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Jin C, Wang S, Sui X, Meng Q, Wu G. Low expression of ELOVL6 may be involved in fat loss in white adipose tissue of cancer-associated cachexia. Lipids Health Dis 2024; 23:144. [PMID: 38760797 PMCID: PMC11100253 DOI: 10.1186/s12944-024-02126-9] [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: 11/14/2023] [Accepted: 04/29/2024] [Indexed: 05/19/2024] Open
Abstract
BACKGROUND Cancer-associated cachexia (CAC) arises from malignant tumors and leads to a debilitating wasting syndrome. In the pathophysiology of CAC, the depletion of fat plays an important role. The mechanisms of CAC-induced fat loss include the enhancement of lipolysis, inhibition of lipogenesis, and browning of white adipose tissue (WAT). However, few lipid-metabolic enzymes have been reported to be involved in CAC. This study hypothesized that ELOVL6, a critical enzyme for the elongation of fatty acids, may be involved in fat loss in CAC. METHODS Transcriptome sequencing technology was used to identify CAC-related genes in the WAT of a CAC rodent model. Then, the expression level of ELOVL6 and the fatty acid composition were analyzed in a large clinical sample. Elovl6 was knocked down by siRNA in 3T3-L1 mouse preadipocytes to compare with wild-type 3T3-L1 cells treated with tumor cell conditioned medium. RESULTS In the WAT of patients with CAC, a significant decrease in the expression of ELOVL6 was found, which was linearly correlated with the extent of body mass reduction. Gas chromatographic analysis revealed an increase in palmitic acid (C16:0) and a decrease in linoleic acid (C18:2n-6) in these tissue samples. After treatment with tumor cell-conditioned medium, 3T3-L1 mouse preadipocytes showed a decrease in Elovl6 expression, and Elovl6-knockdown cells exhibited a reduction in preadipocyte differentiation and lipogenesis. Similarly, the knockdown of Elovl6 in 3T3-L1 cells resulted in a significant increase in palmitic acid (C16:0) and a marked decrease in oleic acid (C18:1n-9) content. CONCLUSION Overall, the expression of ELOVL6 was decreased in the WAT of CAC patients. Decreased expression of ELOVL6 might induce fat loss in CAC patients by potentially altering the fatty acid composition of adipocytes. These findings suggest that ELOVL6 may be used as a valuable biomarker for the early diagnosis of CAC and may hold promise as a target for future therapies.
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Affiliation(s)
- Chenyang Jin
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Shuangjie Wang
- Shanghai Institute for Biomedical and Pharmaceutical Technologies, Shanghai, China
| | - Xiangyu Sui
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China
| | - Qingyang Meng
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China.
- Shanghai Clinical Nutrition Research Centre, Shanghai, China.
| | - Guohao Wu
- Department of General Surgery, Zhongshan Hospital of Fudan University, Shanghai, China.
- Shanghai Clinical Nutrition Research Centre, Shanghai, China.
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2
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Hu J, Li S, Zhong X, Wei Y, Sun Q, Zhong L. Human umbilical cord mesenchymal stem cells attenuate diet-induced obesity and NASH-related fibrosis in mice. Heliyon 2024; 10:e25460. [PMID: 38356602 PMCID: PMC10864966 DOI: 10.1016/j.heliyon.2024.e25460] [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: 09/12/2023] [Revised: 01/26/2024] [Accepted: 01/26/2024] [Indexed: 02/16/2024] Open
Abstract
Non-alcoholic steatohepatitis (NASH) is a progressive form of non-alcoholic fatty liver disease (NAFLD) that may progress to cirrhosis and hepatocellular carcinoma but has no available treatment. Mesenchymal stem cells (MSCs) have become increasingly prominent in cell therapy. Human umbilical cord MSCs (hUC-MSCs) are considered superior to other MSCs due to their strong immunomodulatory ability, ease of collection, low immune rejection, and no tumorigenicity. Though hUC-MSCs have received increasing attention in research, they have been rarely applied in any investigations or treatments of NASH and associated fibrosis. Therefore, this study evaluated the therapeutic efficacy of hUC-MSCs in C57BL/6 mice with diet-induced NASH. At week 32, mice were randomized into two groups: phosphate-buffered saline and MSCs, which were injected into the tail vein. At week 40, glucose metabolism was evaluated using glucose and insulin tolerance tests. NASH-related indicators were examined using various biological methods. hUC-MSC administration alleviated obesity, glucose metabolism, hepatic steatosis, inflammation, and fibrosis. Liver RNA-seq showed that the expression of the acyl-CoA thioesterase (ACOT) family members Acot1, Acot2, and Acot3 involved in fatty acid metabolism were altered. The cytochrome P450 (CYP) members Cyp4a10 and Cyp4a14, which are involved in the peroxisome proliferator-activator receptor (PPAR) signaling pathway, were significantly downregulated after hUC-MSC treatment. In conclusion, hUC-MSCs effectively reduced Western diet-induced obesity, NASH, and fibrosis in mice, partly by regulating lipid metabolism and the PPAR signaling pathway.
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Affiliation(s)
- Jiali Hu
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shan Li
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xuan Zhong
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yushuang Wei
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China
| | - Qinjuan Sun
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Lan Zhong
- Department of Gastroenterology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
- Shanghai Institute of Stem Cell Research and Clinical Translation, Shanghai, 200120, China
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3
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de Carvalho CC, Murray IP, Nguyen H, Nguyen T, Cantu DC. Acyltransferase families that act on thioesters: Sequences, structures, and mechanisms. Proteins 2024; 92:157-169. [PMID: 37776148 DOI: 10.1002/prot.26599] [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: 05/09/2023] [Revised: 09/11/2023] [Accepted: 09/19/2023] [Indexed: 10/01/2023]
Abstract
Acyltransferases (AT) are enzymes that catalyze the transfer of acyl group to a receptor molecule. This review focuses on ATs that act on thioester-containing substrates. Although many ATs can recognize a wide variety of substrates, sequence similarity analysis allowed us to classify the ATs into fifteen distinct families. Each AT family is originated from enzymes experimentally characterized to have AT activity, classified according to sequence similarity, and confirmed with tertiary structure similarity for families that have crystallized structures available. All the sequences and structures of the AT families described here are present in the thioester-active enzyme (ThYme) database. The AT sequences and structures classified into families and available in the ThYme database could contribute to enlightening the understanding acyl transfer to thioester-containing substrates, most commonly coenzyme A, which occur in multiple metabolic pathways, mostly with fatty acids.
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Affiliation(s)
- Caio C de Carvalho
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Ian P Murray
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
| | - Hung Nguyen
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - Tin Nguyen
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
- Department of Computer Science and Software Engineering, Auburn University, Auburn, Alabama, USA
| | - David C Cantu
- Department of Chemical and Materials Engineering, University of Nevada, Reno, Reno, Nevada, USA
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4
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Zhong D, Cai J, Hu C, Chen J, Zhang R, Fan C, Li S, Zhang H, Xu Z, Jia Z, Guo D, Sun Y. Inhibition of mPGES-2 ameliorates NASH by activating NR1D1 via heme. Hepatology 2023; 78:547-561. [PMID: 35839302 DOI: 10.1002/hep.32671] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 06/27/2022] [Accepted: 07/12/2022] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND AIMS Nonalcoholic fatty liver disease (NAFLD), a complex metabolic syndrome, has limited therapeutic options. Microsomal prostaglandin E synthase-2 (mPGES-2) was originally discovered as a prostaglandin E 2 (PGE 2 ) synthase; however, it does not produce PGE 2 in the liver. Moreover, the role of mPGES-2 in NAFLD remains undefined. Herein, we aimed to determine the function and mechanism of mPGES-2 in liver steatosis and steatohepatitis. APPROACH AND RESULTS To evaluate the role of mPGES-2 in NAFLD, whole-body or hepatocyte-specific mPGES-2-deficient mice fed a high-fat or methionine-choline-deficient diet were used. Compared with control mice, mPGES-2-deficient mice showed reduced hepatic lipid accumulation, along with ameliorated liver injury, inflammation, and fibrosis. Furthermore, the protective effect of mPGES-2 deficiency against NAFLD was dependent on decreased cytochrome P450 4A14 and increased acyl-CoA thioesterase 4 levels regulated by the heme receptor nuclear receptor subfamily 1 group D member 1 (NR1D1), but not PGE 2 . Heme regulated the increased NR1D1 activity mediated by mPGES-2 deficiency. Further, we confirmed the protective role of the mPGES-2 inhibitor SZ0232 in NAFLD therapy. CONCLUSION Our study indicates the pathogenic role of mPGES-2 and outlines the mechanism in mediating NAFLD, thereby highlighting the therapeutic potential of mPGES-2 inhibition in liver steatosis and steatohepatitis.
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Affiliation(s)
- Dandan Zhong
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Jie Cai
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
- Nanjing Key Laboratory of Pediatrics , Nanjing Children's Hospital , Nanjing Medical University , Nanjing , Jiangsu , P. R. China
- Public Experimental Research Center of Xuzhou Medical University , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Cheng Hu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Jingshuo Chen
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
- Public Experimental Research Center of Xuzhou Medical University , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Rumeng Zhang
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
- Department of Pharmacology , Xuzhou Central Hospital , Xuzhou , Jiangsu , China
| | - Chenyu Fan
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Shanshan Li
- Jiangsu Medical Engineering Research Center of Gene Detection , Xuzhou , Jiangsu , China
| | - Hongxing Zhang
- Jiangsu Province Key Laboratory of Anesthesiology , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Zhou Xu
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
- Public Experimental Research Center of Xuzhou Medical University , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Zhanjun Jia
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
- Nanjing Key Laboratory of Pediatrics , Nanjing Children's Hospital , Nanjing Medical University , Nanjing , Jiangsu , P. R. China
| | - Dong Guo
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
| | - Ying Sun
- Jiangsu Key Laboratory of New Drug Research and Clinical Pharmacy , Xuzhou Medical University , Xuzhou , Jiangsu , P. R. China
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5
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Ranea-Robles P, Houten SM. The biochemistry and physiology of long-chain dicarboxylic acid metabolism. Biochem J 2023; 480:607-627. [PMID: 37140888 PMCID: PMC10214252 DOI: 10.1042/bcj20230041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 04/20/2023] [Accepted: 04/21/2023] [Indexed: 05/05/2023]
Abstract
Mitochondrial β-oxidation is the most prominent pathway for fatty acid oxidation but alternative oxidative metabolism exists. Fatty acid ω-oxidation is one of these pathways and forms dicarboxylic acids as products. These dicarboxylic acids are metabolized through peroxisomal β-oxidation representing an alternative pathway, which could potentially limit the toxic effects of fatty acid accumulation. Although dicarboxylic acid metabolism is highly active in liver and kidney, its role in physiology has not been explored in depth. In this review, we summarize the biochemical mechanism of the formation and degradation of dicarboxylic acids through ω- and β-oxidation, respectively. We will discuss the role of dicarboxylic acids in different (patho)physiological states with a particular focus on the role of the intermediates and products generated through peroxisomal β-oxidation. This review is expected to increase the understanding of dicarboxylic acid metabolism and spark future research.
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Affiliation(s)
- Pablo Ranea-Robles
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, U.S.A
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6
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. Neurobiol Sleep Circadian Rhythms 2023; 14:100092. [PMID: 37020466 PMCID: PMC10068260 DOI: 10.1016/j.nbscr.2023.100092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 03/17/2023] Open
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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7
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Muheim CM, Ford K, Medina E, Singletary K, Peixoto L, Frank MG. Ontogenesis of the molecular response to sleep loss. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.16.524266. [PMID: 36712085 PMCID: PMC9882159 DOI: 10.1101/2023.01.16.524266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Sleep deprivation (SD) results in profound cellular and molecular changes in the adult mammalian brain. Some of these changes may result in, or aggravate, brain disease. However, little is known about how SD impacts gene expression in developing animals. We examined the transcriptional response in the prefrontal cortex (PFC) to SD across postnatal development in male mice. We used RNA sequencing to identify functional gene categories that were specifically impacted by SD. We find that SD has dramatically different effects on PFC genes depending on developmental age. Gene expression differences after SD fall into 3 categories: present at all ages (conserved), present when mature sleep homeostasis is first emerging, and those unique to certain ages in adults. Developmentally conserved gene expression was limited to a few functional categories, including Wnt-signaling which suggests that this pathway is a core mechanism regulated by sleep. In younger ages, genes primarily related to growth and development are affected while changes in genes related to metabolism are specific to the effect of SD in adults.
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Affiliation(s)
- Christine M. Muheim
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Kaitlyn Ford
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Elizabeth Medina
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA
| | - Kristan Singletary
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA
| | - Lucia Peixoto
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
| | - Marcos G. Frank
- Washington State University Spokane, Department of Translational Medicine and Physiology, Sleep and Performance Research Center, Elson S. Floyd College of Medicine, Pharmaceutical and Biomedical Science Building 230, 412 E. Spokane Falls Blvd., Spokane WA 99202, USA,WSU Health Sciences Spokane, Steve Gleason Institute for Neuroscience, 412 E. Spokane Falls Blvd., Spokane, WA 99202, USA,Correspondence: & , Tel.: +01-509 368 6747
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High Expression of ACOT2 Predicts Worse Overall Survival and Abnormal Lipid Metabolism: A Potential Target for Acute Myeloid Leukemia. JOURNAL OF HEALTHCARE ENGINEERING 2022; 2022:2669114. [PMID: 36193167 PMCID: PMC9525752 DOI: 10.1155/2022/2669114] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/04/2022] [Accepted: 08/25/2022] [Indexed: 12/13/2022]
Abstract
Acyl-CoA thioesterase (ACOT) plays a considerable role in lipid metabolism, which is closely related to the occurrence and development of cancer, nevertheless, its role has not been fully elucidated in acute myeloid leukemia (AML). To explore the role of ACOT2 in AML and to provide a potential therapeutic target for AML, the expression pattern of ACOT was investigated based on the TNMplot, Gene Expression Profiling Interactive Analysis (GEPIA), and Cancer Cell Line Encyclopedia (CCLE) database, and diagnostic value, prognostic value, and clinical phenotype of ACOT were explored based on data from The Cancer Genome Atlas (TCGA). Functional annotation and enrichment analysis of the common targets between ACOT2 coexpressed and AML-related genes were further performed by Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Set Enrichment Analysis (GSEA) analyses. The protein-protein interaction (PPI) network of ACOT2 coexpressed genes and functional ACOT2-related metabolites association network were constructed based on GeneMANIA and Human Metabolome Database. Among ACOTs, ACOT2 was highly expressed in AML compared to normal control subjects according to TNMplot, GEPIA, and CCLE database, which was significantly associated with poor overall survival (OS) in AML (
). Moreover, ACOT2 exhibited excellent diagnostic efficiency for AML (AUC: 1.000) and related to French-American-British (FAB) classification and cytogenetics. GO, KEGG, and GSEA analyses of 71 common targets between ACOT2 coexpressed and AML-related genes revealed that ACOT2 is closely related to ACOT1, ACOT4, enoyl-acyl carrier protein reductase, mitochondrial (MECR), puromycin-sensitive aminopeptidase (NPEPPS), SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily B member 1 (SMARCB1), and long-chain fatty acid-CoA ligase 1 (ACSL1) in PPI network, and plays a significant role in lipid metabolism, that is, involved in fatty acid elongation and biosynthesis of unsaturated fatty acids. Collectively, the increase of ACOT2 may be an important characteristic of worse OS and abnormal lipid metabolism, suggesting that ACOT2 may become a potential therapeutic target for AML.
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Caswell BT, de Carvalho CC, Nguyen H, Roy M, Nguyen T, Cantu DC. Thioesterase enzyme families: Functions, structures, and mechanisms. Protein Sci 2022; 31:652-676. [PMID: 34921469 PMCID: PMC8862431 DOI: 10.1002/pro.4263] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 12/12/2022]
Abstract
Thioesterases are enzymes that hydrolyze thioester bonds in numerous biochemical pathways, for example in fatty acid synthesis. This work reports known functions, structures, and mechanisms of updated thioesterase enzyme families, which are classified into 35 families based on sequence similarity. Each thioesterase family is based on at least one experimentally characterized enzyme, and most families have enzymes that have been crystallized and their tertiary structure resolved. Classifying thioesterases into families allows to predict tertiary structures and infer catalytic residues and mechanisms of all sequences in a family, which is particularly useful because the majority of known protein sequence have no experimental characterization. Phylogenetic analysis of experimentally characterized thioesterases that have structures with the two main structural folds reveal convergent and divergent evolution. Based on tertiary structure superimposition, catalytic residues are predicted.
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Affiliation(s)
- Benjamin T. Caswell
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Caio C. de Carvalho
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Hung Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Monikrishna Roy
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - Tin Nguyen
- Department of Computer Science and EngineeringUniversity of Nevada, RenoRenoNevadaUSA
| | - David C. Cantu
- Department of Chemical and Materials EngineeringUniversity of Nevada, RenoRenoNevadaUSA
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10
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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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St Clair LA, Mills SA, Lian E, Soma PS, Nag A, Montgomery C, Ramirez G, Chotiwan N, Gullberg RC, Perera R. Acyl-Coa Thioesterases: A Rheostat That Controls Activated Fatty Acids Modulates Dengue Virus Serotype 2 Replication. Viruses 2022; 14:v14020240. [PMID: 35215835 PMCID: PMC8875275 DOI: 10.3390/v14020240] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/18/2022] [Accepted: 01/20/2022] [Indexed: 02/05/2023] Open
Abstract
During infection with dengue viruses (DENVs), the lipid landscape within host cells is significantly altered to assemble membrane platforms that support viral replication and particle assembly. Fatty acyl-CoAs are key intermediates in the biosynthesis of complex lipids that form these membranes. They also function as key signaling lipids in the cell. Here, we carried out loss of function studies on acyl-CoA thioesterases (ACOTs), a family of enzymes that hydrolyze fatty acyl-CoAs to free fatty acids and coenzyme A, to understand their influence on the lifecycle of DENVs. The loss of function of the type I ACOTs 1 (cytoplasmic) and 2 (mitochondrial) together significantly increased DENV serotype 2 (DENV2) viral replication and infectious particle release. However, isolated knockdown of mitochondrial ACOT2 significantly decreased DENV2 protein translation, genome replication, and infectious virus release. Furthermore, loss of ACOT7 function, a mitochondrial type II ACOT, similarly suppressed DENV2. As ACOT1 and ACOT2 are splice variants, these data suggest that functional differences and substrate specificities due to the location (cytosol and mitochondria, respectively) of these proteins may account for the differences in DENV2 infection phenotype. Additionally, loss of mitochondrial ACOT2 and ACOT7 expression also altered the expression of several ACOTs located in multiple organelle compartments within the cell, highlighting a complex relationship between ACOTs in the DENV2 virus lifecycle.
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Chatfield KC, Sparagna GC, Specht KS, Whitcomb LA, Omar AK, Miyamoto SD, Wolfe LM, Chicco AJ. Long-chain fatty acid oxidation and respiratory complex I deficiencies distinguish Barth Syndrome from idiopathic pediatric cardiomyopathy. J Inherit Metab Dis 2022; 45:111-124. [PMID: 34821394 DOI: 10.1002/jimd.12459] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Revised: 11/14/2021] [Accepted: 11/23/2021] [Indexed: 12/16/2022]
Abstract
Barth syndrome (BTHS) is an X-linked disorder that results from mutations in the TAFAZZIN gene, which encodes a phospholipid transacylase responsible for generating the mature form of cardiolipin in inner mitochondrial membranes. BTHS patients develop early onset cardiomyopathy and a derangement of intermediary metabolism consistent with mitochondrial disease, but the precise alterations in cardiac metabolism that distinguish BTHS from idiopathic forms of cardiomyopathy are unknown. We performed the first metabolic analysis of myocardial tissue from BTHS cardiomyopathy patients compared to age- and sex-matched patients with idiopathic dilated cardiomyopathy (DCM) and nonfailing controls. Results corroborate previous evidence for deficiencies in cardiolipin content and its linoleoyl enrichment as defining features of BTHS cardiomyopathy, and reveal a dramatic accumulation of hydrolyzed (monolyso-) cardiolipin molecular species. Respiratory chain protein deficiencies were observed in both BTHS and DCM, but a selective depletion of complex I was seen only in BTHS after controlling for an apparent loss of mitochondrial density in cardiomyopathic hearts. Distinct shifts in the expression of long-chain fatty acid oxidation enzymes and the tissue acyl-CoA profile of BTHS hearts suggest a specific block in mitochondrial fatty acid oxidation upstream of the conventional matrix beta-oxidation cycle, which may be compensated for by a greater reliance upon peroxisomal fatty acid oxidation and the catabolism of ketones, amino acids, and pyruvate to meet cardiac energy demands. These results provide a comprehensive foundation for exploring novel therapeutic strategies that target the adaptive and maladaptive metabolic features of BTHS cardiomyopathy.
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Affiliation(s)
- Kathryn C Chatfield
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital of Colorado, Aurora, Colorado, USA
| | - Genevieve C Sparagna
- Division of Cardiology, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Kalyn S Specht
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Luke A Whitcomb
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Asma K Omar
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
| | - Shelley D Miyamoto
- Department of Pediatrics, University of Colorado School of Medicine, Children's Hospital of Colorado, Aurora, Colorado, USA
| | - Lisa M Wolfe
- Proteomics and Metabolomics Facility, Colorado State University, Fort Collins, Colorado, USA
| | - Adam J Chicco
- Department of Biomedical Sciences, Colorado State University, Fort Collins, Colorado, USA
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13
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Cavalli M, Diamanti K, Dang Y, Xing P, Pan G, Chen X, Wadelius C. The Thioesterase ACOT1 as a Regulator of Lipid Metabolism in Type 2 Diabetes Detected in a Multi-Omics Study of Human Liver. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:652-659. [PMID: 34520261 PMCID: PMC8812507 DOI: 10.1089/omi.2021.0093] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Type 2 diabetes (T2D) is characterized by pathophysiological alterations in lipid metabolism. One strategy to understand the molecular mechanisms behind these abnormalities is to identify cis-regulatory elements (CREs) located in chromatin-accessible regions of the genome that regulate key genes. In this study we integrated assay for transposase-accessible chromatin followed by sequencing (ATAC-seq) data, widely used to decode chromatin accessibility, with multi-omics data and publicly available CRE databases to identify candidate CREs associated with T2D for further experimental validations. We performed high-sensitive ATAC-seq in nine human liver samples from normal and T2D donors, and identified a set of differentially accessible regions (DARs). We identified seven DARs including a candidate enhancer for the ACOT1 gene that regulates the balance of acyl-CoA and free fatty acids (FFAs) in the cytoplasm. The relevance of ACOT1 regulation in T2D was supported by the analysis of transcriptomics and proteomics data in liver tissue. Long-chain acyl-CoA thioesterases (ACOTs) are a group of enzymes that hydrolyze acyl-CoA esters to FFAs and coenzyme A. ACOTs have been associated with regulation of triglyceride levels, fatty acid oxidation, mitochondrial function, and insulin signaling, linking their regulation to the pathogenesis of T2D. Our strategy integrating chromatin accessibility with DNA binding and other types of omics provides novel insights on the role of genetic regulation in T2D and is extendable to other complex multifactorial diseases.
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Affiliation(s)
- Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Klev Diamanti
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Yonglong Dang
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Pengwei Xing
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Xingqi Chen
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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14
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Li M, Tian X, Li X, Huang M, Huang S, Wu Y, Jiang M, Shi Y, Shi L, Wang Z. Diverse energy metabolism patterns in females in Neodon fuscus, Lasiopodomys brandtii, and Mus musculus revealed by comparative transcriptomics under hypoxic conditions. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 783:147130. [PMID: 34088150 DOI: 10.1016/j.scitotenv.2021.147130] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 03/28/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
The effects of global warming and anthropogenic disturbance force animals to migrate from lower to higher elevations to find suitable new habitats. As such migrations increase hypoxic stress on the animals, it is important to understand how plateau- and plain-dwelling animals respond to low-oxygen environments. We used comparative transcriptomics to explore the response of Neodon fuscus, Lasiopodomys brandtii, and Mus musculus skeletal muscle tissues to hypoxic conditions. Results indicate that these species have adopted different oxygen transport and energy metabolism strategies for dealing with a hypoxic environment. N. fuscus promotes oxygen transport by increasing hemoglobin synthesis and reduces the risk of thrombosis through cooperative regulation of genes, including Fga, Fgb, Alb, and Ttr; genes such as Acs16, Gpat4, and Ndufb7 are involved in regulating lipid synthesis, fatty acid β-oxidation, hemoglobin synthesis, and electron-linked transmission, thereby maintaining a normal energy supply in hypoxic conditions. In contrast, the oxygen-carrying capacity and angiogenesis of red blood cells in L. brandtii are promoted by genes in the CYP and COL families; this species maintains its bodily energy supply by enhancing the pentose phosphate pathway and mitochondrial fatty acid synthesis pathway. However, under hypoxia, M. musculus cannot effectively transport additional oxygen; thus, its cell cycle, proliferation, and migration are somewhat affected. Given its lack of hypoxic tolerance experience, M. musculus also shows significantly reduced oxidative phosphorylation levels under hypoxic conditions. Our results suggest that the glucose capacity of M. musculus skeletal muscle does not provide sufficient energy during hypoxia; thus, we hypothesize that it supplements its bodily energy by synthesizing ketone bodies. For the first time, we describe the energy metabolism pathways of N. fuscus and L. brandtii skeletal muscle tissues under hypoxic conditions. Our findings, therefore, improve our understanding of how vertebrates thrive in high altitude and plain habitats when faced with hypoxic conditions.
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Affiliation(s)
- Mengyang Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiangyu Tian
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Xiujuan Li
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Maolin Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Shuang Huang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yue Wu
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Mengwan Jiang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Yuhua Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China
| | - Luye Shi
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China.
| | - Zhenlong Wang
- School of Life Sciences, Zhengzhou University, Zhengzhou 450001, Henan, China; School of Physical Education (Main campus), Zhengzhou University, Zhengzhou 450001, Henan, China.
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15
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Du S, Jin F, Maneix L, Gedam M, Xu Y, Catic A, Wang MC, Zheng H. FoxO3 deficiency in cortical astrocytes leads to impaired lipid metabolism and aggravated amyloid pathology. Aging Cell 2021; 20:e13432. [PMID: 34247441 PMCID: PMC8373366 DOI: 10.1111/acel.13432] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 06/02/2021] [Accepted: 06/19/2021] [Indexed: 12/13/2022] Open
Abstract
The rise of life expectancy of the human population is accompanied by the drastic increases of age‐associated diseases, in particular Alzheimer's disease (AD), and underscores the need to understand how aging influences AD development. The Forkhead box O transcription factor 3 (FoxO3) is known to mediate aging and longevity downstream of insulin/insulin‐like growth factor signaling across species. However, its function in the adult brain under physiological and pathological conditions is less understood. Here, we report a region and cell‐type‐specific regulation of FoxO3 in the central nervous system (CNS). We found that FoxO3 protein levels were reduced in the cortex, but not hippocampus, of aged mice. FoxO3 was responsive to insulin/AKT signaling in astrocytes, but not neurons. Using CNS Foxo3‐deficient mice, we reveal that loss of FoxO3 led to cortical astrogliosis and altered lipid metabolism. This is associated with impaired metabolic homoeostasis and β‐amyloid (Aβ) uptake in primary astrocyte cultures. These phenotypes can be reversed by expressing a constitutively active FOXO3 but not a FOXO3 mutant lacking the transactivation domain. Loss of FoxO3 in 5xFAD mice led to exacerbated Aβ pathology and synapse loss and altered local response of astrocytes and microglia in the vicinity of Aβ plaques. Astrocyte‐specific overexpression of FOXO3 displayed opposite effects, suggesting that FoxO3 functions cell autonomously to mediate astrocyte activity and also interacts with microglia to address Aβ pathology. Our studies support a protective role of astroglial FoxO3 against brain aging and AD.
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Affiliation(s)
- Shuqi Du
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX USA
| | - Feng Jin
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
| | - Laure Maneix
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Stem Cells and Regenerative Medicine Center Baylor College of Medicine Houston TX USA
| | - Manasee Gedam
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Graduate Program in Translational Biology and Molecular Medicine Baylor College of Medicine Houston TX USA
| | - Yin Xu
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
| | - Andre Catic
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX USA
- Stem Cells and Regenerative Medicine Center Baylor College of Medicine Houston TX USA
| | - Meng C. Wang
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX USA
- Department of Pharmacology and Chemical Biology Baylor College of Medicine Houston TX USA
- Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA
- Howard Hughes Medical Institute Baylor College of Medicine Houston TX USA
| | - Hui Zheng
- Huffington Center on Aging Baylor College of Medicine Houston TX USA
- Department of Molecular and Cellular Biology Baylor College of Medicine Houston TX USA
- Department of Molecular and Human Genetics Baylor College of Medicine Houston TX USA
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16
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Ranea-Robles P, Violante S, Argmann C, Dodatko T, Bhattacharya D, Chen H, Yu C, Friedman SL, Puchowicz M, Houten SM. Murine deficiency of peroxisomal L-bifunctional protein (EHHADH) causes medium-chain 3-hydroxydicarboxylic aciduria and perturbs hepatic cholesterol homeostasis. Cell Mol Life Sci 2021; 78:5631-5646. [PMID: 34110423 PMCID: PMC8263512 DOI: 10.1007/s00018-021-03869-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/29/2021] [Accepted: 05/29/2021] [Indexed: 02/07/2023]
Abstract
Peroxisomes play an essential role in the β-oxidation of dicarboxylic acids (DCAs), which are metabolites formed upon ω-oxidation of fatty acids. Genetic evidence linking transporters and enzymes to specific DCA β-oxidation steps is generally lacking. Moreover, the physiological functions of DCA metabolism remain largely unknown. In this study, we aimed to characterize the DCA β-oxidation pathway in human cells, and to evaluate the biological role of DCA metabolism using mice deficient in the peroxisomal L-bifunctional protein (Ehhadh KO mice). In vitro experiments using HEK-293 KO cell lines demonstrate that ABCD3 and ACOX1 are essential in DCA β-oxidation, whereas both the bifunctional proteins (EHHADH and HSD17B4) and the thiolases (ACAA1 and SCPx) have overlapping functions and their contribution may depend on expression level. We also show that medium-chain 3-hydroxydicarboxylic aciduria is a prominent feature of EHHADH deficiency in mice most notably upon inhibition of mitochondrial fatty acid oxidation. Using stable isotope tracing methodology, we confirmed that products of peroxisomal DCA β-oxidation can be transported to mitochondria for further metabolism. Finally, we show that, in liver, Ehhadh KO mice have increased mRNA and protein expression of cholesterol biosynthesis enzymes with decreased (in females) or similar (in males) rate of cholesterol synthesis. We conclude that EHHADH plays an essential role in the metabolism of medium-chain DCAs and postulate that peroxisomal DCA β-oxidation is a regulator of hepatic cholesterol biosynthesis.
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Affiliation(s)
- Pablo Ranea-Robles
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
| | - Sara Violante
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
- The Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Carmen Argmann
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
| | - Tetyana Dodatko
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
| | - Dipankar Bhattacharya
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Hongjie Chen
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT, 06902, USA
| | - Chunli Yu
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA
- Mount Sinai Genomics, Inc, Stamford, CT, 06902, USA
| | - Scott L Friedman
- Division of Liver Diseases, Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michelle Puchowicz
- Department of Nutrition, School of Medicine, Case Western Reserve University, Cleveland, OH, 44106, USA
- Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN, 38163, USA
| | - Sander M Houten
- Department of Genetics and Genomic Sciences, Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, Box 1498, New York, NY, 10029, USA.
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17
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The Mystery of Extramitochondrial Proteins Lysine Succinylation. Int J Mol Sci 2021; 22:ijms22116085. [PMID: 34199982 PMCID: PMC8200203 DOI: 10.3390/ijms22116085] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 05/31/2021] [Accepted: 06/02/2021] [Indexed: 12/19/2022] Open
Abstract
Lysine succinylation is a post-translational modification which alters protein function in both physiological and pathological processes. Mindful that it requires succinyl-CoA, a metabolite formed within the mitochondrial matrix that cannot permeate the inner mitochondrial membrane, the question arises as to how there can be succinylation of proteins outside mitochondria. The present mini-review examines pathways participating in peroxisomal fatty acid oxidation that lead to succinyl-CoA production, potentially supporting succinylation of extramitochondrial proteins. Furthermore, the influence of the mitochondrial status on cytosolic NAD+ availability affecting the activity of cytosolic SIRT5 iso1 and iso4—in turn regulating cytosolic protein lysine succinylations—is presented. Finally, the discovery that glia in the adult human brain lack subunits of both alpha-ketoglutarate dehydrogenase complex and succinate-CoA ligase—thus being unable to produce succinyl-CoA in the matrix—and yet exhibit robust pancellular lysine succinylation, is highlighted.
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18
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Duan S, Zhang M, Li J, Tian J, Yin H, Wang X, Zhang L. Uterine metabolic disorder induced by silica nanoparticles: biodistribution and bioactivity revealed by labeling with FITC. J Nanobiotechnology 2021; 19:62. [PMID: 33639958 PMCID: PMC7916316 DOI: 10.1186/s12951-021-00810-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 02/19/2021] [Indexed: 12/16/2022] Open
Abstract
Extensive application of nanomaterials has dramatically increased the risk of silica nanoparticle (SiNP, SiO2) exposure, yet their biological effect on reproduction has not been fully elucidated. By tracking the uterine biodistribution of SiNP in pregnant mice, this study was conducted to evaluate the biological effect of SiNP on reproduction. First, SiNP was conjugated with FITC, and then the FITC-SiNP was administrated to trophoblast (100 µg/mL, 24 h) in vitro and pregnant mice (0.25 mg/mouse, 2-24 h) in vivo. It was found that the FITC-SiNP was internalized by trophoblast and deposited in the uterus. The internalization of SiNP caused trophoblast dysfunction and apoptosis, while SiNP accumulation in the uterus induced diffuse inflammatory infiltration. The genome-wide alteration of gene expression was studied by high throughput sequencing analysis, where 75 genes were found to be dysregulated after SiNP exposure, among which ACOT2, SCD1, and CPT1A were demonstrated to regulate the biosynthesis of unsaturated fatty acids. Moreover, the suppression of unsaturated fatty acids caused mitochondrial overload of long-chain fatty acyl-CoA (LACoA), which further induced both trophoblast apoptosis and endometrial inflammation. In conclusion, the successful conjugation of FITC onto SiNP facilitated the tracking of SiNP in vitro and in vivo, while exposure to FITC-SiNP induced uterine metabolic disorder, which was regulated by the ACOT/CPT1A/SCD1 axis through the biosynthesis of unsaturated fatty acids signaling pathway.
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Affiliation(s)
- Shuyin Duan
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province, Shandong University, 250001, Jinan, China.,School of Public Health, Zhengzhou University, 450001, Zhengzhou, China
| | - Meihua Zhang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province, Shandong University, 250001, Jinan, China
| | - Junxia Li
- School of Public Health, Weifang Medical University, 261053, Weifang, China
| | - Jiaqi Tian
- School of Public Health, Weifang Medical University, 261053, Weifang, China
| | - Haoyu Yin
- School of Public Health, Weifang Medical University, 261053, Weifang, China
| | - Xietong Wang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province, Shandong University, 250001, Jinan, China.,Department of Obstetrics and Gynecology, Shandong Provincial Hospital, 250001, Jinan, China
| | - Lin Zhang
- Key Laboratory of Birth Regulation and Control Technology of National Health Commission of China, Maternal and Child Health Care Hospital of Shandong Province, Shandong University, 250001, Jinan, China.
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19
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Malgapo MIP, Safadi JM, Linder ME. Metallo-β-lactamase domain-containing protein 2 is S-palmitoylated and exhibits acyl-CoA hydrolase activity. J Biol Chem 2021; 296:100106. [PMID: 33219126 PMCID: PMC7949124 DOI: 10.1074/jbc.ra120.015701] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/12/2020] [Accepted: 11/20/2020] [Indexed: 11/24/2022] Open
Abstract
Members of the metallo-β-lactamase (MBL) superfamily of enzymes harbor a highly conserved αββα MBL-fold domain and were first described as inactivators of common β-lactam antibiotics. In humans, these enzymes have been shown to exhibit diverse functions, including hydrolase activity toward amides, esters, and thioesters. An uncharacterized member of the human MBL family, MBLAC2, was detected in multiple palmitoylproteomes, identified as a zDHHC20 S-acyltransferase interactor, and annotated as a potential thioesterase. In this study, we confirmed that MBLAC2 is palmitoylated and identified the likely S-palmitoylation site as Cys254. S-palmitoylation of MBLAC2 is increased in cells when expressed with zDHHC20, and MBLAC2 is a substrate for purified zDHHC20 in vitro. To determine its biochemical function, we tested the ability of MBLAC2 to hydrolyze a variety of small molecules and acylprotein substrates. MBLAC2 has acyl-CoA thioesterase activity with kinetic parameters and acyl-CoA selectivity comparable with acyl-CoA thioesterase 1 (ACOT1). Two predicted zinc-binding residues, Asp87 and His88, are required for MBLAC2 hydrolase activity. Consistent with a role in fatty acid metabolism in cells, MBLAC2 was cross-linked to a photoactivatable fatty acid in a manner that was independent of its S-fatty acylation at Cys254. Our study adds to previous investigations demonstrating the versatility of the MBL-fold domain in supporting a variety of enzymatic reactions.
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Affiliation(s)
- Martin Ian P Malgapo
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Jenelle M Safadi
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA
| | - Maurine E Linder
- Department of Molecular Medicine, College of Veterinary Medicine, Cornell University, Ithaca, New York, USA.
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20
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Park J, Kim YJ, Lee D, Kim KJ. Structural basis for nucleotide-independent regulation of acyl-CoA thioesterase from Bacillus cereus ATCC 14579. Int J Biol Macromol 2020; 170:390-396. [PMID: 33383082 DOI: 10.1016/j.ijbiomac.2020.12.174] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 12/15/2020] [Accepted: 12/23/2020] [Indexed: 11/30/2022]
Abstract
Acyl-CoA thioesterase is an enzyme that catalyzes the cleavage of thioester bonds and regulates the cellular concentrations of CoASH, fatty acids, and acyl-CoA. In this study, we report the crystal structure of acyl-CoA thioesterase from Bacillus cereus ATCC 14579 (BcACT1) complexed with the CoA product. BcACT1 possesses a monomeric structure of a hotdog-fold and forms a hexamer via the trimerization of three dimers. We identified the active site of BcACT1 and revealed that residues Asn23 and Asp38 are crucial for enzyme catalysis, indicating that BcACT1 belongs to the TE6 family. We also propose that BcACT1 might undergo an open-closed conformational change on the acyl-CoA binding pocket upon binding of the acyl-CoA substrate. Interestingly, the BcACT1 variants with dramatically increased activities were obtained during the site-directed mutagenesis experiments to confirm the residues involved in CoA binding. Finally, we found that BcACT1 is not nucleotide-regulated and suggest that the length and shape of the additional α2-helix are crucial in determining a regulation mode by nucleotides.
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Affiliation(s)
- Jiyoung Park
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Yeo-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Donghoon Lee
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Kyung-Jin Kim
- School of Life Sciences, KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea; KNU Institute for Microorganisms, Kyungpook National University, Daegu 41566, Republic of Korea.
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21
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Montoni F, Andreotti DZ, Eichler RADS, Santos WDS, Kisaki CY, Arcos SSS, Lima IF, Soares MAM, Nishiyama-Jr MY, Nava-Rodrigues D, Ferro ES, Carvalho VM, Iwai LK. The impact of rattlesnake venom on mice cerebellum proteomics points to synaptic inhibition and tissue damage. J Proteomics 2020; 221:103779. [DOI: 10.1016/j.jprot.2020.103779] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Revised: 03/30/2020] [Accepted: 04/02/2020] [Indexed: 02/06/2023]
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22
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Swarbrick CMD, Nanson JD, Patterson EI, Forwood JK. Structure, function, and regulation of thioesterases. Prog Lipid Res 2020; 79:101036. [PMID: 32416211 DOI: 10.1016/j.plipres.2020.101036] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 04/30/2020] [Accepted: 05/01/2020] [Indexed: 01/15/2023]
Abstract
Thioesterases are present in all living cells and perform a wide range of important biological functions by catalysing the cleavage of thioester bonds present in a diverse array of cellular substrates. Thioesterases are organised into 25 families based on their sequence conservation, tertiary and quaternary structure, active site configuration, and substrate specificity. Recent structural and functional characterisation of thioesterases has led to significant changes in our understanding of the regulatory mechanisms that govern enzyme activity and their respective cellular roles. The resulting dogma changes in thioesterase regulation include mechanistic insights into ATP and GDP-mediated regulation by oligomerisation, the role of new key regulatory regions, and new insights into a conserved quaternary structure within TE4 family members. Here we provide a current and comparative snapshot of our understanding of thioesterase structure, function, and regulation across the different thioesterase families.
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Affiliation(s)
| | - Jeffrey D Nanson
- School of Chemistry and Molecular Biosciences, Institute for Molecular Bioscience, Australian Infectious Diseases Research Centre, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Edward I Patterson
- Centre for Neglected Tropical Diseases, Departments of Vector Biology and Tropical Disease Biology, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool L3 5QA, UK
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales, Australia.
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23
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Ju Z, Ya J, Li X, Wang H, Zhao H. The effects of chronic cadmium exposure on Bufo gargarizans larvae: Histopathological impairment, gene expression alteration and fatty acid metabolism disorder in the liver. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2020; 222:105470. [PMID: 32199138 DOI: 10.1016/j.aquatox.2020.105470] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 02/16/2020] [Accepted: 03/10/2020] [Indexed: 06/10/2023]
Abstract
Cadmium (Cd) a highly toxic metal to human and wildlife health and it is hazardous to both terrestrial and aquatic life. In this study, we used RNA sequencing analysis to examine the effects of chronic cadmium exposure on liver lipid metabolism of Bufo gargarizans larvae. Tadpoles were exposed to cadmium concentrations at 0, 5, 10, 50, 100 and 200 μg L-1 from Gosner stage 26-42 of metamorphic climax. The results showed high dose cadmium (50, 100 and 200 μg L-1) caused obvious histological changes characterized by hepatocytes deformation, nuclear pyknosis, increasing melanomacrophage centers (MMCs) and aggregated lipid droplets. Moreover, transcriptome analysis showed that liver function was seriously affected by cadmium exposure. Furthermore, high dose cadmium significantly upregulated the mRNA expression of elongation of very-long-chain fatty acids 1 (ELOVL1), Mitochondrial trans-2-enoyl-CoA reductase (MECR), Trans-2, 3-enoyl-CoA reductase (TER) and Hydroxysteroid (17β) dehydrogenase type 12 (HSD17B12) which are related with fatty acid synthesis. Meanwhile, mRNA levels of genes related with fat acid oxidation such as acetyl-CoA acyltransferase 2 (ACAA2) and enoyl-coenzyme A (CoA) hydratase short chain 1 (ECHS1) were significantly upregulated while the expression of Acyl-coA thioesterase 1 (ACOT1), 3-hydroxyacyl-CoA dehydrogenase (HADH), Palmitoyl-protein thioesterase 1(PPT1) and Acetyl-CoA acyltransferase 1(ACAA1) was significantly downregulated by high dose cadmium exposure. Furthermore, the mRNA level of ATP-binding cassette subfamily B member 11 (ABCB11) related with bile secretion was significantly decreased exposed to high dose cadmium. Our results suggested cadmium can cause liver dysfunction by inducing histopathological damages, genetic expression alterations and fatty acid metabolism disorder.
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Affiliation(s)
- Zongqi Ju
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Jing Ya
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Xinyi Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an, 710119, China.
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24
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Kalinger RS, Pulsifer IP, Hepworth SR, Rowland O. Fatty Acyl Synthetases and Thioesterases in Plant Lipid Metabolism: Diverse Functions and Biotechnological Applications. Lipids 2020; 55:435-455. [PMID: 32074392 DOI: 10.1002/lipd.12226] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/29/2020] [Accepted: 01/30/2020] [Indexed: 11/09/2022]
Abstract
Plants use fatty acids to synthesize acyl lipids for many different cellular, physiological, and defensive roles. These roles include the synthesis of essential membrane, storage, or surface lipids, as well as the production of various fatty acid-derived metabolites used for signaling or defense. Fatty acids are activated for metabolic processing via a thioester linkage to either coenzyme A or acyl carrier protein. Acyl synthetases metabolically activate fatty acids to their thioester forms, and acyl thioesterases deactivate fatty acyl thioesters to free fatty acids by hydrolysis. These two enzyme classes therefore play critical roles in lipid metabolism. This review highlights the surprisingly complex and varying roles of fatty acyl synthetases in plant lipid metabolism, including roles in the intracellular trafficking of fatty acids. This review also surveys the many specialized fatty acyl thioesterases characterized to date in plants, which produce a great diversity of fatty acid products in a tissue-specific manner. While some acyl thioesterases produce fatty acids that clearly play roles in plant-insect or plant-microbial interactions, most plant acyl thioesterases have yet to be fully characterized both in terms of their substrate specificities and their functions. The biotechnological applications of plant acyl thioesterases and synthetases are also discussed, as there is significant interest in these enzymes as catalysts for the sustainable production of fatty acids and their derivatives for industrial uses.
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Affiliation(s)
- Rebecca S Kalinger
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Ian P Pulsifer
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Shelley R Hepworth
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
| | - Owen Rowland
- Department of Biology and Institute of Biochemistry, Carleton University, 1125 Colonel By Drive, Ottawa, ON, K1S 5B6, Canada
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25
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Bekeova C, Anderson-Pullinger L, Boye K, Boos F, Sharpadskaya Y, Herrmann JM, Seifert EL. Multiple mitochondrial thioesterases have distinct tissue and substrate specificity and CoA regulation, suggesting unique functional roles. J Biol Chem 2019; 294:19034-19047. [PMID: 31676684 PMCID: PMC6916504 DOI: 10.1074/jbc.ra119.010901] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 10/16/2019] [Indexed: 12/13/2022] Open
Abstract
Acyl-CoA thioesterases (Acots) hydrolyze fatty acyl-CoA esters. Acots in the mitochondrial matrix are poised to mitigate β-oxidation overload and maintain CoA availability. Several Acots associate with mitochondria, but whether they all localize to the matrix, are redundant, or have different roles is unresolved. Here, we compared the suborganellar localization, activity, expression, and regulation among mitochondrial Acots (Acot2, -7, -9, and -13) in mitochondria from multiple mouse tissues and from a model of Acot2 depletion. Acot7, -9, and -13 localized to the matrix, joining Acot2 that was previously shown to localize there. Mitochondria from heart, skeletal muscle, brown adipose tissue, and kidney robustly expressed Acot2, -9, and -13; Acot9 levels were substantially higher in brown adipose tissue and kidney mitochondria, as was activity for C4:0-CoA, a unique Acot9 substrate. In all tissues, Acot2 accounted for about half of the thioesterase activity for C14:0-CoA and C16:0-CoA. In contrast, liver mitochondria from fed and fasted mice expressed little Acot activity, which was confined to long-chain CoAs and due mainly to Acot7 and Acot13 activities. Matrix Acots occupied different functional niches, based on substrate specificity (Acot9 versus Acot2 and -13) and strong CoA inhibition (Acot7, -9, and -13, but not Acot2). Interpreted in the context of β-oxidation, CoA inhibition would prevent Acot-mediated suppression of β-oxidation, while providing a release valve when CoA is limiting. In contrast, CoA-insensitive Acot2 could provide a constitutive siphon for long-chain fatty acyl-CoAs. These results reveal how the family of matrix Acots can mitigate β-oxidation overload and prevent CoA limitation.
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Affiliation(s)
- Carmen Bekeova
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Lauren Anderson-Pullinger
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Kevin Boye
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Felix Boos
- Division of Cellular Biology, Department of Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Yana Sharpadskaya
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
| | - Johannes M Herrmann
- Division of Cellular Biology, Department of Biology, University of Kaiserslautern, 67663 Kaiserslautern, Germany
| | - Erin L Seifert
- MitoCare Center, Department of Pathology, Anatomy, and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania 19107
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26
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Fu CZ, Guang XM, Wan QH, Fang SG. Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon). Genome Biol Evol 2019; 11:2125-2135. [PMID: 31298688 PMCID: PMC6685491 DOI: 10.1093/gbe/evz149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0-45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.
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Affiliation(s)
- Chun-Zheng Fu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Xuan-Min Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
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27
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Andres EM, Hafeez H, Yousaf A, Riazuddin S, Rice ML, Basra MAR, Raza MH. A genome-wide analysis in consanguineous families reveals new chromosomal loci in specific language impairment (SLI). Eur J Hum Genet 2019; 27:1274-1285. [PMID: 30976110 DOI: 10.1038/s41431-019-0398-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Revised: 03/19/2019] [Accepted: 03/26/2019] [Indexed: 12/31/2022] Open
Abstract
Language is a uniquely human ability, and failure to attain this ability can have a life-long impact on the affected individuals. This is particularly true for individuals with specific language impairment (SLI), which is defined as an impairment in normal language development in the absence of any other developmental disability. Although SLI displays high heritability, family-based linkage studies have been hampered by an unclear mode of Mendelian segregation, variable disease penetrance, and heterogeneity of diagnostic criteria. We performed genome-wide parametric linkage analysis and homozygosity mapping in 14 consanguineous families from Pakistan segregating SLI. Linkage analysis revealed a multipoint LOD score of 4.18 at chromosome 2q in family PKSLI05 under a recessive mode of inheritance. A second linkage score of 3.85 was observed in family PKSLI12 at a non-overlapping locus on chromosome 2q. Two other suggestive linkage loci were found in family PKSLI05 on 14q and 22q with LOD scores of 2.37 and 2.23, respectively, that were also identified in homozygosity mapping. Reduction to homozygosity was observed on chromosomes 2q, 5p, 8q, 14q, 17q, and 22q. Each homozygosity region occurred in multiple PKSLI families. We report new SLI loci on chromosomes 2 and 8 and confirm suggestive SLI linkage loci on chromosomes 5, 14, 17, and 22 reported previously in the population of Robinson Crusoe Island. These findings indicate that linkage and homozygosity mapping in consanguineous families can improve genetic analyses in SLI and suggest the involvement of additional genes in the causation of this disorder.
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Affiliation(s)
- Erin M Andres
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | - Huma Hafeez
- Institute of Chemistry, University of the Punjab, Lahore, Pakistan
| | - Adnan Yousaf
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.,Department of Biotechnology, International Islamic University, Islamabad, Pakistan
| | | | - Mabel L Rice
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA
| | | | - Muhammad Hashim Raza
- Child Language Doctoral Program (CLDP), University of Kansas, Lawrence, KS, USA.
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28
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Makwana K, Gosai N, Poe A, Kondratov RV. Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism. FASEB J 2018; 33:4473-4489. [PMID: 30566374 DOI: 10.1096/fj.201802167r] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Calorie restriction (CR) delays aging and affects the circadian clocks by reprogramming circadian rhythms in gene expression. To expand on the circadian mechanisms in CR, we assayed rhythms in the protein translation by analyzing polysome-associated mRNAs in the liver of mice fed ad libitum (AL) and CR diets. Global comparison of the diets revealed that <1% of transcripts were differentially abundant in the polysomes. In contrast, the large differential, up to 10%, was detected when CR and AL diets were compared at individual times throughout the day. Most transcripts that were rhythmic under AL lost their rhythms, and many new transcripts gained rhythms under CR. Only a small fraction of transcripts, including the circadian clock genes, were rhythmic under both diets. Thus, CR strongly reprograms translation. CR affected translation of enzymes regulating long-chain acetyl-coenzyme A (Acyl-CoA) metabolism. The expression of the Acyl-CoA thioesterase (ACOT) family was induced upon CR, leading to the increased transcriptional activity of peroxisome proliferator-activated receptor α, the transcriptional factor regulated by the ACOT products. We propose that the differential translation induced by CR leads to a temporal partition and reprogramming of metabolic processes and provides a link between CR, lipid metabolism, and the circadian clock.-Makwana, K., Gosai, N., Poe, A., Kondratov, R. V. Calorie restriction reprograms diurnal rhythms in protein translation to regulate metabolism.
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Affiliation(s)
- Kuldeep Makwana
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Neha Gosai
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Allan Poe
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
| | - Roman V Kondratov
- Department of Biological, Geological, and Environmental Sciences, Center for Gene Regulation in Health and Diseases, Cleveland State University, Cleveland, Ohio, USA
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29
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Ikenoya C, Takemi S, Kaminoda A, Aizawa S, Ojima S, Gong Z, Chacrabati R, Kondo D, Wada R, Tanaka T, Tsuda S, Sakai T, Sakata I. β-Oxidation in ghrelin-producing cells is important for ghrelin acyl-modification. Sci Rep 2018; 8:9176. [PMID: 29907775 PMCID: PMC6003948 DOI: 10.1038/s41598-018-27458-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 06/01/2018] [Indexed: 12/30/2022] Open
Abstract
Ghrelin is a unique fatty acid-modified peptide hormone produced in the stomach and has important roles in energy homeostasis and gastrointestinal motility. However, the medium-chain fatty acid source for ghrelin acyl-modification is not known. We found that a fat-free diet and the removal of intestinal microbiota did not decrease acyl-ghrelin production in the stomach or plasma acyl-ghrelin levels in mice. RT-PCR analysis showed that genes involving fatty acid synthesis, metabolism, and transport were expressed in pancreas-derived ghrelinoma (PG-1) cells. Treatment with an irreversible inhibitor of carnitine palmitoyltransferase-1 (CPT-1) strongly decreased acylated ghrelin levels but did not affect ghrelin or ghrelin o-acyl transferase (GOAT) mRNA levels in PG-1 cells. Our results suggest that the medium-chain fatty acid used for the acyl-modification of ghrelin is produced in ghrelin-producing cells themselves by β-oxidation of long-chain fatty acids provided from the circulation.
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Affiliation(s)
- Chika Ikenoya
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Shota Takemi
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Arisa Kaminoda
- Department of Biology, Graduate School of Natural Science and Technology, Okayama University, 3-1-1, Tsushimanaka, Kita-ku, Okayama, 700-8530, Japan
| | - Sayaka Aizawa
- Department of Biology, Graduate School of Natural Science and Technology, Okayama University, 3-1-1, Tsushimanaka, Kita-ku, Okayama, 700-8530, Japan
| | - Shiomi Ojima
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Zhi Gong
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Rakhi Chacrabati
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Daisuke Kondo
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Reiko Wada
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Toru Tanaka
- Faculty of Pharmaceutical Sciences, Department of Pharmaceutical and Health Sciences, Josai University, 1-1 Keiyaki dai, Sakado, Saitama, 350-0295, Japan
| | - Sachiko Tsuda
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan.,Research and Development Bureau, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan
| | - Takafumi Sakai
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan.,Area of Life-NanoBio, Division of Strategy Research, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Ichiro Sakata
- Area of Regulatory Biology, Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-ohkubo, Sakuraku, Saitama, 338-8570, Japan.
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30
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Steensels S, Ersoy BA. Fatty acid activation in thermogenic adipose tissue. Biochim Biophys Acta Mol Cell Biol Lipids 2018; 1864:79-90. [PMID: 29793055 DOI: 10.1016/j.bbalip.2018.05.008] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Revised: 03/10/2018] [Accepted: 05/17/2018] [Indexed: 02/07/2023]
Abstract
Channeling carbohydrates and fatty acids to thermogenic tissues, including brown and beige adipocytes, have garnered interest as an approach for the management of obesity-related metabolic disorders. Mitochondrial fatty acid oxidation (β-oxidation) is crucial for the maintenance of thermogenesis. Upon cellular fatty acid uptake or following lipolysis from triglycerides (TG), fatty acids are esterified to coenzyme A (CoA) to form active acyl-CoA molecules. This enzymatic reaction is essential for their utilization in β-oxidation and thermogenesis. The activation and deactivation of fatty acids are regulated by two sets of enzymes called acyl-CoA synthetases (ACS) and acyl-CoA thioesterases (ACOT), respectively. The expression levels of ACS and ACOT family members in thermogenic tissues will determine the substrate availability for β-oxidation, and consequently the thermogenic capacity. Although the role of the majority of ACS and ACOT family members in thermogenesis remains unclear, recent proceedings link the enzymatic activities of ACS and ACOT family members to metabolic disorders and thermogenesis. Elucidating the contributions of specific ACS and ACOT family members to trafficking of fatty acids towards thermogenesis may reveal novel targets for modulating thermogenic capacity and treating metabolic disorders.
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Affiliation(s)
- Sandra Steensels
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA
| | - Baran A Ersoy
- Department of Medicine, Division of Gastroenterology and Hepatology, Weill Cornell Medical College, New York, NY, USA.
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31
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Kim J, Weber JA, Jho S, Jang J, Jun J, Cho YS, Kim HM, Kim H, Kim Y, Chung O, Kim CG, Lee H, Kim BC, Han K, Koh I, Chae KS, Lee S, Edwards JS, Bhak J. KoVariome: Korean National Standard Reference Variome database of whole genomes with comprehensive SNV, indel, CNV, and SV analyses. Sci Rep 2018; 8:5677. [PMID: 29618732 PMCID: PMC5885007 DOI: 10.1038/s41598-018-23837-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 03/16/2018] [Indexed: 01/05/2023] Open
Abstract
High-coverage whole-genome sequencing data of a single ethnicity can provide a useful catalogue of population-specific genetic variations, and provides a critical resource that can be used to more accurately identify pathogenic genetic variants. We report a comprehensive analysis of the Korean population, and present the Korean National Standard Reference Variome (KoVariome). As a part of the Korean Personal Genome Project (KPGP), we constructed the KoVariome database using 5.5 terabases of whole genome sequence data from 50 healthy Korean individuals in order to characterize the benign ethnicity-relevant genetic variation present in the Korean population. In total, KoVariome includes 12.7M single-nucleotide variants (SNVs), 1.7M short insertions and deletions (indels), 4K structural variations (SVs), and 3.6K copy number variations (CNVs). Among them, 2.4M (19%) SNVs and 0.4M (24%) indels were identified as novel. We also discovered selective enrichment of 3.8M SNVs and 0.5M indels in Korean individuals, which were used to filter out 1,271 coding-SNVs not originally removed from the 1,000 Genomes Project when prioritizing disease-causing variants. KoVariome health records were used to identify novel disease-causing variants in the Korean population, demonstrating the value of high-quality ethnic variation databases for the accurate interpretation of individual genomes and the precise characterization of genetic variations.
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Affiliation(s)
- Jungeun Kim
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | - Jessica A Weber
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Sungwoong Jho
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | - Jinho Jang
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - JeHoon Jun
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
- Geromics, Ulsan, 44919, Republic of Korea
| | | | - Hak-Min Kim
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - Yumi Kim
- Geromics, Ulsan, 44919, Republic of Korea
| | - OkSung Chung
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
- Geromics, Ulsan, 44919, Republic of Korea
| | - Chang Geun Kim
- National Standard Reference Center, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - HyeJin Lee
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea
| | | | - Kyudong Han
- Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea
| | - InSong Koh
- Department of Physiology, College of Medicine, Hanyang University, Seoul, 04763, Republic of Korea
| | - Kyun Shik Chae
- National Standard Reference Center, Korea Research Institute of Standards and Science, Daejeon, 34113, Republic of Korea
| | - Semin Lee
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea
| | - Jeremy S Edwards
- Chemistry and Chemical Biology, UNM Comprehensive Cancer Center, University of New Mexico, Albuquerque, NM, 87131, USA.
| | - Jong Bhak
- Personal Genomics Institute, Genome Research Foundation, Cheongju, 28190, Republic of Korea.
- Department of Biomedical Engineering, School of Life Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- The Genomics Institute, Ulsan National Institute of Science and Technology (UNIST), Ulsan, 44919, Republic of Korea.
- Geromics, Ulsan, 44919, Republic of Korea.
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32
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Wanders RJA, Waterham HR, Ferdinandusse S. Peroxisomes and Their Central Role in Metabolic Interaction Networks in Humans. Subcell Biochem 2018; 89:345-365. [PMID: 30378031 DOI: 10.1007/978-981-13-2233-4_15] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Peroxisomes catalyze a number of essential metabolic functions and impairments in any of these are usually associated with major clinical signs and symptoms. In contrast to mitochondria which are autonomous organelles that can catalyze the degradation of fatty acids, certain amino acids and other compounds all by themselves, peroxisomes are non-autonomous organelles which are highly dependent on the interaction with other organelles and compartments to fulfill their role in metabolism. This includes mitochondria, the endoplasmic reticulum, lysosomes, and the cytosol. In this paper we will discuss the central role of peroxisomes in different metabolic interaction networks in humans, including fatty acid oxidation, ether phospholipid biosynthesis, bile acid synthesis, fatty acid alpha-oxidation and glyoxylate metabolism.
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Affiliation(s)
- Ronald J A Wanders
- Laboratory Genetic Metabolic Diseases, Departments Clinical Chemistry and Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.
| | - Hans R Waterham
- Laboratory Genetic Metabolic Diseases, Departments Clinical Chemistry and Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
| | - Sacha Ferdinandusse
- Laboratory Genetic Metabolic Diseases, Departments Clinical Chemistry and Pediatrics, Emma Children's Hospital, Academic Medical Center, University of Amsterdam, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands
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Tillander V, Alexson SEH, Cohen DE. Deactivating Fatty Acids: Acyl-CoA Thioesterase-Mediated Control of Lipid Metabolism. Trends Endocrinol Metab 2017; 28:473-484. [PMID: 28385385 PMCID: PMC5474144 DOI: 10.1016/j.tem.2017.03.001] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 03/01/2017] [Indexed: 12/28/2022]
Abstract
The cellular uptake of free fatty acids (FFA) is followed by esterification to coenzyme A (CoA), generating fatty acyl-CoAs that are substrates for oxidation or incorporation into complex lipids. Acyl-CoA thioesterases (ACOTs) constitute a family of enzymes that hydrolyze fatty acyl-CoAs to form FFA and CoA. Although biochemically and biophysically well characterized, the metabolic functions of these enzymes remain incompletely understood. Existing evidence suggests regulatory roles in controlling rates of peroxisomal and mitochondrial fatty acyl-CoA oxidation, as well as in the subcellular trafficking of fatty acids. Emerging data implicate ACOTs in the pathogenesis of metabolic diseases, suggesting that better understanding their pathobiology could reveal unique targets in the management of obesity, diabetes, and nonalcoholic fatty liver disease.
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Affiliation(s)
- Veronika Tillander
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - Stefan E H Alexson
- Division of Clinical Chemistry, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital, Stockholm, 14186, Sweden
| | - David E Cohen
- Division of Gastroenterology and Hepatology, Joan & Sanford I. Weill Department of Medicine, Weill Cornell Medical College, New York, NY 10021, USA.
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Nie J, DuBois DC, Xue B, Jusko WJ, Almon RR. Effects of High-Fat Feeding on Skeletal Muscle Gene Expression in Diabetic Goto-Kakizaki Rats. GENE REGULATION AND SYSTEMS BIOLOGY 2017; 11:1177625017710009. [PMID: 28607540 PMCID: PMC5457139 DOI: 10.1177/1177625017710009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 04/17/2017] [Indexed: 12/16/2022]
Abstract
In the present report, we examined the responses of diabetic Goto-Kakizaki (GK) rats and control Wistar-Kyoto (WKY) rats fed either a standard chow or high-fat diet (HFD) from weaning to 20 weeks of age. This comparison included gene expression profiling of skeletal muscle using Affymetrix gene array chips. The expression profiling is interpreted within the context of a wide array of physiological measurements. Genes whose expressions are different between the 2 strains regardless of diet, as well as genes that differ between strains only with HFD, were identified. In addition, genes that were regulated by diet in 1 or both strains were identified. The results suggest that both strains respond to HFD by an increased capacity to oxidize lipid fuels in the musculature but that this adaptation occurs more rapidly in WKY rats. The results also demonstrated an impaired cytokine signalling and heightened inflammatory status in the GK rats.
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Affiliation(s)
- Jing Nie
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Debra C DuBois
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Bai Xue
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - William J Jusko
- Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Richard R Almon
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo, NY, USA.,Department of Pharmaceutical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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35
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Cui H, Yang S, Zheng M, Liu R, Zhao G, Wen J. High-salt intake negatively regulates fat deposition in mouse. Sci Rep 2017; 7:2053. [PMID: 28515432 PMCID: PMC5435674 DOI: 10.1038/s41598-017-01560-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 03/20/2017] [Indexed: 01/14/2023] Open
Abstract
High-salt (HS) intake contributes to hypertension and cardiopathy, but the effect of HS on fat deposition is controversial. Feed intake, fat mass, the percentage of abdominal fat, heat production, rate of oxygen consumption and the respiratory exchange ratio of mice on a HS diet were significantly decreased (P < 0.01 or 0.05) compared with mice on a normal-salt (NS) diet. An in vitro experiment with differentiating pre-adipocytes showed reduced fat deposition in the presence of high concentrations of NaCl (>0.05 M). Abdominal fat mRNA profiles and protein measurements showed that 5 known genes involved in lipolysis were up-regulated significantly and 9 genes related to lipogenesis were down-regulated in HS mice. Abundant genes and some proteins (ATP2a1, AGT, and ANGPTL4) related to calcium ion metabolism or the renin-angiotensin system (RAS) were differentially expressed between HS and NS mice. Of special interest, CREB1 phosphorylation (S133 and S142), a key factor involved in calcium signaling and other pathways, was up-regulated in HS mice. By IPA analysis, a network mediated by calcium was established providing the molecular mechanisms underlying the negative effect of HS on fat deposition.
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Affiliation(s)
- Huanxian Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Animal Nutrition, Beijing, 100193, China
| | - Shuyan Yang
- Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Animal Nutrition, Beijing, 100193, China
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,State Key Laboratory of Animal Nutrition, Beijing, 100193, China
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,State Key Laboratory of Animal Nutrition, Beijing, 100193, China.
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China. .,State Key Laboratory of Animal Nutrition, Beijing, 100193, China.
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Grau C, Starkovich M, Azamian MS, Xia F, Cheung SW, Evans P, Henderson A, Lalani SR, Scott DA. Xp11.22 deletions encompassing CENPVL1, CENPVL2, MAGED1 and GSPT2 as a cause of syndromic X-linked intellectual disability. PLoS One 2017; 12:e0175962. [PMID: 28414775 PMCID: PMC5393878 DOI: 10.1371/journal.pone.0175962] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 04/03/2017] [Indexed: 12/27/2022] Open
Abstract
By searching a clinical database of over 60,000 individuals referred for array-based CNV analyses and online resources, we identified four males from three families with intellectual disability, developmental delay, hypotonia, joint hypermobility and relative macrocephaly who carried small, overlapping deletions of Xp11.22. The maximum region of overlap between their deletions spanned ~430 kb and included two pseudogenes, CENPVL1 and CENPVL2, whose functions are not known, and two protein coding genes-the G1 to S phase transition 2 gene (GSPT2) and the MAGE family member D1 gene (MAGED1). Deletions of this ~430 kb region have not been previously implicated in human disease. Duplications of GSPT2 have been documented in individuals with intellectual disability, but the phenotypic consequences of a loss of GSPT2 function have not been elucidated in humans or mouse models. Changes in MAGED1 have not been associated with intellectual disability in humans, but loss of MAGED1 function is associated with neurocognitive and neurobehavioral phenotypes in mice. In all cases, the Xp11.22 deletion was inherited from an unaffected mother. Studies performed on DNA from one of these mothers did not show evidence of skewed X-inactivation. These results suggest that deletions of an ~430 kb region on chromosome Xp11.22 that encompass CENPVL1, CENPVL2, GSPT2 and MAGED1 cause a distinct X-linked syndrome characterized by intellectual disability, developmental delay, hypotonia, joint hypermobility and relative macrocephaly. Loss of GSPT2 and/or MAGED1 function may contribute to the intellectual disability and developmental delay seen in males with these deletions.
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Affiliation(s)
- Christina Grau
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Molly Starkovich
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Mahshid S. Azamian
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Fan Xia
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, Unite States of America
| | - Sau Wai Cheung
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Baylor Genetics, Houston, Texas, Unite States of America
| | - Patricia Evans
- Departments of Pediatrics and Neurology, University of Texas Southwestern Medical School, Dallas, Texas, United States of America
| | - Alex Henderson
- The Newcastle upon Tyne Hospitals, Newcastle upon Tyne, England
| | - Seema R. Lalani
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Daryl A. Scott
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas, United States of America
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37
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Jiang TT, Wei LL, Shi LY, Chen ZL, Wang C, Liu CM, Li ZJ, Li JC. Microarray expression profile analysis of mRNAs and long non-coding RNAs in pulmonary tuberculosis with different traditional Chinese medicine syndromes. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2016; 16:472. [PMID: 27855662 PMCID: PMC5114807 DOI: 10.1186/s12906-016-1436-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 10/27/2016] [Indexed: 02/04/2023]
Abstract
Background Combination chemotherapy with Western anti-tuberculosis (TB) drugs is the mainstay of TB treatment. Chinese herbal medicines with either heat clearing and detoxifying effects or nourishing Yin and reducing fire effects have been used to treat TB based on the Traditional Chinese Medicine (TCM) syndromes of TB patients. This study analyzed the expression profiles of long non-coding RNAs (lncRNAs) and mRNAs in TB patients with different TCM syndromes. Methods TB patients were classified as pulmonary Yin deficiency (PYD) syndrome, hyperactivity of fire due to Yin deficiency (HFYD) syndrome, and deficiency of Qi and Yin (DQY) syndrome. Total RNA from 44 TB patients and healthy controls was extracted and hybridized with a human lncRNA microarray containing 30586 lncRNAs and 26109 mRNAs probes. Bioinformatics analyses, including gene ontology (GO) and pathways, were performed. Related clinical data were also analyzed. Results Differentially expressed mRNAs and lncRNAs were identified (fold change >2, and P < 0.05) in PYD (634 mRNAs and 566 lncRNAs), HFYD (47 mRNAs and 55 lncRNAs), and DQY (63 mRNAs and 60 lncRNAs) patients. The most enriched pathways were the hippo signaling pathway (P = 0.000164) and the protein digestion and absorption pathway (P = 5.89017E-05). Clinical analyses revealed that the lipid indexes of TB patients were abnormal and that the triglyceride concentration was significantly higher in DQY patients (P = 0.0252). Our study is the first to acquire the microarray expression profiles of lncRNAs and mRNAs and analyze pathway enrichment in PYD, HFYD, and DQY patients with TB. Conclusions Our analyses of the expression profiles of lncRNAs and mRNAs may represent a novel method to explore the biological essence of TCM syndromes of TB. Electronic supplementary material The online version of this article (doi:10.1186/s12906-016-1436-y) contains supplementary material, which is available to authorized users.
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38
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Vongsangnak W, Chumnanpuen P, Sriboonlert A. Transcriptome analysis reveals candidate genes involved in luciferin metabolism in Luciola aquatilis (Coleoptera: Lampyridae). PeerJ 2016; 4:e2534. [PMID: 27761329 PMCID: PMC5068357 DOI: 10.7717/peerj.2534] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/06/2016] [Indexed: 12/31/2022] Open
Abstract
Bioluminescence, which living organisms such as fireflies emit light, has been studied extensively for over half a century. This intriguing reaction, having its origins in nature where glowing insects can signal things such as attraction or defense, is now widely used in biotechnology with applications of bioluminescence and chemiluminescence. Luciferase, a key enzyme in this reaction, has been well characterized; however, the enzymes involved in the biosynthetic pathway of its substrate, luciferin, remains unsolved at present. To elucidate the luciferin metabolism, we performed a de novo transcriptome analysis using larvae of the firefly species, Luciola aquatilis. Here, a comparative analysis is performed with the model coleopteran insect Tribolium casteneum to elucidate the metabolic pathways in L. aquatilis. Based on a template luciferin biosynthetic pathway, combined with a range of protein and pathway databases, and various prediction tools for functional annotation, the candidate genes, enzymes, and biochemical reactions involved in luciferin metabolism are proposed for L. aquatilis. The candidate gene expression is validated in the adult L. aquatilis using reverse transcription PCR (RT-PCR). This study provides useful information on the bio-production of luciferin in the firefly and will benefit to future applications of the valuable firefly bioluminescence system.
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Affiliation(s)
- Wanwipa Vongsangnak
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Pramote Chumnanpuen
- Department of Zoology, Kasetsart University, Bangkok, Thailand; Computational Biomodelling Laboratory for Agricultural Science and Technology (CBLAST), Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Ajaraporn Sriboonlert
- Department of Genetics, Kasetsart University, Bangkok, Thailand; Centre for Advanced Studies in Tropical Natural Resources, Kasetsart University, Bangkok, Thailand
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39
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Ratman D, Mylka V, Bougarne N, Pawlak M, Caron S, Hennuyer N, Paumelle R, De Cauwer L, Thommis J, Rider MH, Libert C, Lievens S, Tavernier J, Staels B, De Bosscher K. Chromatin recruitment of activated AMPK drives fasting response genes co-controlled by GR and PPARα. Nucleic Acids Res 2016; 44:10539-10553. [PMID: 27576532 PMCID: PMC5159533 DOI: 10.1093/nar/gkw742] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Revised: 08/08/2016] [Accepted: 08/15/2016] [Indexed: 12/21/2022] Open
Abstract
Adaptation to fasting involves both Glucocorticoid Receptor (GRα) and Peroxisome Proliferator-Activated Receptor α (PPARα) activation. Given both receptors can physically interact we investigated the possibility of a genome-wide cross-talk between activated GR and PPARα, using ChIP- and RNA-seq in primary hepatocytes. Our data reveal extensive chromatin co-localization of both factors with cooperative induction of genes controlling lipid/glucose metabolism. Key GR/PPAR co-controlled genes switched from transcriptional antagonism to cooperativity when moving from short to prolonged hepatocyte fasting, a phenomenon coinciding with gene promoter recruitment of phosphorylated AMP-activated protein kinase (AMPK) and blocked by its pharmacological inhibition. In vitro interaction studies support trimeric complex formation between GR, PPARα and phospho-AMPK. Long-term fasting in mice showed enhanced phosphorylation of liver AMPK and GRα Ser211. Phospho-AMPK chromatin recruitment at liver target genes, observed upon prolonged fasting in mice, is dampened by refeeding. Taken together, our results identify phospho-AMPK as a molecular switch able to cooperate with nuclear receptors at the chromatin level and reveal a novel adaptation mechanism to prolonged fasting.
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Affiliation(s)
- Dariusz Ratman
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Viacheslav Mylka
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Nadia Bougarne
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Michal Pawlak
- UNIV LILLE, 59000 Lille, France.,INSERM UMR 1011, 59000 Lille, France.,European Genomic Institute for Diabetes E.G.I.D., FR 3508, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Sandrine Caron
- UNIV LILLE, 59000 Lille, France.,INSERM UMR 1011, 59000 Lille, France.,European Genomic Institute for Diabetes E.G.I.D., FR 3508, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Nathalie Hennuyer
- UNIV LILLE, 59000 Lille, France.,INSERM UMR 1011, 59000 Lille, France.,European Genomic Institute for Diabetes E.G.I.D., FR 3508, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Réjane Paumelle
- UNIV LILLE, 59000 Lille, France.,INSERM UMR 1011, 59000 Lille, France.,European Genomic Institute for Diabetes E.G.I.D., FR 3508, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France
| | - Lode De Cauwer
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Jonathan Thommis
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium.,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
| | - Mark H Rider
- de Duve Institute and Université catholique de Louvain, 1200 Brussels, Belgium
| | - Claude Libert
- Inflammation Research Center, VIB, 9052 Ghent, Belgium.,Department of Biomedical Molecular Biology, Ghent University, 9052 Ghent, Belgium
| | - Sam Lievens
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.,Receptor Research Laboratories, Cytokine Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium
| | - Jan Tavernier
- Department of Biochemistry, Ghent University, 9000 Ghent, Belgium.,Receptor Research Laboratories, Cytokine Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium
| | - Bart Staels
- UNIV LILLE, 59000 Lille, France.,INSERM UMR 1011, 59000 Lille, France.,European Genomic Institute for Diabetes E.G.I.D., FR 3508, 59000 Lille, France.,Institut Pasteur de Lille, 59000 Lille, France.,CHU Lille, Department of Biology, 59000 Lille, France
| | - Karolien De Bosscher
- Receptor Research Laboratories, Nuclear Receptor Lab, Medical Biotechnology Center, VIB, 9000 Ghent, Belgium .,Department of Biochemistry, Ghent University, 9000 Ghent, Belgium
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Navia-Paldanius D, Patel JZ, López Navarro M, Jakupović H, Goffart S, Pasonen-Seppänen S, Nevalainen TJ, Jääskeläinen T, Laitinen T, Laitinen JT, Savinainen JR. Chemoproteomic, biochemical and pharmacological approaches in the discovery of inhibitors targeting human α/β-hydrolase domain containing 11 (ABHD11). Eur J Pharm Sci 2016; 93:253-63. [PMID: 27544863 DOI: 10.1016/j.ejps.2016.08.031] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 07/28/2016] [Accepted: 08/16/2016] [Indexed: 10/21/2022]
Abstract
ABHD11 (α/β-hydrolase domain containing 11) is a non-annotated enzyme belonging to the family of metabolic serine hydrolases (mSHs). Its natural substrates and products are unknown. Using competitive activity-based protein profiling (ABPP) to identify novel inhibitors of human (h)ABHD11, three compounds from our chemical library exhibited low nanomolar potency towards hABHD11. Competitive ABPP of various proteomes revealed fatty acid amide hydrolase (FAAH) as the sole off-target among the mSHs. Our fluorescent activity assays designed for natural lipase substrates revealed no activity of hABHD11 towards mono- or diacylglycerols. A broader profiling using para-nitrophenyl (pNP)-linked substrates indicated no amidase/protease, phosphatase, sulfatase, phospholipase C or phosphodiesterase activity. Instead, hABHD11 readily utilized para-nitrophenyl butyrate (pNPC4), indicating lipase/esterase-type activity that could be exploited in inhibitor discovery. Additionally, a homology model was created based on the crystal structure of bacterial esterase YbfF. In contrast to YbfF, which reportedly hydrolyze long-chain acyl-CoA, hABHD11 did not utilize oleoyl-CoA or arachidonoyl-CoA. In conclusion, the present study reports the discovery of potent hABHD11 inhibitors with good selectivity among mSHs. We developed substrate-based activity assays for hABHD11 that could be further exploited in inhibitor discovery and created the first homology-based hABHD11 model, offering initial insights into the active site of this poorly characterized enzyme.
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Affiliation(s)
- Dina Navia-Paldanius
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland.
| | - Jayendra Z Patel
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Miriam López Navarro
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Hermina Jakupović
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Steffi Goffart
- Department of Biology, University of Eastern Finland, P.O Box 111, 80101 Joensuu, Finland
| | - Sanna Pasonen-Seppänen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tapio J Nevalainen
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tiina Jääskeläinen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland; Institute of Dentistry, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Tuomo Laitinen
- School of Pharmacy, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Jarmo T Laitinen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
| | - Juha R Savinainen
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, P.O Box 1627, 70211 Kuopio, Finland
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Jiang P, Vegge A, Thymann T, Wan JMF, Sangild PT. Glucagon-Like Peptide 2 Stimulates Postresection Intestinal Adaptation in Preterm Pigs by Affecting Proteins Related to Protein, Carbohydrate, and Sulphur Metabolism. JPEN J Parenter Enteral Nutr 2016; 41:1293-1300. [DOI: 10.1177/0148607116662971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pingping Jiang
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- School of Biological Sciences, The University of Hong Kong, Hong Kong, China
| | - Andreas Vegge
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
- Global Research, Novo Nordisk, Måløv, Denmark
| | - Thomas Thymann
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Per Torp Sangild
- Department of Veterinary Clinical and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
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Rai S, Bhatnagar S. Hyperlipidemia, Disease Associations, and Top 10 Potential Drug Targets: A Network View. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2016; 20:152-68. [DOI: 10.1089/omi.2015.0172] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Sneha Rai
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Computational and Structural Biology Laboratory, Division of Biotechnology, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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Metzger J, Karwath M, Tonda R, Beltran S, Águeda L, Gut M, Gut IG, Distl O. Runs of homozygosity reveal signatures of positive selection for reproduction traits in breed and non-breed horses. BMC Genomics 2015; 16:764. [PMID: 26452642 PMCID: PMC4600213 DOI: 10.1186/s12864-015-1977-3] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2015] [Accepted: 10/03/2015] [Indexed: 11/24/2022] Open
Abstract
Background Modern horses represent heterogeneous populations specifically selected for appearance and performance. Genomic regions under high selective pressure show characteristic runs of homozygosity (ROH) which represent a low genetic diversity. This study aims at detecting the number and functional distribution of ROHs in different horse populations using next generation sequencing data. Methods Next generation sequencing was performed for two Sorraia, one Dülmen Horse, one Arabian, one Saxon-Thuringian Heavy Warmblood, one Thoroughbred and four Hanoverian. After quality control reads were mapped to the reference genome EquCab2.70. ROH detection was performed using PLINK, version 1.07 for a trimmed dataset with 11,325,777 SNPs and a mean read depth of 12. Stretches with homozygous genotypes of >40 kb as well as >400 kb were defined as ROHs. SNPs within consensus ROHs were tested for neutrality. Functional classification was done for genes annotated within ROHs using PANTHER gene list analysis and functional variants were tested for their distribution among breed or non-breed groups. Results ROH detection was performed using whole genome sequences of ten horses of six populations representing various breed types and non-breed horses. In total, an average number of 3492 ROHs were detected in windows of a minimum of 50 consecutive homozygous SNPs and an average number of 292 ROHs in windows of 500 consecutive homozygous SNPs. Functional analyses of private ROHs in each horse revealed a high frequency of genes affecting cellular, metabolic, developmental, immune system and reproduction processes. In non-breed horses, 198 ROHs in 50-SNP windows and seven ROHs in 500-SNP windows showed an enrichment of genes involved in reproduction, embryonic development, energy metabolism, muscle and cardiac development whereas all seven breed horses revealed only three common ROHs in 50-SNP windows harboring the fertility-related gene YES1. In the Hanoverian, a total of 18 private ROHs could be shown to be located in the region of genes potentially involved in neurologic control, signaling, glycogen balance and reproduction. Comparative analysis of homozygous stretches common in all ten horses displayed three ROHs which were all located in the region of KITLG, the ligand of KIT known to be involved in melanogenesis, haematopoiesis and gametogenesis. Conclusions The results of this study give a comprehensive insight into the frequency and number of ROHs in various horses and their potential influence on population diversity and selection pressures. Comparisons of breed and non-breed horses suggest a significant artificial as well as natural selection pressure on reproduction performance in all types of horse populations. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1977-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany.
| | - Matthias Karwath
- Lower Saxony State Office for the Environment, Agriculture and Geology, Unit 74, Animal Breeding and Hygiene, Schlossallee 1, 01468, Moritzburg, Germany.
| | - Raul Tonda
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain.
| | - Sergi Beltran
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain.
| | - Lídia Águeda
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain.
| | - Marta Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain.
| | - Ivo Glynne Gut
- Centro Nacional de Análisis Genómico, Parc Científic de Barcelona, Torre I Baldiri Reixac, 4, 08028, Barcelona, Spain.
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany.
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Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS. Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project. JAMA Neurol 2015; 72:781-8. [PMID: 25961151 PMCID: PMC4673986 DOI: 10.1001/jamaneurol.2015.0582] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
IMPORTANCE Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk. OBJECTIVE To investigate the contribution of rare and common genetic variants to ischemic stroke risk by targeting the protein-coding regions of the human genome. DESIGN, SETTING, AND PARTICIPANTS The National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) analyzed approximately 6000 participants from numerous cohorts of European and African ancestry. For discovery, 365 cases of ischemic stroke (small-vessel and large-vessel subtypes) and 809 European ancestry controls were sequenced; for replication, 47 affected sibpairs concordant for stroke subtype and an African American case-control series were sequenced, with 1672 cases and 4509 European ancestry controls genotyped. The ESP's exome sequencing and genotyping started on January 1, 2010, and continued through June 30, 2012. Analyses were conducted on the full data set between July 12, 2012, and July 13, 2013. MAIN OUTCOMES AND MEASURES Discovery of new variants or genes contributing to ischemic stroke risk and subtype (primary analysis) and determination of support for protein-coding variants contributing to risk in previously published candidate genes (secondary analysis). RESULTS We identified 2 novel genes associated with an increased risk of ischemic stroke: a protein-coding variant in PDE4DIP (rs1778155; odds ratio, 2.15; P = 2.63 × 10(-8)) with an intracellular signal transduction mechanism and in ACOT4 (rs35724886; odds ratio, 2.04; P = 1.24 × 10(-7)) with a fatty acid metabolism; confirmation of PDE4DIP was observed in affected sibpair families with large-vessel stroke subtype and in African Americans. Replication of protein-coding variants in candidate genes was observed for 2 previously reported GWAS associations: ZFHX3 (cardioembolic stroke) and ABCA1 (large-vessel stroke). CONCLUSIONS AND RELEVANCE Exome sequencing discovered 2 novel genes and mechanisms, PDE4DIP and ACOT4, associated with increased risk for ischemic stroke. In addition, ZFHX3 and ABCA1 were discovered to have protein-coding variants associated with ischemic stroke. These results suggest that genetic variation in novel pathways contributes to ischemic stroke risk and serves as a target for prediction, prevention, and therapy.
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Affiliation(s)
- Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee2Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | - W T Longstreth
- Department of Neurology, University of Washington, Seattle
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathleen M Burger
- Department of Neurology, George Washington University Hospital, Washington, DC
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cara L Carty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Myriam Fornage
- Institute for Molecular Medicine, University of Texas Health Science Center, Houston
| | - John Hardy
- Department of Neuroscience, Reta Lila Weston Institute, University College London, London, England
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Rebecca D Jackson
- Department of Internal Medicine, The Ohio State University, Columbus
| | - Gail P Jarvik
- Department of Medicine, University of Washington, Seattle
| | - Daniel S Kim
- Department of Genome Sciences, University of Washington, Seattle
| | | | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Aaron R Quinlan
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
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Yevglevskis M, Bowskill CR, Chan CCY, Heng JHJ, Threadgill MD, Woodman TJ, Lloyd MD. A study on the chiral inversion of mandelic acid in humans. Org Biomol Chem 2015; 12:6737-44. [PMID: 25050409 DOI: 10.1039/c3ob42515k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mandelic acid is a chiral metabolite of the industrial pollutant styrene and is used in chemical skin peels, as a urinary antiseptic and as a component of other medicines. In humans, S-mandelic acid undergoes rapid chiral inversion to R-mandelic acid by an undefined pathway but it has been proposed to proceed via the acyl-CoA esters, S- and R-2-hydroxy-2-phenylacetyl-CoA, in an analogous pathway to that for Ibuprofen. This study investigates chiral inversion of mandelic acid using purified human recombinant enzymes known to be involved in the Ibuprofen chiral inversion pathway. Both S- and R-2-hydroxy-2-phenylacetyl-CoA were hydrolysed to mandelic acid by human acyl-CoA thioesterase-1 and -2 (ACOT1 and ACOT2), consistent with a possible role in the chiral inversion pathway. However, human α-methylacyl-CoA racemase (AMACR; P504S) was not able to catalyse exchange of the α-proton of S- and R-2-hydroxy-2-phenylacetyl-CoA, a requirement for chiral inversion. Both S- and R-2-phenylpropanoyl-CoA were epimerised by AMACR, showing that it is the presence of the hydroxy group that prevents epimerisation of R- and S-2-hydroxy-2-phenylacetyl-CoAs. The results show that it is unlikely that 2-hydroxy-2-phenylacetyl-CoA is an intermediate in the chiral inversion of mandelic acid, and that the chiral inversion of mandelic acid is via a different pathway to that of Ibuprofen and related drugs.
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Affiliation(s)
- Maksims Yevglevskis
- Medicinal Chemistry, Department of Pharmacy & Pharmacology, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.
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Ellis JM, Bowman CE, Wolfgang MJ. Metabolic and tissue-specific regulation of acyl-CoA metabolism. PLoS One 2015; 10:e0116587. [PMID: 25760036 PMCID: PMC4356623 DOI: 10.1371/journal.pone.0116587] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 12/11/2014] [Indexed: 01/22/2023] Open
Abstract
Acyl-CoA formation initiates cellular fatty acid metabolism. Acyl-CoAs are generated by the ligation of a fatty acid to Coenzyme A mediated by a large family of acyl-CoA synthetases (ACS). Conversely, acyl-CoAs can be hydrolyzed by a family of acyl-CoA thioesterases (ACOT). Here, we have determined the transcriptional regulation of all ACS and ACOT enzymes across tissues and in response to metabolic perturbations. We find patterns of coordinated regulation within and between these gene families as well as distinct regulation occurring in a tissue- and physiologically-dependent manner. Due to observed changes in long-chain ACOT mRNA and protein abundance in liver and adipose tissue, we determined the consequence of increasing cytosolic long-chain thioesterase activity on fatty acid metabolism in these tissues by generating transgenic mice overexpressing a hyperactive mutant of Acot7 in the liver or adipose tissue. Doubling cytosolic acyl-CoA thioesterase activity failed to protect mice from diet-induced obesity, fatty liver or insulin resistance, however, overexpression of Acot7 in adipocytes rendered mice cold intolerant. Together, these data suggest distinct modes of regulation of the ACS and ACOT enzymes and that these enzymes act in a coordinated fashion to control fatty acid metabolism in a tissue-dependent manner.
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Affiliation(s)
- Jessica M. Ellis
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Center for Metabolism and Obesity Research, Baltimore, Maryland 21205 United States of America
| | - Caitlyn E. Bowman
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Center for Metabolism and Obesity Research, Baltimore, Maryland 21205 United States of America
| | - Michael J. Wolfgang
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Center for Metabolism and Obesity Research, Baltimore, Maryland 21205 United States of America
- * E-mail:
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47
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Baldoceda L, Gagné D, Ferreira CR, Robert C. Genetic influence on the reduction in bovine embryo lipid content by l-carnitine. Reprod Fertil Dev 2015; 28:RD14215. [PMID: 25568931 DOI: 10.1071/rd14215] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 12/02/2014] [Indexed: 02/28/2024] Open
Abstract
The decreased rate of pregnancy obtained in cattle using frozen in vitro embryos compared with in vivo embryos has been associated with over-accumulation of intracellular lipid, which causes cell damage during cryopreservation. It is believed that the higher lipid content of blastomeres of bovine embryos produced in vitro results in darker-coloured cytoplasm, which could be a consequence of impaired mitochondrial function. In this study, l-carnitine was used as a treatment to reduce embryonic lipid content by increasing metabolism in cultured bovine embryos. We have observed previously that in vivo embryos of different dairy breeds collected from cows housed and fed under the same conditions differed in lipid content and metabolism. As such, breed effects between Holstein and Jersey were also examined in terms of general appearance, lipid composition, mitochondrial activity and gene expression. Adding l-carnitine to the embryo culture medium reduced the lipid content in both breeds due to increased mitochondrial activity. The response to l-carnitine was weaker in Jersey than in Holstein embryos. Our results thus show that genetics influence the response of bovine embryos to stimulation of mitochondrial metabolism.
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48
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Shen C, Huo LR, Zhao XL, Wang PR, Zhong N. Novel Interactive Partners of Neuroligin 3: New Aspects for Pathogenesis of Autism. J Mol Neurosci 2014; 56:89-101. [DOI: 10.1007/s12031-014-0470-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 11/17/2014] [Indexed: 12/25/2022]
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Hunt MC, Tillander V, Alexson SEH. Regulation of peroxisomal lipid metabolism: the role of acyl-CoA and coenzyme A metabolizing enzymes. Biochimie 2014; 98:45-55. [PMID: 24389458 DOI: 10.1016/j.biochi.2013.12.018] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 12/19/2013] [Indexed: 12/11/2022]
Abstract
Peroxisomes are nearly ubiquitous organelles involved in a number of metabolic pathways that vary between organisms and tissues. A common metabolic function in mammals is the partial degradation of various (di)carboxylic acids via α- and β-oxidation. While only a small number of enzymes catalyze the reactions of β-oxidation, numerous auxiliary enzymes have been identified to be involved in uptake of fatty acids and cofactors required for β-oxidation, regulation of β-oxidation and transport of metabolites across the membrane. These proteins include membrane transporters/channels, acyl-CoA thioesterases, acyl-CoA:amino acid N-acyltransferases, carnitine acyltransferases and nudix hydrolases. Here we review the current view of the role of these auxiliary enzymes in peroxisomal lipid metabolism and propose that they function in concert to provide a means to regulate fatty acid metabolism and transport of products across the peroxisomal membrane.
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Affiliation(s)
- Mary C Hunt
- Dublin Institute of Technology, College of Sciences & Health, School of Biological Sciences, Kevin Street, Dublin 8, Ireland.
| | - Veronika Tillander
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska University Hospital, SE 141 86, Stockholm, Sweden
| | - Stefan E H Alexson
- Karolinska Institutet, Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska University Hospital, SE 141 86, Stockholm, Sweden
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50
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Tillander V, Arvidsson Nordström E, Reilly J, Strozyk M, Van Veldhoven PP, Hunt MC, Alexson SEH. Acyl-CoA thioesterase 9 (ACOT9) in mouse may provide a novel link between fatty acid and amino acid metabolism in mitochondria. Cell Mol Life Sci 2014; 71:933-48. [PMID: 23864032 PMCID: PMC11114068 DOI: 10.1007/s00018-013-1422-1] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2013] [Revised: 06/13/2013] [Accepted: 07/04/2013] [Indexed: 02/03/2023]
Abstract
Acyl-CoA thioesterase (ACOT) activities are found in prokaryotes and in several compartments of eukaryotes where they hydrolyze a wide range of acyl-CoA substrates and thereby regulate intracellular acyl-CoA/CoA/fatty acid levels. ACOT9 is a mitochondrial ACOT with homologous genes found from bacteria to humans and in this study we have carried out an in-depth kinetic characterization of ACOT9 to determine its possible physiological function. ACOT9 showed unusual kinetic properties with activity peaks for short-, medium-, and saturated long-chain acyl-CoAs with highest V max with propionyl-CoA and (iso) butyryl-CoA while K cat/K m was highest with saturated long-chain acyl-CoAs. Further characterization of the short-chain acyl-CoA activity revealed that ACOT9 also hydrolyzes a number of short-chain acyl-CoAs and short-chain methyl-branched CoA esters that suggest a role for ACOT9 in regulation also of amino acid metabolism. In spite of markedly different K ms, ACOT9 can hydrolyze both short- and long-chain acyl-CoAs simultaneously, indicating that ACOT9 may provide a novel regulatory link between fatty acid and amino acid metabolism in mitochondria. Based on similar acyl-CoA chain-length specificities of recombinant ACOT9 and ACOT activity in mouse brown adipose tissue and kidney mitochondria, we conclude that ACOT9 is the major mitochondrial ACOT hydrolyzing saturated C2-C20-CoA in these tissues. Finally, ACOT9 activity is strongly regulated by NADH and CoA, suggesting that mitochondrial metabolic state regulates the function of ACOT9.
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Affiliation(s)
- Veronika Tillander
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Elisabet Arvidsson Nordström
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Jenny Reilly
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Malgorzata Strozyk
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
| | - Paul P. Van Veldhoven
- Department of Cellular and Molecular Medicine, LIPIT, Campus Gasthuisberg, Katholieke Universiteit Leuven, Herestraat, Leuven, Belgium
| | - Mary C. Hunt
- Dublin Institute of Technology, School of Biological Sciences, Kevin Street, Dublin 8, Ireland
| | - Stefan E. H. Alexson
- Department of Laboratory Medicine, Division of Clinical Chemistry, Karolinska Institutet, C1-74, Karolinska University Hospital, SE-141 86 Stockholm, Sweden
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