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Green SL, Silvester E, Dworkin S, Shakya M, Klein A, Lowe R, Datta K, Holland A. Molecular variations to the proteome of zebrafish larvae induced by environmentally relevant copper concentrations. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2024; 272:106963. [PMID: 38776608 DOI: 10.1016/j.aquatox.2024.106963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 05/14/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
Contaminants are increasingly accumulating in aquatic environments and biota, with potential adverse effects on individual organisms, communities and ecosystems. However, studies that explore the molecular changes in fish caused by environmentally relevant concentrations of metals, such as copper (Cu), are limited. This study uses embryos of the model organism zebrafish (Danio rerio) to investigate effect of Cu on the proteome and amino acid (AA) composition of fish. Wild-type embryos at 24 h post-fertilisation were exposed to Cu (2 µg L-1 to 120 µg L-1) for 96 h and the number of healthy larvae were determined based on larvae that had hatched and did not display loss of equilibrium (LOE). The effect concentrations where Cu caused a 10 % (EC10) or 50 % (EC50) decrease in the number of healthy larvae were calculated as 3.7 µg L-1 and 10.9 µg L-1, respectively. Proteomics analysis of embryos exposed to the EC10 and EC50 concentrations of Cu revealed the proteome to differ more strongly after 48 h than 96 h, suggesting the acclimatisation of some larvae. Exposure to excess Cu caused differentially expressed proteins (DEPs) involved in oxidative stress, mitochondrial respiration, and neural transduction as well as the modulation of the AAs (Proline, Glycine and Alanine). This is the first study to suggest that LOE displayed by Cu-stressed fish may involve the disruption to GABAergic proteins and the calcium-dependent inhibitory neurotransmitter GABA. Moreover, this study highlights that proteomics and AA analysis can be used to identify potential biomarkers for environmental monitoring.
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Affiliation(s)
- Sarah L Green
- Department of Environment and Genetics, La Trobe University, 133 Mckoy Street, West Wodonga, Albury-Wodonga Campus, Victoria 3690, Australia.
| | - Ewen Silvester
- Department of Environment and Genetics, La Trobe University, 133 Mckoy Street, West Wodonga, Albury-Wodonga Campus, Victoria 3690, Australia
| | - Sebastian Dworkin
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora Campus, Victoria, Australia
| | - Manisha Shakya
- School of Environmental and Rural Science, Faculty of Science, Agriculture, Business and Law, University of New England, Armidale, New South Wales, Australia
| | - Annaleise Klein
- Australian Synchrotron, ANSTO, 800 Blackburn Road, Clayton, Victoria 3168, Australia
| | - Rohan Lowe
- Proteomics and Metabolomics Platform, La Trobe University, Bundoora Campus, Victoria, Australia
| | - Keshava Datta
- Proteomics and Metabolomics Platform, La Trobe University, Bundoora Campus, Victoria, Australia
| | - Aleicia Holland
- Department of Environment and Genetics, La Trobe University, 133 Mckoy Street, West Wodonga, Albury-Wodonga Campus, Victoria 3690, Australia
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Sun W, Gu S, Zhang F, Xu M, Chang P, Zhao Y. Congenital cataracts affect the retinal visual cycle and mitochondrial function: A multi-omics study of GJA8 knockout rabbits. J Proteomics 2023; 287:104972. [PMID: 37467890 DOI: 10.1016/j.jprot.2023.104972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/30/2023] [Accepted: 07/08/2023] [Indexed: 07/21/2023]
Abstract
Congenital cataracts are a threat to visual development in children, and the visual impairment persists after surgical treatment; however, the mechanisms involved remain unclear. Previous clinical studies have identified the effect of congenital cataracts on retinal morphology and function. To further understand the molecular mechanisms by which congenital cataracts affect retinal development, we analyzed retina samples from 7-week-old GJA8-knockout rabbits with congenital cataracts and controls by four-dimensional label-free quantification proteomics and untargeted metabolomics. Bioinformatics analysis of proteomic data showed that retinol metabolism, oxidative phosphorylation, and fatty acid degradation pathways were downregulated in the retinas of rabbits with congenital cataracts, indicating that their visual cycle and mitochondrial function were affected. Additional validation of differentially abundant proteins related to the visual cycle and mitochondrial function was performed using Parallel reaction monitoring and western blot experiments. Untargeted metabolome analysis showed significant upregulation of the antioxidant glutathione and ascorbic acid in the retinas of rabbits with congenital cataracts, indicating that their oxidative stress balance was not dysregulated. SIGNIFICANCE: Congenital cataracts in children can alter retinal structure and function, yet the mechanisms are uncertain. Here is the first study to use proteomics and metabolomics approaches to investigate the effects of congenital cataracts on retinal development in the early postnatal period. Our findings suggest that congenital cataracts have an impact on the retinal visual cycle and mitochondrial function. These findings give insight on the molecular pathways behind congenital cataract-induced visual function impairment in the early postnatal period.
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Affiliation(s)
- Weijie Sun
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Siyi Gu
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Fan Zhang
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Mengxiang Xu
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China
| | - Pingjun Chang
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China.
| | - Yune Zhao
- Wenzhou Medical University School of Optometry and Ophthalmology, Eye Hospital, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; The State Key Laboratory of Optometry, Ophthalmology and Vision Science, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China; National Center for Clinical and Medical Research, 270 Xueyuan Road, Wenzhou, Zhejiang 325003, China.
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Gebicki JM, Nauser T. Initiation and Prevention of Biological Damage by Radiation-Generated Protein Radicals. Int J Mol Sci 2021; 23:ijms23010396. [PMID: 35008823 PMCID: PMC8745036 DOI: 10.3390/ijms23010396] [Citation(s) in RCA: 6] [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: 11/28/2021] [Revised: 12/27/2021] [Accepted: 12/27/2021] [Indexed: 12/23/2022] Open
Abstract
Ionizing radiations cause chemical damage to proteins. In aerobic aqueous solutions, the damage is commonly mediated by the hydroxyl free radicals generated from water, resulting in formation of protein radicals. Protein damage is especially significant in biological systems, because proteins are the most abundant targets of the radiation-generated radicals, the hydroxyl radical-protein reaction is fast, and the damage usually results in loss of their biological function. Under physiological conditions, proteins are initially oxidized to carbon-centered radicals, which can propagate the damage to other molecules. The most effective endogenous antioxidants, ascorbate, GSH, and urate, are unable to prevent all of the damage under the common condition of oxidative stress. In a promising development, recent work demonstrates the potential of polyphenols, their metabolites, and other aromatic compounds to repair protein radicals by the fast formation of less damaging radical adducts, thus potentially preventing the formation of a cascade of new reactive species.
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Affiliation(s)
- Janusz M. Gebicki
- Department of Biological Sciences, Macquarie University, Sydney 2109, Australia
- Correspondence:
| | - Thomas Nauser
- Departement für Chemie und Angewandte Biowissenschaften, Eidgenössische Technische Hochschule, 8093 Zurich, Switzerland;
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Filipiak P, Bobrowski K, Hug GL, Schöneich C, Marciniak B. N-Terminal Decarboxylation as a Probe for Intramolecular Contact Formation in γ-Glu-(Pro) n-Met Peptides. J Phys Chem B 2020; 124:8082-8098. [PMID: 32813519 PMCID: PMC7503560 DOI: 10.1021/acs.jpcb.0c04371] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The kinetics of intramolecular-contact formation between remote functional groups in peptides with restricted conformational flexibility were examined using designed peptides with variable-length proline bridges. As probes for this motion, free radicals were produced using the •OH-induced oxidation at the C-terminal methionine residue of γ-Glu-(Pro)n-Met peptides (n = 0-3). The progress of the radicals' motion along the proline bridges was monitored as the radicals underwent reactions along the peptides' backbones. Of particular interest was the reaction between the sulfur atom located in the side chain of the oxidized Met residue and the unprotonated amino group of the glutamic acid moiety. Interactions between them were probed by the radiation-chemical yields (expressed as G values) of the formation of C-centered, α-aminoalkyl radicals (αN) on the Glu residue. These radicals were monitored directly or via their reaction with p-nitroacetophenone (PNAP) to generate the optically detected PNAP•- radical anions. The yields of these αN radicals were found to be linearly dependent on the number of Pro residues. A constant decrease by 0.09 μM J-1 per spacing Pro residue of the radiation-chemical yields of G(αN) was observed. Previous reports support the conclusion that the αN radicals in these cases would have to result from (S∴N)+-bonded cyclic radical cations that arose as a result from direct contact between the ends of the peptides. Furthermore, by analogy with the rate constants for the formation of intramolecularly (S∴S)+-bonded radical cations in Met-(Pro)n-Met peptides ( J. Phys. Chem. B 2016, 120, 9732), the rate constants for the formation of intramolecularly (S∴N)+-bonded radical cations are activated to the same extent for all of the γ-Glu-(Pro)n-Met peptides. Thus, the continuous decrease of G(αN) with the number of Pro residues (from 0 to 3) suggests that the formation of a contact between the S-atom in the C-terminal Met residue and the N-atom of a deprotonated N-terminal amino group of Glu is controlled in peptides with 0 to 3 Pro residues by the relative diffusion of the S•+ and unoxidized N-atom. The overall rate constants of cyclization to form the (S∴N)-bonded radical cations were estimated to be 3.8 × 106, 1.8 × 106, and 8.1 × 105 s-1 for peptides with n = 0, 1, and 2 Pro residues, respectively. If activation is the same for all of the peptides, then these rate constants are a direct indication for the end-to-end dynamics along the chain.
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Affiliation(s)
- Piotr Filipiak
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland.,Center for Advanced Technology, Adam Mickiewicz University, 61-614 Poznan, Poland
| | - Krzysztof Bobrowski
- Institute of Nuclear Chemistry and Technology, 03-195 Warsaw, Poland.,Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Gordon L Hug
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland.,Radiation Laboratory, University of Notre Dame, Notre Dame, Indiana 46556, United States
| | - Christian Schöneich
- School of Pharmacy, Department of Pharmaceutical Chemistry, University of Kansas, Lawrence, Kansas 66047, United States
| | - Bronislaw Marciniak
- Faculty of Chemistry, Adam Mickiewicz University, 61-614 Poznan, Poland.,Center for Advanced Technology, Adam Mickiewicz University, 61-614 Poznan, Poland
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Nauser T, Gebicki JM. Fast reaction of carbon free radicals with flavonoids and other aromatic compounds. Arch Biochem Biophys 2019; 674:108107. [DOI: 10.1016/j.abb.2019.108107] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 08/27/2019] [Accepted: 09/13/2019] [Indexed: 12/26/2022]
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Nauser T, Gebicki JM. Physiological Concentrations of Ascorbate Cannot Prevent the Potentially Damaging Reactions of Protein Radicals in Humans. Chem Res Toxicol 2017; 30:1702-1710. [PMID: 28745873 DOI: 10.1021/acs.chemrestox.7b00160] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The principal initial biological targets of free radicals formed under conditions of oxidative stress are the proteins. The most common products of the interaction are carbon-centered alkyl radicals which react rapidly with oxygen to form peroxyl radicals and hydroperoxides. All these species are reactive, capable of propagating the free radical damage to enzymes, nucleic acids, lipids, and endogenous antioxidants, leading finally to the pathologies associated with oxidative stress. The best chance of preventing this chain of damage is in early repair of the protein radicals by antioxidants. Estimate of the effectiveness of the physiologically significant antioxidants requires knowledge of the antioxidant tissue concentrations and rate constants of their reaction with protein radicals. Previous studies by pulse radiolysis have shown that only ascorbate can repair the Trp and Tyr protein radicals before they form peroxyl radicals under physiological concentrations of oxygen. We have now extended this work to other protein C-centered radicals generated by hydroxyl radicals because these and many other free radicals formed under oxidative stress can produce secondary radicals on virtually any amino acid residue. Pulse radiolysis identified two classes of rate constants for reactions of protein radicals with ascorbate, a faster one in the range (9-60) × 107 M-1 s-1 and a slow one with a range of (0.5-2) × 107 M-1 s-1. These results show that ascorbate can prevent further reactions of protein radicals only in the few human tissues where its concentration exceeds about 2.5 mM.
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Affiliation(s)
- Thomas Nauser
- Department of Chemistry and Applied Biosciences, Swiss Federal Institute of Technology , Zurich CH8093, Switzerland
| | - Janusz M Gebicki
- Department of Biological Sciences, Macquarie University , Sydney, New South Wales 2109, Australia
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Oxidative stress, free radicals and protein peroxides. Arch Biochem Biophys 2016; 595:33-9. [PMID: 27095212 DOI: 10.1016/j.abb.2015.10.021] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 06/02/2015] [Accepted: 10/28/2015] [Indexed: 01/17/2023]
Abstract
Primary free radicals generated under oxidative stress in cells and tissues produce a cascade of reactive secondary radicals, which attack biomolecules with efficiency determined by the reaction rate constants and target concentration. Proteins are prominent targets because they constitute the bulk of the organic content of cells and tissues and react readily with many of the secondary radicals. The reactions commonly lead to the formation of carbon-centered radicals, which generally convert in vivo to peroxyl radicals and finally to semistable hydroperoxides. All of these intermediates can initiate biological damage. This article outlines the advantages of the application of ionizing radiations to studies of radicals, with particular reference to the generation of desired radicals, studies of the kinetics of their reactions and correlating the results with events in biological systems. In one such application, formation of protein hydroperoxides in irradiated cells was inhibited by the intracellular ascorbate and glutathione.
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Trnková L, Dršata J, Boušová I. Oxidation as an important factor of protein damage: Implications for Maillard reaction. J Biosci 2015; 40:419-39. [DOI: 10.1007/s12038-015-9523-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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9
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Pogocki D, Bobrowski K. Oxidative Degradation of Thiaproline Derivatives in Aqueous Solutions Induced by•OH Radicals. Isr J Chem 2014. [DOI: 10.1002/ijch.201300110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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11
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Liochev SI. Free radicals: how do we stand them? Anaerobic and aerobic free radical (chain) reactions involved in the use of fluorogenic probes and in biological systems. Med Princ Pract 2014; 23:195-203. [PMID: 24356000 PMCID: PMC5586870 DOI: 10.1159/000357120] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2013] [Accepted: 11/07/2013] [Indexed: 01/21/2023] Open
Abstract
Biologically significant conclusions have been based on the use of fluorogenic and luminogenic probes for the detection of reactive species. The basic mechanisms of the processes involved have not been satisfactorily elucidated. In the present work, the mechanism of the enzyme and photosensitized oxidation of NAD(P)H by resorufin is analyzed and appears to involve both aerobic and anaerobic free radical chain reactions. There are two major fallouts of this analysis. Many of the conclusions about the participation of radicals based on the use of probes such as resorufin and Amplex red need reevaluation. It is also concluded that anaerobic free radical reactions may be biologically significant, and the possible existence of enzymatic systems to eliminate certain free radicals is discussed.
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Abstract
PVDF membrane was modified by grafting cross-linked collagen after plasma treatment. The modified PVDF membrane has high OD value compared to original PVDF membrane, which means modified PVDF membrane has good hydrophilicity and biocompatibility.
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Affiliation(s)
- Lishun Wu
- Department of Chemistry and Chemical Engineering
- Heze University
- Heze, P.R. China
| | - Junfen Sun
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials
- College of Material Science & Engineering
- Donghua University
- Shanghai 201620, P.R. China
| | - Faqin Tong
- State Key Laboratory for Modification of Chemical Fibers and Polymer Materials
- College of Material Science & Engineering
- Donghua University
- Shanghai 201620, P.R. China
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Houée-Levin C, Bobrowski K. The use of the methods of radiolysis to explore the mechanisms of free radical modifications in proteins. J Proteomics 2013; 92:51-62. [PMID: 23454334 DOI: 10.1016/j.jprot.2013.02.014] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2013] [Revised: 02/01/2013] [Accepted: 02/02/2013] [Indexed: 10/27/2022]
Abstract
The method of radiolysis is based upon the interaction of ionising radiation with the solvent (water). One can form the same free radicals as in conditions of oxidative stress ((•)OH, O2(•)(-), NO2(•)…). Moreover, the quantity of reactive oxygen (ROS) or nitrogen (RNS) species formed in the irradiated medium can be calculated knowing the dose and the radiation chemical yield, G, thus this method is quantitative. The use of the method of radiolysis has provided a wealth of data, especially about the kinetics of the oxidation by various free radicals and their mechanisms, the identification of transients formed, their lifetimes and the possibility to repair them by the so-called antioxidants. In this review we have collected the most recent data about protein oxidation that might be useful to a proteomic approach. This article is part of a Special Issue entitled: Posttranslational Protein modifications in biology and Medicine.
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Affiliation(s)
- Chantal Houée-Levin
- Laboratoire de Chimie Physique, UMR 8000, Université Paris Sud, (France), also at CNRS, France
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