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Gerber M, Suppanz I, Oeljeklaus S, Niemann M, Käser S, Warscheid B, Schneider A, Dewar CE. A Msp1-containing complex removes orphaned proteins in the mitochondrial outer membrane of T. brucei. Life Sci Alliance 2023; 6:e202302004. [PMID: 37586887 PMCID: PMC10432679 DOI: 10.26508/lsa.202302004] [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: 02/22/2023] [Revised: 07/27/2023] [Accepted: 07/31/2023] [Indexed: 08/18/2023] Open
Abstract
The AAA-ATPase Msp1 extracts mislocalised outer membrane proteins and thus contributes to mitochondrial proteostasis. Using pulldown experiments, we show that trypanosomal Msp1 localises to both glycosomes and the mitochondrial outer membrane, where it forms a complex with four outer membrane proteins. The trypanosome-specific pATOM36 mediates complex assembly of α-helically anchored mitochondrial outer membrane proteins such as protein translocase subunits. Inhibition of their assembly triggers a pathway that results in the proteasomal digestion of unassembled substrates. Using inducible single, double, and triple RNAi cell lines combined with proteomic analyses, we demonstrate that not only Msp1 but also the trypanosomal homolog of the AAA-ATPase VCP are implicated in this quality control pathway. Moreover, in the absence of VCP three out of the four Msp1-interacting mitochondrial proteins are required for efficient proteasomal digestion of pATOM36 substrates, suggesting they act in concert with Msp1. pATOM36 is a functional analog of the yeast mitochondrial import complex complex and possibly of human mitochondrial animal-specific carrier homolog 2, suggesting that similar mitochondrial quality control pathways linked to Msp1 might also exist in yeast and humans.
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Affiliation(s)
- Markus Gerber
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Ida Suppanz
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
| | - Silke Oeljeklaus
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - Moritz Niemann
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Sandro Käser
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Bettina Warscheid
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany
- Faculty of Chemistry and Pharmacy, Biochemistry II, Theodor Boveri-Institute, University of Würzburg, Würzburg, Germany
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
- Institute for Advanced Study (Wissenschaftskolleg) Berlin, Berlin, Germany
| | - Caroline E Dewar
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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2
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Dutta D, Kanca O, Byeon SK, Marcogliese PC, Zuo Z, Shridharan RV, Park JH, Lin G, Ge M, Heimer G, Kohler JN, Wheeler MT, Kaipparettu BA, Pandey A, Bellen HJ. A defect in mitochondrial fatty acid synthesis impairs iron metabolism and causes elevated ceramide levels. Nat Metab 2023; 5:1595-1614. [PMID: 37653044 PMCID: PMC11151872 DOI: 10.1038/s42255-023-00873-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Accepted: 07/21/2023] [Indexed: 09/02/2023]
Abstract
In most eukaryotic cells, fatty acid synthesis (FAS) occurs in the cytoplasm and in mitochondria. However, the relative contribution of mitochondrial FAS (mtFAS) to the cellular lipidome is not well defined. Here we show that loss of function of Drosophila mitochondrial enoyl coenzyme A reductase (Mecr), which is the enzyme required for the last step of mtFAS, causes lethality, while neuronal loss of Mecr leads to progressive neurodegeneration. We observe a defect in Fe-S cluster biogenesis and increased iron levels in flies lacking mecr, leading to elevated ceramide levels. Reducing the levels of either iron or ceramide suppresses the neurodegenerative phenotypes, indicating an interplay between ceramide and iron metabolism. Mutations in human MECR cause pediatric-onset neurodegeneration, and we show that human-derived fibroblasts display similar elevated ceramide levels and impaired iron homeostasis. In summary, this study identifies a role of mecr/MECR in ceramide and iron metabolism, providing a mechanistic link between mtFAS and neurodegeneration.
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Affiliation(s)
- Debdeep Dutta
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Oguz Kanca
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Seul Kee Byeon
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Paul C Marcogliese
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Zhongyuan Zuo
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Rishi V Shridharan
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Jun Hyoung Park
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Guang Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Ming Ge
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA
| | - Gali Heimer
- Pediatric Neurology Unit, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Ramat Gan, Israel
- The Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jennefer N Kohler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew T Wheeler
- Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Benny A Kaipparettu
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
- Manipal Academy of Higher Education, Manipal, India
| | - Hugo J Bellen
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
- Jan and Dan Duncan Neurological Research Institute, Texas Children's Hospital, Houston, TX, USA.
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3
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Xiao PP, Luo BQ, Fan W, Chen XY, Dong ZG, Huang JM, Zhang Y, Chen YQ. Simultaneous Presentation of Multiple Myeloma and Lung Cancer: Case Report and Gene Bioinformatics Analysis. Front Oncol 2022; 12:859735. [PMID: 35769716 PMCID: PMC9235397 DOI: 10.3389/fonc.2022.859735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 12/16/2022] Open
Abstract
Patients diagnosed with more than one cancer generally develop the individual tumors sequentially. There are a few cases of co-occurring multiple myeloma and lung cancer reported in the literature. Here, we report two cases of co-occurring multiple myeloma and lung cancer in patients who presented with the chief complaint of pain. The diagnoses of multiple myeloma and lung cancer were supported by hematologic and biochemical investigations, as well as bone marrow and lung histopathologic examination. We provided suitable interventions for both two patients. The patients are still currently undergoing treatment and followed up closely. We first performed a bioinformatic analysis to determine commonly shared genes and pathways in the two types of cancer types. Fortunately, we identified the hub gene mitochondrial trans-2-enoyl-CoA reductase (MECR), which was overexpressed in both tumors. Survival analysis correlated higher MECR expression with poorer overall survival. Signaling pathway analysis suggested possible transduction pathways implicated in the co-occurrence of both tumors. The clinical cases combined with bioinformatic analysis may provide insight for the pathogenesis of synchronous tumors.
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Affiliation(s)
- Ping-Ping Xiao
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
- *Correspondence: Ping-Ping Xiao,
| | - Bing-Qing Luo
- Department of Respiratory Oncology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Wei Fan
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Xu-Yan Chen
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Zhi-Gao Dong
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Jin-Mei Huang
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Yi Zhang
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
| | - Yong-Quan Chen
- Department of Hematology and Rheumatology, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, China
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4
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Wang S, Yang C, Pan C, Feng X, Lei Z, Huang J, Wei X, Li F, Ma Y. Identification of key genes and functional enrichment pathways involved in fat deposition in Xinyang buffalo by WGCNA. Gene X 2022; 818:146225. [PMID: 35063576 DOI: 10.1016/j.gene.2022.146225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/06/2021] [Accepted: 01/13/2022] [Indexed: 01/02/2023] Open
Abstract
The Xinyang buffalo is a valuable and endangered domestic heritage resource in the Dabie Mountain region in China. With the increasing mechanization of agriculture, the Xinyang buffalo, mainly used for labor, faces unprecedented challenges. One of the feasible approaches to conserve and expand the species is to transfer Xinyang buffalo from service-use to meat-use, but the main hindrance to this transformation is the inferior meat quality of Xinyang buffalo, which is not popular with consumers. Based on the above, this study was conducted to evaluate the growth performance (n = 120) and slaughter performance (n = 3) of Xinyang buffalo and to measure the amino acid levels of the eye muscle (EM), and assess the meat quality. Later, transcriptome sequencing was performed on the subcutaneous fat of the back at six (n = 3) and 30 months of age (n = 3), together with the excavation of candidate genes associated with fat deposition using the weighted co-expression network analysis (WGCNA) method. The results showed that the slaughter rate of Xinyang buffalo was 43.09%, net meat percentage was 33.04%, the ocular area was 59.16 ± 7.58, the backfat thickness was 1.03 ± 0.16, and meat bone ratio was 3.29. The total amino acid contents were 0.63 g per gram of beef, which contained 0.05 g of essential amino acids, and the three most abundant amino acids were Ser (447.17 mg/g), Asp (29.8 mg/g), and Pro (27.24 mg/g). The WGCNA results showed that six phenotypes measured were significantly correlated with the turquoise module (r > 0.97, P < 0.001), and the genes in these modules were significantly enriched in the pathways related to substance metabolism and energy metabolisms, such as metabolic pathways, citrate cycle, and fatty acid metabolism. Meanwhile, six key candidate genes (FH, MECR, GPI, PANK3, ATP6V1A, PHYH) were identified, which were associated with growth and development, fat deposition, and intra-muscular amino acid levels (P < 0.05). In short, this study provides another feasible way to preserve buffalo and enriches the theory of its molecular genetic breeding.
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Affiliation(s)
- Shuzhe Wang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China; College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Chaoyun Yang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Cuili Pan
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Xue Feng
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Zhaoxiong Lei
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Jieping Huang
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China; State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Xuefeng Wei
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China; College of Life Sciences, Xinyang Normal University, Xinyang 464000, Henan, China
| | - Fen Li
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China
| | - Yun Ma
- Ningxia Key Laboratory of Ruminant Molecular and Cellular Breeding, School of Agriculture, Ningxia University, Yinchuan, China.
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5
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Fairbrother-Browne A, Ali AT, Reynolds RH, Garcia-Ruiz S, Zhang D, Chen Z, Ryten M, Hodgkinson A. Mitochondrial-nuclear cross-talk in the human brain is modulated by cell type and perturbed in neurodegenerative disease. Commun Biol 2021; 4:1262. [PMID: 34737414 PMCID: PMC8569145 DOI: 10.1038/s42003-021-02792-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Accepted: 10/15/2021] [Indexed: 01/13/2023] Open
Abstract
Mitochondrial dysfunction contributes to the pathogenesis of many neurodegenerative diseases. The mitochondrial genome encodes core respiratory chain proteins, but the vast majority of mitochondrial proteins are nuclear-encoded, making interactions between the two genomes vital for cell function. Here, we examine these relationships by comparing mitochondrial and nuclear gene expression across different regions of the human brain in healthy and disease cohorts. We find strong regional patterns that are modulated by cell-type and reflect functional specialisation. Nuclear genes causally implicated in sporadic Parkinson's and Alzheimer's disease (AD) show much stronger relationships with the mitochondrial genome than expected by chance, and mitochondrial-nuclear relationships are highly perturbed in AD cases, particularly through synaptic and lysosomal pathways, potentially implicating the regulation of energy balance and removal of dysfunction mitochondria in the etiology or progression of the disease. Finally, we present MitoNuclearCOEXPlorer, a tool to interrogate key mitochondria-nuclear relationships in multi-dimensional brain data.
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Affiliation(s)
- Aine Fairbrother-Browne
- Institute of Neurology, University College London (UCL), London, UK
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Aminah T Ali
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK
| | - Regina H Reynolds
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK
| | - Sonia Garcia-Ruiz
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - David Zhang
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK
| | - Zhongbo Chen
- Institute of Neurology, University College London (UCL), London, UK
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK
| | - Mina Ryten
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London, WC1E 6BT, UK.
- NIHR Great Ormond Street Hospital Biomedical Research Centre, University College London, London, UK.
| | - Alan Hodgkinson
- Department of Medical and Molecular Genetics, School of Basic and Medical Biosciences, King's College London, London, UK.
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6
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Bakhtiarizadeh MR, Alamouti AA. RNA-Seq based genetic variant discovery provides new insights into controlling fat deposition in the tail of sheep. Sci Rep 2020; 10:13525. [PMID: 32782325 PMCID: PMC7419499 DOI: 10.1038/s41598-020-70527-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/27/2020] [Indexed: 01/09/2023] Open
Abstract
Genetic basis of fat deposition in sheep tail have not been completely elucidated yet. Understanding the genetic mechanisms controlling fat-tail size can improve breeding strategies to modulate fat deposition. RNA sequencing has made it possible to discover genetic variants that may underlie various phenotypic differences. Hence, to identify genetic variants that are important for describing different fat-tail phenotypes in sheep, RNA sequencing was used for single nucleotide polymorphism (SNP) calling in two Iranian sheep breeds (Lori-Bakhtiari, fat-tailed; n = 4, vs Zel, thin-tailed; n = 4). Using a stringent pipeline, a total of 112,344 known SNPs were genotyped, of which 30,550 and 42,906 SNPs were shared by at least two Lori-Bakhtiari and Zel, respectively. Comparing these SNPs showed 2,774 (including 209 missense and 25 deleterious SNPs) and 10,470 (including 1,054 missense and 116 deleterious SNPs) breed-specific SNPs in Lori-Bakhtiari and Zel sheep, respectively. Potential breed-specific SNPs were detected by considering those located in QTL regions associated with fatness or reported as important candidates in previous similar studies. Of the breed-specific SNPs, 724 and 2,905 were located in the QTL regions. Functional enrichment analysis of the affected genes revealed several enriched gene ontologies and KEGG pathways related to fat metabolism. Based on the results, several affected genes were proposed to be strongly linked with fat deposition such as DGAT2, ACSL1, ACACA, ADIPOQ, ACLY, FASN, CPT2, SCD, ADCY6, PER3, CSF1R, SLC22A4, GFPT1, CDS2, BMP6, ACSS2, ELOVL6, HOXA10 and FABP4. Moreover, several SNPs were found in the candidate genes related to fatty acid oxidation introducing them as promising candidates responsible for lower fat content in tail of Zel. Our findings provided new insights into the genetic mechanisms of fat deposition in sheep, which can serve to designing appropriate breeding programs.
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Affiliation(s)
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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7
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Kastaniotis AJ, Autio KJ, R Nair R. Mitochondrial Fatty Acids and Neurodegenerative Disorders. Neuroscientist 2020; 27:143-158. [PMID: 32644907 DOI: 10.1177/1073858420936162] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Fatty acids in mitochondria, in sensu stricto, arise either as β-oxidation substrates imported via the carnitine shuttle or through de novo synthesis by the mitochondrial fatty acid synthesis (mtFAS) pathway. Defects in mtFAS or processes involved in the generation of the mtFAS product derivative lipoic acid (LA), including iron-sulfur cluster synthesis required for functional LA synthase, have emerged only recently as etiology for neurodegenerative disease. Intriguingly, mtFAS deficiencies very specifically affect CNS function, while LA synthesis and attachment defects have a pleiotropic presentation beyond neurodegeneration. Typical mtFAS defect presentations include optical atrophy, as well as basal ganglia defects associated with dystonia. The phenotype display of patients with mtFAS defects can resemble the presentation of disorders associated with coenzyme A (CoA) synthesis. A recent publication links these processes together based on the requirement of CoA for acyl carrier protein maturation. MtFAS defects, CoA synthesis- as well as Fe-S cluster-deficiencies share lack of LA as a common symptom.
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Affiliation(s)
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Remya R Nair
- Mammalian Genetics Unit, MRC Harwell Institute, Oxfordshire, UK
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8
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Yang Y, Wang W, Liu X, Song X, Chai L. Probing the effects of hexavalent chromium exposure on histology and fatty acid metabolism in liver of Bufo gargarizans tadpoles. CHEMOSPHERE 2020; 243:125437. [PMID: 31995885 DOI: 10.1016/j.chemosphere.2019.125437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
Hexavalent chromium is one of the major detrimental heavy metal pollutants. B. gargarizans tadpoles were treated with different concentrations of Cr6+ (0, 13, 52, 104, 208, and 416 μg Cr6+ L-1) from Gs 2 to Gs 42. The effect of Cr6+ on histopathological alterations and transcript levels of fatty acid metabolism-related genes as well as fatty acids composition and content in liver were examined. Histopathological changes were observed in liver at 52, 104, 208, and 416 μg Cr6+ L-1. Moreover, RT-qPCR analyses showed the downregulated mRNA levels of the genes related to fatty acid synthesis (SCD, MECR, TECR and ELOVL1) and fatty acid β-oxidation (ACOT1, PPT1, HADH and ACAA2) at 416 μg Cr6+ L-1. However, the mRNA expression of fatty acid β-oxidation-related genes (ECHS1, HADHA and ACAA1) were significantly upregulated at 13, 52, 104, 208 and 416 μg Cr6+ L-1. In situ hybridization revealed BSEP was expressed in hepatocyte nucleus and plasma membrane, and HSD17B12 was abundantly expressed in the plasma membrane. The HSD17B12 mRNA levels were significantly upregulated in tadpoles exposed to all Cr6+ treatment groups, while the BSEP mRNA levels were downregulated at 104, 208 and 416 μg Cr6+ L-1 groups compared to control. In addition, an increase in polyunsaturated fatty acids and a decrease in monounsaturated fatty acids were found in 52, 104 and 416 μg Cr6+ L-1 groups. Overall, chronic exposure to Cr6+ may suppress fatty acid synthesis, disturb fatty acid β-oxidation, aggravate disorders of hepatic function and induce hepatic impairment in B. gargarizans tadpoles.
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Affiliation(s)
- Yijie Yang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Wenxiang Wang
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Xiaoli Liu
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Xiuling Song
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China
| | - Lihong Chai
- School of Water and Environment, Chang'an University, Xi'an, 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effect in Arid Region of Ministry of Education, Chang'an University, Xi'an, 710054, China.
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9
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Exploration of targets regulated by miR-125b in porcine adipocytes. In Vitro Cell Dev Biol Anim 2020; 56:103-111. [PMID: 31912457 DOI: 10.1007/s11626-019-00427-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 11/25/2019] [Indexed: 12/14/2022]
Abstract
MicroRNA (miRNA) has been proved to play a key role in lipid metabolism. In our previous study, miR-125b was validated to be differentially expressed in preadipocytes and adipocytes, which was also proved to involve in lipid metabolism. To explore the comprehensive targets of miR-125b in adipocytes, isobaric tag for relative and absolute quantitation (iTRAQ) analysis was performed to obtain differentially expressed proteins in adipocytes comparing negative control (NC) and miR-125b mimic, combining with digital gene expression (DGE) profiling of mRNA incorporated into RNA-induced silencing complex (RISC) pulled down by biotinylated miR-125b mimic and targets prediction of miR-125b by three algorithms, acyl-CoA dehydrogenase short chain (ACADS) and mitochondrial trans-2-enoyl-CoA reductase (MECR) were screened out as miR-125b direct targets. Luciferase reporter assay further validated that miR-125b mimic significantly inhibited the luciferase activity by targeting wild type (WT) 3'-UTR compared with NC. qPCR analysis of ACADS and MECR mRNA from adipose tissues of miR-125b knockout (KO) mice further confirmed the inhibition of miR-125b on ACADS and MECR expressions. Here we report miR-125b play a vital role in maintaining homeostasis of fatty acid metabolism by targeting key enzyme ACADS and MECR in the process of fatty acid elongation and degradation.
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10
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Cai Y, Lin Y, Xiong X, Lu J, Zhou R, Jin Y, You Z, Ye H, Li F, Cheng N. Knockdown expression of MECR, a novel gene of mitochondrial FAS II inhibits growth and colony-formation, promotes apoptosis of hepatocelluar carcinoma cells. Biosci Trends 2019; 13:234-244. [PMID: 31178528 DOI: 10.5582/bst.2019.01109] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Mitochondrial trans-2-enoyl-CoA reductase (MECR) is a protein-coding gene, and the protein encoded by this gene is an oxidoreductase that catalyzes the last step in mitochondrial fatty acid synthesis (mtFASII). Numerous studies have shown disorder of lipid metabolism is closely related with malignance, especially in liver cancer. Through pre-experiment, we found that the expression of MECR gene was highly expressed in hepatocelluar carcinoma (HCC) cell lines in vitro. This suggests that the MECR gene may play a role of oncogene in HCC. Therefore, we conducted a preliminary experimental study on the role of MECR gene in HCC cells in vitro. Objective to explore whether the MECR gene can affect the malignant biological behavior of HCC. We selected HCC cell line BEL-7404 as experimental cell, which involves the highest expression of MECR in the pre-experiment. We constructed MECR knockdwon lentivirus vector, and then infected HCC cell lines to down-regulate MECR expression, and establish negative control group (NC). Through various experiments of cytology, our study showed that knockdown of MECR inhibited cell proliferation and colony formation, promoted apoptosis, and inhibited metastasis in HCC cell lines BEL-7404. MECR might serve as a novel gene therapeutic target for the treatment of HCC. Further study is needed to elucidate the signaling pathway through which MECR functions in HCC.
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Affiliation(s)
- Yulong Cai
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Yixin Lin
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Xianze Xiong
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Jiong Lu
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Rongxing Zhou
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Yanwen Jin
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Zhen You
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Hui Ye
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Fuyu Li
- Department of Biliary Surgery, West China Hospital, Sichuan University
| | - Nansheng Cheng
- Department of Biliary Surgery, West China Hospital, Sichuan University
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11
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Genome-wide analysis of Chongqing native intersexual goats using next-generation sequencing. 3 Biotech 2019; 9:99. [PMID: 30800610 DOI: 10.1007/s13205-019-1612-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Accepted: 02/01/2019] [Indexed: 10/27/2022] Open
Abstract
Sex reversal has been studied extensively in vertebrate species, particularly in domestic goats, because polled intersex syndrome (PIS) has seriously affected their production efficiency. In the present study, we used histopathologically diagnosed cases of PIS to identify correlated genomic regions and variants using representative selection signatures and performed GWAS using Restriction-Site Associated Resequencing DNA. We identified 171 single-nucleotide polymorphisms (SNPs) that may have contributed to this phenotype, and 53 SNPs were determined to be located in coding regions using a general linear model. The transcriptome data sets of differentially expressed genes (DEGs) in the pituitary tissues of intersexual and nonintersexual goats were examined using high-throughput technology. A total of 10,063 DEGs and 337 long noncoding RNAs were identified. The DEGs were clustered into 56 GO categories and determined to be significantly enriched in 53 signaling pathways by KEGG analysis. In addition, according to qPCR results, PSPO2 and FSH were significantly more highly expressed in sexually mature pituitary tissues of intersexual goats compared to healthy controls (nonintersexual). These results demonstrate that certain novel potential genomic regions may be responsible for intersexual goats, and the transcriptome data indicate that the regulation of various physiological systems is involved in intersexual goat development. Therefore, these results provide helpful data for understanding the molecular mechanisms of intersex syndrome in goats.
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Yao CH, Liu GY, Wang R, Moon SH, Gross RW, Patti GJ. Identifying off-target effects of etomoxir reveals that carnitine palmitoyltransferase I is essential for cancer cell proliferation independent of β-oxidation. PLoS Biol 2018; 16:e2003782. [PMID: 29596410 PMCID: PMC5892939 DOI: 10.1371/journal.pbio.2003782] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Revised: 04/10/2018] [Accepted: 02/22/2018] [Indexed: 02/06/2023] Open
Abstract
It has been suggested that some cancer cells rely upon fatty acid oxidation (FAO) for energy. Here we show that when FAO was reduced approximately 90% by pharmacological inhibition of carnitine palmitoyltransferase I (CPT1) with low concentrations of etomoxir, the proliferation rate of various cancer cells was unaffected. Efforts to pharmacologically inhibit FAO more than 90% revealed that high concentrations of etomoxir (200 μM) have an off-target effect of inhibiting complex I of the electron transport chain. Surprisingly, however, when FAO was reduced further by genetic knockdown of CPT1, the proliferation rate of these same cells decreased nearly 2-fold and could not be restored by acetate or octanoic acid supplementation. Moreover, CPT1 knockdowns had altered mitochondrial morphology and impaired mitochondrial coupling, whereas cells in which CPT1 had been approximately 90% inhibited by etomoxir did not. Lipidomic profiling of mitochondria isolated from CPT1 knockdowns showed depleted concentrations of complex structural and signaling lipids. Additionally, expression of a catalytically dead CPT1 in CPT1 knockdowns did not restore mitochondrial coupling. Taken together, these results suggest that transport of at least some long-chain fatty acids into the mitochondria by CPT1 may be required for anabolic processes that support healthy mitochondrial function and cancer cell proliferation independent of FAO.
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Affiliation(s)
- Cong-Hui Yao
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gao-Yuan Liu
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Rencheng Wang
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Sung Ho Moon
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Richard W. Gross
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Internal Medicine, Division of Bioorganic and Molecular Pharmacology, Washington University School of Medicine, St. Louis, Missouri, United States of America
| | - Gary J. Patti
- Department of Chemistry, Washington University, St. Louis, Missouri, United States of America
- Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, United States of America
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13
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Tucci S, Mingirulli N, Wehbe Z, Dumit VI, Kirschner J, Spiekerkoetter U. Mitochondrial fatty acid biosynthesis and muscle fiber plasticity in very long-chain acyl-CoA dehydrogenase-deficient mice. FEBS Lett 2018; 592:219-232. [PMID: 29237229 DOI: 10.1002/1873-3468.12940] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/27/2017] [Accepted: 12/04/2017] [Indexed: 12/31/2022]
Abstract
The white skeletal muscle of very long-chain acyl-CoA-dehydrogenase-deficient (VLCAD-/- ) mice undergoes metabolic modification to compensate for defective β-oxidation in a progressive and time-dependent manner by upregulating glucose oxidation. This metabolic regulation seems to be accompanied by morphologic adaptation of muscle fibers toward the glycolytic fiber type II with the concomitant upregulation of mitochondrial fatty acid biosynthesis (mFASII) and lipoic acid biosynthesis. Dietary supplementation of VLCAD-/- mice with different medium-chain triglycerides over 1 year revealed that odd-chain species has no effect on muscle fiber switch, whereas even-chain species inhibit progressive metabolic adaptation. Our study shows that muscle may undergo adaptive mechanisms that are modulated by dietary supplementation. We describe for the first time a concomitant change of mFASII in this muscular adaptation process.
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Affiliation(s)
- Sara Tucci
- Department of General Pediatrics, Center for Paediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, Germany
| | - Nadja Mingirulli
- Department of General Pediatrics, Center for Paediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, Germany
| | - Zeinab Wehbe
- Department of General Pediatrics, Center for Paediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, Germany
| | - Verónica I Dumit
- Core Facility Proteomics, Center for Biological Systems Analysis (ZBSA), University of Freiburg, Germany
| | - Janbernd Kirschner
- Department of Neuropaediatrics, Center for Paediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, Germany
| | - Ute Spiekerkoetter
- Department of General Pediatrics, Center for Paediatrics and Adolescent Medicine, Faculty of Medicine and Medical Centre, University of Freiburg, Germany
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14
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van der Plaat DA, de Jong K, Lahousse L, Faiz A, Vonk JM, van Diemen CC, Nedeljkovic I, Amin N, Obeidat M, van Duijn CM, Boezen HM, Postma DS. The Well-Known Gene HHIP and Novel Gene MECR Are Implicated in Small Airway Obstruction. Am J Respir Crit Care Med 2017; 194:1299-1302. [PMID: 27845578 DOI: 10.1164/rccm.201604-0843le] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Affiliation(s)
- Diana A van der Plaat
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | - Kim de Jong
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | - Lies Lahousse
- 2 Erasmus Medical Center Rotterdam, the Netherlands.,3 Ghent University Hospital Ghent, Belgium and
| | - Alen Faiz
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | - Judith M Vonk
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | - Cleo C van Diemen
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | | | - Najaf Amin
- 2 Erasmus Medical Center Rotterdam, the Netherlands
| | | | | | - H Marike Boezen
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
| | - Dirkje S Postma
- 1 University of Groningen, University Medical Center Groningen, Groningen Research Institute for Asthma and COPD (GRIAC) Groningen, the Netherlands
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15
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Nair RR, Kerätär JM, Autio KJ, Masud AJ, Finnilä MA, Autio-Harmainen HI, Miinalainen IJ, Nieminen PA, Hiltunen JK, Kastaniotis AJ. Genetic modifications of Mecr reveal a role for mitochondrial 2-enoyl-CoA/ACP reductase in placental development in mice. Hum Mol Genet 2017; 26:2104-2117. [DOI: 10.1093/hmg/ddx105] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 03/13/2017] [Indexed: 01/23/2023] Open
Affiliation(s)
- Remya R. Nair
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Juha M. Kerätär
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Kaija J. Autio
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Ali J. Masud
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Mikko A.J. Finnilä
- Department of Applied Physics, University of Eastern Finland, FI-70211 Kuopio, Finland
- Research Unit of Medical Imaging, Physics and Technology, Faculty of Medicine, University of Oulu, FI-90014 Oulu, Finland
| | - Helena I. Autio-Harmainen
- Department of Pathology and Medical Research Center Oulu, Oulu University Hospital, FI-90220 Oulu, Finland
| | - Ilkka J. Miinalainen
- Electron Microscopy Core Facility, Biocenter Oulu, University of Oulu, FI-90014 Oulu, Finland
| | - Pentti A. Nieminen
- Medical Informatics and Statistics Research group, University of Oulu, FI-90014 Oulu, Finland
| | - J. Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, FI-90014 Oulu, Finland
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16
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Heimer G, Kerätär J, Riley L, Balasubramaniam S, Eyal E, Pietikäinen L, Hiltunen JK, Marek-Yagel D, Hamada J, Gregory A, Rogers C, Hogarth P, Nance MA, Shalva N, Veber A, Tzadok M, Nissenkorn A, Tonduti D, Renaldo F, Kraoua I, Panteghini C, Valletta L, Garavaglia B, Cowley MJ, Gayevskiy V, Roscioli T, Silberstein JM, Hoffmann C, Raas-Rothschild A, Tiranti V, Anikster Y, Christodoulou J, Kastaniotis AJ, Ben-Zeev B, Hayflick SJ, Bamshad M, Leal S, Nickerson D, Anderson P, Annable M, Blue E, Buckingham K, Chin J, Chong J, Cornejo R, Davis C, Frazar C, He Z, Jarvik G, Jimenez G, Johanson E, Kolar T, Krauter S, Luksic D, Marvin C, McGee S, McGoldrick D, Patterson K, Perez M, Phillips S, Pijoan J, Robertson P, Santos-Cortez R, Shankar A, Slattery K, Shively K, Siegel D, Smith J, Tackett M, Wang G, Wegener M, Weiss J, Wernick R, Wheeler M, Yi Q. MECR Mutations Cause Childhood-Onset Dystonia and Optic Atrophy, a Mitochondrial Fatty Acid Synthesis Disorder. Am J Hum Genet 2016; 99:1229-1244. [PMID: 27817865 DOI: 10.1016/j.ajhg.2016.09.021] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/26/2016] [Indexed: 11/24/2022] Open
Abstract
Mitochondrial fatty acid synthesis (mtFAS) is an evolutionarily conserved pathway essential for the function of the respiratory chain and several mitochondrial enzyme complexes. We report here a unique neurometabolic human disorder caused by defective mtFAS. Seven individuals from five unrelated families presented with childhood-onset dystonia, optic atrophy, and basal ganglia signal abnormalities on MRI. All affected individuals were found to harbor recessive mutations in MECR encoding the mitochondrial trans-2-enoyl-coenzyme A-reductase involved in human mtFAS. All six mutations are extremely rare in the general population, segregate with the disease in the families, and are predicted to be deleterious. The nonsense c.855T>G (p.Tyr285∗), c.247_250del (p.Asn83Hisfs∗4), and splice site c.830+2_830+3insT mutations lead to C-terminal truncation variants of MECR. The missense c.695G>A (p.Gly232Glu), c.854A>G (p.Tyr285Cys), and c.772C>T (p.Arg258Trp) mutations involve conserved amino acid residues, are located within the cofactor binding domain, and are predicted by structural analysis to have a destabilizing effect. Yeast modeling and complementation studies validated the pathogenicity of the MECR mutations. Fibroblast cell lines from affected individuals displayed reduced levels of both MECR and lipoylated proteins as well as defective respiration. These results suggest that mutations in MECR cause a distinct human disorder of the mtFAS pathway. The observation of decreased lipoylation raises the possibility of a potential therapeutic strategy.
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17
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Kastaniotis AJ, Autio KJ, Kerätär JM, Monteuuis G, Mäkelä AM, Nair RR, Pietikäinen LP, Shvetsova A, Chen Z, Hiltunen JK. Mitochondrial fatty acid synthesis, fatty acids and mitochondrial physiology. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1862:39-48. [PMID: 27553474 DOI: 10.1016/j.bbalip.2016.08.011] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/20/2016] [Accepted: 08/17/2016] [Indexed: 02/07/2023]
Abstract
Mitochondria and fatty acids are tightly connected to a multiplicity of cellular processes that go far beyond mitochondrial fatty acid metabolism. In line with this view, there is hardly any common metabolic disorder that is not associated with disturbed mitochondrial lipid handling. Among other aspects of mitochondrial lipid metabolism, apparently all eukaryotes are capable of carrying out de novo fatty acid synthesis (FAS) in this cellular compartment in an acyl carrier protein (ACP)-dependent manner. The dual localization of FAS in eukaryotic cells raises the questions why eukaryotes have maintained the FAS in mitochondria in addition to the "classic" cytoplasmic FAS and what the products are that cannot be substituted by delivery of fatty acids of extramitochondrial origin. The current evidence indicates that mitochondrial FAS is essential for cellular respiration and mitochondrial biogenesis. Although both β-oxidation and FAS utilize thioester chemistry, CoA acts as acyl-group carrier in the breakdown pathway whereas ACP assumes this role in the synthetic direction. This arrangement metabolically separates these two pathways running towards opposite directions and prevents futile cycling. A role of this pathway in mitochondrial metabolic sensing has recently been proposed. This article is part of a Special Issue entitled: Lipids of Mitochondria edited by Guenther Daum.
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Affiliation(s)
- Alexander J Kastaniotis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland.
| | - Kaija J Autio
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Juha M Kerätär
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Geoffray Monteuuis
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Anne M Mäkelä
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Remya R Nair
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Laura P Pietikäinen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Antonina Shvetsova
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Zhijun Chen
- State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China
| | - J Kalervo Hiltunen
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland; State Key Laboratory of Supramolecular Structure and Materials and Institute of Theoretical Chemistry, Jilin University, 2699 Qianjin Street, Changchun 130012, PR China.
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18
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Clay HB, Parl AK, Mitchell SL, Singh L, Bell LN, Murdock DG. Altering the Mitochondrial Fatty Acid Synthesis (mtFASII) Pathway Modulates Cellular Metabolic States and Bioactive Lipid Profiles as Revealed by Metabolomic Profiling. PLoS One 2016; 11:e0151171. [PMID: 26963735 PMCID: PMC4786287 DOI: 10.1371/journal.pone.0151171] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Accepted: 02/24/2016] [Indexed: 01/10/2023] Open
Abstract
Despite the presence of a cytosolic fatty acid synthesis pathway, mitochondria have retained their own means of creating fatty acids via the mitochondrial fatty acid synthesis (mtFASII) pathway. The reason for its conservation has not yet been elucidated. Therefore, to better understand the role of mtFASII in the cell, we used thin layer chromatography to characterize the contribution of the mtFASII pathway to the fatty acid composition of selected mitochondrial lipids. Next, we performed metabolomic analysis on HeLa cells in which the mtFASII pathway was either hypofunctional (through knockdown of mitochondrial acyl carrier protein, ACP) or hyperfunctional (through overexpression of mitochondrial enoyl-CoA reductase, MECR). Our results indicate that the mtFASII pathway contributes little to the fatty acid composition of mitochondrial lipid species examined. Additionally, loss of mtFASII function results in changes in biochemical pathways suggesting alterations in glucose utilization and redox state. Interestingly, levels of bioactive lipids, including lysophospholipids and sphingolipids, directly correlate with mtFASII function, indicating that mtFASII may be involved in the regulation of bioactive lipid levels. Regulation of bioactive lipid levels by mtFASII implicates the pathway as a mediator of intracellular signaling.
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Affiliation(s)
- Hayley B. Clay
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- Neuroscience Graduate Program, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Angelika K. Parl
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Sabrina L. Mitchell
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Larry Singh
- Center for Mitochondrial and Epigenomic Medicine, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, United States of America
| | - Lauren N. Bell
- Metabolon, Incorporated, Durham, North Carolina, United States of America
| | - Deborah G. Murdock
- Center for Human Genetics Research, Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, Tennessee, United States of America
- * E-mail:
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19
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Jha A, Panzade G, Pandey R, Shankar R. A legion of potential regulatory sRNAs exists beyond the typical microRNAs microcosm. Nucleic Acids Res 2015; 43:8713-24. [PMID: 26354861 PMCID: PMC4605316 DOI: 10.1093/nar/gkv871] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Post ENCODE, regulatory sRNAs (rsRNAs) like miRNAs have established their status as one of the core regulatory elements of cell systems. However, large number of rsRNAs are compromised due to traditional approaches to identify miRNAs, limiting the otherwise vast world of rsRNAs mainly to hair-pin loop bred typical miRNAs. The present study has analyzed for the first time a huge volume of sequencing data from 4997 individuals and 25 cancer types to report 11 234 potentially regulatory small RNAs which appear to have deep reaching impact. The rsRNA-target interactions have been studied and validated extensively using experimental data from AGO-crosslinking, DGCR8 knockdown, CLASH, proteome and expression data. A subset of such interactions was also validated independently in the present study using multiple cell lines, by qPCR. Several of the potential rsRNAs have emerged as a critical cancer biomarker controlling some important spots of cell system. The entire study has been presented into an interactive info-analysis portal handling more than 260 GB of processed data. The possible degree of cell system regulation by sRNAs appears to be much higher than previously assumed.
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Affiliation(s)
- Ashwani Jha
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
| | - Ganesh Panzade
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
| | - Rajesh Pandey
- CSIR Ayurgenomics Unit -TRISUTRA, CSIR-Institute of Genomics & Integrative Biology (CSIR-IGIB), New Delhi, India
| | - Ravi Shankar
- Studio of Computational Biology & Bioinformatics, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur 176061, HP, India Academy of Scientific & Innovative Research, Chennai, India
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20
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Discovery of bacterial fatty acid synthase type II inhibitors using a novel cellular bioluminescent reporter assay. Antimicrob Agents Chemother 2015; 59:5775-87. [PMID: 26169404 DOI: 10.1128/aac.00686-15] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 07/06/2015] [Indexed: 12/11/2022] Open
Abstract
Novel, cellular, gain-of-signal, bioluminescent reporter assays for fatty acid synthesis type II (FASII) inhibitors were constructed in an efflux-deficient strain of Pseudomonas aeruginosa and based on the discovery that FASII genes in P. aeruginosa are coordinately upregulated in response to pathway disruption. A screen of 115,000 compounds identified a series of sulfonamidobenzamide (SABA) analogs, which generated strong luminescent signals in two FASII reporter strains but not in four control reporter strains designed to respond to inhibitors of pathways other than FASII. The SABA analogs selectively inhibited lipid biosynthesis in P. aeruginosa and exhibited minimal cytotoxicity to mammalian cells (50% cytotoxic concentration [CC50] ≥ 80 μM). The most potent SABA analogs had MICs of 0.5 to 7.0 μM (0.2 to 3.0 μg/ml) against an efflux-deficient Escherichia coli (ΔtolC) strain but had no detectable MIC against efflux-proficient E. coli or against P. aeruginosa (efflux deficient or proficient). Genetic, molecular genetic, and biochemical studies revealed that SABA analogs target the enzyme (AccC) catalyzing the biotin carboxylase half-reaction of the acetyl coenzyme A (acetyl-CoA) carboxylase step in the initiation phase of FASII in E. coli and P. aeruginosa. These results validate the capability and the sensitivity of this novel bioluminescent reporter screen to identify inhibitors of E. coli and P. aeruginosa FASII.
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21
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Zhang D, Lu K, Jiang G, Liu W, Dong Z, Tian H, Li X. A global transcriptional analysis of Megalobrama amblycephala revealing the molecular determinants of diet-induced hepatic steatosis. Gene 2015; 570:255-63. [PMID: 26074088 DOI: 10.1016/j.gene.2015.06.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/19/2015] [Accepted: 06/09/2015] [Indexed: 02/07/2023]
Abstract
Blunt snout bream (Megalobrama amblycephala), a prevalent species in China's intensive polyculture systems, is highly susceptible to hepatic steatosis, resulting in considerable losses to the fish farming industry. Due to a lack of genomic resources, the molecular mechanisms of lipid metabolism in M. amblycephala are poorly understood. Here, a hepatic cDNA library was generated from equal amounts of mRNAs isolated from M. amblycephala fed normal-fat and high-fat diets. Sequencing of this library using the Illumina/Solexa platform produced approximately 51.87 million clean reads, which were assembled into 48,439 unigenes with an average length of 596 bp and an N50 value of 800 bp. These unigenes were searched against the nucleotide (NT), non-redundant (NR), Swiss-Prot, Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genome (KEGG) databases using the BLASTn or BLASTx algorithms (E-value ≤ 10(-5)). A total of 8602 unigenes and 22,155 unigenes were functionally classified into 25 COG categories and 259 KEGG pathways, respectively. Furthermore, 22,072 unigenes were grouped into 62 sub-categories belonging to three main Gene Ontology (GO) terms. Using a digital gene expression analysis and the M. amblycephala transcriptome as a reference, 477 genes (134 up-regulated and 343 down-regulated) were identified as differentially expressed in fish fed a high-fat diet versus a normal-fat diet. KEGG and GO functional enrichment analyses of the differentially expressed unigenes were performed and 12 candidate genes related to lipid metabolism were identified. This study provides a global survey of hepatic transcriptome profiles and identifies candidate genes that may be related to lipid metabolism in M. amblycephala. These findings will facilitate further investigations of the mechanisms underlying hepatic steatosis in M. amblycephala.
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Affiliation(s)
- Dingdong Zhang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
| | - Kangle Lu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Guangzhen Jiang
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Wenbin Liu
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Hongyan Tian
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiangfei Li
- Key Laboratory of Aquatic Nutrition and Feed Science of Jiangsu Province, College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
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22
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Weber S, Salabei JK, Möller G, Kremmer E, Bhatnagar A, Adamski J, Barski OA. Aldo-keto Reductase 1B15 (AKR1B15): a mitochondrial human aldo-keto reductase with activity toward steroids and 3-keto-acyl-CoA conjugates. J Biol Chem 2015; 290:6531-45. [PMID: 25577493 DOI: 10.1074/jbc.m114.610121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Aldo-keto reductases (AKRs) comprise a superfamily of proteins involved in the reduction and oxidation of biogenic and xenobiotic carbonyls. In humans, at least 15 AKR superfamily members have been identified so far. One of these is a newly identified gene locus, AKR1B15, which clusters on chromosome 7 with the other human AKR1B subfamily members (i.e. AKR1B1 and AKR1B10). We show that alternative splicing of the AKR1B15 gene transcript gives rise to two protein isoforms with different N termini: AKR1B15.1 is a 316-amino acid protein with 91% amino acid identity to AKR1B10; AKR1B15.2 has a prolonged N terminus and consists of 344 amino acid residues. The two gene products differ in their expression level, subcellular localization, and activity. In contrast with other AKR enzymes, which are mostly cytosolic, AKR1B15.1 co-localizes with the mitochondria. Kinetic studies show that AKR1B15.1 is predominantly a reductive enzyme that catalyzes the reduction of androgens and estrogens with high positional selectivity (17β-hydroxysteroid dehydrogenase activity) as well as 3-keto-acyl-CoA conjugates and exhibits strong cofactor selectivity toward NADP(H). In accordance with its substrate spectrum, the enzyme is expressed at the highest levels in steroid-sensitive tissues, namely placenta, testis, and adipose tissue. Placental and adipose expression could be reproduced in the BeWo and SGBS cell lines, respectively. In contrast, AKR1B15.2 localizes to the cytosol and displays no enzymatic activity with the substrates tested. Collectively, these results demonstrate the existence of a novel catalytically active AKR, which is associated with mitochondria and expressed mainly in steroid-sensitive tissues.
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Affiliation(s)
- Susanne Weber
- From the Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, 85764 Neuherberg, Germany
| | - Joshua K Salabei
- the Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, Kentucky 40202
| | - Gabriele Möller
- From the Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, 85764 Neuherberg, Germany
| | - Elisabeth Kremmer
- the Institute of Molecular Immunology, German Research Center for Environmental Health, Helmholtz Zentrum Muenchen, 81377 Muenchen, Germany
| | - Aruni Bhatnagar
- the Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, Kentucky 40202
| | - Jerzy Adamski
- From the Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, 85764 Neuherberg, Germany, the Lehrstuhl für Experimentelle Genetik, Technische Universitaet Muenchen, 85356 Freising-Weihenstephan, Germany, and the German Center for Diabetes Research, 85764 Neuherberg, Germany
| | - Oleg A Barski
- the Diabetes and Obesity Center, School of Medicine, University of Louisville, Louisville, Kentucky 40202,
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