1
|
Landowski M, Gogoi P, Ikeda S, Ikeda A. Roles of transmembrane protein 135 in mitochondrial and peroxisomal functions - implications for age-related retinal disease. FRONTIERS IN OPHTHALMOLOGY 2024; 4:1355379. [PMID: 38576540 PMCID: PMC10993500 DOI: 10.3389/fopht.2024.1355379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Abstract
Aging is the most significant risk factor for age-related diseases in general, which is true for age-related diseases in the eye including age-related macular degeneration (AMD). Therefore, in order to identify potential therapeutic targets for these diseases, it is crucial to understand the normal aging process and how its mis-regulation could cause age-related diseases at the molecular level. Recently, abnormal lipid metabolism has emerged as one major aspect of age-related symptoms in the retina. Animal models provide excellent means to identify and study factors that regulate lipid metabolism in relation to age-related symptoms. Central to this review is the role of transmembrane protein 135 (TMEM135) in the retina. TMEM135 was identified through the characterization of a mutant mouse strain exhibiting accelerated retinal aging and positional cloning of the responsible mutation within the gene, indicating the crucial role of TMEM135 in regulating the normal aging process in the retina. Over the past decade, the molecular functions of TMEM135 have been explored in various models and tissues, providing insights into the regulation of metabolism, particularly lipid metabolism, through its action in multiple organelles. Studies indicated that TMEM135 is a significant regulator of peroxisomes, mitochondria, and their interaction. Here, we provide an overview of the molecular functions of TMEM135 which is crucial for regulating mitochondria, peroxisomes, and lipids. The review also discusses the age-dependent phenotypes in mice with TMEM135 perturbations, emphasizing the importance of a balanced TMEM135 function for the health of the retina and other tissues including the heart, liver, and adipose tissue. Finally, we explore the potential roles of TMEM135 in human age-related retinal diseases, connecting its functions to the pathobiology of AMD.
Collapse
Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Purnima Gogoi
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
| | - Sakae Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, United States
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, United States
| |
Collapse
|
2
|
Singin Ö, Astapenka A, Costina V, Kühl S, Bonekamp N, Drews O, Islinger M. Analysis of the Mouse Hepatic Peroxisome Proteome-Identification of Novel Protein Constituents Using a Semi-Quantitative SWATH-MS Approach. Cells 2024; 13:176. [PMID: 38247867 PMCID: PMC10814758 DOI: 10.3390/cells13020176] [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: 12/21/2023] [Revised: 01/12/2024] [Accepted: 01/15/2024] [Indexed: 01/23/2024] Open
Abstract
Ongoing technical and bioinformatics improvements in mass spectrometry (MS) allow for the identifying and quantifying of the enrichment of increasingly less-abundant proteins in individual fractions. Accordingly, this study reassessed the proteome of mouse liver peroxisomes by the parallel isolation of peroxisomes from a mitochondria- and a microsome-enriched prefraction, combining density-gradient centrifugation with a semi-quantitative SWATH-MS proteomics approach to unveil novel peroxisomal or peroxisome-associated proteins. In total, 1071 proteins were identified using MS and assessed in terms of their distribution in either high-density peroxisomal or low-density gradient fractions, containing the bulk of organelle material. Combining the data from both fractionation approaches allowed for the identification of specific protein profiles characteristic of mitochondria, the ER and peroxisomes. Among the proteins significantly enriched in the peroxisomal cluster were several novel peroxisomal candidates. Five of those were validated by colocalization in peroxisomes, using confocal microscopy. The peroxisomal import of HTATIP2 and PAFAH2, which contain a peroxisome-targeting sequence 1 (PTS1), could be confirmed by overexpression in HepG2 cells. The candidates SAR1B and PDCD6, which are known ER-exit-site proteins, did not directly colocalize with peroxisomes, but resided at ER sites, which frequently surrounded peroxisomes. Hence, both proteins might concentrate at presumably co-purified peroxisome-ER membrane contacts. Intriguingly, the fifth candidate, OCIA domain-containing protein 1, was previously described as decreasing mitochondrial network formation. In this work, we confirmed its peroxisomal localization and further observed a reduction in peroxisome numbers in response to OCIAD1 overexpression. Hence, OCIAD1 appears to be a novel protein, which has an impact on both mitochondrial and peroxisomal maintenance.
Collapse
Affiliation(s)
- Öznur Singin
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Artur Astapenka
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Victor Costina
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
| | - Sandra Kühl
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Nina Bonekamp
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| | - Oliver Drews
- Institute of Clinical Chemistry, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (V.C.); (O.D.)
- Biomedical Mass Spectrometry, Center for Medical Research, Johannes Kepler University Linz, 4020 Linz, Austria
| | - Markus Islinger
- Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, D-68167 Mannheim, Germany; (Ö.S.); (A.A.); (S.K.); (N.B.)
| |
Collapse
|
3
|
Liu Y, Chen W, Li C, Li L, Yang M, Jiang N, Luo S, Xi Y, Liu C, Han Y, Zhao H, Zhu X, Yuan S, Xiao L, Sun L. DsbA-L interacting with catalase in peroxisome improves tubular oxidative damage in diabetic nephropathy. Redox Biol 2023; 66:102855. [PMID: 37597421 PMCID: PMC10458997 DOI: 10.1016/j.redox.2023.102855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 08/21/2023] Open
Abstract
Peroxisomes are metabolically active organelles that are known for exerting oxidative metabolism, but the precise mechanism remains unclear in diabetic nephropathy (DN). Here, we used proteomics to uncover a correlation between the antioxidant protein disulfide-bond A oxidoreductase-like protein (DsbA-L) and peroxisomal function. In vivo, renal tubular injury, oxidative stress, and cell apoptosis in high-fat diet plus streptozotocin (STZ)-induced diabetic mice were significantly increased, and these changes were accompanied by a "ghost" peroxisomal phenotype, which was further aggravated in DsbA-L-deficient diabetic mice. In vitro, the overexpression of DsbA-L in peroxisomes could improve peroxisomal phenotype and function, reduce oxidative stress and cell apoptosis induced by high glucose (HG, 30 mM) and palmitic acid (PA, 250 μM), but this effect was reversed by 3-Amino-1,2,4-triazole (3-AT, a catalase inhibitor). Mechanistically, DsbA-L regulated the activity of catalase by binding to it, thereby reducing peroxisomal leakage and proteasomal degradation of peroxisomal matrix proteins induced by HG and PA. Additionally, the expression of DsbA-L in renal tubules of patients with DN significantly decreased and was positively correlated with peroxisomal function. Taken together, these results highlight an important role of DsbA-L in ameliorating tubular injury in DN by improving peroxisomal function.
Collapse
Affiliation(s)
- Yan Liu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Wei Chen
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Chenrui Li
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Li Li
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Ming Yang
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Na Jiang
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Shilu Luo
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Yiyun Xi
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Chongbin Liu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Yachun Han
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Hao Zhao
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Xuejing Zhu
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Shuguang Yuan
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Li Xiao
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China
| | - Lin Sun
- Department of Nephrology, The Second Xiangya Hospital of Central South University, Hunan Key Laboratory of Kidney Disease and Blood Purification, Changsha, Hunan, China.
| |
Collapse
|
4
|
Landowski M, Bhute VJ, Grindel S, Haugstad Z, Gyening YK, Tytanic M, Brush RS, Moyer LJ, Nelson DW, Davis CR, Yen CLE, Ikeda S, Agbaga MP, Ikeda A. Transmembrane protein 135 regulates lipid homeostasis through its role in peroxisomal DHA metabolism. Commun Biol 2023; 6:8. [PMID: 36599953 PMCID: PMC9813353 DOI: 10.1038/s42003-022-04404-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 12/23/2022] [Indexed: 01/05/2023] Open
Abstract
Transmembrane protein 135 (TMEM135) is thought to participate in the cellular response to increased intracellular lipids yet no defined molecular function for TMEM135 in lipid metabolism has been identified. In this study, we performed a lipid analysis of tissues from Tmem135 mutant mice and found striking reductions of docosahexaenoic acid (DHA) across all Tmem135 mutant tissues, indicating a role of TMEM135 in the production of DHA. Since all enzymes required for DHA synthesis remain intact in Tmem135 mutant mice, we hypothesized that TMEM135 is involved in the export of DHA from peroxisomes. The Tmem135 mutation likely leads to the retention of DHA in peroxisomes, causing DHA to be degraded within peroxisomes by their beta-oxidation machinery. This may lead to generation or alteration of ligands required for the activation of peroxisome proliferator-activated receptor a (PPARa) signaling, which in turn could result in increased peroxisomal number and beta-oxidation enzymes observed in Tmem135 mutant mice. We confirmed this effect of PPARa signaling by detecting decreased peroxisomes and their proteins upon genetic ablation of Ppara in Tmem135 mutant mice. Using Tmem135 mutant mice, we also validated the protective effect of increased peroxisomes and peroxisomal beta-oxidation on the metabolic disease phenotypes of leptin mutant mice which has been observed in previous studies. Thus, we conclude that TMEM135 has a role in lipid homeostasis through its function in peroxisomes.
Collapse
Affiliation(s)
- Michael Landowski
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Vijesh J Bhute
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemical Engineering, Imperial College London, South Kensington, London, UK
| | - Samuel Grindel
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachary Haugstad
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - Yeboah K Gyening
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Madison Tytanic
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Richard S Brush
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Lucas J Moyer
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
| | - David W Nelson
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Christopher R Davis
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Chi-Liang Eric Yen
- Department of Nutritional Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Sakae Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Martin-Paul Agbaga
- Department of Cell Biology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Department of Ophthalmology, University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
- Dean A. McGee Eye Institute, Oklahoma City, OK, USA
| | - Akihiro Ikeda
- Department of Medical Genetics, University of Wisconsin-Madison, Madison, WI, USA.
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
| |
Collapse
|
5
|
Ansermet C, Centeno G, Pradervand S, Harmacek D, Garcia A, Daraspe J, Kocherlakota S, Baes M, Bignon Y, Firsov D. Renal tubular peroxisomes are dispensable for normal kidney function. JCI Insight 2022; 7:155836. [PMID: 35191396 PMCID: PMC8876468 DOI: 10.1172/jci.insight.155836] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 01/12/2022] [Indexed: 12/04/2022] Open
Abstract
Peroxisomes are specialized cellular organelles involved in a variety of metabolic processes. In humans, mutations leading to complete loss of peroxisomes cause multiorgan failure (Zellweger’s spectrum disorders, ZSD), including renal impairment. However, the (patho)physiological role of peroxisomes in the kidney remains unknown. We addressed the role of peroxisomes in renal function in mice with conditional ablation of peroxisomal biogenesis in the renal tubule (cKO mice). Functional analyses did not reveal any overt kidney phenotype in cKO mice. However, infant male cKO mice had lower body and kidney weights, and adult male cKO mice exhibited substantial reductions in kidney weight and kidney weight/body weight ratio. Stereological analysis showed an increase in mitochondria density in proximal tubule cells of cKO mice. Integrated transcriptome and metabolome analyses revealed profound reprogramming of a number of metabolic pathways, including metabolism of glutathione and biosynthesis/biotransformation of several major classes of lipids. Although this analysis suggested compensated oxidative stress, challenge with high-fat feeding did not induce significant renal impairments in cKO mice. We demonstrate that renal tubular peroxisomes are dispensable for normal renal function. Our data also suggest that renal impairments in patients with ZSD are of extrarenal origin.
Collapse
Affiliation(s)
| | | | | | | | | | - Jean Daraspe
- Electron Microscopy Facility, University of Lausanne, Lausanne, Switzerland
| | - Sai Kocherlakota
- Department for Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven, Belgium
| | - Myriam Baes
- Department for Pharmaceutical and Pharmacological Sciences, University of Leuven, Leuven, Belgium
| | | | | |
Collapse
|
6
|
van Roermund CWT, IJlst L, Linka N, Wanders RJA, Waterham HR. Peroxisomal ATP Uptake Is Provided by Two Adenine Nucleotide Transporters and the ABCD Transporters. Front Cell Dev Biol 2022; 9:788921. [PMID: 35127709 PMCID: PMC8807639 DOI: 10.3389/fcell.2021.788921] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Accepted: 12/27/2021] [Indexed: 11/13/2022] Open
Abstract
Peroxisomes are essential organelles involved in various metabolic processes, including fatty acid β-oxidation. Their metabolic functions require a controlled exchange of metabolites and co-factors, including ATP, across the peroxisomal membrane. We investigated which proteins are involved in the peroxisomal uptake of ATP in the yeast Saccharomyces cerevisiae. Using wild-type and targeted deletion strains, we measured ATP-dependent peroxisomal octanoate β-oxidation, intra-peroxisomal ATP levels employing peroxisome-targeted ATP-sensing reporter proteins, and ATP uptake in proteoliposomes prepared from purified peroxisomes. We show that intra-peroxisomal ATP levels are maintained by different peroxisomal membrane proteins each with different modes of action: 1) the previously reported Ant1p protein, which catalyzes the exchange of ATP for AMP or ADP, 2) the ABC transporter protein complex Pxa1p/Pxa2p, which mediates both uni-directional acyl-CoA and ATP uptake, and 3) the mitochondrial Aac2p protein, which catalyzes ATP/ADP exchange and has a dual localization in both mitochondria and peroxisomes. Our results provide compelling evidence for a complementary system for the uptake of ATP in peroxisomes.
Collapse
Affiliation(s)
- Carlo W. T. van Roermund
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam University Medical Centers—Location AMC, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Carlo W. T. van Roermund, ; Hans R. Waterham,
| | - Lodewijk IJlst
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam University Medical Centers—Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Nicole Linka
- Department of Plant Biochemistry, Heinrich-Heine University Düsseldorf, Düsseldorf, Germany
| | - Ronald J. A. Wanders
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam University Medical Centers—Location AMC, University of Amsterdam, Amsterdam, Netherlands
| | - Hans R. Waterham
- Laboratory Genetic Metabolic Diseases, Amsterdam Gastroenterology, Endocrinology and Metabolism, Amsterdam University Medical Centers—Location AMC, University of Amsterdam, Amsterdam, Netherlands
- *Correspondence: Carlo W. T. van Roermund, ; Hans R. Waterham,
| |
Collapse
|
7
|
Khalil Y, Carrino S, Lin F, Ferlin A, Lad HV, Mazzacuva F, Falcone S, Rivers N, Banks G, Concas D, Aguilar C, Haynes AR, Blease A, Nicol T, Al-Shawi R, Heywood W, Potter P, Mills K, Gale DP, Clayton PT. Tissue Proteome of 2-Hydroxyacyl-CoA Lyase Deficient Mice Reveals Peroxisome Proliferation and Activation of ω-Oxidation. Int J Mol Sci 2022; 23:ijms23020987. [PMID: 35055171 PMCID: PMC8781152 DOI: 10.3390/ijms23020987] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 01/11/2022] [Indexed: 02/04/2023] Open
Abstract
Peroxisomal fatty acid α-oxidation is an essential pathway for the degradation of β-carbon methylated fatty acids such as phytanic acid. One enzyme in this pathway is 2-hydroxyacyl CoA lyase (HACL1), which is responsible for the cleavage of 2-hydroxyphytanoyl-CoA into pristanal and formyl-CoA. Hacl1 deficient mice do not present with a severe phenotype, unlike mice deficient in other α-oxidation enzymes such as phytanoyl-CoA hydroxylase deficiency (Refsum disease) in which neuropathy and ataxia are present. Tissues from wild-type and Hacl1−/− mice fed a high phytol diet were obtained for proteomic and lipidomic analysis. There was no phenotype observed in these mice. Liver, brain, and kidney tissues underwent trypsin digestion for untargeted proteomic liquid chromatography-mass spectrometry analysis, while liver tissues also underwent fatty acid hydrolysis, extraction, and derivatisation for fatty acid gas chromatography-mass spectrometry analysis. The liver fatty acid profile demonstrated an accumulation of phytanic and 2-hydroxyphytanic acid in the Hacl1−/− liver and significant decrease in heptadecanoic acid. The liver proteome showed a significant decrease in the abundance of Hacl1 and a significant increase in the abundance of proteins involved in PPAR signalling, peroxisome proliferation, and omega oxidation, particularly Cyp4a10 and Cyp4a14. In addition, the pathway associated with arachidonic acid metabolism was affected; Cyp2c55 was upregulated and Cyp4f14 and Cyp2b9 were downregulated. The kidney proteome revealed fewer significantly upregulated peroxisomal proteins and the brain proteome was not significantly different in Hacl1−/− mice. This study demonstrates the powerful insight brought by proteomic and metabolomic profiling of Hacl1−/− mice in better understanding disease mechanism in fatty acid α-oxidation disorders.
Collapse
Affiliation(s)
- Youssef Khalil
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Sara Carrino
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Department of Experimental, Diagnostic and Specialty Medicine, University of Bologna, 40138 Bologna, Italy
| | - Fujun Lin
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
- Department of Nephrology, Xin Hua Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200082, China
| | - Anna Ferlin
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
- Clinical Genetics and Genomics Laboratory, Royal Brompton Hospital, London SW3 6NP, UK
| | - Heena V. Lad
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Francesca Mazzacuva
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Department of Bioscience, University of East London, London E15 4LZ, UK
| | - Sara Falcone
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Natalie Rivers
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Gareth Banks
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Danilo Concas
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Carlos Aguilar
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Andrew R. Haynes
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Andy Blease
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Thomas Nicol
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Raya Al-Shawi
- Genetics Unit and Wolfson Drug Discovery Unit, Centre for Amyloidosis and Acute Phase Proteins, University College London, London NW3 2PF, UK;
| | - Wendy Heywood
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Paul Potter
- MRC Harwell Institute, Harwell Campus, Oxfordshire OX11 0RD, UK; (H.V.L.); (S.F.); (N.R.); (G.B.); (D.C.); (C.A.); (A.R.H.); (A.B.); (T.N.); (P.P.)
| | - Kevin Mills
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
| | - Daniel P. Gale
- Department of Renal Medicine, University College London, London NW3 2PF, UK; (F.L.); (A.F.); (D.P.G.)
| | - Peter T. Clayton
- Genetics and Genomic Medicine, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK; (Y.K.); (S.C.); (F.M.); (W.H.); (K.M.)
- Correspondence:
| |
Collapse
|
8
|
Quantitative proteomics to study aging in rabbit liver. Mech Ageing Dev 2020; 187:111227. [PMID: 32126221 DOI: 10.1016/j.mad.2020.111227] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 01/24/2020] [Accepted: 02/27/2020] [Indexed: 12/23/2022]
Abstract
Aging globally effects cellular and organismal metabolism across a range of mammalian species, including humans and rabbits. Rabbits (Oryctolagus cuniculus are an attractive model system of aging due to their genetic similarity with humans and their short lifespans. This model can be used to understand metabolic changes in aging especially in major organs such as liver where we detected pronounced variations in fat metabolism, mitochondrial dysfunction, and protein degradation. Such changes in the liver are consistent across several mammalian species however in rabbits the downstream effects of these changes have not yet been explored. We have applied proteomics to study changes in the liver proteins from young, middle, and old age rabbits using a multiplexing cPILOT strategy. This resulted in the identification of 2,586 liver proteins, among which 45 proteins had significant p < 0.05) changes with aging. Seven proteins were differentially-expressed at all ages and include fatty acid binding protein, aldehyde dehydrogenase, enoyl-CoA hydratase, 3-hydroxyacyl CoA dehydrogenase, apolipoprotein C3, peroxisomal sarcosine oxidase, adhesion G-protein coupled receptor, and glutamate ionotropic receptor kinate. Insights to how alterations in metabolism affect protein expression in liver have been gained and demonstrate the utility of rabbit as a model of aging.
Collapse
|
9
|
Pan R, Reumann S, Lisik P, Tietz S, Olsen LJ, Hu J. Proteome analysis of peroxisomes from dark-treated senescent Arabidopsis leaves. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2018; 60:1028-1050. [PMID: 29877633 DOI: 10.1111/jipb.12670] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 05/29/2018] [Indexed: 05/21/2023]
Abstract
Peroxisomes compartmentalize a dynamic suite of biochemical reactions and play a central role in plant metabolism, such as the degradation of hydrogen peroxide, metabolism of fatty acids, photorespiration, and the biosynthesis of plant hormones. Plant peroxisomes have been traditionally classified into three major subtypes, and in-depth mass spectrometry (MS)-based proteomics has been performed to explore the proteome of the two major subtypes present in green leaves and etiolated seedlings. Here, we carried out a comprehensive proteome analysis of peroxisomes from Arabidopsis leaves given a 48-h dark treatment. Our goal was to determine the proteome of the third major subtype of plant peroxisomes from senescent leaves, and further catalog the plant peroxisomal proteome. We identified a total of 111 peroxisomal proteins and verified the peroxisomal localization for six new proteins with potential roles in fatty acid metabolism and stress response by in vivo targeting analysis. Metabolic pathways compartmentalized in the three major subtypes of peroxisomes were also compared, which revealed a higher number of proteins involved in the detoxification of reactive oxygen species in peroxisomes from senescent leaves. Our study takes an important step towards mapping the full function of plant peroxisomes.
Collapse
Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Sigrun Reumann
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
- Center of Organelle Research, University of Stavanger, N-4021 Stavanger, Norway
- Department of Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, University of Hamburg, D-22609 Hamburg, Germany
| | - Piotr Lisik
- Center of Organelle Research, University of Stavanger, N-4021 Stavanger, Norway
| | - Stefanie Tietz
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
| | - Laura J Olsen
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Plant Biology Department, Michigan State University, East Lansing, MI 48824, USA
| |
Collapse
|
10
|
Kunze M. Predicting Peroxisomal Targeting Signals to Elucidate the Peroxisomal Proteome of Mammals. Subcell Biochem 2018; 89:157-199. [PMID: 30378023 DOI: 10.1007/978-981-13-2233-4_7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Peroxisomes harbor a plethora of proteins, but the peroxisomal proteome as the entirety of all peroxisomal proteins is still unknown for mammalian species. Computational algorithms can be used to predict the subcellular localization of proteins based on their amino acid sequence and this method has been amply used to forecast the intracellular fate of individual proteins. However, when applying such algorithms systematically to all proteins of an organism the prediction of its peroxisomal proteome in silico should be possible. Therefore, a reliable detection of peroxisomal targeting signals (PTS ) acting as postal codes for the intracellular distribution of the encoding protein is crucial. Peroxisomal proteins can utilize different routes to reach their destination depending on the type of PTS. Accordingly, independent prediction algorithms have been developed for each type of PTS, but only those for type-1 motifs (PTS1) have so far reached a satisfying predictive performance. This is partially due to the low number of peroxisomal proteins limiting the power of statistical analyses and partially due to specific properties of peroxisomal protein import, which render functional PTS motifs inactive in specific contexts. Moreover, the prediction of the peroxisomal proteome is limited by the high number of proteins encoded in mammalian genomes, which causes numerous false positive predictions even when using reliable algorithms and buries the few yet unidentified peroxisomal proteins. Thus, the application of prediction algorithms to identify all peroxisomal proteins is currently ineffective as stand-alone method, but can display its full potential when combined with other methods.
Collapse
Affiliation(s)
- Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Vienna, Austria.
| |
Collapse
|
11
|
Abstract
Plant peroxisomes are required for a number of fundamental physiological processes, such as primary and secondary metabolism, development and stress response. Indexing the dynamic peroxisome proteome is prerequisite to fully understanding the importance of these organelles. Mass Spectrometry (MS)-based proteome analysis has allowed the identification of novel peroxisomal proteins and pathways in a relatively high-throughput fashion and significantly expanded the list of proteins and biochemical reactions in plant peroxisomes. In this chapter, we summarize the experimental proteomic studies performed in plants, compile a list of ~200 confirmed Arabidopsis peroxisomal proteins, and discuss the diverse plant peroxisome functions with an emphasis on the role of Arabidopsis MS-based proteomics in discovering new peroxisome functions. Many plant peroxisome proteins and biochemical pathways are specific to plants, substantiating the complexity, plasticity and uniqueness of plant peroxisomes. Mapping the full plant peroxisome proteome will provide a knowledge base for the improvement of crop production, quality and stress tolerance.
Collapse
Affiliation(s)
- Ronghui Pan
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA
| | - Jianping Hu
- MSU-Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, USA.
- Plant Biology Department, Michigan State University, East Lansing, MI, 48824, USA.
| |
Collapse
|
12
|
Abstract
The current view on peroxisomes has changed dramatically from being human cell oddities to vital organelles that host several key metabolic pathways. To fulfil over 50 different enzymatic functions, human peroxisomes host either unique peroxisomal proteins or dual-localized proteins. The identification and characterization of the complete peroxisomal proteome in humans is important for diagnosis and treatment of patients with peroxisomal disorders as well as for uncovering novel peroxisomal functions and regulatory modules. Hence, here we compiled a comprehensive list of mammalian peroxisomal and peroxisome-associated proteins by curating results of several quantitative and non-quantitative proteomic studies together with entries in the UniProtKB and Compartments knowledge channel databases. Our analysis gives a holistic view on the mammalian peroxisomal proteome and brings to light potential new peroxisomal and peroxisome-associated proteins. We believe that this dataset, represents a valuable surrogate map of the human peroxisomal proteome.
Collapse
|
13
|
Deb R, Nagotu S. Versatility of peroxisomes: An evolving concept. Tissue Cell 2017; 49:209-226. [DOI: 10.1016/j.tice.2017.03.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2017] [Revised: 03/05/2017] [Accepted: 03/06/2017] [Indexed: 02/04/2023]
|
14
|
Yofe I, Soliman K, Chuartzman SG, Morgan B, Weill U, Yifrach E, Dick TP, Cooper SJ, Ejsing CS, Schuldiner M, Zalckvar E, Thoms S. Pex35 is a regulator of peroxisome abundance. J Cell Sci 2017; 130:791-804. [PMID: 28049721 DOI: 10.1242/jcs.187914] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 11/24/2016] [Indexed: 12/12/2022] Open
Abstract
Peroxisomes are cellular organelles with vital functions in lipid, amino acid and redox metabolism. The cellular formation and dynamics of peroxisomes are governed by PEX genes; however, the regulation of peroxisome abundance is still poorly understood. Here, we use a high-content microscopy screen in Saccharomyces cerevisiae to identify new regulators of peroxisome size and abundance. Our screen led to the identification of a previously uncharacterized gene, which we term PEX35, which affects peroxisome abundance. PEX35 encodes a peroxisomal membrane protein, a remote homolog to several curvature-generating human proteins. We systematically characterized the genetic and physical interactome as well as the metabolome of mutants in PEX35, and we found that Pex35 functionally interacts with the vesicle-budding-inducer Arf1. Our results highlight the functional interaction between peroxisomes and the secretory pathway.
Collapse
Affiliation(s)
- Ido Yofe
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Kareem Soliman
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
| | - Silvia G Chuartzman
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Bruce Morgan
- Department of Cellular Biochemistry, University of Kaiserslautern, Kaiserslautern 67653, Germany.,Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Uri Weill
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Eden Yifrach
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Tobias P Dick
- Division of Redox Regulation, ZMBH-DKFZ Alliance, German Cancer Research Center (DKFZ), Heidelberg 69121, Germany
| | - Sara J Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Christer S Ejsing
- Department of Biochemistry and Molecular Biology, VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense 5230, Denmark
| | - Maya Schuldiner
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Einat Zalckvar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Sven Thoms
- Department of Child and Adolescent Health, University Medical Center, Göttingen 37075, Germany
| |
Collapse
|
15
|
Berger J, Dorninger F, Forss-Petter S, Kunze M. Peroxisomes in brain development and function. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:934-55. [PMID: 26686055 PMCID: PMC4880039 DOI: 10.1016/j.bbamcr.2015.12.005] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 12/04/2015] [Accepted: 12/09/2015] [Indexed: 12/26/2022]
Abstract
Peroxisomes contain numerous enzymatic activities that are important for mammalian physiology. Patients lacking either all peroxisomal functions or a single enzyme or transporter function typically develop severe neurological deficits, which originate from aberrant development of the brain, demyelination and loss of axonal integrity, neuroinflammation or other neurodegenerative processes. Whilst correlating peroxisomal properties with a compilation of pathologies observed in human patients and mouse models lacking all or individual peroxisomal functions, we discuss the importance of peroxisomal metabolites and tissue- and cell type-specific contributions to the observed brain pathologies. This enables us to deconstruct the local and systemic contribution of individual metabolic pathways to specific brain functions. We also review the recently discovered variability of pathological symptoms in cases with unexpectedly mild presentation of peroxisome biogenesis disorders. Finally, we explore the emerging evidence linking peroxisomes to more common neurological disorders such as Alzheimer’s disease, autism and amyotrophic lateral sclerosis. This article is part of a Special Issue entitled: Peroxisomes edited by Ralf Erdmann.
Collapse
Affiliation(s)
- Johannes Berger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria.
| | - Fabian Dorninger
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria.
| | - Sonja Forss-Petter
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria.
| | - Markus Kunze
- Department of Pathobiology of the Nervous System, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090 Vienna, Austria.
| |
Collapse
|
16
|
Baes M, Van Veldhoven PP. Hepatic dysfunction in peroxisomal disorders. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:956-70. [PMID: 26453805 DOI: 10.1016/j.bbamcr.2015.09.035] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/18/2022]
Abstract
The peroxisomal compartment in hepatocytes hosts several essential metabolic conversions. These are defective in peroxisomal disorders that are either caused by failure to import the enzymes in the organelle or by mutations in the enzymes or in transporters needed to transfer the substrates across the peroxisomal membrane. Hepatic pathology is one of the cardinal features in disorders of peroxisome biogenesis and peroxisomal β-oxidation although it only rarely determines the clinical fate. In mouse models of these diseases liver pathologies also occur, although these are not always concordant with the human phenotype which might be due to differences in diet, expression of enzymes and backup mechanisms. Besides the morphological changes, we overview the impact of peroxisome malfunction on other cellular compartments including mitochondria and the ER. We further focus on the metabolic pathways that are affected such as bile acid formation, and dicarboxylic acid and branched chain fatty acid degradation. It appears that the association between deregulated metabolites and pathological events remains unclear.
Collapse
Affiliation(s)
- Myriam Baes
- Laboratory for Cell Metabolism, Department of Pharmaceutical and Pharmacological Sciences, KU Leuven, B-3000 Leuven, Belgium.
| | - Paul P Van Veldhoven
- Laboratory for Lipid Biochemistry and Protein Interactions, Department of Cellular and Molecular Medicine, KU Leuven, B-3000 Leuven, Belgium.
| |
Collapse
|
17
|
Disturbances in cholesterol, bile acid and glucose metabolism in peroxisomal 3-ketoacylCoA thiolase B deficient mice fed diets containing high or low fat contents. Biochimie 2013; 98:86-101. [PMID: 24287293 DOI: 10.1016/j.biochi.2013.11.014] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Accepted: 11/15/2013] [Indexed: 12/29/2022]
Abstract
The peroxisomal 3-ketoacyl-CoA thiolase B (ThB) catalyzes the thiolytic cleavage of straight chain 3-ketoacyl-CoAs. Up to now, the ability of ThB to interfere with lipid metabolism was studied in mice fed a laboratory chow enriched or not with the synthetic agonist Wy14,643, a pharmacological activator of the nuclear hormone receptor PPARα. The aim of the present study was therefore to determine whether ThB could play a role in obesity and lipid metabolism when mice are chronically fed a synthetic High Fat Diet (HFD) or a Low Fat Diet (LFD) as a control diet. To investigate this possibility, wild-type (WT) mice and mice deficient for Thb (Thb(-/-)) were subjected to either a synthetic LFD or a HFD for 25 weeks, and their responses were compared. First, when fed a normal regulatory laboratory chow, Thb(-/-) mice displayed growth retardation as well as a severe reduction in the plasma level of Growth Hormone (GH) and Insulin Growth Factor-I (IGF-I), suggesting alterations in the GH/IGF-1 pathway. When fed the synthetic diets, the corrected energy intake to body mass was significantly higher in Thb(-/-) mice, yet those mice were protected from HFD-induced adiposity. Importantly, Thb(-/-) mice also suffered from hypoglycemia, exhibited reduction in liver glycogen stores and circulating insulin levels under the LFD and the HFD. Thb deficiency was also associated with higher levels of plasma HDL (High Density Lipoproteins) cholesterol and increased liver content of cholesterol under both the LFD and the HFD. As shown by the plasma lathosterol to cholesterol ratio, a surrogate marker for cholesterol biosynthesis, whole body cholesterol de novo synthesis was increased in Thb(-/-) mice. By comparing liver RNA from WT mice and Thb(-/-) mice using oligonucleotide microarray and RT-qPCR, a coordinated decrease in the expression of critical cholesterol synthesizing genes and an increased expression of genes involved in bile acid synthesis (Cyp7a1, Cyp17a1, Akr1d1) were observed in Thb(-/-) mice. In parallel, the elevation of the lathosterol to cholesterol ratio as well as the increased expression of cholesterol synthesizing genes were observed in the kidney of Thb(-/-) mice fed the LFD and the HFD. Overall, the data indicate that ThB is not fully interchangeable with the thiolase A isoform. The present study also reveals that modulating the expression of the peroxisomal ThB enzyme can largely reverberate not only throughout fatty acid metabolism but also cholesterol, bile acid and glucose metabolism.
Collapse
|
18
|
Contreras MA, Alzate O, Singh AK, Singh I. PPARα activation induces N(ε)-Lys-acetylation of rat liver peroxisomal multifunctional enzyme type 1. Lipids 2013; 49:119-31. [PMID: 24092543 DOI: 10.1007/s11745-013-3843-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/09/2013] [Indexed: 11/28/2022]
Abstract
Peroxisomes are ubiquitous subcellular organelles that participate in metabolic and disease processes, with few of its proteins undergoing posttranslational modifications. As the role of lysine-acetylation has expanded into the cellular intermediary metabolism, we used a combination of differential centrifugation, organelle isolation by linear density gradient centrifugation, western blot analysis, and peptide fingerprinting and amino acid sequencing by mass spectrometry to investigate protein acetylation in control and ciprofibrate-treated rat liver peroxisomes. Organelle protein samples isolated by density gradient centrifugation from PPARα-agonist treated rat liver screened with an anti-N(ε)-acetyl lysine antibody revealed a single protein band of 75 kDa. Immunoprecipitation with this antibody resulted in the precipitation of a protein from the protein pool of ciprofibrate-induced peroxisomes, but not from the protein pool of non-induced peroxisomes. Peptide mass fingerprinting analysis identified the protein as the peroxisomal multifunctional enzyme type 1. In addition, mass spectrometry-based amino acid sequencing resulted in the identification of unique peptides containing 4 acetylated-Lys residues (K¹⁵⁵, K¹⁷³, K¹⁹⁰, and K⁵⁸³). This is the first report that demonstrates posttranslational acetylation of a peroxisomal enzyme in PPARα-dependent proliferation of peroxisomes in rat liver.
Collapse
Affiliation(s)
- Miguel A Contreras
- Department of Pediatrics, The Darby Children's Research Institute, Medical University of South Carolina, Charleston, SC, 29425, USA,
| | | | | | | |
Collapse
|
19
|
Mammalian SOD2 is exclusively located in mitochondria and not present in peroxisomes. Histochem Cell Biol 2013; 140:105-17. [DOI: 10.1007/s00418-013-1099-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/08/2013] [Indexed: 11/30/2022]
|
20
|
The impact of a ketogenic diet and liver dysfunction on serum very long-chain fatty acids levels. Lipids 2013; 48:405-9. [PMID: 23371825 DOI: 10.1007/s11745-013-3761-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2012] [Accepted: 11/13/2012] [Indexed: 10/27/2022]
Abstract
Peroxisomes play an essential role in mammalian cellular metabolism, particularly in oxidation fatty acid pathways. Serum very long-chain fatty acids (VLCFA), the main biochemical diagnostic parameters for peroxisomal disorders, were examined in 25 neurological patients with epilepsy on a ketogenic diet and 27 patients with liver dysfunction. The data show that patients on a ketogenic diet have increased levels of C22:0 and C24:0, but not C26:0, and normal C24:0/C22:0 and C26:0/C22:0. Patients with liver insufficiency showed a slightly elevated level of C26:0, a normal level of C24:0 and a decreased level of C22:0; thus in 21/27 the ratio of C24:0/C22:0 was increased and 15/27 the ratio of C26:0/C22:0 was increased.
Collapse
|
21
|
Techritz S, Lützkendorf S, Bazant E, Becker S, Klose J, Schuelke M. Quantitative and qualitative 2D electrophoretic analysis of differentially expressed mitochondrial proteins from five mouse organs. Proteomics 2012; 13:179-95. [DOI: 10.1002/pmic.201100539] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 10/02/2012] [Accepted: 10/29/2012] [Indexed: 01/27/2023]
Affiliation(s)
- Sandra Techritz
- Department of Neuropediatrics; Charité University Medical Center; Berlin Germany
| | - Susanne Lützkendorf
- Department of Neuropediatrics; Charité University Medical Center; Berlin Germany
- NeuroCure Clinical Research Center; Charité University Medical Center; Berlin Germany
| | - Esther Bazant
- Department of Neuropediatrics; Charité University Medical Center; Berlin Germany
| | - Silke Becker
- Institute of Human Genetics; Charité University Medical Center; Berlin Germany
| | - Joachim Klose
- Institute of Human Genetics; Charité University Medical Center; Berlin Germany
| | - Markus Schuelke
- Department of Neuropediatrics; Charité University Medical Center; Berlin Germany
- NeuroCure Clinical Research Center; Charité University Medical Center; Berlin Germany
| |
Collapse
|
22
|
Antonenkov VD, Hiltunen JK. Transfer of metabolites across the peroxisomal membrane. Biochim Biophys Acta Mol Basis Dis 2011; 1822:1374-86. [PMID: 22206997 DOI: 10.1016/j.bbadis.2011.12.011] [Citation(s) in RCA: 88] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2011] [Revised: 12/08/2011] [Accepted: 12/15/2011] [Indexed: 02/08/2023]
Abstract
Peroxisomes perform a large variety of metabolic functions that require a constant flow of metabolites across the membranes of these organelles. Over the last few years it has become clear that the transport machinery of the peroxisomal membrane is a unique biological entity since it includes nonselective channels conducting small solutes side by side with transporters for 'bulky' solutes such as ATP. Electrophysiological experiments revealed several channel-forming activities in preparations of plant, mammalian, and yeast peroxisomes and in glycosomes of Trypanosoma brucei. The properties of the first discovered peroxisomal membrane channel - mammalian Pxmp2 protein - have also been characterized. The channels are apparently involved in the formation of peroxisomal shuttle systems and in the transmembrane transfer of various water-soluble metabolites including products of peroxisomal β-oxidation. These products are processed by a large set of peroxisomal enzymes including carnitine acyltransferases, enzymes involved in the synthesis of ketone bodies, thioesterases, and others. This review discusses recent data pertaining to solute permeability and metabolite transport systems in peroxisomal membranes and also addresses mechanisms responsible for the transfer of ATP and cofactors such as an ATP transporter and nudix hydrolases.
Collapse
Affiliation(s)
- Vasily D Antonenkov
- Department of Biochemistry and Biocenter, University of Oulu, Oulu, Finland.
| | | |
Collapse
|
23
|
Amelina H, Sjödin MOD, Bergquist J, Cristobal S. Quantitative subproteomic analysis of age-related changes in mouse liver peroxisomes by iTRAQ LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2011; 879:3393-400. [PMID: 21963482 DOI: 10.1016/j.jchromb.2011.08.044] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2011] [Revised: 08/07/2011] [Accepted: 08/26/2011] [Indexed: 10/17/2022]
Abstract
Aging is a complex multifactorial phenomenon, which is believed to result from the accumulation of cellular damage to biological macromolecules. Peroxisomes recently emerged as another important source of reactive oxygen species (ROS) production in addition to mitochondria. However, the role of these organelles in the process of aging is still not clear. The aim of this study was to characterize the changes in protein expression profiles of young (10 weeks old) versus old (18 months old) mouse liver peroxisome-enriched fractions. We have applied shotgun proteomic approach based on liquid chromatography and tandem mass spectrometry (LC-MS/MS) combined with iTRAQ (isobaric tags for relative and absolute quantitation) labeling that allows comparative quantitative multiplex analysis. Our analysis led to identification and quantification of 150 proteins, 8 out of which were differentially expressed between two age groups at a statistically significant level (p<0.05), with folds ranging from 1.2 to 4.1. These proteins involved in peroxisomal β-oxidation, detoxification of xenobiotics and production of ROS. Noteworthy, differences in liver proteome have been observed between as well as within different age groups. In conclusion, our subproteomic quantitative study suggests that mouse liver proteome is sufficiently maintained until certain age.
Collapse
Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.
| | | | | | | |
Collapse
|
24
|
Van Veldhoven PP. Biochemistry and genetics of inherited disorders of peroxisomal fatty acid metabolism. J Lipid Res 2010; 51:2863-95. [PMID: 20558530 DOI: 10.1194/jlr.r005959] [Citation(s) in RCA: 243] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
In humans, peroxisomes harbor a complex set of enzymes acting on various lipophilic carboxylic acids, organized in two basic pathways, alpha-oxidation and beta-oxidation; the latter pathway can also handle omega-oxidized compounds. Some oxidation products are crucial to human health (primary bile acids and polyunsaturated FAs), whereas other substrates have to be degraded in order to avoid neuropathology at a later age (very long-chain FAs and xenobiotic phytanic acid and pristanic acid). Whereas total absence of peroxisomes is lethal, single peroxisomal protein deficiencies can present with a mild or severe phenotype and are more informative to understand the pathogenic factors. The currently known single protein deficiencies equal about one-fourth of the number of proteins involved in peroxisomal FA metabolism. The biochemical properties of these proteins are highlighted, followed by an overview of the known diseases.
Collapse
Affiliation(s)
- Paul P Van Veldhoven
- Katholieke Universiteit Leuven, Department of Molecular Cell Biology, LIPIT, Campus Gasthuisberg, Herestraat, Leuven, Belgium.
| |
Collapse
|
25
|
Abstract
Peroxisomes are organelles bounded by a single membrane that can be found in all major groups of eukaryotes. A single evolutionary origin of this cellular compartment is supported by the presence, in diverse organisms, of a common set of proteins implicated in peroxisome biogenesis and maintenance. Their enzymatic content, however, can vary substantially across species, indicating a high level of evolutionary plasticity. Proteomic analyses have greatly expanded our knowledge on peroxisomes in some model organisms, including plants, mammals and yeasts. However, we still have a limited knowledge about the distribution and functionalities of peroxisomes in the vast majority of groups of microbial eukaryotes. Here, I review recent advances in our understanding of peroxisome diversity and evolution, with a special emphasis on peroxisomes in microbial eukaryotes.
Collapse
Affiliation(s)
- Toni Gabaldón
- Centre for Genomic Regulation (CRG), Dr Aiguader, 88 08003 Barcelona, Spain.
| |
Collapse
|
26
|
Islinger M, Cardoso MJR, Schrader M. Be different--the diversity of peroxisomes in the animal kingdom. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2010; 1803:881-97. [PMID: 20347886 DOI: 10.1016/j.bbamcr.2010.03.013] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2010] [Revised: 03/15/2010] [Accepted: 03/18/2010] [Indexed: 10/19/2022]
Abstract
Peroxisomes represent so-called "multipurpose organelles" as they contribute to various anabolic as well as catabolic pathways. Thus, with respect to the physiological specialization of an individual organ or animal species, peroxisomes exhibit a functional diversity, which is documented by significant variations in their proteome. These differences are usually regarded as an adaptational response to the nutritional and environmental life conditions of a specific organism. Thus, human peroxisomes can be regarded as an in part physiologically unique organellar entity fulfilling metabolic functions that differ from our animal model systems. In line with this, a profound understanding on how peroxisomes acquired functional heterogeneity in terms of an evolutionary and mechanistic background is required. This review summarizes our current knowledge on the heterogeneity of peroxisomal physiology, providing insights into the genetic and cell biological mechanisms, which lead to the differential localization or expression of peroxisomal proteins and further gives an overview on peroxisomal biochemical pathways, which are specialized in different animal species and organs. Moreover, it addresses the impact of proteome studies on our understanding of differential peroxisome function describing the utility of mass spectrometry and computer-assisted algorithms to identify peroxisomal target sequences for the detection of new organ- or species-specific peroxisomal proteins.
Collapse
Affiliation(s)
- M Islinger
- Department of Anatomy and Cell Biology, Ruprecht-Karls University, 69120 Heidelberg, Germany
| | | | | |
Collapse
|
27
|
Chen G, Liu H, Wang X, Li Z. In vitro methylation by methanol: proteomic screening and prevalence investigation. Anal Chim Acta 2009; 661:67-75. [PMID: 20113717 DOI: 10.1016/j.aca.2009.12.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2009] [Revised: 11/21/2009] [Accepted: 12/10/2009] [Indexed: 11/17/2022]
Abstract
It is assumed that much more functional importance for protein activity than expected may be granted by methylation that occurs at the side-chain of aspartate or glutamate residue. In vitro methylation mainly comes from the use of methanol in sample preparation prior to MS analysis. In this study, we first performed the methylation site-directed proteomic screening of bovine serum albumin, ovalbumin and 20S proteasome for gel staining using a meaningfully indicative MS-pattern of peak tag (termed as 4P tag) and manual inspection for mass spectral data. As a result, there were 17 proteolytic peptides with 20 modified sites confirmed to be in vitro methylated. Subsequently, the prevalence investigation was performed, focusing on the reaction kinetic behavior of in vitro methylation. This study provided a simple and robust approach for confirmation of in vitro methylation by methanol, as well as the precautious guide for the use of methanol in proteomic study.
Collapse
Affiliation(s)
- Guoqiang Chen
- Department of Biophysics and Structural Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and School of Basic Medicine, Peking Union Medical College, 5 Dong Dan San Tiao, Beijing 100005, China
| | | | | | | |
Collapse
|
28
|
Gazzana G, Borlak J. An update on the mouse liver proteome. Proteome Sci 2009; 7:35. [PMID: 19737410 PMCID: PMC2752743 DOI: 10.1186/1477-5956-7-35] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2009] [Accepted: 09/08/2009] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Decoding of the liver proteome is subject of intense research, but hampered by methodological constraints. We recently developed an improved protocol for studying rat liver proteins based on 2-DE-MALDI-TOF-MS peptide mass finger printing.This methodology was now applied to develop a mouse liver protein database. RESULTS Liver proteins were extracted by two different lysis buffers in sequence followed by a liquid-phase IEF pre-fractionation and separation of proteins by 2 DE at two different pH ranges, notably 5-8 and 7-10. Based on 9600 in gel digests a total of 643 mouse liver proteins with high sequence coverage (> 20 peptides per protein) could be identified by MALDI-TOF-MS peptide mass finger printing. Notably, 255 proteins are novel and have not been reported so far by conventional two-dimensional electrophoresis proteome mapping. Additionally, the results of the present findings for mouse liver were compared to published data of the rat proteome to compile as many proteins as possible in a rodent liver database. CONCLUSION Based on 2-DE MALDI-TOF-MS a significantly improved proteome map of mouse liver was obtained. We discuss some prominent members of newly identified proteins for a better understanding of liver biology.
Collapse
Affiliation(s)
- Giuseppe Gazzana
- Department of Molecular Medicine and Medical Biotechnology, Fraunhofer Institute of Toxicology and Experimental Medicine, Hannover, Germany.
| | | |
Collapse
|
29
|
The cytosolic domain of PEX3, a protein involved in the biogenesis of peroxisomes, binds membrane lipids. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2009; 1793:1669-75. [PMID: 19715730 DOI: 10.1016/j.bbamcr.2009.08.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2009] [Revised: 08/19/2009] [Accepted: 08/19/2009] [Indexed: 12/31/2022]
Abstract
According to current models, most newly synthesized peroxisomal intrinsic membrane proteins are recognized in the cytosol and targeted to the peroxisomal membrane by PEX19. At the organelle membrane the PEX19-cargo protein complex interacts with PEX3, a protein believed to possess only one transmembrane domain and exposing the majority of its polypeptide chain into the cytosol. In agreement with this topological model, a recombinant protein comprising the cytosolic domain of PEX3 can be purified in a soluble and monomeric form in the absence of detergents or other solubilizing agents. Here, we show that this recombinant protein actually precipitates when incubated with mild detergents, suggesting that this domain of PEX3 interacts with amphipathic molecules. Following this observation, we tested this recombinant protein in lipid-binding assays and found that it interacts strongly with liposomes inducing their flocculation or even partial solubilization. The implications of these findings are discussed.
Collapse
|
30
|
Anthonio EA, Brees C, Baumgart-Vogt E, Hongu T, Huybrechts SJ, Van Dijck P, Mannaerts GP, Kanaho Y, Van Veldhoven PP, Fransen M. Small G proteins in peroxisome biogenesis: the potential involvement of ADP-ribosylation factor 6. BMC Cell Biol 2009; 10:58. [PMID: 19686593 PMCID: PMC3224584 DOI: 10.1186/1471-2121-10-58] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Accepted: 08/17/2009] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Peroxisomes execute diverse and vital functions in virtually every eukaryote. New peroxisomes form by budding from pre-existing organelles or de novo by vesiculation of the ER. It has been suggested that ADP-ribosylation factors and COPI coatomer complexes are involved in these processes. RESULTS Here we show that all viable Saccharomyces cerevisiae strains deficient in one of the small GTPases which have an important role in the regulation of vesicular transport contain functional peroxisomes, and that the number of these organelles in oleate-grown cells is significantly upregulated in the arf1 and arf3 null strains compared to the wild-type strain. In addition, we provide evidence that a portion of endogenous Arf6, the mammalian orthologue of yeast Arf3, is associated with the cytoplasmic face of rat liver peroxisomes. Despite this, ablation of Arf6 did neither influence the regulation of peroxisome abundance nor affect the localization of peroxisomal proteins in cultured fetal hepatocytes. However, co-overexpression of wild-type, GTP hydrolysis-defective or (dominant-negative) GTP binding-defective forms of Arf1 and Arf6 caused mislocalization of newly-synthesized peroxisomal proteins and resulted in an alteration of peroxisome morphology. CONCLUSION These observations suggest that Arf6 is a key player in mammalian peroxisome biogenesis. In addition, they also lend strong support to and extend the concept that specific Arf isoform pairs may act in tandem to regulate exclusive trafficking pathways.
Collapse
Affiliation(s)
- Erin A Anthonio
- Department of Molecular Cell Biology, Catholic University of Leuven, Leuven, Belgium.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
31
|
Amelina H, Cristobal S. Proteomic study on gender differences in aging kidney of mice. Proteome Sci 2009; 7:16. [PMID: 19358702 PMCID: PMC2673210 DOI: 10.1186/1477-5956-7-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2008] [Accepted: 04/09/2009] [Indexed: 11/23/2022] Open
Abstract
Background This study aims to analyze sex differences in mice aging kidney. We applied a proteomic technique based on subfractionation, and liquid chromatography coupled with 2-DE. Samples from male and female CD1-Swiss outbred mice from 28 weeks, 52 weeks, and 76 weeks were analysed by 2-DE, and selected proteins were identified by matrix assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS). Results This proteomic analysis detected age-related changes in protein expression in 55 protein-spots, corresponding to 22 spots in males and 33 spots in females. We found a protein expression signature (PES) of aging composed by 8 spots, common for both genders. The identified proteins indicated increases in oxidative and proteolytic proteins and decreases in glycolytic proteins, and antioxidant enzymes. Conclusion Our results provide insights into the gender differences associated to the decline of kidney function in aging. Thus, we show that proteomics can provide valuable information on age-related changes in expression levels of proteins and related modifications. This pilot study is still far from providing candidates for aging-biomarkers. However, we suggest that the analysis of these proteins could suggest mechanisms of cellular aging in kidney, and improve the kidney selection for transplantation.
Collapse
Affiliation(s)
- Hanna Amelina
- Department of Biochemistry and Biophysics, Stockholm University, Sweden.
| | | |
Collapse
|
32
|
Scaloni A, Codarin E, Di Maso V, Arena S, Renzone G, Tiribelli C, Quadrifoglio F, Tell G. Modern strategies to identify new molecular targets for the treatment of liver diseases: The promising role of Proteomics and Redox Proteomics investigations. Proteomics Clin Appl 2009; 3:242-62. [DOI: 10.1002/prca.200800169] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2008] [Indexed: 12/16/2022]
|
33
|
Sapir-Mir M, Mett A, Belausov E, Tal-Meshulam S, Frydman A, Gidoni D, Eyal Y. Peroxisomal localization of Arabidopsis isopentenyl diphosphate isomerases suggests that part of the plant isoprenoid mevalonic acid pathway is compartmentalized to peroxisomes. PLANT PHYSIOLOGY 2008; 148:1219-28. [PMID: 18988695 PMCID: PMC2577245 DOI: 10.1104/pp.108.127951] [Citation(s) in RCA: 94] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Accepted: 08/26/2008] [Indexed: 05/19/2023]
Affiliation(s)
- Maya Sapir-Mir
- Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, Bet-Dagan 50250, Israel
| | | | | | | | | | | | | |
Collapse
|
34
|
Brites P, Mooyer PAW, el Mrabet L, Waterham HR, Wanders RJA. Plasmalogens participate in very-long-chain fatty acid-induced pathology. Brain 2008; 132:482-92. [DOI: 10.1093/brain/awn295] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
|
35
|
Abstract
More than half a century of research on peroxisomes has revealed unique features of this ubiquitous subcellular organelle, which have often been in disagreement with existing dogmas in cell biology. About 50 peroxisomal enzymes have so far been identified, which contribute to several crucial metabolic processes such as β-oxidation of fatty acids, biosynthesis of ether phospholipids and metabolism of reactive oxygen species, and render peroxisomes indispensable for human health and development. It became obvious that peroxisomes are highly dynamic organelles that rapidly assemble, multiply and degrade in response to metabolic needs. However, many aspects of peroxisome biology are still mysterious. This review addresses recent exciting discoveries on the biogenesis, formation and degradation of peroxisomes, on peroxisomal dynamics and division, as well as on the interaction and cross talk of peroxisomes with other subcellular compartments. Furthermore, recent advances on the role of peroxisomes in medicine and in the identification of novel peroxisomal proteins are discussed.
Collapse
Affiliation(s)
- Michael Schrader
- Centre for Cell Biology and Department of Biology, University of Aveiro, 3810-193 Aveiro, Portugal.
| | | |
Collapse
|
36
|
Mi J, Garcia-Arcos I, Alvarez R, Cristobal S. Age-related subproteomic analysis of mouse liver and kidney peroxisomes. Proteome Sci 2007; 5:19. [PMID: 18042274 PMCID: PMC2231346 DOI: 10.1186/1477-5956-5-19] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 11/27/2007] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Despite major recent advances in the understanding of peroxisomal functions and how peroxisomes arise, only scant information is available regarding this organelle in cellular aging. The aim of this study was to characterize the changes in the protein expression profile of aged versus young liver and kidney peroxisome-enriched fractions from mouse and to suggest possible mechanisms underlying peroxisomal aging. Peroxisome-enriched fractions from 10 weeks, 18 months and 24 months C57bl/6J mice were analyzed by quantitative proteomics. RESULTS Peroxisomal proteins were enriched by differential and density gradient centrifugation and proteins were separated by two-dimensional electrophoresis (2-DE), quantified and identified by mass spectrometry (MS). In total, sixty-five proteins were identified in both tissues. Among them, 14 proteins were differentially expressed in liver and 21 proteins in kidney. The eight proteins differentially expressed in both tissues were involved in beta-oxidation, alpha-oxidation, isoprenoid biosynthesis, amino acid metabolism, and stress response. Quantitative proteomics, clustering methods, and prediction of transcription factors, all indicated that there is a decline in protein expression at 18 months and a recovery at 24 months. CONCLUSION These results indicate that some peroxisomal proteins show a tissue-specific functional response to aging. This response is probably dependent on their differential regeneration capacity. The differentially expressed proteins could lead several cellular effects: such as alteration of fatty acid metabolism that could alert membrane protein functions, increase of the oxidative stress and contribute to decline in bile salt synthesis. The ability to detect age-related variations in the peroxisomal proteome can help in the search for reliable and valid aging biomarkers.
Collapse
Affiliation(s)
- Jia Mi
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Itsaso Garcia-Arcos
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
| | - Ruben Alvarez
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Susana Cristobal
- Department of Cell and Molecular Biology, Biomedical Center, Box 596, Uppsala University, SE-751 24 Uppsala, Sweden
- Department of Biochemistry and Biophysics, The Arrhenius Laboratories for Natural Sciences, Stockholm University, SE-106 91 Stockholm, Sweden
| |
Collapse
|