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Kamoshita M, Kumar R, Anteghini M, Kunze M, Islinger M, Martins dos Santos V, Schrader M. Insights Into the Peroxisomal Protein Inventory of Zebrafish. Front Physiol 2022; 13:822509. [PMID: 35295584 PMCID: PMC8919083 DOI: 10.3389/fphys.2022.822509] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 02/07/2022] [Indexed: 12/19/2022] Open
Abstract
Peroxisomes are ubiquitous, oxidative subcellular organelles with important functions in cellular lipid metabolism and redox homeostasis. Loss of peroxisomal functions causes severe disorders with developmental and neurological abnormalities. Zebrafish are emerging as an attractive vertebrate model to study peroxisomal disorders as well as cellular lipid metabolism. Here, we combined bioinformatics analyses with molecular cell biology and reveal the first comprehensive inventory of Danio rerio peroxisomal proteins, which we systematically compared with those of human peroxisomes. Through bioinformatics analysis of all PTS1-carrying proteins, we demonstrate that D. rerio lacks two well-known mammalian peroxisomal proteins (BAAT and ZADH2/PTGR3), but possesses a putative peroxisomal malate synthase (Mlsl) and verified differences in the presence of purine degrading enzymes. Furthermore, we revealed novel candidate peroxisomal proteins in D. rerio, whose function and localisation is discussed. Our findings confirm the suitability of zebrafish as a vertebrate model for peroxisome research and open possibilities for the study of novel peroxisomal candidate proteins in zebrafish and humans.
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Affiliation(s)
- Maki Kamoshita
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Rechal Kumar
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
| | - Marco Anteghini
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Markus Kunze
- Center for Brain Research, Medical University of Vienna, Vienna, Austria
| | - Markus Islinger
- Institute of Neuroanatomy, Mannheim Center for Translational Neuroscience, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Vítor Martins dos Santos
- LifeGlimmer GmbH, Berlin, Germany
- Systems and Synthetic Biology, Wageningen University & Research, Wageningen, Netherlands
| | - Michael Schrader
- College of Life and Environmental Sciences, Biosciences, University of Exeter, Exeter, United Kingdom
- *Correspondence: Michael Schrader,
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Xu W, Zhang Y, Cao H, Sheng Y, Li H, Li Y, Zhao H, Gui X. Metagenomic insights into the microbiota profiles and bioaugmentation mechanism of organics removal in coal gasification wastewater in an anaerobic/anoxic/oxic system by methanol. BIORESOURCE TECHNOLOGY 2018; 264:106-115. [PMID: 29793117 DOI: 10.1016/j.biortech.2018.05.064] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 06/08/2023]
Abstract
Coal gasification wastewater is a typical high phenol-containing, toxic and refractory industrial wastewater. Here, lab-scale anaerobic-anoxic-oxic system was employed to treat real coal gasification wastewater, and methanol was added to oxic tank as the co-substrate to enhance the removal of refractory organic pollutants. The results showed that the average COD removal in oxic effluent increased from 24.9% to 36.0% by adding methanol, the total phenols concentration decreased from 54.4 to 44.9 mg/L. GC-MS analysis revealed that contents of phenolic components and polycyclic aromatic hydrocarbons (PAHs) were decreased compared to the control and their degradation intermediates were observed. Microbial community revealed that methanol increased the abundance of phenolics and PAHs degraders such as Comamonas, Burkholderia and Sphingopyxis. Moreover, functional analysis revealed the relative abundance of functional genes associated with toluene, benzoate and PAHs degradation pathways was higher than that of control based on KEGG database.
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Affiliation(s)
- Weichao Xu
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China; Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuxiu Zhang
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China.
| | - Hongbin Cao
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuxing Sheng
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China; National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Haibo Li
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Yuping Li
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - He Zhao
- Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Xuefei Gui
- School of Chemical and Environmental Engineering, China University of Mining and Technology (Beijing), Beijing 100083, PR China; Beijing Engineering Research Centre of Process Pollution Control, Division of Environmental Engineering and Technology, Institute of Process Engineering, Chinese Academy of Sciences, Beijing 100190, PR China
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Young JM, Nelson JW, Cheng J, Zhang W, Mader S, Davis CM, Morrison RS, Alkayed NJ. Peroxisomal biogenesis in ischemic brain. Antioxid Redox Signal 2015; 22:109-20. [PMID: 25226217 PMCID: PMC4281844 DOI: 10.1089/ars.2014.5833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
AIMS Peroxisomes are highly adaptable and dynamic organelles, adjusting their size, number, and enzyme composition to changing environmental and metabolic demands. We determined whether peroxisomes respond to ischemia, and whether peroxisomal biogenesis is an adaptive response to cerebral ischemia. RESULTS Focal cerebral ischemia induced peroxisomal biogenesis in peri-infarct neurons, which was associated with a corresponding increase in peroxisomal antioxidant enzyme catalase. Peroxisomal biogenesis was also observed in primary cultured cortical neurons subjected to ischemic insult induced by oxygen-glucose deprivation (OGD). A catalase inhibitor increased OGD-induced neuronal death. Moreover, preventing peroxisomal proliferation by knocking down dynamin-related protein 1 (Drp1) exacerbated neuronal death induced by OGD, whereas enhancing peroxisomal biogenesis pharmacologically using a peroxisome proliferator-activated receptor-alpha agonist protected against neuronal death induced by OGD. INNOVATION This is the first documentation of ischemia-induced peroxisomal biogenesis in mammalian brain using a combined in vivo and in vitro approach, electron microscopy, high-resolution laser-scanning confocal microscopy, and super-resolution structured illumination microscopy. CONCLUSION Our findings suggest that neurons respond to ischemic injury by increasing peroxisome biogenesis, which serves a protective function, likely mediated by enhanced antioxidant capacity of neurons.
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Affiliation(s)
- Jennifer M Young
- 1 Department of Anesthesiology & Perioperative Medicine, The Knight Cardiovascular Institute, Oregon Health & Science University , Portland, Oregon
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Madureira TV, Lopes C, Malhão F, Rocha E. Estimation of volume densities of hepatocytic peroxisomes in a model fish: catalase conventional immunofluorescence versus cytochemistry for electron microscopy. Microsc Res Tech 2014; 78:134-9. [PMID: 25431324 DOI: 10.1002/jemt.22455] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 11/03/2014] [Indexed: 11/12/2022]
Abstract
Accurately accessing changes in the intracellular volumes (or numbers) of peroxisomes within a cell can be a lengthy task, because unbiased estimations can be made only by studies conducted under transmission electron microscopy. Yet, such information is often required, namely for correlations with functional data. The optimization and applicability of a fast and new technical proceeding based on catalase immunofluorescence was implemented herein by using primary hepatocytes from brown trout (Salmo trutta f. fario), exposed during 96 h to two distinct treatments (0.1% ethanol and 50 µM of 17α-ethynylestradiol). The time and cost efficiency, together with the results obtained by stereological analyses, specifically directed to the volume densities of peroxisomes, and additionally of the nucleus in relation to the hepatocyte, were compared with the well-established 3,3'-diaminobenzidine cytochemistry for electron microscopy. With the immuno technique it was possible to correctly distinguish punctate peroxisomal profiles, allowing the selection of the marked organelles for quantification. By both methodologies, a significant reduction in the volume density of the peroxisome within the hepatocyte was obtained after an estrogenic input. The most interesting point here was that the volume density ratios were quite correlated between both techniques. Overall, the immunofluorescence protocol for catalase was evidently faster, cheaper and provided reliable quantitative data that discriminated in the same way the compared groups. After this validation study, we recommend the use of catalase immunofluorescence as the first option for rapid screening of changes of the amount of hepatocytic peroxisomes, using their volume density as an indicator.
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Affiliation(s)
- Tânia Vieira Madureira
- ICBAS-Institute of Biomedical Sciences Abel Salazar, U. Porto-University of Porto, Laboratory of Histology and Embryology, Department of Microscopy, Rua Jorge Viterbo Ferreira 228, P 4050-313, Porto, Portugal; CIIMAR/CIMAR-Interdisciplinary Centre of Marine and Environmental Research, U. Porto-University of Porto, Laboratory of Cellular, Molecular and Analytical Studies, Rua dos Bragas 289, P 4050-123, Porto, Portugal
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Abstract
The correlation of light and electron microscopy (EM) is a powerful tool as it combines the investigation of dynamic processes in vivo with the resolution power of the electron microscope. The green fluorescent proteins (GFPs) and its derivatives revolutionized live-cell light microscopy. Hence, this review outlines correlative microscopy of GFP through photo-oxidation, a method that allows for the direct ultrastructural visualization of fluorophores upon illumination. Oxygen radicals generated during the GFP bleaching process photo-oxidize diaminobenzidine (DAB) into an electron dense precipitate that can be visualized both by routine EM of thin sections and by electron tomography for 3D analysis. There are different levels of correlative microscopy, i.e. the correlation of certain areas, cells, or organelles from light to EM, where photo-oxidation of DAB through GFP allows the highest possible degree--the correlation of specific molecules.
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Affiliation(s)
- Markus Grabenbauer
- Department of Systems Cell Biology, Max-Planck-Institute for Molecular Physiology, Otto-Hahn-Str. 11, D-44227 Dortmund, North Rhine-Westphalia, Germany
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Abstract
Peroxisomes are multifunctional organelles with an important role in the generation and decomposition of reactive oxygen species (ROS). In this review, the ROS-producing enzymes, as well as the antioxidative defense system in mammalian peroxisomes, are described. In addition, various conditions leading to disturbances in peroxisomal ROS metabolism, such as abnormal peroxisomal biogenesis, hypocatalasemia, and proliferation of peroxisomes are discussed. We also review the role of mammalian peroxisomes in some physiological and pathological processes involving ROS that lead to mitochondrial abnormalities, defects in cell proliferation, and alterations in the central nervous system, alcoholic cardiomyopathy, and aging. Antioxid.
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Extending the knowledge in histochemistry and cell biology. Histochem Cell Biol 2009; 133:1-40. [PMID: 19946696 DOI: 10.1007/s00418-009-0665-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2009] [Indexed: 01/21/2023]
Abstract
Central to modern Histochemistry and Cell Biology stands the need for visualization of cellular and molecular processes. In the past several years, a variety of techniques has been achieved bridging traditional light microscopy, fluorescence microscopy and electron microscopy with powerful software-based post-processing and computer modeling. Researchers now have various tools available to investigate problems of interest from bird's- up to worm's-eye of view, focusing on tissues, cells, proteins or finally single molecules. Applications of new approaches in combination with well-established traditional techniques of mRNA, DNA or protein analysis have led to enlightening and prudent studies which have paved the way toward a better understanding of not only physiological but also pathological processes in the field of cell biology. This review is intended to summarize articles standing for the progress made in "histo-biochemical" techniques and their manifold applications.
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