaction but also the activity of all mitochondrial enzymes using that particular cofactor and the metabolic pathways in which the cofactor-dependent enzymes are involved. The mitochondrial transport, metabolism and diseases of the cofactors thiamine pyrophosphate, coenzyme A, FAD and NAD+ are the focus of this review.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- Department of SciencesUniversity of BasilicataPotenzaItaly
| | - Giuseppe Fiermonte
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and BiopharmaceuticsUniversity of BariBariItaly
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM)BariItaly
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15
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Monné M, Marobbio CMT, Agrimi G, Palmieri L, Palmieri F. Mitochondrial transport and metabolism of the major methyl donor and versatile cofactor S-adenosylmethionine, and related diseases: A review †. IUBMB Life 2022; 74:573-591. [PMID: 35730628 DOI: 10.1002/iub.2658] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Accepted: 05/19/2022] [Indexed: 11/08/2022]
Abstract
S-adenosyl-L-methionine (SAM) is a coenzyme and the most commonly used methyl-group donor for the modification of metabolites, DNA, RNA and proteins. SAM biosynthesis and SAM regeneration from the methylation reaction product S-adenosyl-L-homocysteine (SAH) take place in the cytoplasm. Therefore, the intramitochondrial SAM-dependent methyltransferases require the import of SAM and export of SAH for recycling. Orthologous mitochondrial transporters belonging to the mitochondrial carrier family have been identified to catalyze this antiport transport step: Sam5p in yeast, SLC25A26 (SAMC) in humans, and SAMC1-2 in plants. In mitochondria SAM is used by a vast number of enzymes implicated in the following processes: the regulation of replication, transcription, translation, and enzymatic activities; the maturation and assembly of mitochondrial tRNAs, ribosomes and protein complexes; and the biosynthesis of cofactors, such as ubiquinone, lipoate, and molybdopterin. Mutations in SLC25A26 and mitochondrial SAM-dependent enzymes have been found to cause human diseases, which emphasizes the physiological importance of these proteins.
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Affiliation(s)
- Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,Department of Sciences, University of Basilicata, Potenza, Italy
| | - Carlo M T Marobbio
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Bari, Italy.,CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Bari, Italy
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16
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Savvateeva M, Kudryavtseva A, Lukyanova E, Kobelyatskaya A, Pavlov V, Fedorova M, Pudova E, Guvatova Z, Kalinin D, Golovyuk A, Bulavkina E, Katunina I, Krasnov G, Snezhkina A. Somatic Mutation Profiling in Head and Neck Paragangliomas. J Clin Endocrinol Metab 2022; 107:1833-1842. [PMID: 35460558 PMCID: PMC9202733 DOI: 10.1210/clinem/dgac250] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Indexed: 11/19/2022]
Abstract
CONTEXT Head and neck paragangliomas (HNPGLs) are rare neoplasms with a high degree of heritability. Paragangliomas present as polygenic diseases caused by combined alterations in multiple genes; however, many driver changes remain unknown. OBJECTIVE The objective of the study was to analyze somatic mutation profiles in HNPGLs. METHODS Whole-exome sequencing of 42 tumors and matched normal tissues obtained from Russian patients with HNPGLs was carried out. Somatic mutation profiling included variant calling and utilizing MutSig and SigProfiler packages. RESULTS 57% of patients harbored germline and somatic variants in paraganglioma (PGL) susceptibility genes or potentially related genes. Somatic variants in novel genes were found in 17% of patients without mutations in any known PGL-related genes. The studied cohort was characterized by 6 significantly mutated genes: SDHD, BCAS4, SLC25A14, RBM3, TP53, and ASCC1, as well as 4 COSMIC single base substitutions (SBS)-96 mutational signatures (SBS5, SBS29, SBS1, and SBS7b). Tumors with germline variants specifically displayed SBS11 and SBS19, when an SBS33-specific mutational signature was identified for cases without those. Beta allele frequency analysis of copy number variations revealed loss of heterozygosity of the wild-type allele in 1 patient with germline mutation c.287-2A>G in the SDHB gene. In patients with germline mutation c.A305G in the SDHD gene, frequent potential loss of chromosome 11 was observed. CONCLUSION These results give an understanding of somatic changes and the mutational landscape associated with HNPGLs and are important for the identification of molecular mechanisms involved in tumor development.
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Affiliation(s)
- Maria Savvateeva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Lukyanova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Vladislav Pavlov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena Pudova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Zulfiya Guvatova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Dmitry Kalinin
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Alexander Golovyuk
- Vishnevsky Institute of Surgery, Ministry of Health of the Russian Federation, 117997 Moscow, Russia
| | - Elizaveta Bulavkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Irina Katunina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anastasiya Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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17
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Miniero DV, Monné M, Di Noia MA, Palmieri L, Palmieri F. Evidence for Non-Essential Salt Bridges in the M-Gates of Mitochondrial Carrier Proteins. Int J Mol Sci 2022; 23:ijms23095060. [PMID: 35563451 PMCID: PMC9104175 DOI: 10.3390/ijms23095060] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 01/05/2023] Open
Abstract
Mitochondrial carriers, which transport metabolites, nucleotides, and cofactors across the mitochondrial inner membrane, have six transmembrane α-helices enclosing a translocation pore with a central substrate binding site whose access is controlled by a cytoplasmic and a matrix gate (M-gate). The salt bridges formed by the three PX[DE]XX[RK] motifs located on the odd-numbered transmembrane α-helices greatly contribute to closing the M-gate. We have measured the transport rates of cysteine mutants of the charged residue positions in the PX[DE]XX[RK] motifs of the bovine oxoglutarate carrier, the yeast GTP/GDP carrier, and the yeast NAD+ transporter, which all lack one of these charged residues. Most single substitutions, including those of the non-charged and unpaired charged residues, completely inactivated transport. Double mutations of charged pairs showed that all three carriers contain salt bridges non-essential for activity. Two double substitutions of these non-essential charge pairs exhibited higher transport rates than their corresponding single mutants, whereas swapping the charged residues in these positions did not increase activity. The results demonstrate that some of the residues in the charged residue positions of the PX[DE]XX[KR] motifs are important for reasons other than forming salt bridges, probably for playing specific roles related to the substrate interaction-mediated conformational changes leading to the M-gate opening/closing.
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Affiliation(s)
- Daniela Valeria Miniero
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- Department of Sciences, University of Basilicata, Via Ateneo Lucano 10, 85100 Potenza, Italy
| | - Maria Antonietta Di Noia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- Correspondence: (L.P.); (F.P.)
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari, Via E. Orabona 4, 70125 Bari, Italy; (D.V.M.); (M.M.); (M.A.D.N.)
- CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), 70126 Bari, Italy
- Correspondence: (L.P.); (F.P.)
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18
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Kushnareva Y, Moraes V, Suess J, Peters B, Newmeyer DD, Kuwana T. Disruption of mitochondrial quality control genes promotes caspase-resistant cell survival following apoptotic stimuli. J Biol Chem 2022; 298:101835. [PMID: 35304098 PMCID: PMC9018395 DOI: 10.1016/j.jbc.2022.101835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/24/2022] Open
Abstract
In cells undergoing cell-intrinsic apoptosis, mitochondrial outer membrane permeabilization (MOMP) typically marks an irreversible step in the cell death process. However, in some cases, a subpopulation of treated cells can exhibit a sublethal response, termed "minority MOMP." In this phenomenon, the affected cells survive, despite a low level of caspase activation and subsequent limited activation of the endonuclease caspase-activated DNase (DNA fragmentation factor subunit beta). Consequently, these cells can experience DNA damage, increasing the probability of oncogenesis. However, little is known about the minority MOMP response. To discover genes that affect the MOMP response in individual cells, we conducted an imaging-based phenotypic siRNA screen. We identified multiple candidate genes whose downregulation increased the heterogeneity of MOMP within single cells, among which were genes related to mitochondrial dynamics and mitophagy that participate in the mitochondrial quality control (MQC) system. Furthermore, to test the hypothesis that functional MQC is important for reducing the frequency of minority MOMP, we developed an assay to measure the clonogenic survival of caspase-engaged cells. We found that cells deficient in various MQC genes were indeed prone to aberrant post-MOMP survival. Our data highlight the important role of proteins involved in mitochondrial dynamics and mitophagy in preventing apoptotic dysregulation and oncogenesis.
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Affiliation(s)
- Yulia Kushnareva
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Vivian Moraes
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Julian Suess
- Department of Biochemical Pharmacology, University of Konstanz, Konstanz, Germany
| | - Bjoern Peters
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Donald D Newmeyer
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California, USA
| | - Tomomi Kuwana
- Division of Immune Regulation, La Jolla Institute for Immunology, La Jolla, California, USA.
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Drosophila melanogaster Uncoupling Protein-4A (UCP4A) Catalyzes a Unidirectional Transport of Aspartate. Int J Mol Sci 2022; 23:ijms23031020. [PMID: 35162943 PMCID: PMC8834685 DOI: 10.3390/ijms23031020] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/14/2022] [Accepted: 01/16/2022] [Indexed: 12/23/2022] Open
Abstract
Uncoupling proteins (UCPs) form a distinct subfamily of the mitochondrial carrier family (MCF) SLC25. Four UCPs, DmUCP4A-C and DmUCP5, have been identified in Drosophila melanogaster on the basis of their sequence homology with mammalian UCP4 and UCP5. In a Parkinson’s disease model, DmUCP4A showed a protective role against mitochondrial dysfunction, by increasing mitochondrial membrane potential and ATP synthesis. To date, DmUCP4A is still an orphan of a biochemical function, although its possible involvement in mitochondrial uncoupling has been ruled out. Here, we show that DmUCP4A expressed in bacteria and reconstituted in phospholipid vesicles catalyzes a unidirectional transport of aspartate, which is saturable and inhibited by mercurials and other mitochondrial carrier inhibitors to various degrees. Swelling experiments carried out in yeast mitochondria have demonstrated that the unidirectional transport of aspartate catalyzed by DmUCP4 is not proton-coupled. The biochemical function of DmUCP4A has been further confirmed in a yeast cell model, in which growth has required an efflux of aspartate from mitochondria. Notably, DmUCP4A is the first UCP4 homolog from any species to be biochemically characterized. In Drosophila melanogaster, DmUCP4A could be involved in the transport of aspartate from mitochondria to the cytosol, in which it could be used for protein and nucleotide synthesis, as well as in the biosynthesis of ß-alanine and N-acetylaspartate, which play key roles in signal transmission in the central nervous system.
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Marra F, Lunetti P, Curcio R, Lasorsa FM, Capobianco L, Porcelli V, Dolce V, Fiermonte G, Scarcia P. An Overview of Mitochondrial Protein Defects in Neuromuscular Diseases. Biomolecules 2021; 11:1633. [PMID: 34827632 PMCID: PMC8615828 DOI: 10.3390/biom11111633] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/29/2021] [Accepted: 11/01/2021] [Indexed: 11/18/2022] Open
Abstract
Neuromuscular diseases (NMDs) are dysfunctions that involve skeletal muscle and cause incorrect communication between the nerves and muscles. The specific causes of NMDs are not well known, but most of them are caused by genetic mutations. NMDs are generally progressive and entail muscle weakness and fatigue. Muscular impairments can differ in onset, severity, prognosis, and phenotype. A multitude of possible injury sites can make diagnosis of NMDs difficult. Mitochondria are crucial for cellular homeostasis and are involved in various metabolic pathways; for this reason, their dysfunction can lead to the development of different pathologies, including NMDs. Most NMDs due to mitochondrial dysfunction have been associated with mutations of genes involved in mitochondrial biogenesis and metabolism. This review is focused on some mitochondrial routes such as the TCA cycle, OXPHOS, and β-oxidation, recently found to be altered in NMDs. Particular attention is given to the alterations found in some genes encoding mitochondrial carriers, proteins of the inner mitochondrial membrane able to exchange metabolites between mitochondria and the cytosol. Briefly, we discuss possible strategies used to diagnose NMDs and therapies able to promote patient outcome.
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Affiliation(s)
- Federica Marra
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Paola Lunetti
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Rosita Curcio
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Francesco Massimo Lasorsa
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Loredana Capobianco
- Department of Biological and Environmental Sciences and Technologies, University of Salento, 73100 Lecce, Italy; (P.L.); (L.C.)
| | - Vito Porcelli
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
| | - Vincenza Dolce
- Department of Pharmacy, Health, and Nutritional Sciences, University of Calabria, 87036 Arcavacata di Rende, Italy; (F.M.); (R.C.); (V.D.)
| | - Giuseppe Fiermonte
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
- Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies, National Research Council, 00155 Rome, Italy
| | - Pasquale Scarcia
- Laboratory of Biochemistry and Molecular Biology, Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy; (F.M.L.); (V.P.)
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21
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Mitochondrial Uncoupling Proteins (UCPs) as Key Modulators of ROS Homeostasis: A Crosstalk between Diabesity and Male Infertility? Antioxidants (Basel) 2021; 10:antiox10111746. [PMID: 34829617 PMCID: PMC8614977 DOI: 10.3390/antiox10111746] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/14/2022] Open
Abstract
Uncoupling proteins (UCPs) are transmembrane proteins members of the mitochondrial anion transporter family present in the mitochondrial inner membrane. Currently, six homologs have been identified (UCP1-6) in mammals, with ubiquitous tissue distribution and multiple physiological functions. UCPs are regulators of key events for cellular bioenergetic metabolism, such as membrane potential, metabolic efficiency, and energy dissipation also functioning as pivotal modulators of ROS production and general cellular redox state. UCPs can act as proton channels, leading to proton re-entry the mitochondrial matrix from the intermembrane space and thus collapsing the proton gradient and decreasing the membrane potential. Each homolog exhibits its specific functions, from thermogenesis to regulation of ROS production. The expression and function of UCPs are intimately linked to diabesity, with their dysregulation/dysfunction not only associated to diabesity onset, but also by exacerbating oxidative stress-related damage. Male infertility is one of the most overlooked diabesity-related comorbidities, where high oxidative stress takes a major role. In this review, we discuss in detail the expression and function of the different UCP homologs. In addition, the role of UCPs as key regulators of ROS production and redox homeostasis, as well as their influence on the pathophysiology of diabesity and potential role on diabesity-induced male infertility is debated.
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22
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Kunji ERS, King MS, Ruprecht JJ, Thangaratnarajah C. The SLC25 Carrier Family: Important Transport Proteins in Mitochondrial Physiology and Pathology. Physiology (Bethesda) 2021; 35:302-327. [PMID: 32783608 PMCID: PMC7611780 DOI: 10.1152/physiol.00009.2020] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Members of the mitochondrial carrier family (SLC25) transport a variety of compounds across the inner membrane of mitochondria. These transport steps provide building blocks for the cell and link the pathways of the mitochondrial matrix and cytosol. An increasing number of diseases and pathologies has been associated with their dysfunction. In this review, the molecular basis of these diseases is explained based on our current understanding of their transport mechanism.
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Affiliation(s)
- Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J Ruprecht
- Medical Research Council Mitochondrial Biology Unit, University of Cambridge, Cambridge, United Kingdom
| | - Chancievan Thangaratnarajah
- Groningen Biomolecular Sciences and Biotechnology Institute, Membrane Enzymology, University of Groningen, Groningen, The Netherlands
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Pasquadibisceglie A, Polticelli F. Computational studies of the mitochondrial carrier family SLC25. Present status and future perspectives. BIO-ALGORITHMS AND MED-SYSTEMS 2021. [DOI: 10.1515/bams-2021-0018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Abstract
The members of the mitochondrial carrier family, also known as solute carrier family 25 (SLC25), are transmembrane proteins involved in the translocation of a plethora of small molecules between the mitochondrial intermembrane space and the matrix. These transporters are characterized by three homologous domains structure and a transport mechanism that involves the transition between different conformations. Mutations in regions critical for these transporters’ function often cause several diseases, given the crucial role of these proteins in the mitochondrial homeostasis. Experimental studies can be problematic in the case of membrane proteins, in particular concerning the characterization of the structure–function relationships. For this reason, computational methods are often applied in order to develop new hypotheses or to support/explain experimental evidence. Here the computational analyses carried out on the SLC25 members are reviewed, describing the main techniques used and the outcome in terms of improved knowledge of the transport mechanism. Potential future applications on this protein family of more recent and advanced in silico methods are also suggested.
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Affiliation(s)
| | - Fabio Polticelli
- Department of Sciences , Roma Tre University , Rome , Italy
- National Institute of Nuclear Physics, Roma Tre Section , Rome , Italy
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Han M, Zhang C, Suglo P, Sun S, Wang M, Su T. l-Aspartate: An Essential Metabolite for Plant Growth and Stress Acclimation. Molecules 2021; 26:molecules26071887. [PMID: 33810495 PMCID: PMC8037285 DOI: 10.3390/molecules26071887] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/17/2021] [Accepted: 03/23/2021] [Indexed: 01/07/2023] Open
Abstract
L-aspartate (Asp) serves as a central building block, in addition to being a constituent of proteins, for many metabolic processes in most organisms, such as biosynthesis of other amino acids, nucleotides, nicotinamide adenine dinucleotide (NAD), the tricarboxylic acid (TCA) cycle and glycolysis pathway intermediates, and hormones, which are vital for growth and defense. In animals and humans, lines of data have proved that Asp is indispensable for cell proliferation. However, in plants, despite the extensive study of the Asp family amino acid pathway, little attention has been paid to the function of Asp through the other numerous pathways. This review aims to elucidate the most important aspects of Asp in plants, from biosynthesis to catabolism and the role of Asp and its metabolic derivatives in response to changing environmental conditions. It considers the distribution of Asp in various cell compartments and the change of Asp level, and its significance in the whole plant under various stresses. Moreover, it provides evidence of the interconnection between Asp and phytohormones, which have prominent functions in plant growth, development, and defense. The updated information will help improve our understanding of the physiological role of Asp and Asp-borne metabolic fluxes, supporting the modular operation of these networks.
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Affiliation(s)
- Mei Han
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Can Zhang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Peter Suglo
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Shuyue Sun
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Mingyao Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
| | - Tao Su
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China; (M.H.); (C.Z.); (P.S.); (S.S.); (M.W.)
- Key Laboratory of State Forestry Administration on Subtropical Forest Biodiversity Conservation, Nanjing Forestry University, Nanjing 210037, China
- Correspondence:
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Chaney HL, Grose LF, Charpigny G, Behura SK, Sheldon IM, Cronin JG, Lonergan P, Spencer TE, Mathew DJ. Conceptus-induced, interferon tau-dependent gene expression in bovine endometrial epithelial and stromal cells†. Biol Reprod 2020; 104:669-683. [PMID: 33330929 DOI: 10.1093/biolre/ioaa226] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 11/13/2020] [Accepted: 12/13/2020] [Indexed: 12/21/2022] Open
Abstract
Bovine endometrium consists of epithelial and stromal cells that respond to conceptus interferon tau (IFNT), the maternal recognition of pregnancy (MRP) signal, by increasing expression of IFN-stimulated genes (ISGs). Endometrial epithelial and stromal-cell-specific ISGs are largely unknown but hypothesized to have essential functions during pregnancy establishment. Bovine endometrial epithelial cells were cultured in inserts above stromal fibroblast (SF) cells for 6 h in medium alone or with IFNT. The epithelial and SF transcriptomic response was analyzed separately using RNA sequencing and compared to a list of 369 DEGs recently identified in intact bovine endometrium in response to elongating bovine conceptuses and IFNT. Bovine endometrial epithelial and SF shared 223 and 70 DEGs in common with the list of 369 endometrial DEGs. Well-known ISGs identified in the epithelial and SF were ISG15, MX1, MX2, and OAS2. DEGs identified in the epithelial but not SF included a number of IRF molecules (IRF1, IRF2, IRF3, and IRF8), mitochondria SLC transporters (SLC25A19, SLC25A28, and SLC25A30), and a ghrelin receptor. Expression of ZC3HAV1, an anti-retroviral gene, increased specifically within the SF. Gene ontology analysis identified the type I IFN signaling pathway and activation of nuclear factor kappa B transcription factors as biological processes associated with the epithelial cell DEGs. This study has identified biologically relevant IFNT-stimulated genes within specific endometrial cell types. The findings provide critical information regarding the effects of conceptus IFNT on specific endometrial compartments during early developmental processes in cattle.
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Affiliation(s)
- Heather L Chaney
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Lindsay F Grose
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
| | - Gilles Charpigny
- INRA, Biologie du Développement et Reproduction, Jouy en Josas, France
| | - Susanta K Behura
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - I Martin Sheldon
- Swansea University Medical School, Swansea University, Swansea, UK
| | - James G Cronin
- Swansea University Medical School, Swansea University, Swansea, UK
| | - Patrick Lonergan
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Thomas E Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, USA
| | - Daniel J Mathew
- Department of Animal Science, University of Tennessee, Knoxville, TN, USA
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26
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Yuzbasheva EY, Scarcia P, Yuzbashev TV, Messina E, Kosikhina IM, Palmieri L, Shutov AV, Taratynova MO, Amaro RL, Palmieri F, Sineoky SP, Agrimi G. Engineering Yarrowia lipolytica for the selective and high-level production of isocitric acid through manipulation of mitochondrial dicarboxylate-tricarboxylate carriers. Metab Eng 2020; 65:156-166. [PMID: 33161142 DOI: 10.1016/j.ymben.2020.11.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Revised: 10/14/2020] [Accepted: 11/01/2020] [Indexed: 11/18/2022]
Abstract
During cultivation under nitrogen starvation, Yarrowia lipolytica produces a mixture of citric acid and isocitric acid whose ratio is mainly determined by the carbon source used. We report that mitochondrial succinate-fumarate carrier YlSfc1 controls isocitric acid efflux from mitochondria. YlSfc1 purified and reconstituted into liposomes transports succinate, fumarate, oxaloacetate, isocitrate and α-ketoglutarate. YlSFC1 overexpression determined the inversion of isocitric acid/citric acid ratio towards isocitric acid, resulting in 33.4 ± 1.9 g/L and 43.3 ± 2.8 g/L of ICA production in test-tube cultivation with glucose and glycerol, respectively. These titers represent a 4.0 and 6.3-fold increase compared to the wild type. YlSFC1 gene expression was repressed in the wild type strain grown in glucose-based medium compared to olive oil medium explaining the reason for the preferred citric acid production during Y. lipolytica growth on carbohydrates. Coexpression of YlSFC1 and adenosine monophosphate deaminase YlAMPD genes together with inactivation of citrate mitochondrial carrier YlYHM2 gene enhanced isocitric acid accumulation up to 41.4 ± 4.1 g/L with an isocitric acid/citric acid ratio of 14.3 in a small-scale cultivation with glucose as a carbon source. During large-scale cultivation with glucose pulse-feeding, the engineered strain produced 136.7 ± 2.5 g/L of ICA with a process selectivity of 88.1%, the highest reported titer and selectivity to date. These results represent the first reported isocitric acid secretion by Y. lipolytica as a main organic acid during cultivation on carbohydrate. Moreover, we demonstrate for the first time that the replacement of one mitochondrial transport system for another can be an efficient tool for switching product accumulation.
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Affiliation(s)
- Evgeniya Y Yuzbasheva
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK; NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia; BioMediCan Inc., 40471 Encyclopedia Circle, Fremont, 94538, CA, USA.
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy
| | - Tigran V Yuzbashev
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK; Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Eugenia Messina
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy
| | - Iuliia M Kosikhina
- NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia; NRC «Kurchatov Institute», 1 Kurchatov Square, Moscow, 123182, Russia
| | - Luigi Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Campus Universitario, Via Orabona 4, 70125, Bari, Italy
| | - Artem V Shutov
- NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia; NRC «Kurchatov Institute», 1 Kurchatov Square, Moscow, 123182, Russia
| | - Maria O Taratynova
- NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia; NRC «Kurchatov Institute», 1 Kurchatov Square, Moscow, 123182, Russia
| | - Rodrigo Ledesma Amaro
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK; Centre for Synthetic Biology, Imperial College London, London, SW7 2AZ, UK
| | - Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy; CNR Institute of Biomembranes, Bioenergetics and Molecular Biotechnologies (IBIOM), Campus Universitario, Via Orabona 4, 70125, Bari, Italy
| | - Sergey P Sineoky
- NRC «Kurchatov Institute» - GOSNIIGENETIKA, Kurchatov Genomic Center, 1-st Dorozhny Pr., 1, Moscow, 117545, Russia; NRC «Kurchatov Institute», 1 Kurchatov Square, Moscow, 123182, Russia
| | - Gennaro Agrimi
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Campus Universitario, Via Orabona 4, 70125, Bari, Italy.
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Drosophila melanogaster Mitochondrial Carriers: Similarities and Differences with the Human Carriers. Int J Mol Sci 2020; 21:ijms21176052. [PMID: 32842667 PMCID: PMC7504413 DOI: 10.3390/ijms21176052] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 12/15/2022] Open
Abstract
Mitochondrial carriers are a family of structurally related proteins responsible for the exchange of metabolites, cofactors and nucleotides between the cytoplasm and mitochondrial matrix. The in silico analysis of the Drosophila melanogaster genome has highlighted the presence of 48 genes encoding putative mitochondrial carriers, but only 20 have been functionally characterized. Despite most Drosophila mitochondrial carrier genes having human homologs and sharing with them 50% or higher sequence identity, D. melanogaster genes display peculiar differences from their human counterparts: (1) in the fruit fly, many genes encode more transcript isoforms or are duplicated, resulting in the presence of numerous subfamilies in the genome; (2) the expression of the energy-producing genes in D. melanogaster is coordinated from a motif known as Nuclear Respiratory Gene (NRG), a palindromic 8-bp sequence; (3) fruit-fly duplicated genes encoding mitochondrial carriers show a testis-biased expression pattern, probably in order to keep a duplicate copy in the genome. Here, we review the main features, biological activities and role in the metabolism of the D. melanogaster mitochondrial carriers characterized to date, highlighting similarities and differences with their human counterparts. Such knowledge is very important for obtaining an integrated view of mitochondrial function in D. melanogaster metabolism.
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Rochette L, Meloux A, Zeller M, Malka G, Cottin Y, Vergely C. Mitochondrial SLC25 Carriers: Novel Targets for Cancer Therapy. Molecules 2020; 25:molecules25102417. [PMID: 32455902 PMCID: PMC7288124 DOI: 10.3390/molecules25102417] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/20/2020] [Accepted: 05/21/2020] [Indexed: 01/11/2023] Open
Abstract
The transfer of metabolites through the mitochondrial membranes is a vital process that is highly controlled and regulated by the inner membrane. A variety of metabolites, nucleotides, and cofactors are transported across the inner mitochondrial membrane (IMM) by a superfamily of membrane transporters which are known as the mitochondrial carrier family (MCF) or the solute carrier family 25 (SLC25 protein family). In humans, the MCF has 53 members encoded by nuclear genes. Members of the SLC25 family of transporters, which is the largest group of solute carriers, are also known as mitochondrial carriers (MCs). Because MCs are nuclear-coded proteins, they must be imported into the IMM. When compared with normal cells, the mitochondria of cancer cells exhibit significantly increased transmembrane potentials and a number of their transporters are altered. SLC25 members were identified as potential biomarkers for various cancers. The objective of this review is to summarize what is currently known about the involvement of mitochondrial SLC25 carriers in associated diseases. This review suggests that the SLC25 family could be used for the development of novel points of attack for targeted cancer therapy.
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Affiliation(s)
- Luc Rochette
- Equipe d’Accueil (EA 7460) Physiopathologie et Epidémiologie Cérébro-Cardiovasculaires (PEC2), Faculté des Sciences de Santé, Université de Bourgogne—Franche Comté, 7 Bd Jeanne d’Arc, 21000 Dijon, France; (A.M.); (M.Z.); (Y.C.); (C.V.)
- Correspondence: ; Tel.: +33-380-393-292
| | - Alexandre Meloux
- Equipe d’Accueil (EA 7460) Physiopathologie et Epidémiologie Cérébro-Cardiovasculaires (PEC2), Faculté des Sciences de Santé, Université de Bourgogne—Franche Comté, 7 Bd Jeanne d’Arc, 21000 Dijon, France; (A.M.); (M.Z.); (Y.C.); (C.V.)
| | - Marianne Zeller
- Equipe d’Accueil (EA 7460) Physiopathologie et Epidémiologie Cérébro-Cardiovasculaires (PEC2), Faculté des Sciences de Santé, Université de Bourgogne—Franche Comté, 7 Bd Jeanne d’Arc, 21000 Dijon, France; (A.M.); (M.Z.); (Y.C.); (C.V.)
| | - Gabriel Malka
- Centre Interface Applications Médicales (CIAM), Université Mohammed VI Polytechnique, Ben-Guerir 43 150, Morocco;
| | - Yves Cottin
- Equipe d’Accueil (EA 7460) Physiopathologie et Epidémiologie Cérébro-Cardiovasculaires (PEC2), Faculté des Sciences de Santé, Université de Bourgogne—Franche Comté, 7 Bd Jeanne d’Arc, 21000 Dijon, France; (A.M.); (M.Z.); (Y.C.); (C.V.)
- Department of cardiology, CHU Dijon Bourgogne, 21000 Dijon, France
| | - Catherine Vergely
- Equipe d’Accueil (EA 7460) Physiopathologie et Epidémiologie Cérébro-Cardiovasculaires (PEC2), Faculté des Sciences de Santé, Université de Bourgogne—Franche Comté, 7 Bd Jeanne d’Arc, 21000 Dijon, France; (A.M.); (M.Z.); (Y.C.); (C.V.)
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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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30
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Palmieri F, Scarcia P, Monné M. Diseases Caused by Mutations in Mitochondrial Carrier Genes SLC25: A Review. Biomolecules 2020; 10:biom10040655. [PMID: 32340404 PMCID: PMC7226361 DOI: 10.3390/biom10040655] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 04/15/2020] [Accepted: 04/17/2020] [Indexed: 12/13/2022] Open
Abstract
In the 1980s, after the mitochondrial DNA (mtDNA) had been sequenced, several diseases resulting from mtDNA mutations emerged. Later, numerous disorders caused by mutations in the nuclear genes encoding mitochondrial proteins were found. A group of these diseases are due to defects of mitochondrial carriers, a family of proteins named solute carrier family 25 (SLC25), that transport a variety of solutes such as the reagents of ATP synthase (ATP, ADP, and phosphate), tricarboxylic acid cycle intermediates, cofactors, amino acids, and carnitine esters of fatty acids. The disease-causing mutations disclosed in mitochondrial carriers range from point mutations, which are often localized in the substrate translocation pore of the carrier, to large deletions and insertions. The biochemical consequences of deficient transport are the compartmentalized accumulation of the substrates and dysfunctional mitochondrial and cellular metabolism, which frequently develop into various forms of myopathy, encephalopathy, or neuropathy. Examples of diseases, due to mitochondrial carrier mutations are: combined D-2- and L-2-hydroxyglutaric aciduria, carnitine-acylcarnitine carrier deficiency, hyperornithinemia-hyperammonemia-homocitrillinuria (HHH) syndrome, early infantile epileptic encephalopathy type 3, Amish microcephaly, aspartate/glutamate isoform 1 deficiency, congenital sideroblastic anemia, Fontaine progeroid syndrome, and citrullinemia type II. Here, we review all the mitochondrial carrier-related diseases known until now, focusing on the connections between the molecular basis, altered metabolism, and phenotypes of these inherited disorders.
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Affiliation(s)
- Ferdinando Palmieri
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
- Correspondence: (F.P.); (M.M.); Tel.: +39-0805443323 (F.P.)
| | - Pasquale Scarcia
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
| | - Magnus Monné
- Department of Biosciences, Biotechnologies and Biopharmaceutics, Laboratory of Biochemistry and Molecular Biology, University of Bari Aldo Moro, via E. Orabona 4, 70125 Bari, Italy;
- Department of Sciences, University of Basilicata, via Ateneo Lucano 10, 85100 Potenza, Italy
- Correspondence: (F.P.); (M.M.); Tel.: +39-0805443323 (F.P.)
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31
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Mitochondrial Carriers for Aspartate, Glutamate and Other Amino Acids: A Review. Int J Mol Sci 2019; 20:ijms20184456. [PMID: 31510000 PMCID: PMC6769469 DOI: 10.3390/ijms20184456] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/05/2019] [Accepted: 09/06/2019] [Indexed: 12/19/2022] Open
Abstract
Members of the mitochondrial carrier (MC) protein family transport various molecules across the mitochondrial inner membrane to interlink steps of metabolic pathways and biochemical processes that take place in different compartments; i.e., are localized partly inside and outside the mitochondrial matrix. MC substrates consist of metabolites, inorganic anions (such as phosphate and sulfate), nucleotides, cofactors and amino acids. These compounds have been identified by in vitro transport assays based on the uptake of radioactively labeled substrates into liposomes reconstituted with recombinant purified MCs. By using this approach, 18 human, plant and yeast MCs for amino acids have been characterized and shown to transport aspartate, glutamate, ornithine, arginine, lysine, histidine, citrulline and glycine with varying substrate specificities, kinetics, influences of the pH gradient, and capacities for the antiport and uniport mode of transport. Aside from providing amino acids for mitochondrial translation, the transport reactions catalyzed by these MCs are crucial in energy, nitrogen, nucleotide and amino acid metabolism. In this review we dissect the transport properties, phylogeny, regulation and expression levels in different tissues of MCs for amino acids, and summarize the main structural aspects known until now about MCs. The effects of their disease-causing mutations and manipulation of their expression levels in cells are also considered as clues for understanding their physiological functions.
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