1
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Lin L, Liao ZH, Li CQ. Insight into the role of mitochondrion-related gene anchor signature in mitochondrial dysfunction of neutrophilic asthma. J Asthma 2024:1-42. [PMID: 38294718 DOI: 10.1080/02770903.2024.2311241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 01/23/2024] [Indexed: 02/01/2024]
Abstract
OBJECTIVE At present, targeting molecular-pharmacological therapy is still difficult in neutrophilic asthma. The investigation aims to identify and validate mitochondrion-related gene signatures for diagnosis and specific targeting therapeutics in neutrophilic asthma. METHODS Bronchial biopsy samples of neutrophilic asthma and healthy people were identified from GSE143304 dataset and then matched with human mitochondrial gene data to obtain mitochondria-related differential genes (MitoDEGs). Signature mitochondria-related diagnostic markers were jointly screened by support vector machine (SVM) analysis, least absolute shrinkage, and selection operator (LASSO) regression. The expression of marker MitoDEGs was evaluated by validation datasets GSE147878 and GSE43696. The diagnostic value was evaluated by receiver operating characteristic (ROC) curve analysis. Meanwhile, the infiltrating immune cells were analyzed by the CIBERSORT. Finally, oxidative stress level and mitochondrial functional morphology for asthmatic mice and BEAS-2B cells were evaluated. The expression of signature MitoDEGs was verified by qPCR. RESULTS 67 MitoDEGs were identified. Five signature MitoDEGs (SOD2, MTHFD2, PPTC7, NME6, and SLC25A18) were further screened out. The area under the curve (AUC) of signature MitoDEGs presented a good diagnostic performance (more than 0.9). There were significant differences in the expression of signature MitoDEGs between neutrophilic asthma and non-neutrophilic asthma. In addition, the basic features of mitochondrial dysfunction were demonstrated by in vitro and in vivo experiments. The expression of signature MitoDEGs in the neutrophilic asthma mice presented a significant difference from the control group. CONCLUSIONS These MitoDEGs signatures in neutrophilic asthma may hold potential as anchor diagnostic and therapeutic targets in neutrophilic asthma.
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Affiliation(s)
- Lu Lin
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, 530021
| | - Zeng-Hua Liao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, 530021
| | - Chao-Qian Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Guangxi Medical University, Nanning Guangxi, 530021
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2
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Wei L, Oguz Gok M, Svoboda JD, Forny M, Friedman JR, Niemi NM. PPTC7 limits mitophagy through proximal and dynamic interactions with BNIP3 and NIX. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.24.576953. [PMID: 38328188 PMCID: PMC10849627 DOI: 10.1101/2024.01.24.576953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
PPTC7 is a mitochondrial-localized PP2C phosphatase that maintains mitochondrial protein content and metabolic homeostasis. We previously demonstrated that knockout of Pptc7 elevates mitophagy in a BNIP3- and NIX-dependent manner, but the mechanisms by which PPTC7 influences receptor-mediated mitophagy remain ill-defined. Here, we demonstrate that loss of PPTC7 upregulates BNIP3 and NIX post-transcriptionally and independent of HIF-1α stabilization. On a molecular level, loss of PPTC7 prolongs the half-life of BNIP3 and NIX while blunting their accumulation in response to proteasomal inhibition, suggesting that PPTC7 promotes the ubiquitin-mediated turnover of BNIP3 and NIX. Consistently, overexpression of PPTC7 limits the accumulation of BNIP3 and NIX protein levels in response to pseudohypoxia, a well-known inducer of mitophagy. This PPTC7-mediated suppression of BNIP3 and NIX protein expression requires an intact PP2C catalytic motif but is surprisingly independent of its mitochondrial targeting, indicating that PPTC7 influences mitophagy outside of the mitochondrial matrix. We find that PPTC7 exists in at least two distinct states in cells: a longer isoform, which likely represents full length protein, and a shorter isoform, which likely represents an imported, matrix-localized phosphatase pool. Importantly, anchoring PPTC7 to the outer mitochondrial membrane is sufficient to blunt BNIP3 and NIX accumulation, and proximity labeling and fluorescence co-localization experiments suggest that PPTC7 associates with BNIP3 and NIX within the native cellular environment. Importantly, these associations are enhanced in cellular conditions that promote BNIP3 and NIX turnover, demonstrating that PPTC7 is dynamically recruited to BNIP3 and NIX to facilitate their degradation. Collectively, these data reveal that a fraction of PPTC7 dynamically localizes to the outer mitochondrial membrane to promote the proteasomal turnover of BNIP3 and NIX.
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Affiliation(s)
- Lianjie Wei
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Mehmet Oguz Gok
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jordyn D. Svoboda
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Merima Forny
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
| | - Jonathan R. Friedman
- Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Natalie M. Niemi
- Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO, 63110, USA
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3
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Sun Y, Cao Y, Wan H, Memetimin A, Cao Y, Li L, Wu C, Wang M, Chen S, Li Q, Ma Y, Dong M, Jiang H. A mitophagy sensor PPTC7 controls BNIP3 and NIX degradation to regulate mitochondrial mass. Mol Cell 2024; 84:327-344.e9. [PMID: 38151018 DOI: 10.1016/j.molcel.2023.11.038] [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: 04/04/2023] [Revised: 09/15/2023] [Accepted: 11/29/2023] [Indexed: 12/29/2023]
Abstract
Mitophagy mediated by BNIP3 and NIX critically regulates mitochondrial mass. Cellular BNIP3 and NIX levels are tightly controlled by SCFFBXL4-mediated ubiquitination to prevent excessive mitochondrial loss and lethal disease. Here, we report that knockout of PPTC7, a mitochondrial matrix protein, hyperactivates BNIP3-/NIX-mediated mitophagy and causes perinatal lethality that is rescued by NIX knockout in mice. Biochemically, the PPTC7 precursor is trapped by BNIP3 and NIX to the mitochondrial outer membrane, where PPTC7 scaffolds assembly of a substrate-PPTC7-SCFFBXL4 holocomplex to degrade BNIP3 and NIX, forming a homeostatic regulatory loop. PPTC7 possesses an unusually weak mitochondrial targeting sequence to facilitate its outer membrane retention and mitophagy control. Starvation upregulates PPPTC7 expression in mouse liver to repress mitophagy, which critically maintains hepatic mitochondrial mass, bioenergetics, and gluconeogenesis. Collectively, PPTC7 functions as a mitophagy sensor that integrates homeostatic and physiological signals to dynamically control BNIP3 and NIX degradation, thereby maintaining mitochondrial mass and cellular homeostasis.
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Affiliation(s)
- Yuqiu Sun
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Yu Cao
- College of Life Sciences, Beijing Normal University, Beijing 100875, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Huayun Wan
- National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Adalet Memetimin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Yang Cao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Lin Li
- National Institute of Biological Sciences, Beijing 102206, China
| | - Chongyang Wu
- National Institute of Biological Sciences, Beijing 102206, China
| | - Meng Wang
- National Institute of Biological Sciences, Beijing 102206, China
| | - She Chen
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Qi Li
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Yan Ma
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China
| | - Mengqiu Dong
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China
| | - Hui Jiang
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing 102206, China; National Institute of Biological Sciences, Beijing 102206, China; Beijing Key Laboratory of Cell Biology for Animal Aging, Beijing 102206, China.
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4
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Nicoll CR, Alvigini L, Gottinger A, Cecchini D, Mannucci B, Corana F, Mascotti ML, Mattevi A. In vitro construction of the COQ metabolon unveils the molecular determinants of coenzyme Q biosynthesis. Nat Catal 2024; 7:148-160. [PMID: 38425362 PMCID: PMC7615680 DOI: 10.1038/s41929-023-01087-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 11/20/2023] [Indexed: 03/02/2024]
Abstract
Metabolons are protein assemblies that perform a series of reactions in a metabolic pathway. However, the general importance and aptitude of metabolons for enzyme catalysis remain poorly understood. In animals, biosynthesis of coenzyme Q is currently attributed to ten different proteins, with COQ3, COQ4, COQ5, COQ6, COQ7 and COQ9 forming the iconic COQ metabolon. Yet several reaction steps conducted by the metabolon remain enigmatic. To elucidate the prerequisites for animal coenzyme Q biosynthesis, we sought to construct the entire metabolon in vitro. Here we show that this approach, rooted in ancestral sequence reconstruction, reveals the enzymes responsible for the uncharacterized steps and captures the biosynthetic pathway in vitro. We demonstrate that COQ8, a kinase, increases and streamlines coenzyme Q production. Our findings provide crucial insight into how biocatalytic efficiency is regulated and enhanced by these biosynthetic engines in the context of the cell.
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Affiliation(s)
- Callum R. Nicoll
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Laura Alvigini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Andrea Gottinger
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | - Domiziana Cecchini
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
| | | | - Federica Corana
- ’Centro Grandi Strumenti’, University of Pavia, Pavia, Italy
| | - María Laura Mascotti
- Molecular Enzymology Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
- IMIBIO-SL CONICET, Facultad de Química Bioquímica y Farmacia, Universidad Nacional de San Luis, San Luis, Argentina
| | - Andrea Mattevi
- Department of Biology and Biotechnology ‘Lazzaro Spallanzani’, University of Pavia, Pavia, Italy
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5
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Samidurai A, Olex AL, Ockaili R, Kraskauskas D, Roh SK, Kukreja RC, Das A. Integrated Analysis of lncRNA-miRNA-mRNA Regulatory Network in Rapamycin-Induced Cardioprotection against Ischemia/Reperfusion Injury in Diabetic Rabbits. Cells 2023; 12:2820. [PMID: 38132140 PMCID: PMC10742118 DOI: 10.3390/cells12242820] [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: 09/12/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023] Open
Abstract
The inhibition of mammalian target of rapamycin (mTOR) with rapamycin (RAPA) provides protection against myocardial ischemia/reperfusion (I/R) injury in diabetes. Since interactions between transcripts, including long non-coding RNA (lncRNA), microRNA(miRNA) and mRNA, regulate the pathophysiology of disease, we performed unbiased miRarray profiling in the heart of diabetic rabbits following I/R injury with/without RAPA treatment to identify differentially expressed (DE) miRNAs and their predicted targets of lncRNAs/mRNAs. Results showed that among the total of 806 unique miRNAs targets, 194 miRNAs were DE after I/R in diabetic rabbits. Specifically, eight miRNAs, including miR-199a-5p, miR-154-5p, miR-543-3p, miR-379-3p, miR-379-5p, miR-299-5p, miR-140-3p, and miR-497-5p, were upregulated and 10 miRNAs, including miR-1-3p, miR-1b, miR-29b-3p, miR-29c-3p, miR-30e-3p, miR-133c, miR-196c-3p, miR-322-5p, miR-499-5p, and miR-672-5p, were significantly downregulated after I/R injury. Interestingly, RAPA treatment significantly reversed these changes in miRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated the participation of miRNAs in the regulation of several signaling pathways related to I/R injury, including MAPK signaling and apoptosis. Furthermore, in diabetic hearts, the expression of lncRNAs, HOTAIR, and GAS5 were induced after I/R injury, but RAPA suppressed these lncRNAs. In contrast, MALAT1 was significantly reduced following I/R injury, with the increased expression of miR-199a-5p and suppression of its target, the anti-apoptotic protein Bcl-2. RAPA recovered MALAT1 expression with its sponging effect on miR-199-5p and restoration of Bcl-2 expression. The identification of novel targets from the transcriptome analysis in RAPA-treated diabetic hearts could potentially lead to the development of new therapeutic strategies for diabetic patients with myocardial infarction.
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Affiliation(s)
- Arun Samidurai
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Amy L. Olex
- Wright Center for Clinical and Translational Research, Virginia Commonwealth University, Richmond, VA 23298, USA;
| | - Ramzi Ockaili
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Donatas Kraskauskas
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Sean K. Roh
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Rakesh C. Kukreja
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
| | - Anindita Das
- Division of Cardiology, Pauley Heart Center, Internal Medicine, Virginia Commonwealth University, Richmond, VA 23298, USA; (A.S.); (R.O.); (D.K.); (S.K.R.)
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6
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Flores L, Shene C, Asenjo JA, Chisti Y. Coenzyme Q in Thraustochytrium sp. RT2316-16: Effect of the Medium Composition. Mar Drugs 2023; 21:586. [PMID: 37999410 PMCID: PMC10672569 DOI: 10.3390/md21110586] [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: 10/11/2023] [Revised: 11/05/2023] [Accepted: 11/07/2023] [Indexed: 11/25/2023] Open
Abstract
Coenzyme Q (CoQ; ubiquinone) is an essential component of the respiratory chain. It is also a potent antioxidant that prevents oxidative damage to DNA, biological membranes, and lipoproteins. CoQ comprises a six-carbon ring with polar substituents that interact with electron acceptors and donors, and a hydrophobic polyisoprenoid chain that allows for its localization in cellular membranes. Human CoQ has 10 isoprenoid units (CoQ10) within the polyisoprenoid chain. Few microorganisms produce CoQ10. This work shows that Thraustochytrium sp. RT2316-16 produces CoQ10 and CoQ9. The CoQ10 content in RT2316-16 depended strongly on the composition of the growth medium and the age of the culture, whereas the CoQ9 content was less variable probably because it served a different function in the cell. Adding p-hydroxybenzoic acid to the culture media positively influenced the CoQ10 content of the cell. The absence of some B vitamins and p-aminobenzoic acid in the culture medium negatively affected the growth of RT2316-16, but reduced the decline in CoQ10 that otherwise occurred during growth. The highest content of CoQ9 and CoQ10 in the biomass were 855 μg g-1 and 10 mg g-1, respectively. The results presented here suggest that the thraustochytrid RT2316-16 can be a potential vehicle for producing CoQ10. Metabolic signals that trigger the synthesis of CoQ10 in RT2316-16 need to be determined for optimizing culture conditions.
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Affiliation(s)
- Liset Flores
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Carolina Shene
- Department of Chemical Engineering, Center of Food Biotechnology and Bioseparations, BIOREN, and Centre of Biotechnology and Bioengineering (CeBiB), Universidad de La Frontera, Temuco 4811230, Chile;
| | - Juan A. Asenjo
- Centre for Biotechnoloy and Bioengineering (CeBiB), Department of Chemical Engineering, Biotechnology and Materials, Universidad de Chile, Beauchef 851, Santiago 8370459, Chile;
| | - Yusuf Chisti
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Terengganu, Malaysia;
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7
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González-Arzola K, Díaz-Quintana A. Mitochondrial Factors in the Cell Nucleus. Int J Mol Sci 2023; 24:13656. [PMID: 37686461 PMCID: PMC10563088 DOI: 10.3390/ijms241713656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 08/31/2023] [Accepted: 08/31/2023] [Indexed: 09/10/2023] Open
Abstract
The origin of eukaryotic organisms involved the integration of mitochondria into the ancestor cell, with a massive gene transfer from the original proteobacterium to the host nucleus. Thus, mitochondrial performance relies on a mosaic of nuclear gene products from a variety of genomes. The concerted regulation of their synthesis is necessary for metabolic housekeeping and stress response. This governance involves crosstalk between mitochondrial, cytoplasmic, and nuclear factors. While anterograde and retrograde regulation preserve mitochondrial homeostasis, the mitochondria can modulate a wide set of nuclear genes in response to an extensive variety of conditions, whose response mechanisms often merge. In this review, we summarise how mitochondrial metabolites and proteins-encoded either in the nucleus or in the organelle-target the cell nucleus and exert different actions modulating gene expression and the chromatin state, or even causing DNA fragmentation in response to common stress conditions, such as hypoxia, oxidative stress, unfolded protein stress, and DNA damage.
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Affiliation(s)
- Katiuska González-Arzola
- Centro Andaluz de Biología Molecular y Medicina Regenerativa—CABIMER, Consejo Superior de Investigaciones Científicas—Universidad de Sevilla—Universidad Pablo de Olavide, 41092 Seville, Spain
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
| | - Antonio Díaz-Quintana
- Departamento de Bioquímica Vegetal y Biología Molecular, Universidad de Sevilla, 41012 Seville, Spain
- Instituto de Investigaciones Químicas—cicCartuja, Universidad de Sevilla—C.S.I.C, 41092 Seville, Spain
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8
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Mishra A, Duplaà C, Vojinovic D, Suzuki H, Sargurupremraj M, Zilhão NR, Li S, Bartz TM, Jian X, Zhao W, Hofer E, Wittfeld K, Harris SE, van der Auwera-Palitschka S, Luciano M, Bis JC, Adams HHH, Satizabal CL, Gottesman RF, Gampawar PG, Bülow R, Weiss S, Yu M, Bastin ME, Lopez OL, Vernooij MW, Beiser AS, Völker U, Kacprowski T, Soumare A, Smith JA, Knopman DS, Morris Z, Zhu Y, Rotter JI, Dufouil C, Valdés Hernández M, Muñoz Maniega S, Lathrop M, Boerwinkle E, Schmidt R, Ihara M, Mazoyer B, Yang Q, Joutel A, Tournier-Lasserve E, Launer LJ, Deary IJ, Mosley TH, Amouyel P, DeCarli CS, Psaty BM, Tzourio C, Kardia SLR, Grabe HJ, Teumer A, van Duijn CM, Schmidt H, Wardlaw JM, Ikram MA, Fornage M, Gudnason V, Seshadri S, Matthews PM, Longstreth WT, Couffinhal T, Debette S. Gene-mapping study of extremes of cerebral small vessel disease reveals TRIM47 as a strong candidate. Brain 2022; 145:1992-2007. [PMID: 35511193 PMCID: PMC9255380 DOI: 10.1093/brain/awab432] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 10/11/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cerebral small vessel disease is a leading cause of stroke and a major contributor to cognitive decline and dementia, but our understanding of specific genes underlying the cause of sporadic cerebral small vessel disease is limited. We report a genome-wide association study and a whole-exome association study on a composite extreme phenotype of cerebral small vessel disease derived from its most common MRI features: white matter hyperintensities and lacunes. Seventeen population-based cohorts of older persons with MRI measurements and genome-wide genotyping (n = 41 326), whole-exome sequencing (n = 15 965), or exome chip (n = 5249) data contributed 13 776 and 7079 extreme small vessel disease samples for the genome-wide association study and whole-exome association study, respectively. The genome-wide association study identified significant association of common variants in 11 loci with extreme small vessel disease, of which the chr12q24.11 locus was not previously reported to be associated with any MRI marker of cerebral small vessel disease. The whole-exome association study identified significant associations of extreme small vessel disease with common variants in the 5' UTR region of EFEMP1 (chr2p16.1) and one probably damaging common missense variant in TRIM47 (chr17q25.1). Mendelian randomization supports the causal association of extensive small vessel disease severity with increased risk of stroke and Alzheimer's disease. Combined evidence from summary-based Mendelian randomization studies and profiling of human loss-of-function allele carriers showed an inverse relation between TRIM47 expression in the brain and blood vessels and extensive small vessel disease severity. We observed significant enrichment of Trim47 in isolated brain vessel preparations compared to total brain fraction in mice, in line with the literature showing Trim47 enrichment in brain endothelial cells at single cell level. Functional evaluation of TRIM47 by small interfering RNAs-mediated knockdown in human brain endothelial cells showed increased endothelial permeability, an important hallmark of cerebral small vessel disease pathology. Overall, our comprehensive gene-mapping study and preliminary functional evaluation suggests a putative role of TRIM47 in the pathophysiology of cerebral small vessel disease, making it an important candidate for extensive in vivo explorations and future translational work.
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Affiliation(s)
- Aniket Mishra
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
| | - Cécile Duplaà
- University of Bordeaux, INSERM, Biologie des Maladies Cardiovasculaires, U1034, F-33600 Pessac, France
| | - Dina Vojinovic
- Department of Epidemiology, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Biomedical Data Sciences, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
| | - Hideaki Suzuki
- Department of Cardiovascular Medicine, Tohoku University Hospital, 1-1, Seiryo, Aoba, Sendai 980-8574, Japan
- Tohoku Medical Megabank Organization, Tohoku University, 2-1, Seiryo, Aoba, Sendai 980-8573, Japan
- Department of Brain Sciences and UK Dementia Research Institute Centre, Imperial College, London, W12 0NN, UK
| | - Muralidharan Sargurupremraj
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
| | | | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02115, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Xueqiu Jian
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
| | - Wei Zhao
- Department of Epidemiology, School of Public Health, University of Michigan, Michigan, MI 48104, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
- Institute for Medical Informatics, Statistics and Documentation, Medical University of Graz, 8036 Graz, Austria
| | - Katharina Wittfeld
- German Centre for Neurodegenerative Diseases (DZNE), Rostock/Greifswald, 17489 Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Sarah E Harris
- Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Sandra van der Auwera-Palitschka
- German Centre for Neurodegenerative Diseases (DZNE), Rostock/Greifswald, 17489 Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Michelle Luciano
- Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hieab H H Adams
- Department of Epidemiology, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Clinical Genetics, Erasmus University Medical Centre Rotterdam, 3015 GD Rotterdam, The Netherlands
| | - Claudia L Satizabal
- Glenn Biggs Institute for Alzheimer's and Neurodegenerative Diseases, University of Texas Health Sciences Center, San Antonio, TX, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 2115, USA
| | - Rebecca F Gottesman
- National Institute of Neurological Disorders and Stroke Intramural Research Program, Bethesda, MD 20814, USA
| | - Piyush G Gampawar
- Institute of Molecular Biology & Biochemistry, Gottfried Schatz Research Centre (for Cell Signalling, Metabolism and Aging), Medical University of Graz, 8036 Graz, Austria
| | - Robin Bülow
- Department of Diagnostic Radiology and Neuroradiology, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Stefan Weiss
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Miao Yu
- Department of Epidemiology, School of Public Health, University of Michigan, Michigan, MI 48104, USA
| | - Mark E Bastin
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9AB, UK
- Division of Neuroimaging Sciences, Brain Research Imaging Centre, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Oscar L Lopez
- Department of Neurology, University of Pittsburgh, Pittsburgh, PA 15213, USA
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Meike W Vernooij
- Department of Epidemiology, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Alexa S Beiser
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02115, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 2115, USA
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Tim Kacprowski
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17489 Greifswald, Germany
- TUM School of Life Sciences Weihenstephan (WZW), Technical University of Munich (TUM), 85354 Freising-Weihenstephan, Germany
| | - Aicha Soumare
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Michigan, MI 48104, USA
| | | | - Zoe Morris
- Neuroradiology Department, Department of Clinical Neurosciences, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Yicheng Zhu
- Department of Neurology, Peking Union Medical College Hospital, Beijing 100730, China
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Carole Dufouil
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
| | - Maria Valdés Hernández
- Division of Neuroimaging Sciences, Brain Research Imaging Centre, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Susana Muñoz Maniega
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9AB, UK
| | - Mark Lathrop
- University of McGill Genome Center, Montreal, Quebec H3A 0G1, Canada
| | - Erik Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University of Graz, 8036 Graz, Austria
| | - Masafumi Ihara
- Department of Neurology, National Cerebral and Cardiovascular Center, Suita, Osaka 564-8565, Japan
| | - Bernard Mazoyer
- University of Bordeaux, Institut des Maladies Neurodégénératives, CNRS-CEA UMR 5293, 33000 Bordeaux, France
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, MA 02115, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
| | - Anne Joutel
- Institute of Psychiatry and Neurosciences of Paris, INSERM UMR1266, Université de Paris, France
| | | | - Lenore J Launer
- Intramural Research Program, National Institute on Aging, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ian J Deary
- Department of Psychology, University of Edinburgh, EH8 9JZ Edinburgh, UK
| | - Thomas H Mosley
- Memory Impairment and Neurodegenerative Dementia (MIND) Center, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Philippe Amouyel
- University of Lille, INSERM, Institut Pasteur de Lille, UMR1167-RID-AGE—Risk Factors and Molecular Determinants of Aging-Related Diseases, F-59000 Lille, France
- LabEx DISTALZ, Institut Pasteur de Lille, 59000 Lille, France
- Department of Epidemiology and Public Health, Centre Hospital University of Lille, F-59000 Lille, France
| | - Charles S DeCarli
- Department of Neurology and Center for Neuroscience, University of California at Davis, Sacramento, CA 95816, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Health Systems and Population Health, University of Washington, Seattle, WA
| | - Christophe Tzourio
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
- CHU de Bordeaux, Pole de santé publique, Service d’information médicale, F-33000 Bordeaux, France
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Michigan, MI 48104, USA
| | - Hans J Grabe
- German Centre for Neurodegenerative Diseases (DZNE), Rostock/Greifswald, 17489 Greifswald, Germany
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, 17489 Greifswald, Germany
| | - Alexander Teumer
- Institute for Community Medicine, University Medicine Greifswald, D-17475 Greifswald, Germany
| | - Cornelia M van Duijn
- Department of Biomedical Data Sciences, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
- Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Helena Schmidt
- Institute of Molecular Biology & Biochemistry, Gottfried Schatz Research Centre (for Cell Signalling, Metabolism and Aging), Medical University of Graz, 8036 Graz, Austria
| | - Joanna M Wardlaw
- Division of Neuroimaging Sciences, Brain Research Imaging Centre, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - M Arfan Ikram
- Department of Biomedical Data Sciences, Leiden University Medical Centre, 2333 ZA Leiden, The Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus MC, University Medical Centre, 3015 GD Rotterdam, The Netherlands
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, 200 Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Sudha Seshadri
- Department of Epidemiology, School of Public Health, University of Michigan, Michigan, MI 48104, USA
- The Framingham Heart Study, Framingham, MA 01701, USA
- Department of Neurology, Boston University School of Medicine, Boston, MA 2115, USA
| | - Paul M Matthews
- Department of Brain Sciences and UK Dementia Research Institute Centre, Imperial College, London, W12 0NN, UK
| | - William T Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Department of Neurology, University of Washington, Seattle, WA 98104-2420, USA
| | - Thierry Couffinhal
- University of Bordeaux, INSERM, Biologie des Maladies Cardiovasculaires, U1034, F-33600 Pessac, France
| | - Stephanie Debette
- University of Bordeaux, INSERM, Bordeaux Population Health Research Centre, Team ELEANOR, UMR 1219, F-33000 Bordeaux, France
- Department of Neurology, Boston University School of Medicine, Boston, MA 2115, USA
- CHU de Bordeaux, Department of Neurology, F-33000 Bordeaux, France
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9
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Li X, Zhang Y, He F, Gao D, Che B, Cao X, Huang S, Zheng M, Han H. miR-582 Suppresses the Proliferation of B-Cell Precursor Acute Lymphoblastic Leukemia (BCP-ALL) Cells and Protects Them From Natural Killer Cell-Mediated Cytotoxicity. Front Immunol 2022; 13:853094. [PMID: 35514986 PMCID: PMC9065596 DOI: 10.3389/fimmu.2022.853094] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2022] [Accepted: 03/16/2022] [Indexed: 12/02/2022] Open
Abstract
B-cell precursor acute lymphoblastic leukemia (BCP-ALL) is a malignancy characterized by the aberrant accumulation of immature B-cell precursors in bone marrow and other lymphoid organs. Although several intrinsic regulatory signals participating in BCP-ALL have been clarified, detailed intrinsic and extrinsic mechanisms that regulate BCP-ALL progression have not been fully understood. In the current study, we report that miR-582 is downregulated in BCP-ALL cells compared with normal B cells. Forced overexpression of miR-582 attenuated BCP-ALL cell proliferation and survival. We found that miR-582 overexpression disturbed the mitochondrial metabolism of BCP-ALL cells, leading to less ATP but more ROS production. Mechanistically, we identified PPTC7 as a direct target of miR-582. MiR-582 overexpression inhibited the activity of CoQ10, which is downstream of PPTC7 and played an important positive regulatory role in mitochondrial electron transportation. Finally, we found that overexpression of miR-582 upregulated the expression of immune checkpoint molecule CD276 and reduced NK cell-mediated cytotoxicity against BCP-ALL cells. CD276 blockade significantly increased NK cell-mediated cytotoxicity against miR-582-overexpressing BCP-ALL cells. Together, our research demonstrates that miR-582 acts as a negative regulator of BCP-ALL cells by reducing proliferation and survival, but protects BCP-ALL cells from NK cell-mediated cytotoxicity, suggesting that miR-582 may be a new therapeutic biomarker for BCP-ALL with CD276 blocker.
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Affiliation(s)
- Xinxin Li
- Xi'an Key Laboratory of Stem Cell and Regenerative Medicine, Institute of Medical Research, Northwestern Polytechnical University, Xi'an, China.,Research and Development Institute of Northwestern Polytechnical University in Shenzhen, Shenzhen, China
| | - Yufei Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Fei He
- Department of Hepatobiliary Surgery, Xijing Hospital, Fourth Military Medical University, Xi'an, China
| | - Dan Gao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Bo Che
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xiuli Cao
- Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, China
| | - Siyong Huang
- Department of Hematology, Xi'an International Medical Center Hospital, Xi'an, China
| | - Minhua Zheng
- Department of Medical Genetics and Developmental Biology, Fourth Military Medical University, Xi'an, China
| | - Hua Han
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
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10
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miR-193a-3p increases glycolysis under hypoxia by facilitating Akt phosphorylation and PFKFB3 activation in human macrophages. Cell Mol Life Sci 2022; 79:89. [PMID: 35072776 PMCID: PMC8786749 DOI: 10.1007/s00018-022-04146-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 11/21/2022]
Abstract
Human macrophages infiltrating hypoxic regions alter their metabolism, because oxygen becomes limited. Increased glycolysis is one of the most common cellular adaptations to hypoxia and mostly is regulated via hypoxia-inducible factor (HIF) and RAC-alpha serine/threonine–protein kinase (Akt) signaling, which gets activated under reduced oxygen content. We noticed that micro RNA (miR)-193a-3p enhances Akt phosphorylation at threonine 308 under hypoxia. In detail, miR-193a-3p suppresses the protein abundance of phosphatase PTC7 homolog (PPTC7), which in turn increases Akt phosphorylation. Lowering PPTC7 expression by siRNA or overexpressing miR-193a-3p increases Akt phosphorylation. Vice versa, inhibition of miR-193a-3p attenuates Akt activation and prevents a subsequent increase of glycolysis under hypoxia. Excluding effects of miR-193a-3p and Akt on HIF expression, stabilization, and function, we noticed phosphorylation of 6 phosphofructo-2-kinase/fructose 2,6-bisphosphatase PFKFB3 in response to the PI3K/Akt/mTOR signaling cascade. Inhibition of PFKFB3 blocked an increased glycolytic flux under hypoxia. Apparently, miR-193a-3p balances Akt phosphorylation and dephosphorylation by affecting PPTC7 protein amount. Suppression of PPTC7 increases Akt activation and phosphorylation of PFKFB3, which culminates in higher rates of glycolysis under hypoxia.
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11
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Nguyen T, Gronauer TF, Nast‐Kolb T, Sieber SA, Lang K. Substrate Profiling of Mitochondrial Caseinolytic Protease P via a Site‐Specific Photocrosslinking Approach. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202111085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Tuan‐Anh Nguyen
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Thomas F. Gronauer
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Timon Nast‐Kolb
- Center for Protein Assemblies (CPA) and Lehrstuhl für Biophysik (E27) Physics Department Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Stephan A. Sieber
- Center for Protein Assemblies (CPA) Department of Chemistry Chair of Organic Chemistry II Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
| | - Kathrin Lang
- Department of Chemistry Group of Synthetic Biochemistry Technical University of Munich Lichtenbergstr. 4 85748 Garching Germany
- Laboratory of Organic Chemistry Department of Chemistry and Applied Biosciences Chair of Chemical Biology ETH Zürich Vladimir-Prelog-Weg 3 8093 Zurich Switzerland
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12
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Nguyen TA, Gronauer T, Nast-Kolb T, Sieber S, Lang K. Substrate profiling of mitochondrial caseinolytic protease P via a site-specific photocrosslinking approach. Angew Chem Int Ed Engl 2021; 61:e202111085. [PMID: 34847623 PMCID: PMC9306725 DOI: 10.1002/anie.202111085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Indexed: 11/17/2022]
Abstract
Approaches for profiling protease substrates are critical for defining protease functions, but remain challenging tasks. We combine genetic code expansion, photocrosslinking and proteomics to identify substrates of the mitochondrial (mt) human caseinolytic protease P (hClpP). Site‐specific incorporation of the diazirine‐bearing amino acid DiazK into the inner proteolytic chamber of hClpP, followed by UV‐irradiation of cells, allows to covalently trap substrate proteins of hClpP and to substantiate hClpP's major involvement in maintaining overall mt homeostasis. In addition to confirming many of the previously annotated hClpP substrates, our approach adds a diverse set of new proteins to the hClpP interactome. Importantly, our workflow allows identifying substrate dynamics upon application of external cues in an unbiased manner. Identification of unique hClpP‐substrate proteins upon induction of mt oxidative stress, suggests that hClpP counteracts oxidative stress by processing of proteins that are involved in respiratory chain complex synthesis and maturation as well as in catabolic pathways.
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Affiliation(s)
- Tuan-Anh Nguyen
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Thomas Gronauer
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Timon Nast-Kolb
- Technische Universität München: Technische Universitat Munchen, Physics, GERMANY
| | - Stephan Sieber
- Technical University of Munich: Technische Universitat Munchen, Chemistry, Lichtenbergstr. 4, 85748, Garching, GERMANY
| | - Kathrin Lang
- ETH-Zürich LOC: Eidgenossische Technische Hochschule Zurich Laboratorium fur Organische Chemie, Chemistry and Applied Biosciences, Vladimir-Prelog-Weg. 3, 8093, Zürich, SWITZERLAND
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13
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Microarray and qPCR Analysis of Mitochondrial Metabolism Activation during Prenatal and Early Postnatal Development in Rats and Humans with Emphasis on CoQ10 Biosynthesis. BIOLOGY 2021; 10:biology10050418. [PMID: 34066731 PMCID: PMC8150536 DOI: 10.3390/biology10050418] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 11/16/2022]
Abstract
At the end of the mammalian intra-uterine foetal development, a rapid switch from glycolytic to oxidative metabolism must proceed. Using microarray techniques, qPCR, enzyme activities and coenzyme Q content measurements, we describe perinatal mitochondrial metabolism acceleration in rat liver and skeletal muscle during the perinatal period and correlate the results with those in humans. Out of 1546 mitochondrial genes, we found significant changes in expression in 1119 and 827 genes in rat liver and skeletal muscle, respectively. The most remarkable expression shift occurred in the rat liver at least two days before birth. Coenzyme Q-based evaluation in both the rat model and human tissues showed the same trend: the total CoQ content is low prenatally, significantly increasing after birth in both the liver and skeletal muscle. We propose that an important regulator of rat coenzyme Q biosynthesis might be COQ8A, an atypical kinase involved in the biosynthesis of coenzyme Q. Our microarray data, a total of 16,557 RefSeq (Entrez) genes, have been deposited in NCBI’s Gene Expression Omnibus and are freely available to the broad scientific community. Our microarray data could serve as a suitable background for finding key factors regulating mitochondrial metabolism and the preparation of the foetus for the transition to extra-uterine conditions.
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14
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Villalba JM, Navas P. Regulation of coenzyme Q biosynthesis pathway in eukaryotes. Free Radic Biol Med 2021; 165:312-323. [PMID: 33549646 DOI: 10.1016/j.freeradbiomed.2021.01.055] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/22/2021] [Accepted: 01/30/2021] [Indexed: 12/21/2022]
Abstract
Coenzyme Q (CoQ, ubiquinone/ubiquinol) is a ubiquitous and unique molecule that drives electrons in mitochondrial respiratory chain and an obligatory step for multiple metabolic pathways in aerobic metabolism. Alteration of CoQ biosynthesis or its redox stage are causing mitochondrial dysfunctions as hallmark of heterogeneous disorders as mitochondrial/metabolic, cardiovascular, and age-associated diseases. Regulation of CoQ biosynthesis pathway is demonstrated to affect all steps of proteins production of this pathway, posttranslational modifications and protein-protein-lipid interactions inside mitochondria. There is a bi-directional relationship between CoQ and the epigenome in which not only the CoQ status determines the epigenetic regulation of many genes, but CoQ biosynthesis is also a target for epigenetic regulation, which adds another layer of complexity to the many pathways by which CoQ levels are regulated by environmental and developmental signals to fulfill its functions in eukaryotic aerobic metabolism.
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Affiliation(s)
- José Manuel Villalba
- Departamento de Biología Celular, Fisiología e Inmunología, Universidad de Córdoba, Campus de Excelencia Internacional Agroalimentario, ceiA3, Spain
| | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo and CIBERER, Instituto de Salud Carlos III, Universidad Pablo de Olavide-CSIC-JA, Sevilla, 41013, Spain.
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15
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The ubiquinone synthesis pathway is a promising drug target for Chagas disease. PLoS One 2021; 16:e0243855. [PMID: 33539347 PMCID: PMC7861437 DOI: 10.1371/journal.pone.0243855] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 11/27/2020] [Indexed: 12/16/2022] Open
Abstract
Chagas disease is caused by infection with the protozoan parasite Trypanosoma cruzi (T. cruzi). It was originally a Latin American endemic health problem, but now is expanding worldwide as a result of increasing migration. The currently available drugs for Chagas disease, benznidazole and nifurtimox, provoke severe adverse effects, and thus the development of new drugs is urgently required. Ubiquinone (UQ) is essential for respiratory chain and redox balance in trypanosomatid protozoans, therefore we aimed to provide evidence that inhibitors of the UQ biosynthesis have trypanocidal activities. In this study, inhibitors of the human COQ7, a key enzyme of the UQ synthesis, were tested for their trypanocidal activities because they were expected to cross-react and inhibit trypanosomal COQ7 due to their genetic homology. We show the trypanocidal activity of a newly found human COQ7 inhibitor, an oxazinoquinoline derivative. The structurally similar compounds were selected from the commercially available compounds by 2D and 3D ligand-based similarity searches. Among 38 compounds selected, 12 compounds with the oxazinoquinoline structure inhibited significantly the growth of epimastigotes of T. cruzi. The most effective 3 compounds also showed the significant antitrypanosomal activity against the mammalian stage of T. cruzi at lower concentrations than benznidazole, a commonly used drug today. We found that epimastigotes treated with the inhibitor contained reduced levels of UQ9. Further, the growth of epimastigotes treated with the inhibitors was partially rescued by UQ10 supplementation to the culture medium. These results suggest that the antitrypanosomal mechanism of the oxazinoquinoline derivatives results from inhibition of the trypanosomal UQ synthesis leading to a shortage of the UQ pool. Our data indicate that the UQ synthesis pathway of T. cruzi is a promising drug target for Chagas disease.
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16
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Frankovsky J, Vozáriková V, Nosek J, Tomáška Ľ. Mitochondrial protein phosphorylation in yeast revisited. Mitochondrion 2021; 57:148-162. [PMID: 33412333 DOI: 10.1016/j.mito.2020.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Revised: 12/23/2020] [Accepted: 12/30/2020] [Indexed: 12/16/2022]
Abstract
Protein phosphorylation is one of the best-known post-translational modifications occurring in all domains of life. In eukaryotes, protein phosphorylation affects all cellular compartments including mitochondria. High-throughput techniques of mass spectrometry combined with cell fractionation and biochemical methods yielded thousands of phospho-sites on hundreds of mitochondrial proteins. We have compiled the information on mitochondrial protein kinases and phosphatases and their substrates in Saccharomyces cerevisiae and provide the current state-of-the-art overview of mitochondrial protein phosphorylation in this model eukaryote. Using several examples, we describe emerging features of the yeast mitochondrial phosphoproteome and present challenges lying ahead in this exciting field.
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Affiliation(s)
- Jan Frankovsky
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Veronika Vozáriková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Jozef Nosek
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 842 15 Bratislava, Slovakia.
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17
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Nakano Y, Moriuchi M, Fukushima Y, Hayashi K, Suico MA, Kai H, Koutaki G, Shuto T. Intrapopulation analysis of longitudinal lifespan in Caenorhabditis elegans identifies W09D10.4 as a novel AMPK-associated healthspan shortening factor. J Pharmacol Sci 2020; 145:241-252. [PMID: 33602504 DOI: 10.1016/j.jphs.2020.12.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/11/2020] [Accepted: 12/17/2020] [Indexed: 11/27/2022] Open
Abstract
Caenorhabditis elegans is a model organism widely used for longevity studies. Current advances have been made in the methods that allow automated monitoring of C. elegans behavior. However, ordinary manual assays as well as automated methods have yet to achieve qualitative whole-life analysis of C. elegans longevity based on intrapopulation variation. Here, we utilized live-cell analysis system to determine the parameters of nematode lifespans. Image-based superposition method enabled to determine not only frailty in worms, but also to measure individual and longitudinal lifespan, healthspan, and frailspan. Notably, k-means clustering via principal component analysis revealed four clusters with distinct longevity patterns in wild-type C. elegans. Physiological relevance of clustering was confirmed by assays with pharmacological and/or genetic manipulation of AMP-activated protein kinase (AMPK), a crucial regulator of healthspan. Finally, we focused on W09D10.4 among the possible regulators extracted by integrative expression analysis with existing data sets. Importantly, W09D10.4 knockdown increased the high-healthspan populations only in the presence of AMPK, suggesting that W09D10.4 is a novel AMPK-associated healthspan shortening factor in C. elegans. Overall, the study establishes a novel platform of longitudinal lifespan in C. elegans, which is user-friendly, and may be a useful pharmacological tool to identify healthspan modulatory factors.
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Affiliation(s)
- Yoshio Nakano
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Masataka Moriuchi
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Yutaro Fukushima
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health Life Science: Interdisciplinary and Global Oriented) Program", 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Kyotaro Hayashi
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan
| | - Go Koutaki
- Department of Electrical and Computer Engineering, Kumamoto University, 2-39-1 Kurokami, Chuo-ku, Kumamoto, 860-8555, Japan
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Science, Kumamoto University, 5-1 Oe-honmachi, Chuo-ku, Kumamoto, 862-0973, Japan.
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18
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Swan AL, Schütt C, Rozman J, del Mar Muñiz Moreno M, Brandmaier S, Simon M, Leuchtenberger S, Griffiths M, Brommage R, Keskivali-Bond P, Grallert H, Werner T, Teperino R, Becker L, Miller G, Moshiri A, Seavitt JR, Cissell DD, Meehan TF, Acar EF, Lelliott CJ, Flenniken AM, Champy MF, Sorg T, Ayadi A, Braun RE, Cater H, Dickinson ME, Flicek P, Gallegos J, Ghirardello EJ, Heaney JD, Jacquot S, Lally C, Logan JG, Teboul L, Mason J, Spielmann N, McKerlie C, Murray SA, Nutter LMJ, Odfalk KF, Parkinson H, Prochazka J, Reynolds CL, Selloum M, Spoutil F, Svenson KL, Vales TS, Wells SE, White JK, Sedlacek R, Wurst W, Lloyd KCK, Croucher PI, Fuchs H, Williams GR, Bassett JHD, Gailus-Durner V, Herault Y, Mallon AM, Brown SDM, Mayer-Kuckuk P, Hrabe de Angelis M. Mouse mutant phenotyping at scale reveals novel genes controlling bone mineral density. PLoS Genet 2020; 16:e1009190. [PMID: 33370286 PMCID: PMC7822523 DOI: 10.1371/journal.pgen.1009190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Revised: 01/22/2021] [Accepted: 10/13/2020] [Indexed: 12/18/2022] Open
Abstract
The genetic landscape of diseases associated with changes in bone mineral density (BMD), such as osteoporosis, is only partially understood. Here, we explored data from 3,823 mutant mouse strains for BMD, a measure that is frequently altered in a range of bone pathologies, including osteoporosis. A total of 200 genes were found to significantly affect BMD. This pool of BMD genes comprised 141 genes with previously unknown functions in bone biology and was complementary to pools derived from recent human studies. Nineteen of the 141 genes also caused skeletal abnormalities. Examination of the BMD genes in osteoclasts and osteoblasts underscored BMD pathways, including vesicle transport, in these cells and together with in silico bone turnover studies resulted in the prioritization of candidate genes for further investigation. Overall, the results add novel pathophysiological and molecular insight into bone health and disease. Patients affected by osteoporosis frequently present with decreased BMD and increased fracture risk. Genes are known to control the onset and progression of bone diseases such as osteoporosis. Therefore, we aimed to identify osteoporosis-related genes using BMD measures obtained from a large pool of mutant mice genetically modified for deletion of individual genes (knockout mice). In a collaborative endeavor involving several research sites world-wide, we generated and phenotyped 3,823 knockout mice and identified 200 genes which regulated BMD. Of the 200 BMD genes, 141 genes were previously not known to affect BMD. The discovery and study of novel BMD genes will help to better understand the causes and therapeutic options for patients with low BMD. In the long run, this will improve the clinical management of osteoporosis.
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Affiliation(s)
- Anna L. Swan
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Christine Schütt
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Jan Rozman
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | | | - Stefan Brandmaier
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Michelle Simon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Stefanie Leuchtenberger
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Mark Griffiths
- Mouse Informatics Group, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Robert Brommage
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Piia Keskivali-Bond
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Harald Grallert
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Institute of Epidemiology, Helmholtz Zentrum München, Neuherberg, Germany
| | - Thomas Werner
- Internal Medicine Nephrology and Center for Computational Medicine & Bioinformatics, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Raffaele Teperino
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Lore Becker
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Gregor Miller
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Ala Moshiri
- University of California-Davis School of Medicine, Sacramento, California, United States of America
| | - John R. Seavitt
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Derek D. Cissell
- Department of Surgical & Radiological Sciences, University of California, Davis, California, United States of America
| | - Terrence F. Meehan
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Elif F. Acar
- The Center for Phenogenomics, Toronto, Ontario, Canada
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
- Department of Statistics, University of Manitoba, Winnipeg, Manitoba, Canada
| | | | - Ann M. Flenniken
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Marie-France Champy
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Tania Sorg
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Abdel Ayadi
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Robert E. Braun
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Heather Cater
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Mary E. Dickinson
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Paul Flicek
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Juan Gallegos
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Elena J. Ghirardello
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Jason D. Heaney
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, One Baylor Plaza, Houston, Texas, United States of America
| | - Sylvie Jacquot
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Connor Lally
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - John G. Logan
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Lydia Teboul
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jeremy Mason
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nadine Spielmann
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Colin McKerlie
- The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen A. Murray
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Lauryl M. J. Nutter
- The Center for Phenogenomics, Toronto, Ontario, Canada
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Kristian F. Odfalk
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Helen Parkinson
- European Molecular Biology Laboratory- European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Jan Prochazka
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Corey L. Reynolds
- Departments of Molecular Physiology & Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston,Texas, United States of America
| | - Mohammed Selloum
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Frantisek Spoutil
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Karen L. Svenson
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Taylor S. Vales
- Advanced Technologies Cores, Baylor College of Medicine, One Baylor Plaza, Houston Texas, United States of America
| | - Sara E. Wells
- MRC Harwell Institute, Mary Lyon Centre, Harwell Campus, Oxfordshire, United Kingdom
| | - Jacqueline K. White
- The Jackson Laboratory, 600 Main Street, Bar Harbor, Maine, United States of America
| | - Radislav Sedlacek
- Czech Center for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences,Vestec, Czech Republic
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Developmental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- Deutsches Institut für Neurodegenerative Erkrankungen (DZNE) Site Munich, Munich, Germany
- Munich Cluster for Systems Neurology (SyNergy), Adolf-Butenandt-Institut, Ludwig-Maximilians-Universität München, Munich, Germany
| | - K. C. Kent Lloyd
- Department of Surgery, School of Medicine and Mouse Biology Program, University of California Davis
| | - Peter I. Croucher
- Garvan Institute of Medical Research, Sydney, New South Wales, Australia
- St Vincent’s Clinical School, Faculty of Medicine, Sydney, New South Wales, Australia
- School of Biotechnology and Biomolecular Sciences, UNSW Australia, Sydney, New South Wales, Australia
| | - Helmut Fuchs
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Graham R. Williams
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - J. H. Duncan Bassett
- Molecular Endocrinology Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, Hammersmith Campus, London, United Kingdom
| | - Valerie Gailus-Durner
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Yann Herault
- Université de Strasbourg, CNRS, INSERM, IGBMC, Illkirch, France
- Université de Strasbourg, CNRS, INSERM, IGBMC, PHENOMIN-ICS, Illkirch, France
| | - Ann-Marie Mallon
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Steve D. M. Brown
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
| | - Philipp Mayer-Kuckuk
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
| | - Martin Hrabe de Angelis
- German Mouse Clinic, Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- German Center for Diabetes Research (DZD), Neuherberg, Germany
- Institute of Experimental Genetics, Helmholtz Zentrum München, German Research Center for Environmental Health GmbH, Neuherberg, Germany
- Chair of Experimental Genetics, TUM School of Life Sciences (SoLS), Technische Universität München, Freising, Germany
- * E-mail:
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19
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Sánchez-Cuesta A, Cortés-Rodríguez AB, Navas-Enamorado I, Lekue JA, Viar T, Axpe M, Navas P, López-Lluch G. High coenzyme Q10 plasma levels improve stress and damage markers in professional soccer players during competition. INT J VITAM NUTR RES 2020; 92:192-203. [PMID: 32639220 DOI: 10.1024/0300-9831/a000659] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Ubiquinol, the reduced form of Coenzyme Q10 (CoQ10), is a key factor in bioenergetics and antioxidant protection. During competition, professional soccer players suffer from considerable physical stress causing high risk of muscle damage. For athletes, supplementation with several antioxidants, including CoQ10, is widely recommended to avoid oxidative stress and muscle damage. We performed an observational study of plasma parameters associated with CoQ10 levels in professional soccer players of the Spanish First League team Athletic Club de Bilbao over two consecutive seasons (n = 24-25) in order determine their relationship with damage, stress and performance during competition. We analyzed three different moments of the competition: preterm, initial phase and mid phase. Metabolites and factors related with stress (testosterone/cortisol) and muscle damage (creatine kinase) were determined. Physical activity during matches was analyzed over the 2015/16 season in those players participating in complete matches. In the mid phase of competition, CoQ10 levels were higher in 2015/16 (906.8 ± 307.9 vs. 584.3 ± 196.3 pmol/mL, p = 0.0006) High levels of CoQ10 in the hardest phase of competition were associated with a reduction in the levels of the muscle-damage marker creatine kinase (Pearsons' correlation coefficient (r) = - 0.460, p = 0.00168) and a trend for the stress marker cortisol (r = -0.252, p = 0.150). Plasma ubiquinol was also associated with better kidney function (r = -0.287, p = 0.0443 for uric acid). Furthermore, high CoQ10 levels were associated with higher muscle performance during matches. Our results suggest that high levels of plasma CoQ10 can prevent muscle damage, improve kidney function and are associated with higher performance in professional soccer players during competition.
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Affiliation(s)
- Ana Sánchez-Cuesta
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Ana Belén Cortés-Rodríguez
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Ignacio Navas-Enamorado
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | | | | | | | - Plácido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
| | - Guillermo López-Lluch
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC-JA, and CIBERER, Instituto de Salud Carlos III, Sevilla, Spain
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20
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Metal-dependent Ser/Thr protein phosphatase PPM family: Evolution, structures, diseases and inhibitors. Pharmacol Ther 2020; 215:107622. [PMID: 32650009 DOI: 10.1016/j.pharmthera.2020.107622] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 06/29/2020] [Indexed: 02/06/2023]
Abstract
Protein phosphatases and kinases control multiple cellular events including proliferation, differentiation, and stress responses through regulating reversible protein phosphorylation, the most important post-translational modification. Members of metal-dependent protein phosphatase (PPM) family, also known as PP2C phosphatases, are Ser/Thr phosphatases that bind manganese/magnesium ions (Mn2+/Mg2+) in their active center and function as single subunit enzymes. In mammals, there are 20 isoforms of PPM phosphatases: PPM1A, PPM1B, PPM1D, PPM1E, PPM1F, PPM1G, PPM1H, PPM1J, PPM1K, PPM1L, PPM1M, PPM1N, ILKAP, PDP1, PDP2, PHLPP1, PHLPP2, PP2D1, PPTC7, and TAB1, whereas there are only 8 in yeast. Phylogenetic analysis of the DNA sequences of vertebrate PPM isoforms revealed that they can be divided into 12 different classes: PPM1A/PPM1B/PPM1N, PPM1D, PPM1E/PPM1F, PPM1G, PPM1H/PPM1J/PPM1M, PPM1K, PPM1L, ILKAP, PDP1/PDP2, PP2D1/PHLPP1/PHLPP2, TAB1, and PPTC7. PPM-family members have a conserved catalytic core region, which contains the metal-chelating residues. The different isoforms also have isoform specific regions within their catalytic core domain and terminal domains, and these regions may be involved in substrate recognition and/or functional regulation of the phosphatases. The twenty mammalian PPM phosphatases are involved in regulating diverse cellular functions, such as cell cycle control, cell differentiation, immune responses, and cell metabolism. Mutation, overexpression, or deletion of the PPM phosphatase gene results in abnormal cellular responses, which lead to various human diseases. This review focuses on the structures and biological functions of the PPM-phosphatase family and their associated diseases. The development of specific inhibitors against the PPM phosphatase family as a therapeutic strategy will also be discussed.
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21
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Wang Y, Hekimi S. The Complexity of Making Ubiquinone. Trends Endocrinol Metab 2019; 30:929-943. [PMID: 31601461 DOI: 10.1016/j.tem.2019.08.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Revised: 08/19/2019] [Accepted: 08/20/2019] [Indexed: 12/15/2022]
Abstract
Ubiquinone (UQ, coenzyme Q) is an essential electron transfer lipid in the mitochondrial respiratory chain. It is a main source of mitochondrial reactive oxygen species (ROS) but also has antioxidant properties. This mix of characteristics is why ubiquinone supplementation is considered a potential therapy for many diseases involving mitochondrial dysfunction. Mutations in the ubiquinone biosynthetic pathway are increasingly being identified in patients. Furthermore, secondary ubiquinone deficiency is a common finding associated with mitochondrial disorders and might exacerbate these conditions. Recent developments have suggested that ubiquinone biosynthesis occurs in discrete domains of the mitochondrial inner membrane close to ER-mitochondria contact sites. This spatial requirement for ubiquinone biosynthesis could be the link between secondary ubiquinone deficiency and mitochondrial dysfunction, which commonly results in loss of mitochondrial structural integrity.
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Affiliation(s)
- Ying Wang
- Department of Biology, McGill University, Montreal, Canada
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22
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Tsuganezawa K, Sekimata K, Nakagawa Y, Utata R, Nakamura K, Ogawa N, Koyama H, Shirouzu M, Fukami T, Kita K, Tanaka A. Identification of small molecule inhibitors of human COQ7. Bioorg Med Chem 2019; 28:115182. [PMID: 31753803 DOI: 10.1016/j.bmc.2019.115182] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/23/2019] [Accepted: 10/24/2019] [Indexed: 12/29/2022]
Abstract
Given that the associated clinical manifestations of ubiquinone (UQ, or coenzyme Q) deficiency diseases are highly heterogeneous and complicated, effective new research tools for UQ homeostasis studies are awaited. We set out to develop human COQ7 inhibitors that interfere with UQ synthesis. Systematic structure-activity relationship development starting from a screening hit compound led to the identification of highly potent COQ7 inhibitors that did not disturb physiological cell growth of human normal culture cells. These new COQ7 inhibitors may serve as useful tools for studying the balance between UQ supplementation pathways: de novo UQ synthesis and extracellular UQ uptake.
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Affiliation(s)
- Keiko Tsuganezawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Katsuhiko Sekimata
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Yukari Nakagawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Rei Utata
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Kana Nakamura
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Naoko Ogawa
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Hiroo Koyama
- RIKEN Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Mikako Shirouzu
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Takehiro Fukami
- RIKEN Program for Drug Discovery and Medical Technology Platforms, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Kiyoshi Kita
- School of Tropical Medicine and Global Health, Nagasaki University, 1-12-4, Sakamoto, Nagasaki 852-8523, Japan
| | - Akiko Tanaka
- RIKEN Systems and Structural Biology Center, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
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23
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Niemi NM, Wilson GM, Overmyer KA, Vögtle FN, Myketin L, Lohman DC, Schueler KL, Attie AD, Meisinger C, Coon JJ, Pagliarini DJ. Pptc7 is an essential phosphatase for promoting mammalian mitochondrial metabolism and biogenesis. Nat Commun 2019; 10:3197. [PMID: 31324765 PMCID: PMC6642090 DOI: 10.1038/s41467-019-11047-6] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Accepted: 06/14/2019] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial proteins are replete with phosphorylation, yet its functional relevance remains largely unclear. The presence of multiple resident mitochondrial phosphatases, however, suggests that protein dephosphorylation may be broadly important for calibrating mitochondrial activities. To explore this, we deleted the poorly characterized matrix phosphatase Pptc7 from mice using CRISPR-Cas9 technology. Strikingly, Pptc7−/− mice exhibit hypoketotic hypoglycemia, elevated acylcarnitines and serum lactate, and die soon after birth. Pptc7−/− tissues have markedly diminished mitochondrial size and protein content despite normal transcript levels, and aberrantly elevated phosphorylation on select mitochondrial proteins. Among these, we identify the protein translocase complex subunit Timm50 as a putative Pptc7 substrate whose phosphorylation reduces import activity. We further find that phosphorylation within or near the mitochondrial targeting sequences of multiple proteins could disrupt their import rates and matrix processing. Overall, our data define Pptc7 as a protein phosphatase essential for proper mitochondrial function and biogenesis during the extrauterine transition. The mitochondria houses several phosphatases, but their function is not well characterized. Here, the authors show that mitochondrial phosphatase Pptc7 is important during development for proper mitochondrial function and has a role regulating protein import with the translocase subunit Timm50.
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Affiliation(s)
- Natalie M Niemi
- Morgridge Institute for Research, Madison, WI, 53715, USA.,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Gary M Wilson
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Katherine A Overmyer
- Morgridge Institute for Research, Madison, WI, 53715, USA.,Genome Center of Wisconsin, Madison, WI, 53706, USA
| | - F-Nora Vögtle
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, 79104, Germany
| | - Lisa Myketin
- Institute of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg im Breisgau, 79104, Germany
| | | | - Kathryn L Schueler
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Alan D Attie
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Chris Meisinger
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg im Breisgau, 79104, Germany
| | - Joshua J Coon
- Morgridge Institute for Research, Madison, WI, 53715, USA.,Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.,Genome Center of Wisconsin, Madison, WI, 53706, USA.,Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - David J Pagliarini
- Morgridge Institute for Research, Madison, WI, 53715, USA. .,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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24
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Ariño J, Velázquez D, Casamayor A. Ser/Thr protein phosphatases in fungi: structure, regulation and function. MICROBIAL CELL 2019; 6:217-256. [PMID: 31114794 PMCID: PMC6506691 DOI: 10.15698/mic2019.05.677] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Reversible phospho-dephosphorylation of proteins is a major mechanism for the control of cellular functions. By large, Ser and Thr are the most frequently residues phosphorylated in eukar-yotes. Removal of phosphate from these amino acids is catalyzed by a large family of well-conserved enzymes, collectively called Ser/Thr protein phosphatases. The activity of these enzymes has an enormous impact on cellular functioning. In this work we pre-sent the members of this family in S. cerevisiae and other fungal species, and review the most recent findings concerning their regu-lation and the roles they play in the most diverse aspects of cell biology.
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Affiliation(s)
- Joaquín Ariño
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Diego Velázquez
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
| | - Antonio Casamayor
- Departament de Bioquímica i Biologia Molecular and Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Barcelona, Spain
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