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Badhe MR, Das P, Sahoo S, Paul A, Sahoo PK, Reddy RRK, Suryawanshi AR, Nandanpawar PC, Das Mahapatra K, Nagpure NS, Goswami M, Mohanty J. Physiological Responses to Acute Heat Stress in Rohu, Labeo rohita: Insights from Liver Proteomics. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2024:10.1007/s10126-024-10360-6. [PMID: 39207653 DOI: 10.1007/s10126-024-10360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 08/15/2024] [Indexed: 09/04/2024]
Abstract
Heat stress is a major problem in aquaculture species, causing changes in physiology such as decreased feed intake, growth rate, reproduction, and internal cellular damage, thereby affecting fish's health. The effects of an acute heat stress simulating a daily rise and fall in temperature on summer days were evaluated in the liver proteome of rohu (Labeo rohita) fingerlings in the present study. The fish maintained at 30 °C were gradually exposed to a higher temperature of 36 °C at an increment rate of 1 °C per 1.5 h, and after 3 h at that temperature, it was gradually reduced to 30 °C. The liver tissue samples were collected at 5 am, 5 pm, and 5 am the next day from the exposed and control fish. Protein samples were prepared from the liver tissues, and the extracted proteins were compared using 2-dimensional (2D) gel electrophoresis (2DGE) and mass spectrometry (MS) using a MALDI-TOF/TOF mass spectrometer. A total of 44 differentially expressed protein spots were visualized in 2D gel analysis from heat stress exposed fish at three time points, out of which 21 proteins including one hypothetical protein could be identified by MS. The abundance of five selected differentially expressed proteins (DEPs) was validated using qPCR. The majority of DEPs were found to be involved primarily in lipid, protein and energy metabolism, immune system regulation, cytoskeletal stability, and ROS management. The findings of this study would help in the development of strategies to mitigate heat stress in L. rohita.
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Affiliation(s)
- Mohan R Badhe
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Priyanka Das
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Sonalina Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Anirban Paul
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Pramoda Kumar Sahoo
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | | | | | | | - Kanta Das Mahapatra
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India
| | - Naresh S Nagpure
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Mukunda Goswami
- ICAR-Central Institute of Fisheries Education, Mumbai, 400061, India
| | - Jyotirmaya Mohanty
- ICAR-Central Institute of Freshwater Aquaculture, Bhubaneswar, 751002, India.
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Bai Z, Yin J, Cheng L, Song L, Zhang YY, Wang M. Multistress Interplay: Time and Duration of Ocean Acidification Modulate the Toxicity of Mercury and Other Metals. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:6487-6498. [PMID: 38579165 DOI: 10.1021/acs.est.3c09112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/07/2024]
Abstract
The current understanding of multistress interplay assumes stresses occur in perfect synchrony, but this assumption is rarely met in the natural marine ecosystem. To understand the interplay between nonperfectly overlapped stresses in the ocean, we manipulated a multigenerational experiment (F0-F3) to explore how different temporal scenarios of ocean acidification will affect mercury toxicity in a marine copepod Pseudodiaptomus annandalei. We found that the scenario of past acidification aggravated mercury toxicity but current and persistent acidification mitigated its toxicity. We specifically performed a proteomics analysis for the copepods of F3. The results indicated that current and persistent acidification initiated the energy compensation for development and mercury efflux, whereas past acidification lacked the barrier of H+ and had dysfunction in the detoxification and efflux system, providing a mechanistic understanding of mercury toxicity under different acidification scenarios. Furthermore, we conducted a meta-analysis on marine animals, demonstrating that different acidification scenarios could alter the toxicity of several other metals, despite evidence from nonsynchronous scenarios remaining limited. Our study thus demonstrates that time and duration of ocean acidification modulate mercury toxicity in marine copepods and suggests that future studies should move beyond the oversimplified scenario of perfect synchrony in understanding multistress interaction.
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Affiliation(s)
- Zhuoan Bai
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Junjie Yin
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Luman Cheng
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Luting Song
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Yuan-Ye Zhang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
| | - Minghua Wang
- Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems, College of the Environment & Ecology, Xiamen University, Xiamen 361102, China
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361102, China
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de Souza HM, de Almeida RF, Lopes AP, Hauser-Davis RA. Review: Fish bile, a highly versatile biomarker for different environmental pollutants. Comp Biochem Physiol C Toxicol Pharmacol 2024; 278:109845. [PMID: 38280442 DOI: 10.1016/j.cbpc.2024.109845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 01/05/2024] [Accepted: 01/21/2024] [Indexed: 01/29/2024]
Abstract
Ecotoxicological assessments encompass a broad spectrum of biochemical endpoints and ecological factors, allowing for comprehensive assessments concerning pollutant exposure levels and their effects on both fish populations and surrounding ecosystems. While these evaluations offer invaluable insights into the overall health and dynamics of aquatic environments, they often provide an integrated perspective, making it challenging to pinpoint the precise sources and individual-level responses to environmental contaminants. In contrast, biliary pollutant excretion assessments represent a focused approach aimed at understanding how fish at the individual level respond to environmental stressors. In this sense, the analysis of pollutant profiles in fish bile not only serves as a valuable exposure indicator, but also provides critical information concerning the uptake, metabolism, and elimination of specific contaminants. Therefore, by investigating unique and dynamic fish responses to various pollutants, biliary assessments can contribute significantly to the refinement of ecotoxicological studies. This review aims to discuss the multifaceted utility of bile as a potent biomarker for various environmental pollutants in fish in targeted monitoring strategies, such as polycyclic aromatic hydrocarbons, metals, pesticides, pharmaceuticals, estrogenic compounds, resin acids, hepatotoxins and per- and polyfluorinated substances. The main caveats of this type of assessment are also discussed, as well as future directions of fish bile studies.
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Affiliation(s)
- Heloise Martins de Souza
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil; Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Regina Fonsêca de Almeida
- Departamento de Química, Pontifícia Universidade Católica do Rio de Janeiro (PUC-Rio), Rio de Janeiro, RJ CEP 22453-900, Brazil
| | - Amanda Pontes Lopes
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil; Programa de Pós-Graduação em Biodiversidade e Saúde, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil
| | - Rachel Ann Hauser-Davis
- Laboratório de Avaliação e Promoção da Saúde Ambiental, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Av. Brasil, 4.365, Manguinhos, Rio de Janeiro 21040-360, Brazil.
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Li X, Li M, Xue X, Wang X. Proteomic analysis reveals oxidative stress-induced activation of Hippo signaling in thiamethoxam-exposed Drosophila. CHEMOSPHERE 2023; 338:139448. [PMID: 37437626 DOI: 10.1016/j.chemosphere.2023.139448] [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: 12/14/2022] [Revised: 03/12/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
Thiamethoxam (THIA) is a widely used neonicotinoid insecticide. However, the toxicity and defense mechanisms activated in THIA-exposed insects are unclear. Here, we used isobaric tags for relative and absolute quantitation (iTRAQ) proteomics technology to identify changes in protein expression in THIA-exposed Drosophila. We found that the antioxidant proteins Cyp6a23 and Dys were upregulated, whereas vir-1 was downregulated, which may have been detoxification in response to THIA exposure. Prx5 downregulation promoted the generation of reactive oxygen species. Furthermore, the accumulation of reactive oxygen species led to the induction of antioxidant defenses in THIA-exposed Drosophila, thereby enhancing the levels of oxidative stress markers (e.g., superoxide dismutase, glutathione S-transferase, and glutathione) and reducing catalase expression. Furthermore, the Hippo signaling transcription coactivator Yki was inactivated by THIA. Our results suggesting that Hippo signaling may be necessary to promote insect survival in response to neonicotinoid insecticide toxicity.
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Affiliation(s)
- Xiaoqin Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Mingquan Li
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China
| | - Xianle Xue
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China
| | - Xing Wang
- College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China; Beijing Key Laboratory of Biodiversity and Organic Farming, Beijing, 100193, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, Beijing, 100193, China.
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Yogesh K, Venkateshwarlu M. Modulation in carbohydrate and protein metabolism under sublethal concentration of carbosulfan intoxication in the freshwater fish, Cyprinus carpio (L.). BIOCHEM SYST ECOL 2022. [DOI: 10.1016/j.bse.2022.104500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Gajahin Gamage NT, Miyashita R, Takahashi K, Asakawa S, Senevirathna JDM. Proteomic Applications in Aquatic Environment Studies. Proteomes 2022; 10:proteomes10030032. [PMID: 36136310 PMCID: PMC9505238 DOI: 10.3390/proteomes10030032] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 08/28/2022] [Accepted: 08/30/2022] [Indexed: 11/16/2022] Open
Abstract
Genome determines the unique individualities of organisms; however, proteins play significant roles in the generation of the colorful life forms below water. Aquatic systems are usually complex and multifaceted and can take on unique modifications and adaptations to environmental changes by altering proteins at the cellular level. Proteomics is an essential strategy for exploring aquatic ecosystems due to the diverse involvement of proteins, proteoforms, and their complexity in basic and advanced cellular functions. Proteomics can expedite the analysis of molecular mechanisms underlying biological processes in an aquatic environment. Previous proteomic studies on aquatic environments have mainly focused on pollution assessments, ecotoxicology, their role in the food industry, and extraction and identification of natural products. Aquatic protein biomarkers have been comprehensively reported and are currently extensively applied in the pharmaceutical and medical industries. Cellular- and molecular-level responses of organisms can be used as indicators of environmental changes and stresses. Conversely, environmental changes are expedient in predicting aquatic health and productivity, which are crucial for ecosystem management and conservation. Recent advances in proteomics have contributed to the development of sustainable aquaculture, seafood safety, and high aquatic food production. Proteomic approaches have expanded to other aspects of the aquatic environment, such as protein fingerprinting for species identification. In this review, we encapsulated current proteomic applications and evaluated the potential strengths, weaknesses, opportunities, and threats of proteomics for future aquatic environmental studies. The review identifies both pros and cons of aquatic proteomics and projects potential challenges and recommendations. We postulate that proteomics is an emerging, powerful, and integrated omics approach for aquatic environmental studies.
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Affiliation(s)
- Nadeeka Thushari Gajahin Gamage
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
| | - Rina Miyashita
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Kazutaka Takahashi
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Shuichi Asakawa
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Jayan Duminda Mahesh Senevirathna
- Department of Aquatic Bioscience, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
- Department of Animal Science, Faculty of Animal Science and Export Agriculture, Uva Wellassa University, Badulla 90000, Sri Lanka
- Correspondence:
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Yang Z, Zhou J, Zhu L, Chen A, Cheng Y. Label-free quantification proteomics analysis reveals acute hyper-osmotic responsive proteins in the gills of Chinese mitten crab (Eriocheir sinensis). COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY. PART D, GENOMICS & PROTEOMICS 2022; 43:101009. [PMID: 35777161 DOI: 10.1016/j.cbd.2022.101009] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/12/2022] [Accepted: 06/13/2022] [Indexed: 06/15/2023]
Abstract
Chinese mitten crab (Eriocheir sinensis) is a typical euryhaline crustacean to study osmotic regulation of crustaceans. Osmotic-regulation of Chinese mitten crab is a complex process. In order to study the osmotic-regulation related proteins of Chinese mitten crab, we domesticated Chinese mitten crab for 144 h with 25 salinity sea water (SW) and 0 salinity fresh water (FW) respectively, and then analyzed the proteome of its posterior gills. A total of 1453 proteins were identified by label free proteomics. Under the threshold of 2 fold change (FC), 242 differentially expressed proteins (DEPs) were screened, including 122 up-regulated DEPs and 120 down-regulated DEPs. GO database and KEGG database were used to annotate and enrich DEPs. It was found that DEPs were significantly enriched in energy metabolism, signal transduction, ion transport, actin cytoskeleton, immunity, lipid metabolism, amino acid metabolism and other biological functions. After 144 h of high salinity stress, the energy metabolism of Chinese mitten crab decreased and the expression of actin and cytoskeleton protein increased. In order to cope with oxidative damage caused by high salinity, Chinese mitten crab improved its immunity and antioxidant capacity.
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Affiliation(s)
- Zhigang Yang
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Junyu Zhou
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Liangliang Zhu
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China.
| | - Aqin Chen
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
| | - Yongxu Cheng
- Key Laboratory of Freshwater Aquatic Genetic Resources, Ministry of Agriculture, Shanghai Ocean University, Shanghai 201306, China; Centre for Research on Environmental Ecology and Fish Nutrition (CREEFN) of the Ministry of Agriculture, Shanghai Ocean University, Shanghai, China; National Demonstration Center for Experimental Fisheries Science Education, Shanghai Ocean University, Shanghai, China
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Kumar S, Nehra M, Mehta J, Dilbaghi N, Marrazza G, Kaushik A. Point-of-Care Strategies for Detection of Waterborne Pathogens. SENSORS (BASEL, SWITZERLAND) 2019; 19:E4476. [PMID: 31623064 PMCID: PMC6833035 DOI: 10.3390/s19204476] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/11/2019] [Accepted: 10/13/2019] [Indexed: 12/31/2022]
Abstract
Waterborne diseases that originated due to pathogen microorganisms are emerging as a serious global health concern. Therefore, rapid, accurate, and specific detection of these microorganisms (i.e., bacteria, viruses, protozoa, and parasitic pathogens) in water resources has become a requirement of water quality assessment. Significant research has been conducted to develop rapid, efficient, scalable, and affordable sensing techniques to detect biological contaminants. State-of-the-art technology-assisted smart sensors have improved features (high sensitivity and very low detection limit) and can perform in a real-time manner. However, there is still a need to promote this area of research, keeping global aspects and demand in mind. Keeping this view, this article was designed carefully and critically to explore sensing technologies developed for the detection of biological contaminants. Advancements using paper-based assays, microfluidic platforms, and lateral flow devices are discussed in this report. The emerging recent trends, mainly point-of-care (POC) technologies, of water safety analysis are also discussed here, along with challenges and future prospective applications of these smart sensing technologies for water health diagnostics.
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Affiliation(s)
- Sandeep Kumar
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Monika Nehra
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Jyotsana Mehta
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Neeraj Dilbaghi
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar-Haryana 125001, India.
| | - Giovanna Marrazza
- Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence, Italy.
| | - Ajeet Kaushik
- Department of Natural Sciences, Florida Polytechnic University, Lakeland, FL 33805-8531, USA.
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Bourguignon N, Irazusta V, Isaac P, Estévez C, Maizel D, Ferrero MA. Identification of proteins induced by polycyclic aromatic hydrocarbon and proposal of the phenanthrene catabolic pathway in Amycolatopsis tucumanensis DSM 45259. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2019; 175:19-28. [PMID: 30878660 DOI: 10.1016/j.ecoenv.2019.02.071] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 02/15/2019] [Accepted: 02/22/2019] [Indexed: 06/09/2023]
Abstract
In the present study the polycyclic aromatic hydrocarbon removal and metabolic adaptation of Amycolatopsis tucumanensis DSM 45259 were investigated. Analysis of one-dimensional gel electrophoresis of crude cell extracts revealed differential synthesis of proteins which were identified by MALDI-TOF. To elucidate the phenanthrene metabolic pathway in A. tucumanensis DSM45259, two-dimensional electrophoresis and detection of phenanthrene degradation intermediates by GS-MS were performed. The presence of aromatic substrates resulted in changes in the abundance of proteins involved in the metabolism of aromatic compounds, oxidative stress response, energy production and protein synthesis. The obtained results allowed us to clarify the phenanthrene catabolic pathway, by confirming the roles of several proteins involved in the degradation process and comprehensive adaptation. This may clear the way for more efficient engineering of bacteria in the direction of more effective bioremediation applications.
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Affiliation(s)
- Natalia Bourguignon
- Universidad Tecnológica Nacional (UTN), Facultad Regional de Haédo, París 532, 1706 Haedo, Buenos Aires, Argentina.
| | - Verónica Irazusta
- Instituto de Investigaciones para la Industria Química (INIQUI), CONICET-UNSa, Argentina; Facultad de Ciencias Naturales, UNSa, Salta, Argentina
| | - Paula Isaac
- Centro de Investigaciones y Transferencia de Villa María (CIT Villa María), CONICET-Instituto de Ciencias Básicas y Aplicadas, Universidad Nacional de Villa María, Córdoba, Argentina
| | - Cristina Estévez
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
| | - Daniela Maizel
- Instituto de Astronomía y Física del Espacio, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Buenos Aires, Intendente Güiraldes 2160, C1428EGA CABA, Argentina
| | - Marcela A Ferrero
- Planta Piloto de Procesos Industriales Microbiológicos (PROIMI, CONICET), Tucumán, Argentina
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Wang EH, Appulage DK, McAllister EA, Schug KA. Investigation of Ion Transmission Effects on Intact Protein Quantification in a Triple Quadrupole Mass Spectrometer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1977-1986. [PMID: 28560561 DOI: 10.1007/s13361-017-1696-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 04/02/2017] [Accepted: 04/18/2017] [Indexed: 06/07/2023]
Abstract
Recently, direct intact protein quantitation using triple quadrupole mass spectrometry (QqQ-MS) and multiple reaction monitoring (MRM) was demonstrated (J. Am. Soc. Mass Spectrom. 27, 886-896 (2016)). Even though QqQ-MS is known to provide extraordinary detection sensitivity for quantitative analysis, we found that intact proteins exhibited a less than 5% ion transmission from the first quadrupole to the third quadrupole mass analyzer in the presence of zero collision energy (ZCE). With the goal to enhance intact protein quantitation sensitivity, ion scattering effects, proton transfer effects, and mass filter resolution widths were examined for their contributions to the lost signal. Protein standards myoglobin and ubiquitin along with small molecules reserpine and vancomycin were analyzed together with various collision induced dissociation (CID) gases (N2, He, and Ar) at different gas pressures. Mass resolution settings played a significant role in reducing ion transmission signal. By narrowing the mass resolution window by 0.35 m/z on each side, roughly 75%-90% of the ion signal was lost. The multiply charged proteins experienced additional proton transfer effects, corresponding to 10-fold signal reduction. A study of increased sensitivity of the method was also conducted with various MRM summation techniques. Although the degree of enhancement was analyte-dependent, an up to 17-fold increase in sensitivity was observed for ubiquitin using a summation of multiple MRM transitions. Biological matrix, human urine, and equine plasma were spiked with proteins to demonstrate the specificity of the method. This study provides additional insight into optimizing the use and sensitivity of QqQ-MS for intact protein quantification. Graphical Abstract ᅟ.
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Affiliation(s)
- Evelyn H Wang
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | - Dananjaya Kalu Appulage
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA
| | | | - Kevin A Schug
- Department of Chemistry and Biochemistry, The University of Texas at Arlington, Arlington, TX, 76019, USA.
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Toxicogenomic applications of Chinese rare minnow (Gobiocypris rarus) in aquatic toxicology. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2016; 19:174-180. [DOI: 10.1016/j.cbd.2016.06.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 06/09/2016] [Accepted: 06/15/2016] [Indexed: 11/22/2022]
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12
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Ghosal D, Ghosh S, Dutta TK, Ahn Y. Current State of Knowledge in Microbial Degradation of Polycyclic Aromatic Hydrocarbons (PAHs): A Review. Front Microbiol 2016; 7:1369. [PMID: 27630626 PMCID: PMC5006600 DOI: 10.3389/fmicb.2016.01369] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2016] [Accepted: 08/18/2016] [Indexed: 12/22/2022] Open
Abstract
Polycyclic aromatic hydrocarbons (PAHs) include a group of organic priority pollutants of critical environmental and public health concern due to their toxic, genotoxic, mutagenic and/or carcinogenic properties and their ubiquitous occurrence as well as recalcitrance. The increased awareness of their various adverse effects on ecosystem and human health has led to a dramatic increase in research aimed toward removing PAHs from the environment. PAHs may undergo adsorption, volatilization, photolysis, and chemical oxidation, although transformation by microorganisms is the major neutralization process of PAH-contaminated sites in an ecologically accepted manner. Microbial degradation of PAHs depends on various environmental conditions, such as nutrients, number and kind of the microorganisms, nature as well as chemical property of the PAH being degraded. A wide variety of bacterial, fungal and algal species have the potential to degrade/transform PAHs, among which bacteria and fungi mediated degradation has been studied most extensively. In last few decades microbial community analysis, biochemical pathway for PAHs degradation, gene organization, enzyme system, genetic regulation for PAH degradation have been explored in great detail. Although, xenobiotic-degrading microorganisms have incredible potential to restore contaminated environments inexpensively yet effectively, but new advancements are required to make such microbes effective and more powerful in removing those compounds, which were once thought to be recalcitrant. Recent analytical chemistry and genetic engineering tools might help to improve the efficiency of degradation of PAHs by microorganisms, and minimize uncertainties of successful bioremediation. However, appropriate implementation of the potential of naturally occurring microorganisms for field bioremediation could be considerably enhanced by optimizing certain factors such as bioavailability, adsorption and mass transfer of PAHs. The main purpose of this review is to provide an overview of current knowledge of bacteria, halophilic archaea, fungi and algae mediated degradation/transformation of PAHs. In addition, factors affecting PAHs degradation in the environment, recent advancement in genetic, genomic, proteomic and metabolomic techniques are also highlighted with an aim to facilitate the development of a new insight into the bioremediation of PAH in the environment.
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Affiliation(s)
- Debajyoti Ghosal
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
| | - Shreya Ghosh
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
| | - Tapan K. Dutta
- Department of Microbiology, Bose InstituteKolkata, India
| | - Youngho Ahn
- Environmental Engineering Laboratory, Department of Civil Engineering, Yeungnam UniversityGyeongsan, South Korea
- Disasters Prevention Research Institute, Yeungnam UniversityGyeongsan, South Korea
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Brandt KK, Amézquita A, Backhaus T, Boxall A, Coors A, Heberer T, Lawrence JR, Lazorchak J, Schönfeld J, Snape JR, Zhu YG, Topp E. Ecotoxicological assessment of antibiotics: A call for improved consideration of microorganisms. ENVIRONMENT INTERNATIONAL 2015; 85:189-205. [PMID: 26411644 DOI: 10.1016/j.envint.2015.09.013] [Citation(s) in RCA: 139] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 09/03/2015] [Accepted: 09/10/2015] [Indexed: 05/06/2023]
Abstract
Antibiotics play a pivotal role in the management of infectious disease in humans, companion animals, livestock, and aquaculture operations at a global scale. Antibiotics are produced, consumed, and released into the environment at an unprecedented scale causing concern that the presence of antibiotic residues may adversely impact aquatic and terrestrial ecosystems. Here we critically review the ecotoxicological assessment of antibiotics as related to environmental risk assessment (ERA). We initially discuss the need for more specific protection goals based on the ecosystem service concept, and suggest that the ERA of antibiotics, through the application of a mode of toxic action approach, should make more use of ecotoxicological endpoints targeting microorganisms (especially bacteria) and microbial communities. Key ecosystem services provided by microorganisms and associated ecosystem service-providing units (e.g. taxa or functional groups) are identified. Approaches currently available for elucidating ecotoxicological effects on microorganisms are reviewed in detail and we conclude that microbial community-based tests should be used to complement single-species tests to offer more targeted protection of key ecosystem services. Specifically, we propose that ecotoxicological tests should not only assess microbial community function, but also microbial diversity (‘species’ richness) and antibiotic susceptibility. Promising areas for future basic and applied research of relevance to ERA are highlighted throughout the text. In this regard, the most fundamental knowledge gaps probably relate to our rudimentary understanding of the ecological roles of antibiotics in nature and possible adverse effects of environmental pollution with subinhibitory levels of antibiotics.
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Affiliation(s)
- Kristian K Brandt
- Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark; Sino Danish Center for Education and Research, Beijing, China.
| | - Alejandro Amézquita
- Unilever-Safety & Environmental Assurance Centre, Sharnbrook, United Kingdom
| | - Thomas Backhaus
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
| | | | - Anja Coors
- ECT Oekotoxikologie GmbH, Flörsheim/Main, Germany
| | - Thomas Heberer
- Federal Office of Consumer Protection and Food Safety, Department 3: Veterinary Drugs, Berlin, Germany
| | | | - James Lazorchak
- Office of Research and Development, U.S. Environmental Protection Agency, Cincinnati, OH, USA
| | - Jens Schönfeld
- Umweltbundesamt, Federal Environment Agency, Dessau, Germany
| | - Jason R Snape
- AstraZeneca Global Environment, Alderley Park, United Kingdom
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Edward Topp
- Agriculture and Agri-Food Canada, London, Ontario, Canada.
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14
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Flores-Nunes F, Gomes T, Company R, Moraes RRM, Sasaki ST, Taniguchi S, Bicego MC, Melo CMR, Bainy ACD, Bebianno MJ. Changes in protein expression of pacific oyster Crassostrea gigas exposed in situ to urban sewage. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2015; 22:17267-17279. [PMID: 25398216 DOI: 10.1007/s11356-014-3821-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 11/04/2014] [Indexed: 06/04/2023]
Abstract
The composition and concentration of substances in urban effluents are complex and difficult to measure. These contaminants elicit biological responses in the exposed organisms. Proteomic analysis is a powerful tool in environmental toxicology by evidencing alterations in protein expression due to exposure to contaminants and by providing a useful framework for the development of new potential biomarkers. The aim of this study was to determine changes in protein expression signatures (PES) in the digestive gland of oysters Crassostrea gigas transplanted to two farming areas (LIS and RIB) and to one area contaminated by sanitary sewage (BUC) after 14 days of exposure. This species is one of the most cultivated molluscs in the world. The identified proteins are related to the cytoskeleton (CKAP5 and ACT2), ubiquitination pathway conjugation (UBE3C), G protein-coupled receptor and signal transduction (SVEP1), and cell cycle/division (CCNB3). CKAP5 showed higher expression in oysters kept at BUC in comparison with those kept at the farming areas, while ACT2, UBE3C, SVEP1, and CCNB3 were suppressed. The results suggest that these changes might lead to DNA damage, apoptosis, and interference with the immune system in oyster C. gigas exposed to sewage and give initial information on PES of C. gigas exposed to sanitary sewage, which can subsequently be useful in the development of more sensitive tools for biomonitoring coastal areas, particularly those devoted mainly to oyster farming activities.
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Affiliation(s)
- Fabrício Flores-Nunes
- Laboratory for Biomarkers of Aquatic Contamination and Immunochemistry, Federal University Santa Catarina, Florianópolis, Brazil
| | - Tânia Gomes
- CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Rui Company
- CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal
| | - Roberta R M Moraes
- Laboratory for Biomarkers of Aquatic Contamination and Immunochemistry, Federal University Santa Catarina, Florianópolis, Brazil
| | - Silvio T Sasaki
- Laboratory of Marine Organic Chemistry, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Satie Taniguchi
- Laboratory of Marine Organic Chemistry, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Márcia C Bicego
- Laboratory of Marine Organic Chemistry, Oceanographic Institute, University of São Paulo, São Paulo, Brazil
| | - Cláudio M R Melo
- Laboratory of Marine Molluscs, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Afonso C D Bainy
- Laboratory for Biomarkers of Aquatic Contamination and Immunochemistry, Federal University Santa Catarina, Florianópolis, Brazil
| | - Maria J Bebianno
- CIMA, Faculty of Science and Technology, University of Algarve, Campus de Gambelas, 8005-139, Faro, Portugal.
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15
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Epelboin Y, Quéré C, Pernet F, Pichereau V, Corporeau C. Energy and Antioxidant Responses of Pacific Oyster Exposed to Trace Levels of Pesticides. Chem Res Toxicol 2015; 28:1831-41. [DOI: 10.1021/acs.chemrestox.5b00269] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Yanouk Epelboin
- Ifremer, UMR 6539
(CNRS, UBO, IRD, Ifremer), Laboratoire des sciences de l’Environnement
Marin (LEMAR), 29280 Plouzané, France
| | - Claudie Quéré
- Ifremer, UMR 6539
(CNRS, UBO, IRD, Ifremer), Laboratoire des sciences de l’Environnement
Marin (LEMAR), 29280 Plouzané, France
| | - Fabrice Pernet
- Ifremer, UMR 6539
(CNRS, UBO, IRD, Ifremer), Laboratoire des sciences de l’Environnement
Marin (LEMAR), 29280 Plouzané, France
| | - Vianney Pichereau
- UBO,
UMR 6539 (CNRS, UBO, IRD, Ifremer), Laboratoire des sciences de l’Environnement
Marin (LEMAR), Institut Universitaire Européen de la Mer (IUEM), Université de Brest, 29280 Plouzané, France
| | - Charlotte Corporeau
- Ifremer, UMR 6539
(CNRS, UBO, IRD, Ifremer), Laboratoire des sciences de l’Environnement
Marin (LEMAR), 29280 Plouzané, France
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16
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Intact cell mass spectrometry as a rapid and specific tool for the differentiation of toxic effects in cell-based ecotoxicological test systems. Anal Bioanal Chem 2015; 407:7721-31. [PMID: 26255296 PMCID: PMC4575386 DOI: 10.1007/s00216-015-8937-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Revised: 07/21/2015] [Accepted: 07/23/2015] [Indexed: 02/04/2023]
Abstract
In the last few decades, MALDI-TOF MS has become a useful technique not only in proteomics, but also as a fast and specific tool for whole cell analysis through intact cell mass spectrometry (IC-MS). The present study evaluated IC-MS as a novel tool for the detection of distinct patterns that can be observed after exposure to a certain toxin or concentration by utilizing the eukaryotic fish cell line RTL-W1. Two different viability assays were performed to define the range for IC-MS investigations, each of which employing copper sulfate, acridine, and β-naphthoflavone (BNF) as model compounds for several classes of environmental toxins. The IC-MS of RTL-W1 cells revealed not only specific spectral patterns for the various toxins, but also that the concentration used had an effect on RTL-W1 profiles. After the exposure with copper sulfate and acridine, the spectra of RTL-W1 showed a significant increase of certain peaks in the higher mass range (m/z >7000), which is probably attributed to the apoptosis of RTL-W1. On the contrary, exposure to BNF showed a distinct change of ion abundances only in the lower mass range (m/z <7000). Furthermore, a set of mass peaks could be identified as a specific biomarker for a single toxin treatment, so IC-MS demonstrates a new method for the distinction of toxic effects in fish cells. Due to fast sample preparation and high throughput, IC-MS offers great potential for ecotoxicological studies to investigate cellular effects of different substances and complex environmental samples. Use of intact cell MALDI-TOF mass spectrometry (IC-MS) to detect and differentiate toxic effects of environmental toxins in rainbow trout liver cell line RTL-W1 ![]()
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17
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Wang SY, Kuo CH, Tseng YJ. Ion Trace Detection Algorithm to Extract Pure Ion Chromatograms to Improve Untargeted Peak Detection Quality for Liquid Chromatography/Time-of-Flight Mass Spectrometry-Based Metabolomics Data. Anal Chem 2015; 87:3048-55. [DOI: 10.1021/ac504711d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- San-Yuan Wang
- Department of Computer Science
and Information Engineering, ‡The Metabolomics
Core Laboratory, Center of Genomic Medicine, §School of Pharmacy, College of Medicine, ∥Department of Pharmacy,
National Taiwan University Hospital, ⊥Graduate Institute of Biomedical
Electronics and Bioinformatics, #Drug Research Center, College of Medicine, National Taiwan University, 106 Taipei, Taiwan
| | - Ching-Hua Kuo
- Department of Computer Science
and Information Engineering, ‡The Metabolomics
Core Laboratory, Center of Genomic Medicine, §School of Pharmacy, College of Medicine, ∥Department of Pharmacy,
National Taiwan University Hospital, ⊥Graduate Institute of Biomedical
Electronics and Bioinformatics, #Drug Research Center, College of Medicine, National Taiwan University, 106 Taipei, Taiwan
| | - Yufeng J. Tseng
- Department of Computer Science
and Information Engineering, ‡The Metabolomics
Core Laboratory, Center of Genomic Medicine, §School of Pharmacy, College of Medicine, ∥Department of Pharmacy,
National Taiwan University Hospital, ⊥Graduate Institute of Biomedical
Electronics and Bioinformatics, #Drug Research Center, College of Medicine, National Taiwan University, 106 Taipei, Taiwan
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18
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Zheng L, Yu J, Shi H, Xia L, Xin Q, Zhang Q, Zhao H, Luo J, Jin W, Li D, Zhou J. Quantitative toxicoproteomic analysis of zebrafish embryos exposed to a retinoid X receptor antagonist UVI3003. J Appl Toxicol 2015; 35:1049-57. [DOI: 10.1002/jat.3099] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 11/03/2014] [Accepted: 11/13/2014] [Indexed: 12/29/2022]
Affiliation(s)
- Liang Zheng
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
- Department of Cancer Biology and Pharmacology; University of Illinois College of Medicine; One Illini Drive Peoria IL 61605 USA
| | - Jianlan Yu
- Asia Pacific Application Support Center; AB SCIEX; 888 Tianlin Road Shanghai 200233 China
| | - Huahong Shi
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Liang Xia
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Qi Xin
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Qiang Zhang
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Heng Zhao
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Ji Luo
- Asia Pacific Application Support Center; AB SCIEX; 888 Tianlin Road Shanghai 200233 China
| | - Wenhai Jin
- Asia Pacific Application Support Center; AB SCIEX; 888 Tianlin Road Shanghai 200233 China
| | - Daoji Li
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
| | - Junliang Zhou
- State Key Laboratory of Estuarine and Coastal Research; East China Normal University; 3663 Zhongshan (N) Road Shanghai 200062 China
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19
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Ge Y, Bruno M, Wallace K, Leavitt S, Andrews D, Spassova MA, Xi M, Roy A, Haykal-Coates N, Lefew W, Swank A, Winnik WM, Chen C, Woodard J, Farraj A, Teichman KY, Ross JA. Systematic proteomic approach to characterize the impacts of chemical interactions on protein and cytotoxicity responses to metal mixture exposures. J Proteome Res 2014; 14:183-92. [PMID: 25285964 DOI: 10.1021/pr500795d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Chemical interactions have posed a big challenge in toxicity characterization and human health risk assessment of environmental mixtures. To characterize the impacts of chemical interactions on protein and cytotoxicity responses to environmental mixtures, we established a systems biology approach integrating proteomics, bioinformatics, statistics, and computational toxicology to measure expression or phosphorylation levels of 21 critical toxicity pathway regulators and 445 downstream proteins in human BEAS-2B cells treated with 4 concentrations of nickel, 2 concentrations each of cadmium and chromium, as well as 12 defined binary and 8 defined ternary mixtures of these metals in vitro. Multivariate statistical analysis and mathematical modeling of the metal-mediated proteomic response patterns showed a high correlation between changes in protein expression or phosphorylation and cellular toxic responses to both individual metals and metal mixtures. Of the identified correlated proteins, only a small set of proteins including HIF-1α is likely to be responsible for selective cytotoxic responses to different metals and metals mixtures. Furthermore, support vector machine learning was utilized to computationally predict protein responses to uncharacterized metal mixtures using experimentally generated protein response profiles corresponding to known metal mixtures. This study provides a novel proteomic approach for characterization and prediction of toxicities of metal and other chemical mixtures.
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Affiliation(s)
- Yue Ge
- National Health and Environmental Effects Research Laboratory, U.S. Environmental Protection Agency , 109 T. W. Alexander Drive, Research Triangle Park, North Carolina 27709, United States
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20
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Schoenfuss HL, Maie T, Moody KN, Lesteberg KE, Blob RW, Schoenfuss TC. Stairway to heaven: evaluating levels of biological organization correlated with the successful ascent of natural waterfalls in the Hawaiian stream goby Sicyopterus stimpsoni. PLoS One 2013; 8:e84851. [PMID: 24386424 PMCID: PMC3873996 DOI: 10.1371/journal.pone.0084851] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 11/19/2013] [Indexed: 12/02/2022] Open
Abstract
Selective pressures generated by locomotor challenges act at the level of the individual. However, phenotypic variation among individuals that might convey a selective advantage may occur across any of multiple levels of biological organization. In this study, we test for differences in external morphology, muscle mechanical advantage, muscle fiber type and protein expression among individuals of the waterfall climbing Hawaiian fish Sicyopterus stimpsoni collected from sequential pools increasing in elevation within a single freshwater stream. Despite predictions from previous laboratory studies of morphological selection, few directional morphometric changes in body shape were observed at successively higher elevations. Similarly, lever arm ratios associated with the main pelvic sucker, central to climbing ability in this species, did not differ between elevations. However, among climbing muscles, the adductor pelvicus complex (largely responsible for generating pelvic suction during climbing) contained a significantly greater red muscle fiber content at upstream sites. A proteomic analysis of the adductor pelvicus revealed two-fold increases in expression levels for two respiratory chain proteins (NADH:ubiquinone reductase and cytochrome b) that are essential for aerobic respiration among individuals from successively higher elevations. Assessed collectively, these evaluations reveal phenotypic differences at some, but not all levels of biological organization that are likely the result of selective pressures experienced during climbing.
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Affiliation(s)
- Heiko L. Schoenfuss
- Aquatic Toxicology Laboratory, Saint Cloud State University, Saint Cloud, Minnesota, United States of America
| | - Takashi Maie
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Kristine N. Moody
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Kelsey E. Lesteberg
- Aquatic Toxicology Laboratory, Saint Cloud State University, Saint Cloud, Minnesota, United States of America
| | - Richard W. Blob
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Tonya C. Schoenfuss
- Department of Food Science and Nutrition, University of Minnesota, Saint Paul, Minnesota, United States of America
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21
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Huang Q, Zhang J, Peng S, Du M, Ow S, Pu H, Pan C, Shen H. Proteomic analysis of perfluorooctane sulfonate-induced apoptosis in human hepatic cells using the iTRAQ technique. J Appl Toxicol 2013; 34:1342-51. [PMID: 24301089 DOI: 10.1002/jat.2963] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/10/2013] [Accepted: 10/14/2013] [Indexed: 01/09/2023]
Abstract
Perfluorooctane sulfonate (PFOS) is one of the most commonly used perfluorinated compounds, whose environmental exposure has been associated with a number of adverse health outcomes. However, the molecular mechanisms involved in PFOS toxicity are still not well elucidated. In the present study, we applied iTRAQ labeling quantitative proteomic technology to investigate the differential protein expression profiles of non-tumor human hepatic cells (L-02) exposed to PFOS. A total of 18 proteins were differentially expressed in a dose-dependent manner in PFOS-treated cells versus the control. Among these, 11 proteins were up-regulated and 7 were down-regulated. Gene ontology analysis indicated that PFOS would exert toxic effects on L-02 cells by affecting multiple biological processes, including protein biosynthesis and degradation, mRNA processing and splicing, transcription, signal transduction and transport. Furthermore, the proteomic results especially proposed that the inhibition of HNRNPC, HUWE1 and UBQLN1, as well as the induction of PAF1 is involved in the activation of the p53 and c-myc signaling pathways, which then trigger the apoptotic process in L-02 cells exposed to PFOS. Overall, these data will aid our understanding of the mechanisms responsible for PFOS-mediated hepatotoxicity, and develop useful biomarkers for monitoring and evaluating PFOS contamination in the environment.
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Affiliation(s)
- Qingyu Huang
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
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22
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Malécot M, Guével B, Pineau C, Holbech BF, Bormans M, Wiegand C. Specific proteomic response of Unio pictorum mussel to a mixture of glyphosate and microcystin-LR. J Proteome Res 2013; 12:5281-92. [PMID: 23972258 DOI: 10.1021/pr4006316] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cyanobacterial toxins and pesticides regularly impact freshwaters. Microcystin-LR is one of the most toxic and common cyanobacterial toxins whereas glyphosate is the active ingredient of a widely use herbicide. As filter feeders, freshwater mussels are particularly exposed. Like many native bivalve species, Unio pictorum suffers from a continuous decline in Europe. In order to get a deeper insight of its response to contaminants, U. pictorum was exposed to either 10 μg L(-1) of microcystin-LR or 10 μg L(-1) of glyphosate or a mixture of both. Proteins of the digestive glands were extracted and analyzed by DIGE. Gel analysis revealed 103 spots with statistical variations, and the response seems to be less toward glyphosate than to microcystin-LR. Specific spots have variations only when exposed to the mixture, showing that there is an interaction of both contaminants in the responses triggered. The proteins of 30 spots have been identified. They belong mostly to the cytoskeleton family, but proteins of the oxidative pathway, detoxification, and energetic metabolism were affected either by glyphosate or microcystin-LR or by the mixture. These results demonstrate the importance to study contaminants at low concentrations representative of those found in the field and that multicontaminations can lead to different response pathways.
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Affiliation(s)
- Mélodie Malécot
- Université Européenne de Bretagne , 5 Boulevard Laënnec, 35000 Rennes, France
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23
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Wu S, Xu X, Zhao S, Shen F, Chen J. Evaluation of phenanthrene toxicity on earthworm (Eisenia fetida): an ecotoxicoproteomics approach. CHEMOSPHERE 2013; 93:963-971. [PMID: 23856470 DOI: 10.1016/j.chemosphere.2013.05.062] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 05/23/2013] [Accepted: 05/25/2013] [Indexed: 06/02/2023]
Abstract
The goal of this study was to identify promising new biomarkers of phenanthrene by identifying differentially expressed proteins in Eisenia fetida after exposure to phenanthrene. Extracts of earthworm epithelium collected at days 2, 7, 14, and 28 after phenanthrene exposure were analyzed by two dimensional electrophoresis (2-DE) and quantitative image analysis. Comparing the intensity of protein spots, 36 upregulated proteins and 45 downregulated proteins were found. Some of the downregulated and upregulated proteins were verified by MALDI-TOF/TOF-MS and database searching. Downregulated proteins in response to phenanthrene exposure were involved in glycolysis, energy metabolism, chaperones, proteolysis, protein folding and electron transport. In contrast, oxidation reduction, oxygen transport, defense systems response to pollutant, protein biosynthesis and fatty acid biosynthesis were upregulated in phenanthrene-treated E. fetida. In addition, ATP synthase b subunit, lysenin-related protein 2, lombricine kinase, glyceraldehyde 3-phosphate dehydrogenase, actinbinding protein, and extracellular globin-4 seem to be potential biomarkers since these biomarker were able to low levels (2.5 mg kg(-1)) of phenanthrene. Our study provides a functional profile of the phenanthrene-responsive proteins in earthworms. The variable levels and trends in these spots could play a potential role as novel biomarkers for monitoring the levels of phenanthrene contamination in soil ecosystems.
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Affiliation(s)
- Shijin Wu
- College of Biological and Environmental Engineering, Zhejiang University of Technology, Hangzhou 310032, People's Republic of China
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24
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Ji C, Wu H, Wei L, Zhao J, Wang Q, Lu H. Responses of Mytilus galloprovincialis to bacterial challenges by metabolomics and proteomics. FISH & SHELLFISH IMMUNOLOGY 2013; 35:489-498. [PMID: 23711471 DOI: 10.1016/j.fsi.2013.05.009] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Revised: 04/26/2013] [Accepted: 05/06/2013] [Indexed: 06/02/2023]
Abstract
Pathogens can cause diseases and lead to massive mortalities of aquaculture animals and substantial economic loss. In this work, we studied the responses induced by Micrococcus luteus and Vibrio anguillarum in gill of mussel Mytilus galloprovincialis at protein and metabolite levels. Metabolic biomarkers (e.g., amino acids, betaine, ATP) suggested that both M. luteus and V. anguillarum induced disturbances in energy metabolism and osmotic regulation. The unique and some more remarkably altered metabolic biomarkers (threonine, alanine, aspartate, taurine, succinate) demonstrated that V. anguillarum could cause more severe disturbances in osmotic regulation and energy metabolism. Proteomic biomarkers (e.g., goose-type lysozyme 2, matrilin, ependymin-related protein, peptidyl-prolyl cis-trans isomerases) indicated that M. luteus caused immune stress, and disturbances in signaling pathways and protein synthesis. However, V. anguillarum mainly induced oxidative stress and disturbance in energy metabolism in mussel gills indicated by altered procollagen-proline dioxygenase, protein disulfide isomerase, nucleoside diphosphate kinases, electron transfer flavoprotein and glutathione S-transferase. This work confirmed that an integration of proteomics and metabolomics could provide an insightful view into the effects of pathogens to the marine mussel M. galloprovincialis.
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Affiliation(s)
- Chenglong Ji
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research (YIC), Chinese Academy of Sciences (CAS), Shandong Provincial Key Laboratory of Coastal Zone Environmental Processes, YICCAS, Yantai 264003, PR China
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25
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Sacheti P, Bhonsle H, Patil R, Kulkarni MJ, Srikanth R, Gade W. Arsenomics of Exiguobacterium sp. PS (NCIM 5463). RSC Adv 2013. [DOI: 10.1039/c3ra40897c] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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26
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Liu F, Wang WX. Proteome pattern in oysters as a diagnostic tool for metal pollution. JOURNAL OF HAZARDOUS MATERIALS 2012; 239-240:241-8. [PMID: 22999020 DOI: 10.1016/j.jhazmat.2012.08.069] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2012] [Revised: 08/27/2012] [Accepted: 08/28/2012] [Indexed: 05/20/2023]
Abstract
The present study investigated whether proteome pattern of an oyster Crassostrea hongkongensis could be used as a diagnostic tool for contamination and toxicity of metals/metalloids in a real multiple metal-contaminated estuary. We collected oysters along a pollution gradient from highly contaminated to relatively clean sites. The oysters showed distinct contamination gradients of Cu, Zn and Cd. Proteomic analysis of the oyster gills as one of major metal targets identified a proteome pattern composed of 13 commonly altered proteins in the contaminated oysters. The discovered proteome pattern completely segregated the contaminated from the clean individuals, and the pattern achieved clear classification of the oysters with different contamination levels. Importantly, the integrated changes of gill proteome were linearly related to the integrated contamination of the metal mixtures present in oyster tissues. It is suggested that proteome pattern is a promising diagnostic tool for metal pollution assessment in environmental monitoring programs.
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Affiliation(s)
- Fengjie Liu
- Division of Life Science, The Hong Kong University of Science and Technology (HKUST), Clear Water Bay, Kowloon, Hong Kong
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27
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Tan F, Jin Y, Liu W, Quan X, Chen J, Liang Z. Global liver proteome analysis using iTRAQ labeling quantitative proteomic technology to reveal biomarkers in mice exposed to perfluorooctane sulfonate (PFOS). ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:12170-12177. [PMID: 23046066 DOI: 10.1021/es3027715] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Proteomic analysis allows detection of changes of proteins expression in organisms exposed to environmental pollutants, leading to the discovery of biomarkers of exposure and understanding of the action mechanism of toxicity. In the present study, we applied iTRAQ labeling quantitative proteomic technology for global characterization of the liver proteome in mice exposed to perfluorooctane sulfonate (PFOS). This successfully identified and quantified 1038 unique proteins. Seventy-one proteins showed a significant expression change in the treated groups (1.0, 2.5, 5.0 mg/kg of body weight) compared with the control group, and 16 proteins displayed strong dose-dependent changes. Gene ontology analysis showed that these differential proteins were significantly enriched and mainly involved in lipid metabolism, transport, biosynthetic processes, and response to stimulus. We detected significantly increased expression levels of enzymes regulating peroxisomal β-oxidation-including long-chain acyl-CoA synthetase, acyl-CoA oxidase 1, bifunctional enzyme, and 3-ketoacyl-CoA thiolase A. PFOS also significantly induced cytochrome P450s and glutathione S-transferases that are responsible for the metabolism of xenobiotic compounds. The expressions of several proteins with important biological functions-such as cysteine sulfinic acid decarboxylase, aldehyde dehydrogenase, and apolipoprotein A-I, also correlated with PFOS exposure. Together, the present results provide insight into the molecular mechanism and biomarkers for PFOS-induced effects.
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Affiliation(s)
- Feng Tan
- Key Laboratory of Industrial Ecology and Environmental Engineering (MOE), School of Environmental Science and Technology, Dalian University of Technology, Dalian 116024, China.
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Ben Fredj F, Han J, Irie M, Funamizu N, Ghrabi A, Isoda H. Assessment of wastewater-irrigated soil containing heavy metals and establishment of specific biomarkers. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2012; 84:54-62. [PMID: 22795889 DOI: 10.1016/j.ecoenv.2012.06.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2012] [Revised: 05/18/2012] [Accepted: 06/20/2012] [Indexed: 06/01/2023]
Abstract
Irrigation with treated wastewater (TWW) is a vital alternative for arid and semi-arid lands but it poses pollution-risk to soil, vegetation and groundwater. Therefore, in the present study, in vitro bioassays were used to evaluate the adverse effects of TWW and irrigated-soil extract sample, on mammalian cells, with respect to heavy metal--Ni, Cd, Pb, Fe, Al-content. The heat shock protein (HSP) 47, E-screen, and transepithelial electrical resistance (TEER) assays served to investigate the stress response of treated-HSP47-transfected Chinese hamster ovary (CHO) cells, the estrogenic activity of the samples in MCF-7 breast cancer cells, and the barrier function (BF) of Caco-2 cells. Furthermore, proteomics analyses were performed to shed light on involved mechanisms and to establish pollution biomarkers. Results showed that the TWW elicited a stress response on HSP cells from 0.1% concentration while soil extract samples exhibited a stress at 1%. TWW induced an estrogenic activity at 10%; up-regulating cell proliferation and tumor-related proteins. Soil extract triggered the enhanced expression of HSP70 family proteins as survival mechanisms against their cytotoxicity toward MCF-7 cells. Moreover, depending on the concentration, 1% of soil extract from 20 cm depth (T20) resulted in a disruption of BF in Caco-2 cells involving cell metabolism, protein synthesis and tumor marker proteins, whereas, 5% of T20 induced the expression of BF-related proteins associated to heat shock, oxidative stress, cell proliferation and glycolytic metabolic pathway. These biological techniques were found to be extremely useful to evaluate the impact of wastewater reuse and to establish specific biomarkers that are common proteins for humans, other mammals and plants. Future studies should focus on exposure quantifications.
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Affiliation(s)
- F Ben Fredj
- Alliance for Research on North Africa (ARENA), University of Tsukuba, 1-1-1 Tennodai, Tsukuba City, Ibaraki 305-8572, Japan.
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Liu F, Wang DZ, Wang WX. Cadmium-induced changes in trace element bioaccumulation and proteomics perspective in four marine bivalves. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2012; 31:1292-1300. [PMID: 22488592 DOI: 10.1002/etc.1823] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/16/2011] [Accepted: 01/13/2012] [Indexed: 05/31/2023]
Abstract
Bivalves are employed widely as biomonitors of metal pollution and proteomics has increasingly been applied to solve ecotoxicological issues. This study aimed to investigate the effects of Cd exposure on the bioaccumulation of other trace elements and reveal the molecular mechanisms using proteomics technologies. The results showed that Cd exposure resulted in remarkable changes in body concentrations of Zn, Cu, Ag, Co, Ni, Pb, and Se in four marine bivalves (scallop Chlamys nobilis, clam Ruditapes philippinarum, mussel Perna viridis, and oyster Saccostrea cucullata). Generally, the bivalves exposed to higher Cd concentration accumulated higher concentrations of Zn, Cu, and Se, but a lower concentration of Co. The accumulation of Ag, Ni, and Pb was specific for different species. The data strongly suggest that the influences of one metal exposure on the bioaccumulation of other metals/metalloids need to be considered in interpreting body concentrations of the elements in the biomonitors. Cd exposure had little effect on bivalve proteomes, and the identified proteins were insufficient to explain the observed disruption of trace element metabolism. However, protein expression signatures composed of the altered proteins could distinguish the clams and the mussels with different body Cd levels. The strong up-regulation of galectin in Cd-exposed oysters indicated the protein as a novel biomarker in environmental monitoring.
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Affiliation(s)
- Fengjie Liu
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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Proteomic research in bivalves: towards the identification of molecular markers of aquatic pollution. J Proteomics 2012; 75:4346-59. [PMID: 22579653 DOI: 10.1016/j.jprot.2012.04.027] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/17/2012] [Accepted: 04/20/2012] [Indexed: 11/21/2022]
Abstract
Biomonitoring of aquatic environment and assessment of ecosystem health play essential roles in the development of effective strategies for the protection of the environment, human health and sustainable development. Biomarkers of pollution exposure have been extensively utilized in the last few decades to monitor the health of organisms and hence assess environmental status. However, the use of single biomarkers against biotic or abiotic stressors may be limited by the lack of sensitivity and specificity. Therefore, more recently, the search for novel biomarkers has been focused on the application of OMICS methodologies. Environmental proteomics focuses on the analysis of an organism's proteome and the detection of changes in the level of individual proteins/peptides in response to environmental stressors. Proteomics can provide a more robust approach for the assessment of environmental stress and therefore exposure to pollutants. This review aims to summarize the proteomic research in bivalves, a group of sessile and filter feeding organisms that play an important function as "sentinels" of the aquatic environment. A description of the main proteomic methodologies is provided. The current knowledge in bivalves' toxicology, achieved with proteomics, is reported describing the main biochemical markers identified. A brief discussion regarding future challenges in this area of research emphasizing the development of more descriptive gene/protein databases that could support the OMICs approaches is presented.
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Gotelli NJ, Ellison AM, Ballif BA. Environmental proteomics, biodiversity statistics and food-web structure. Trends Ecol Evol 2012; 27:436-42. [PMID: 22459246 DOI: 10.1016/j.tree.2012.03.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 01/29/2012] [Accepted: 03/03/2012] [Indexed: 11/17/2022]
Abstract
Pioneering studies in environmental proteomics have revealed links between protein diversity and ecological function in simple ecological communities, such as microbial biofilms. In the near future, high-throughput proteomic methods will be applied to more complex ecological systems in which microbes and macrobes interact. Data structures in biodiversity and protein surveys have many similarities, so the statistical methods that ecologists use for analyzing biodiversity data should be adapted for use with quantitative surveys of protein diversity. However, increasing quantities of protein and bioinformatics data will not, by themselves, reveal the functional significance of proteins. Instead, ecologists should be measuring changes in the abundance of protein cohorts in response to replicated field manipulations, including nutrient enrichment and removal of top predators.
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Affiliation(s)
- Nicholas J Gotelli
- Department of Biology, University of Vermont, 109 Carrigan Drive, Burlington, VT 05405, USA.
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Altenburger R, Scholz S, Schmitt-Jansen M, Busch W, Escher BI. Mixture toxicity revisited from a toxicogenomic perspective. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2012; 46:2508-22. [PMID: 22283441 DOI: 10.1021/es2038036] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
The advent of new genomic techniques has raised expectations that central questions of mixture toxicology such as for mechanisms of low dose interactions can now be answered. This review provides an overview on experimental studies from the past decade that address diagnostic and/or mechanistic questions regarding the combined effects of chemical mixtures using toxicogenomic techniques. From 2002 to 2011, 41 studies were published with a focus on mixture toxicity assessment. Primarily multiplexed quantification of gene transcripts was performed, though metabolomic and proteomic analysis of joint exposures have also been undertaken. It is now standard to explicitly state criteria for selecting concentrations and provide insight into data transformation and statistical treatment with respect to minimizing sources of undue variability. Bioinformatic analysis of toxicogenomic data, by contrast, is still a field with diverse and rapidly evolving tools. The reported combined effect assessments are discussed in the light of established toxicological dose-response and mixture toxicity models. Receptor-based assays seem to be the most advanced toward establishing quantitative relationships between exposure and biological responses. Often transcriptomic responses are discussed based on the presence or absence of signals, where the interpretation may remain ambiguous due to methodological problems. The majority of mixture studies design their studies to compare the recorded mixture outcome against responses for individual components only. This stands in stark contrast to our existing understanding of joint biological activity at the levels of chemical target interactions and apical combined effects. By joining established mixture effect models with toxicokinetic and -dynamic thinking, we suggest a conceptual framework that may help to overcome the current limitation of providing mainly anecdotal evidence on mixture effects. To achieve this we suggest (i) to design studies to establish quantitative relationships between dose and time dependency of responses and (ii) to adopt mixture toxicity models. Moreover, (iii) utilization of novel bioinformatic tools and (iv) stress response concepts could be productive to translate multiple responses into hypotheses on the relationships between general stress and specific toxicity reactions of organisms.
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Affiliation(s)
- Rolf Altenburger
- Department Bioanalytical Ecotoxicology, UFZ - Helmholtz Centre for Environmental Research, Permoser Street 15, 04318 Leipzig, Germany.
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Thompson EL, Taylor DA, Nair SV, Birch G, Haynes PA, Raftos DA. Proteomic discovery of biomarkers of metal contamination in Sydney Rock oysters (Saccostrea glomerata). AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2012; 109:202-12. [PMID: 22030410 DOI: 10.1016/j.aquatox.2011.09.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 09/22/2011] [Accepted: 09/27/2011] [Indexed: 05/20/2023]
Abstract
In the current study we examined the effects of metal contamination on the protein complement of Sydney Rock oysters. Saccostrea glomerata were exposed for 4 days to three environmentally relevant concentrations (100 μg/l, 50 μg/l and 5 μg/l) of cadmium, copper, lead and zinc. Protein abundances in oyster haemolymph from metal-exposed oysters were compared to those from non-exposed controls using two-dimensional electrophoresis to display differentially expressed proteins. Differentially expressed proteins were subsequently identified using tandem mass spectrometry (LC-MS/MS), to assign their putative biological functions. Unique sets of differentially expressed proteins were affected by each metal, in addition to proteins that were affected by more than one metal. The proteins identified included some that are commonly associated with environmental monitoring, such as HSP 70, and other novel proteins not previously considered as candidates for molecular biomonitoring. The most common biological functions of proteins were associated with stress response, cytoskeletal activity and protein synthesis.
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Affiliation(s)
- Emma L Thompson
- Department of Biological Sciences, Macquarie University, NSW 2109, Australia.
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Wang F, Shang Y, Yang L, Zhu C. Comparative proteomic study and functional analysis of translationally controlled tumor protein in rice roots under Hg2+ stress. J Environ Sci (China) 2012; 24:2149-58. [PMID: 23534212 DOI: 10.1016/s1001-0742(11)61062-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
So far, very little is known about mercury stress-induced intercellular metabolic changes in rice roots at the proteome level. To investigate the response of rice roots to mercury stress, changes in protein expression in rice roots were analyzed using a comparative proteomics approach. Six-leaf stage rice seedlings were treated with 50 micromol/L HgCl2 for 3 hr; 29 protein spots showed a significant changes in abundance under stress when compared with the Hg2+ -tolerant rice mutant and wild type (Zhonghua 11). Furthermore, all these protein spots were identified by mass spectrometry to match 27 diverse protein species. The identified proteins were involved in several processes, including stress response, redox homeostasis, signal transduction, regulation and metabolism; some were found to be cellular structure proteins and a few were unknown. Among the up-regulated proteins, OsTCTP (translationally controlled tumor protein) was chosen to perform hetereologous expression in yeast which was presumed to participate in the Hg2+ tolerance of rice, providing evidence for its role in alleviating Hg2+ damage. Among the many tests, we found that OsTCTP-overexpressed yeast strains were more resistant to Hg2+ than wild-type yeast. Thus, we propose that OsTCTP contributes to Hg2+ resistance. Here we present, for the first time, the functional characterization of OsTCTP in connection with Hg2+ stress in plants.
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Affiliation(s)
- Feijuan Wang
- College of Life Sciences, Zhejiang University, Hangzhou 310058, China.
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Hyne RV. Review of the reproductive biology of amphipods and their endocrine regulation: identification of mechanistic pathways for reproductive toxicants. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:2647-2657. [PMID: 21898570 DOI: 10.1002/etc.673] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2011] [Revised: 06/21/2011] [Accepted: 08/02/2011] [Indexed: 05/31/2023]
Abstract
The reproductive biology of amphipods is reviewed to update the knowledge of the male and female reproductive processes of oogenesis and spermatogenesis as well as the endocrine systems of amphipods with the aim of advancing studies of reproductive toxicology. The ovarian and reproduction cycles of female gammaridean amphipods are closely correlated with the molt cycle, which is under direct control by the steroid hormone 20-hydroxyecdysone. The ability of males to copulate and subsequently for females to ovulate is restricted to the early postmolt period of the females. New developments in our understanding of the molt cycle and the endocrine regulatory pathways for reproduction using genomics techniques on other crustacean species are also discussed. The arthropod sterol ponasterone A or xenobiotics such as the fungicide fenarimol have been shown to elicit endocrine disruption in some crustaceans by acting as an agonist for 20-hydroxyecdysone at the ecdysone receptor or by inhibiting the synthesis of 20-hydroxyecdysone, respectively, resulting in disruption of molting and reproduction. Recent studies suggest that cadmium can inhibit secondary vitellogenesis in amphipods. Experimental approaches for examining the metabolic pathways associated with ecdysteroid hormonal signaling or metabolism, exoskeleton maintenance and molting, and the regulation of vitellogenin in amphipods are discussed. This information should aid in the identification of useful biomarkers for reproductive toxicity.
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Affiliation(s)
- Ross V Hyne
- Centre for Ecotoxicology, Office of Environment and Heritage, Lidcombe, New South Wales, Australia.
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Zhang H, Ding L, Fang X, Shi Z, Zhang Y, Chen H, Yan X, Dai J. Biological responses to perfluorododecanoic acid exposure in rat kidneys as determined by integrated proteomic and metabonomic studies. PLoS One 2011; 6:e20862. [PMID: 21677784 PMCID: PMC3108999 DOI: 10.1371/journal.pone.0020862] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2010] [Accepted: 05/15/2011] [Indexed: 11/19/2022] Open
Abstract
Background Perfluorododecanoic acid (PFDoA) is a perfluorinated carboxylic chemical (PFC) that has broad applications and distribution in the environment. While many studies have focused on hepatotoxicity, immunotoxicity, and reproductive toxicity of PFCAs, few have investigated renal toxicity. Methodology/Principal Findings Here, we used comparative proteomic and metabonomic technologies to provide a global perspective on renal response to PFDoA. Male rats were exposed to 0, 0.05, 0.2, and 0.5 mg/kg/day of PFDoA for 110 days. After 2-D DIGE and MALDI TOF/TOF analysis, 79 differentially expressed proteins between the control and the PFDoA treated rats (0.2 and 0.5 mg-dosed groups) were successfully identified. These proteins were mainly involved in amino acid metabolism, the tricarboxylic acid cycle, gluconeogenesis, glycolysis, electron transport, and stress response. Nuclear magnetic resonance-based metabonomic analysis showed an increase in pyruvate, lactate, acetate, choline, and a variety of amino acids in the highest dose group. Furthermore, the profiles of free amino acids in the PFDoA treated groups were investigated quantitatively by high-coverage quantitative iTRAQ-LC MS/MS, which showed levels of sarcosine, asparagine, histidine, 1-methylhistidine, Ile, Leu, Val, Trp, Tyr, Phe, Cys, and Met increased markedly in the 0.5 mg dosed group, while homocitrulline, α-aminoadipic acid, β-alanine, and cystathionine decreased. Conclusion/Significance These observations provide evidence that disorders in glucose and amino acid metabolism may contribute to PFDoA nephrotoxicity. Additionally, α2u globulin may play an important role in protecting the kidneys from PFDoA toxicity.
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Affiliation(s)
- Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Lina Ding
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Xuemei Fang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Zhimin Shi
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Yating Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Hebing Chen
- National Center of Biomedical Analysis, Beijing, People's Republic of China
| | - Xianzhong Yan
- National Center of Biomedical Analysis, Beijing, People's Republic of China
- * E-mail: (XY); (JD)
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, People's Republic of China
- * E-mail: (XY); (JD)
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Son J, Lee SE, Park BS, Jung J, Park HS, Bang JY, Kang GY, Cho K. Biomarker discovery and proteomic evaluation of cadmium toxicity on a collembolan species, Paronychiurus kimi (Lee). Proteomics 2011; 11:2294-307. [PMID: 21548089 DOI: 10.1002/pmic.200900690] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 02/04/2023]
Abstract
The goal of this study was to identify promising new biomarkers of cadmium by identifying differentially expressed proteins in Paronychiurus kimi after exposure to cadmium. Through proteomic analysis of P. kimi using 1-D PAGE and nano-LC-MS/MS, 36 downregulated proteins and 40 upregulated proteins were found. Some of the downregulated and upregulated proteins were verified by LC-MS/MS analysis after 2-D PAGE. Downregulated proteins in response to cadmium exposure were involved in glycolysis and energy metabolism, chaperones, transcription, reproduction, and neuron growth. In contrast, proteins involved in glycolysis and energy production, neurogenesis, defense systems response to bacteria, and protein biosynthesis were upregulated in cadmium-treated collembolans. Cubulin may be a potential biomarker for the detection of cadmium in P. kimi since this biomarker was able to low levels (3.5 mg/kg) of cadmium. The 14-3-3 ζ was also found to be a potential biomarker for the detection of medium levels (14 mg/kg) of cadmium. Collembolans may be an alternative tool to humans because many collembolans proteins show a high homology to human proteins.
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Affiliation(s)
- Jino Son
- Division of Environmental Science and Ecological Engineering, College of Life Sciences and Biotechnology, Korea University, Seoul, South Korea
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A comprehensive analysis of Bordetella pertussis surface proteome and identification of new immunogenic proteins. Vaccine 2011; 29:3583-95. [DOI: 10.1016/j.vaccine.2011.02.086] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2010] [Revised: 02/23/2011] [Accepted: 02/25/2011] [Indexed: 01/26/2023]
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Yıldırım V, Ozcan S, Becher D, Büttner K, Hecker M, Ozcengiz G. Characterization of proteome alterations in Phanerochaete chrysosporium in response to lead exposure. Proteome Sci 2011; 9:12. [PMID: 21388532 PMCID: PMC3063812 DOI: 10.1186/1477-5956-9-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2010] [Accepted: 03/09/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Total soluble proteome alterations of white rot fungus Phanerochaete chrysosporium in response to different doses (25, 50 and 100 μM) of Pb (II) were characterized by 2DE in combination with MALDI-TOF-MS. RESULTS Dose-dependent molecular response to Pb (II) involved a total of 14 up-regulated and 21 down-regulated proteins. The induction of an isoform of glyceraldehyde 3-phosphate dehydrogenase, alcohol dehydrogenase class V, mRNA splicing factor, ATP-dependent RNA helicase, thioredoxin reductase and actin required a Pb (II) dose of at least 50 μM. Analysis of the proteome dynamics of mid-exponential phase cells of P. chrysosporium subjected to 50 μM lead at exposure time intervals of 1, 2, 4 and 8 h, identified a total of 23 proteins in increased and 67 proteins in decreased amount. Overall, the newly induced/strongly up-regulated proteins involved in (i) amelioration of lipid peroxidation products, (ii) defense against oxidative damage and redox metabolism, (iii) transcription, recombination and DNA repair (iv) a yet unknown function represented by a putative protein. CONCLUSION The present study implicated the particular role of the elements of DNA repair, post-tanscriptional regulation and heterotrimeric G protein signaling in response to Pb (II) stress as shown for the first time for a basidiomycete.
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Affiliation(s)
- Volkan Yıldırım
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
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Sanchez BC, Ralston-Hooper K, Sepúlveda MS. Review of recent proteomic applications in aquatic toxicology. ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY 2011; 30:274-282. [PMID: 21072841 DOI: 10.1002/etc.402] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Over the last decade, the environmental sciences have witnessed an incredible movement towards the utilization of high-throughput molecular tools that are capable of detecting simultaneous changes of hundreds, and even thousands, of molecules and molecular components after exposure of organisms to different environmental stressors. These techniques have received a great deal of attention because they not only offer the potential to unravel novel mechanisms of physiological and toxic action but are also amenable to the discovery of biomarkers of exposure and effects. In this article, we review the state of knowledge of one of these tools in ecotoxicological research: proteomics. We summarize the state of proteomics research in fish, and follow with studies conducted with aquatic invertebrates. A brief discussion on proteomic methods is also presented. We conclude with some ideas for future proteomic studies with fish and aquatic invertebrates.
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Abstract
Perchlorate is a known health hazard for humans, fish, and other species. Therefore, it is important to assess the response of an ecosystem exposed to perchlorate contamination. The data reported here show that a liquid chromatography-mass spectrometry-based proteomics approach for the detection of perchlorate-reducing enzymes can be used to measure the ability of microorganisms to degrade perchlorate, including determining the current perchlorate degradation status. Signature peptides derived from chlorite dismutase (CD) and perchlorate reductase can be used as biomarkers of perchlorate presence and biodegradation. Four peptides each derived from CD and perchlorate reductase subunit A (PcrA) and seven peptides derived from perchlorate reductase subunit B (PcrB) were identified as signature biomarkers for perchlorate degradation, as these sequences are conserved in the majority of the pure and mixed perchlorate-degrading microbial cultures examined. However, chlorite dismutase signature biomarker peptides from Dechloromonas agitata CKB were found to be different from those in other cultures used and should also be included with selected CD biomarkers. The combination of these peptides derived from the two enzymes represents a promising perchlorate presence/biodegradation biomarker system. The biomarker peptides were detected at perchlorate concentrations as low as 0.1 mM and at different time points both in pure cultures and within perchlorate-reducing environmental enrichment consortia. The peptide biomarkers were also detected in the simultaneous presence of perchlorate and an alternate electron acceptor, nitrate. We believe that this technique can be useful for monitoring bioremediation processes for other anthropogenic environmental contaminants with known metabolic pathways.
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Spurgeon DJ, Jones OAH, Dorne JLCM, Svendsen C, Swain S, Stürzenbaum SR. Systems toxicology approaches for understanding the joint effects of environmental chemical mixtures. THE SCIENCE OF THE TOTAL ENVIRONMENT 2010; 408:3725-3734. [PMID: 20231031 DOI: 10.1016/j.scitotenv.2010.02.038] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2009] [Revised: 02/15/2010] [Accepted: 02/17/2010] [Indexed: 05/28/2023]
Abstract
Environmental mixtures of chemicals constitute a prevalent issue in ecotoxicology and the development of new methods to reduce the uncertainties associated with their ecological risk assessment is a critical research need. Historically, a number of models have been explored to predict the potential combined effects of chemicals on species. These models, especially concentration addition and the independent action, have been applied to a number of mixtures. While often providing a good prediction of joint effect, there are cases where these models can have limitations: notably in cases where there are interactions for which they fail to adequately predict joint effects. To support the better mechanistic understanding of interactions in mixture toxicology a framework to support experimental studies to investigate the basis of observed interactions is proposed. The conceptual framework is derived from the extension of a three stage scheme which has previously been applied to understand chemical bioavailability. The framework considers that interactions in mixtures result from processes related to 1) the speciation, binding and transport of chemicals in the exposure medium (external exposure); 2) the adsorption, distribution, metabolism and excretion of chemicals within the organisms (toxicokinetics); 3) associations governing the binding and toxicity of the chemical(s) at the target site (toxicodynamics). The current state of the art in (eco)toxicology in relation to investigation of the mechanisms of interactions between chemicals is discussed with particular emphasis towards the multi-disciplinary tools and techniques within environmental chemistry; toxicology; biochemistry and systems biology that can be used to address such effects.
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Affiliation(s)
- David J Spurgeon
- Centre for Ecology and Hydrology, Maclean Building, Benson Lane, Crowmarsh Gifford, Wallingford, Oxon, OX10 8BB, UK.
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Differential protein expression profile in the liver of pikeperch (Sander lucioperca) larvae fed with increasing levels of phospholipids. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2010; 5:130-7. [DOI: 10.1016/j.cbd.2010.03.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 03/23/2010] [Accepted: 03/24/2010] [Indexed: 01/18/2023]
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Wigginton NS, de Titta A, Piccapietra F, Dobias J, Nesatyy VJ, Suter MJF, Bernier-Latmani R. Binding of silver nanoparticles to bacterial proteins depends on surface modifications and inhibits enzymatic activity. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2010; 44:2163-8. [PMID: 20158230 DOI: 10.1021/es903187s] [Citation(s) in RCA: 152] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Here we describe results from a proteomic study of protein-nanoparticle interactions to further the understanding of the ecotoxicological impact of silver nanoparticles (AgNPs) in the environment. We identified a number of proteins from Escherichia coli that bind specifically to bare or carbonate-coated AgNPs. Of these proteins, tryptophanase (TNase) was observed to have an especially high affinity for both surface modifications despite its low abundance in E. coli. Purified TNase loses enzymatic activity upon associating with AgNPs, suggesting that the active site may be in the vicinity of the binding site(s). TNase fragments with high affinities for both types of AgNPs were identified using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Differences in peptide abundance/presence in mass spectra for the two types of AgNPs suggest preferential binding of some protein fragments based on surface coating. One high-binding protein fragment contained a residue (Arg103) that is part of the active site. Ag adducts were identified for some fragments and found to be characteristic of strong binding to AgNPs rather than association of the fragments with ionic silver. These results suggest a probable mechanism for adhesion of proteins to the most commonly used commercial nanoparticles and highlight the potential effect of nanoparticle surface coating on bioavailability.
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Affiliation(s)
- Nicholas S Wigginton
- Environmental Microbiology Laboratory, Ecole Polytechnique Federale de Lausanne, CH-1015 Lausanne, Switzerland
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Werner JJ, Ptak AC, Rahm BG, Zhang S, Richardson RE. Absolute quantification of Dehalococcoides proteins: enzyme bioindicators of chlorinated ethene dehalorespiration. Environ Microbiol 2009; 11:2687-97. [PMID: 19650881 DOI: 10.1111/j.1462-2920.2009.01996.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The quantification of trace proteins in complex environmental samples and mixed microbial communities would be a valuable monitoring tool in countless applications, including the bioremediation of groundwater contaminated with chlorinated solvents. Measuring the concentrations of specific proteins provides unique information about the activity and physiological state of organisms in a sample. We developed sensitive (< 5 fmol), selective bioindicator assays for the absolute quantification of select proteins used by Dehalococcoides spp. when reducing carbon atoms in the common pollutants trichloroethene (TCE) and tetrachloroethene (PCE). From complex whole-sample digests of two different dechlorinating mixed communities, we monitored the chromatographic peaks of selected tryptic peptides chosen to represent 19 specific Dehalococcoides proteins. This was accomplished using multiple-reaction monitoring (MRM) assays using nano-liquid chromatography-tandem mass spectrometry (nLC-MS/MS), which provided the selectivity, sensitivity and reproducibility required to quantify Dehalococcoides proteins in complex samples. We observed reproducible peak areas (average CV = 0.14 over 4 days, n = 3) and linear responses in standard curves (n = 5, R(2) > 0.98) using synthetic peptide standards spiked into a background matrix of sediment peptides. We detected and quantified TCE reductive dehalogenase (TceA) at 7.6 +/- 1.7 x 10(3) proteins cell(-1) in the KB1 bioaugmentation culture, previously thought to be lacking TceA. Fragmentation data from MS/MS shotgun proteomics experiments were helpful in developing the MRM targets. Similar shotgun proteomics data are emerging in labs around the world for many environmentally relevant microbial proteins, and these data are a valuable resource for the future development of MRM assays. We expect targeted peptide quantification in environmental samples to be a useful tool in environmental monitoring.
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Affiliation(s)
- Jeffrey J Werner
- School of Civil and Environmental Engineering, Cornell University, Hollister Hall, Ithaca, NY 14853, USA
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Bacterial degradation of aromatic compounds. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2009; 6:278-309. [PMID: 19440284 PMCID: PMC2672333 DOI: 10.3390/ijerph6010278] [Citation(s) in RCA: 468] [Impact Index Per Article: 31.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2008] [Accepted: 01/06/2009] [Indexed: 11/21/2022]
Abstract
Aromatic compounds are among the most prevalent and persistent pollutants in the environment. Petroleum-contaminated soil and sediment commonly contain a mixture of polycyclic aromatic hydrocarbons (PAHs) and heterocyclic aromatics. Aromatics derived from industrial activities often have functional groups such as alkyls, halogens and nitro groups. Biodegradation is a major mechanism of removal of organic pollutants from a contaminated site. This review focuses on bacterial degradation pathways of selected aromatic compounds. Catabolic pathways of naphthalene, fluorene, phenanthrene, fluoranthene, pyrene, and benzo[a]pyrene are described in detail. Bacterial catabolism of the heterocycles dibenzofuran, carbazole, dibenzothiophene, and dibenzodioxin is discussed. Bacterial catabolism of alkylated PAHs is summarized, followed by a brief discussion of proteomics and metabolomics as powerful tools for elucidation of biodegradation mechanisms.
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Stenuit B, Eyers L, Schuler L, Agathos SN, George I. Emerging high-throughput approaches to analyze bioremediation of sites contaminated with hazardous and/or recalcitrant wastes. Biotechnol Adv 2008; 26:561-75. [DOI: 10.1016/j.biotechadv.2008.07.004] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2007] [Revised: 07/27/2008] [Accepted: 07/28/2008] [Indexed: 12/01/2022]
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Shen W, liu H, Yu Y. Translation initiation proteins, ubiquitin-proteasome system related proteins, and 14-3-3 proteins as response proteins in FL cells exposed to anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide. Proteomics 2008; 8:3450-68. [DOI: 10.1002/pmic.200800085] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Wei Y, Chan LL, Wang D, Zhang H, Wang J, Dai J. Proteomic Analysis of Hepatic Protein Profiles in Rare Minnow (Gobiocypris rarus) Exposed to Perfluorooctanoic Acid. J Proteome Res 2008; 7:1729-39. [DOI: 10.1021/pr7008059] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yanhong Wei
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Leo. L. Chan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Dazhi Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Hongxia Zhang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Jianshe Wang
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
| | - Jiayin Dai
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, P.R. China, State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, P.R. China, and Graduate School of the Chinese Academy of Sciences, Beijing 100080, P.R. China
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