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Zhang B, Tang Y, Yu F, Peng Z, Yao S, Deng X, Long H, Wang X, Huang K. Translatomics and physiological analyses of the detoxification mechanism of green alga Chlamydomonas reinhardtii to cadmium toxicity. JOURNAL OF HAZARDOUS MATERIALS 2023; 448:130990. [PMID: 36860060 DOI: 10.1016/j.jhazmat.2023.130990] [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: 10/24/2022] [Revised: 02/02/2023] [Accepted: 02/09/2023] [Indexed: 06/18/2023]
Abstract
Cadmium (Cd) is one of the most toxic pollutants found in aquatic ecosystems. Although gene expression in algae exposed to Cd has been studied at the transcriptional level, little is known about Cd impacts at the translational level. Ribosome profiling is a novel translatomics method that can directly monitor RNA translation in vivo. Here, we analyzed the translatome of the green alga Chlamydomonas reinhardtii following treatment with Cd to identify the cellular and physiological responses to Cd stress. Interestingly, we found that the cell morphology and cell wall structure were altered, and starch and high-electron-density particles accumulated in the cytoplasm. Several ATP-binding cassette transporters that responded to Cd exposure were identified. Redox homeostasis was adjusted to adapt to Cd toxicity, and GDP-L-galactose phosphorylase (VTC2), glutathione peroxidase (GPX5), and ascorbate were found to play important roles in maintaining reactive oxygen species homeostasis. Moreover, we found that the key enzyme of flavonoid metabolism, i.e., hydroxyisoflavone reductase (IFR1), is also involved in the detoxification of Cd. Thus, in this study, translatome and physiological analyses provided a complete picture of the molecular mechanisms of green algae cell responses to Cd.
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Affiliation(s)
- Baolong Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Yuxin Tang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Fei Yu
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Zhao Peng
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Sheng Yao
- School of Life Sciences and Hubei Key Laboratory of Genetic Regulation and Integrative Biology, Central China Normal University, Wuhan 430079, Hubei, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Huan Long
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China
| | - Xun Wang
- School of Urban Construction, Wuhan University of Science and Technology, Wuhan 430065, Hubei, China
| | - Kaiyao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, Hubei, China.
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Jia X, Pan Y, Zhu X. Salinization and heavy metal cadmium impair growth but have contrasting effects on defensive colony formation of Scenedesmus obliquus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 862:160693. [PMID: 36481135 DOI: 10.1016/j.scitotenv.2022.160693] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 10/30/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Driven by anthropogenic activities, freshwater salinization has become an emerging global environmental issue. Recent studies indicate that salinization increases the mobility of heavy metals in soil and causes higher flux into surface waterbodies. The present study assessed the combined effects of salinization (0, 3, 6 PSU) and the heavy metal Cd2+ (0, 0.2, 0.4 mg L-1) on the anti-grazing colony formation and population growth of Scenedesmus obliquus, a common freshwater alga. The results showed that the increase in salinity promoted colony formation of S. obliquus with or without the presence of grazing cues and, in contrast, Cd2+ contamination depressed the defensive colony formation of S. obliquus to Daphnia filtrate. The increase in both salinity and Cd2+ concentration depressed the population growth of S. obliquus, including impaired photosynthesis and a decreased population growth rate. Salinization moderated the negative effects of Cd2+ on defensive colony formation of S. obliquus, suggesting increased absorption of Cd2+ ions by a thicker outer layer of the algal cell wall under saltier conditions. As a result, larger defensive colonies of S. obliquus under freshwater salinization may cause higher bioaccumulation of heavy metals by algal cells and heavier influence on zooplankton. This study provides evidence that freshwater salinization could interfere with plankton interactions by affecting algal defense and growth, which may lead to bottom-up cascading effects on freshwater food webs.
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Affiliation(s)
- Xuanhe Jia
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing 210098, China.
| | - Yueqiang Pan
- College of Oceanography, Hohai University, 1 Xikang Road, Nanjing 210098, China.
| | - Xuexia Zhu
- The First Institute of Oceanography, Ministry of Natural Resources of the People's Republic of China, 6 Xianxialing Road, Qingdao 266061, China; College of Oceanography, Hohai University, 1 Xikang Road, Nanjing 210098, China.
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Anand S, Singh A, Kumar V. Recent advancements in cadmium-microbe interactive relations and their application for environmental remediation: a mechanistic overview. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:17009-17038. [PMID: 36622611 DOI: 10.1007/s11356-022-25065-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Accepted: 12/26/2022] [Indexed: 01/10/2023]
Abstract
The toxic and persistent nature of cadmium (Cd) in the environment has become a matter of concern with its drastic increase in the concentrations over past few decades. Among the various techniques, the microbial remediation has been accepted as an effective decontamination tool for environmental applications, which is sustainable over a period of time. The Cd decontamination potential of the microbes depends on various internal and external factors that play a crucial role in selection of the microbes for application in a particular environment. Thus, it is important to understand the role of these factors for optimal application of the microbes. This study provides an insight into the mechanisms involved between the microbes and the environmental Cd. The study also briefly reviews the mathematical models that have been used to predict the remediation potential of the microbes and the kinetics involved during the process. A critical analysis of the recent advancements in the techniques for use of bacteria, fungi, and algal cells to remove Cd has been also presented in the manuscript.
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Affiliation(s)
- Saumya Anand
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004
| | - Ankur Singh
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004
| | - Vipin Kumar
- Laboratory of Applied Microbiology, Department of Environmental Science and Engineering, Indian Institute of Technology (Indian School of Mines), Dhanbad, Jharkhand, India, 826004.
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Jean N, Perié L, Dumont E, Bertheau L, Balliau T, Caruana AMN, Amzil Z, Laabir M, Masseret E. Metal stresses modify soluble proteomes and toxin profiles in two Mediterranean strains of the distributed dinoflagellate Alexandrium pacificum. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 818:151680. [PMID: 34793790 DOI: 10.1016/j.scitotenv.2021.151680] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Revised: 10/25/2021] [Accepted: 11/10/2021] [Indexed: 06/13/2023]
Abstract
HABs involving Alexandrium pacificum have been reported in metal-contaminated ecosystems, suggesting that this distributed species adapts to and/or can tolerate the effects of metals. Modifications in soluble proteomes and PST contents were characterized in two Mediterranean A. pacificum strains exposed to mono- or polymetallic stresses (zinc, lead, copper, cadmium). These strains were isolated from two anthropized locations: Santa Giusta Lagoon (Italy, SG C10-3) and the Tarragona seaport (Spain, TAR C5-4F). In both strains, metals primarily downregulated key photosynthesis proteins. Metals also upregulated other proteins involved in photosynthesis (PCP in both strains), the oxidative stress response (HSP 60, proteasome and SOD in SG C10-3; HSP 70 in TAR C5-4F), energy metabolism (AdK in TAR C5-4F), neoglucogenesis/glycolysis (GAPDH and PEP synthase in SG C10-3) and protein modification (PP in TAR C5-4F). These proteins, possibly involved in adaptive proteomic responses, may explain the development of these A. pacificum strains in metal-contaminated ecosystems. The two strains showed different proteomic responses to metals, with SG C10-3 upregulating more proteins, particularly PCP. Among the PSTs, regardless of the metal and the strain studied, C2 and GTX4 predominated, followed by GTX5. Under the polymetallic cocktail, (i) total PSTs, C2 and GTX4 reached the highest levels in SG C10-3 only, and (ii) total PSTs, C2, GTX5 and neoSTX were higher in SG C10-3 than in TAR C5-4F, whereas in SG C10-3 under copper stress, total PSTs, GTX5, GTX1 and C1 were higher than in the controls, revealing variability in PST biosynthesis between the two strains. Total PSTs, C2, GTX4 and GTX1 showed significant positive correlations with PCP, indicating that PST production may be positively related to photosynthesis. Our results showed that the A. pacificum strains adapt their proteomic and physiological responses to metals, which may contribute to their ecological success in highly anthropized areas.
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Affiliation(s)
- Natacha Jean
- Université de Toulon, Aix Marseille Univ, CNRS, IRD, MIO, Toulon, France.
| | - Luce Perié
- Division of Endocrinology, Diabetes and Metabolism, Department of Medicine, New York University, 30(th) St., New York, NY 10016, USA
| | - Estelle Dumont
- UMR_MD1, Aix-Marseille Univ, U-1261-INSERM, SSA, IRBA, MCT, Marseille, France
| | - Lucie Bertheau
- UMR PAM A 02.102 Procédés Alimentaires et Microbiologiques, Université de Bourgogne Franche-Comté, AgroSup Dijon, esplanade Erasme, 21 000 Dijon, France
| | - Thierry Balliau
- PAPPSO-GQE-Le Moulon, INRA, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, 91 190 Gif-sur-Yvette, France
| | - Amandine M N Caruana
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| | - Zouher Amzil
- IFREMER, Phycotoxin Laboratory, rue de l'île d'Yeu, BP 21105, 44 311 Nantes, France
| | - Mohamed Laabir
- Marbec, Univ Montpellier, IRD, Ifremer, CNRS, Montpellier, France
| | - Estelle Masseret
- Marbec, Univ Montpellier, IRD, Ifremer, CNRS, Montpellier, France
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5
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Wang W, Sheng Y, Jiang M. Physiological and metabolic responses of Microcystis aeruginosa to a salinity gradient. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:13226-13237. [PMID: 34585353 DOI: 10.1007/s11356-021-16590-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Microcystis is a well-known toxic cyanobacterium in eutrophic environments, and an increasing number of Microcystis blooms have emerged in salty reservoirs and coastal rivers. This study observed that many Microcystis were identified in a coastal river in June 2020. The relative abundance of Microcystis decreased from 81.2 to 10.2% in the sampling sites from a salinity of 0 (Sal. 0) to a salinity of 12 (Sal. 12). Hepatotoxic microcystins (MCs) were identified in the coastal river and its estuary. Of the samples, those with a salinity of 5 (Sal. 5) had the highest concentration of MCs at 7.81 ± 0.67 μg L-1. In a saline water simulation experiment, the results showed that salt inhibited Microcystis (M.) aeruginosa growth, enhanced the activity levels of superoxide dismutase (SOD) and catalase (CAT) and stimulated microcystin production. Transcription analysis showed that the expression levels of the psaB and rbcL genes controlling photosymbiotic processes were downregulated, and capD and csaBgene-related polysaccharide productions were upregulated by salt incubation. Notably, metabolism analysis showed that the total polysaccharides, proteins and small molecular matter, such as sucrose, methionine and N-acetyl-D-glucosamine, in the Microcystis cells increased substantially to resist the extracellular hyperosmotic pressure caused by the high salinity levels in culture. These findings indicate that increased salt in a natural aquatic body shifts the phytoplankton community by influencing the physiological metabolism of cyanobacteria and poses a high risk of microcystin exposure during cyanobacterial blooms in coastal rivers.
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Affiliation(s)
- Wenjing Wang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 7 Chunhui Road, Yantai, 264003, People's Republic of China
| | - Yanqing Sheng
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 7 Chunhui Road, Yantai, 264003, People's Republic of China.
| | - Ming Jiang
- Key Laboratory of Coastal Zone Environmental Processes, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, 7 Chunhui Road, Yantai, 264003, People's Republic of China
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Carrasco-Reinado R, Bermudez-Sauco M, Escobar-Niño A, Cantoral JM, Fernández-Acero FJ. Development of the "Applied Proteomics" Concept for Biotechnology Applications in Microalgae: Example of the Proteome Data in Nannochloropsis gaditana. Mar Drugs 2021; 20:38. [PMID: 35049892 PMCID: PMC8780095 DOI: 10.3390/md20010038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/26/2021] [Indexed: 11/23/2022] Open
Abstract
Most of the marine ecosystems on our planet are still unknown. Among these ecosystems, microalgae act as a baseline due to their role as primary producers. The estimated millions of species of these microorganisms represent an almost infinite source of potentially active biocomponents offering unlimited biotechnology applications. This review considers current research in microalgae using the "omics" approach, which today is probably the most important biotechnology tool. These techniques enable us to obtain a large volume of data from a single experiment. The specific focus of this review is proteomics as a technique capable of generating a large volume of interesting information in a single proteomics assay, and particularly the concept of applied proteomics. As an example, this concept has been applied to the study of Nannochloropsis gaditana, in which proteomics data generated are transformed into information of high commercial value by identifying proteins with direct applications in the biomedical and agri-food fields, such as the protein designated UCA01 which presents antitumor activity, obtained from N. gaditana.
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Affiliation(s)
- Rafael Carrasco-Reinado
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research (IVAGRO), Marine and Environmental Sciences Faculty, University of Cadiz (UCA), 11500 Puerto Real, Spain; (R.C.-R.); (M.B.-S.); (A.E.-N.); (J.M.C.)
| | - María Bermudez-Sauco
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research (IVAGRO), Marine and Environmental Sciences Faculty, University of Cadiz (UCA), 11500 Puerto Real, Spain; (R.C.-R.); (M.B.-S.); (A.E.-N.); (J.M.C.)
| | - Almudena Escobar-Niño
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research (IVAGRO), Marine and Environmental Sciences Faculty, University of Cadiz (UCA), 11500 Puerto Real, Spain; (R.C.-R.); (M.B.-S.); (A.E.-N.); (J.M.C.)
| | - Jesús M. Cantoral
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research (IVAGRO), Marine and Environmental Sciences Faculty, University of Cadiz (UCA), 11500 Puerto Real, Spain; (R.C.-R.); (M.B.-S.); (A.E.-N.); (J.M.C.)
| | - Francisco Javier Fernández-Acero
- Microbiology Laboratory, Institute of Viticulture and Agri-Food Research (IVAGRO), Marine and Environmental Sciences Faculty, University of Cadiz (UCA), 11500 Puerto Real, Spain; (R.C.-R.); (M.B.-S.); (A.E.-N.); (J.M.C.)
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7
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Ye X, Zheng X, Zhang D, Niu X, Fan Y, Deng W, Lin Z, Hu H, Zhou S. The efficient biomineralization and adsorption of cadmium (Cd 2+) using secretory organo-biominerals (SOBs) produced by screened Alcaligenes faecalis K2. ENVIRONMENTAL RESEARCH 2021; 199:111330. [PMID: 34010625 DOI: 10.1016/j.envres.2021.111330] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/07/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
Cadmium-contaminated wastewater has attracted increasing concerns due to its non-biodegradable properties and high toxicity. To explore eco-friendly and economically feasible strategies, the screened Alcaligenes faecalis K2 were employed for the biomineralization and recovery of Cd2+ from wastewater while producing considerable secretory organo-biominerals (SOBs) as bioadsorbents. At 75 mg/L Cd2+ exposure, 85.5% of Cd2+ was removed by K2, 43.0% of which was fixed in the granular SOBs. SOBs were convenient for separating from the solution. The adsorption capacity of granular sorbent made from SOBs was verified to be greater than 77.1 mg/g. Practically, 89.5% of 75 mg/L of Cd2+ could be stably removed while ereK2 continuously generated SOBs in a moving-bed biofilm reactor (MBBR). To sum up, the production of bioadsorbents can be achieved by K2, while removing Cd with live microorganisms, which was conducive to making full use of materials and improving Cd removal efficiency.
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Affiliation(s)
- Xingyao Ye
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Xiaoxian Zheng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Dongqing Zhang
- Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, College of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, PR China.
| | - Xiaojun Niu
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China; Guangdong Provincial Key Laboratory of Petrochemical Pollution Processes and Control, College of Environmental Science and Engineering, Guangdong University of Petrochemical Technology, Maoming, 525000, PR China; Guangdong Provincial Key Laboratory of Atmospheric Environment and Pollution Control, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China; The Key Lab of Pollution Control and Ecosystem Restoration in Industry Clusters, Ministry of Education, South China University of Technology, Guangzhou Higher Education Mega Centre, Guangzhou, 510006, PR China.
| | - Yiming Fan
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Wangde Deng
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Zhang Lin
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
| | - Huijian Hu
- Guangdong Institute of Applied Biological Resources, Guangzhou, 510260, PR China
| | - Shaoqi Zhou
- School of Environment and Energy, South China University of Technology, Guangzhou, 510006, PR China
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Mahana A, Guliy OI, Mehta SK. Accumulation and cellular toxicity of engineered metallic nanoparticle in freshwater microalgae: Current status and future challenges. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111662. [PMID: 33396172 DOI: 10.1016/j.ecoenv.2020.111662] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 11/05/2020] [Accepted: 11/11/2020] [Indexed: 06/12/2023]
Abstract
Metal nanoparticles (MNPs) are employed in a variety of medical and non-medical applications. Over the past two decades, there has been substantial research on the impact of metallic nanoparticles on algae and cyanobacteria, which are at the base of aquatic food webs. In this review, the current status of our understanding of mechanisms of uptake and toxicity of MNPs and metal ions released from MNPs after dissolution in the surrounding environment were discussed. Also, the trophic transfer of MNPs in aquatic food webs was analyzed in this review. Approximately all metallic nanoparticles cause toxicity in algae. Predominantly, MNPs are less toxic compared to their corresponding metal ions. There is a sufficient evidence for the trophic transfer of MNPs in aquatic food webs. Internalization of MNPs is indisputable in algae, however, mechanisms of their transmembrane transport are inadequately known. Most of the toxicity studies are carried out with solitary species of MNPs under laboratory conditions rarely found in natural ecosystems. Oxidative stress is the primary toxicity mechanism of MNPs, however, oxidative stress seems a general response predictable to other abiotic stresses. MNP-specific toxicity in an algal cell is yet unknown. Lastly, the mechanism of MNP internalization, toxicity, and excretion in algae needs to be understood carefully for the risk assessment of MNPs to aquatic biota.
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Affiliation(s)
- Abhijeet Mahana
- Laboratory of Algal Biology, Department of Botany, Mizoram University, Aizawl 796004, India
| | - Olga I Guliy
- Leading Researcher Microbial Physiology Lab., Institute of Biochemistry & Physiology of Plants & Microorganisms, Russian Academy of Sciences, Entuziastov av., 13, 410049 Saratov, Russia
| | - Surya Kant Mehta
- Laboratory of Algal Biology, Department of Botany, Mizoram University, Aizawl 796004, India.
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Reis LLD, Alho LDOG, Abreu CBD, Melão MDGG. Using multiple endpoints to assess the toxicity of cadmium and cobalt for chlorophycean Raphidocelis subcapitata. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 208:111628. [PMID: 33396148 DOI: 10.1016/j.ecoenv.2020.111628] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 10/31/2020] [Accepted: 11/05/2020] [Indexed: 06/12/2023]
Abstract
Metals may cause damage to the biota of contaminated environments. Moreover, using multiple endpoints in ecotoxicological studies is useful to better elucidate the mechanisms of toxicity of these compounds. Therefore, this study aimed to evaluate the effects of cadmium (Cd) and cobalt (Co) on growth, biochemical and photosynthetic parameters of the microalgae Raphidocelis subcapitata, through quantification of lipid classes composition, chlorophyll a (Chl a) content, maximum (ΦM) and effective (Φ'M) quantum yields and efficiency of the oxygen-evolving complex (OEC). Both metals affected the algal population growth, with an IC50-96h of 0.67 and 1.53 μM of Cd and Co, respectively. Moreover, the metals led to an increase in the total lipid content and reduced efficiency of OEC and ΦM. Cell density was the most sensitive endpoint to detect Cd toxicity after 96 h of treatment. Regarding Co, the photosynthetic parameters were the most affected and the total lipid content was the most sensitive endpoint as it was altered by the exposure to this metal in all concentrations. Cd led to increased contents of the lipid class wax esters (0.89 μM) and phospholipids (PL - at 0.89 and 1.11 μM) and decreased values of triglycerides (at 0.22 μM) and acetone-mobile polar lipids (AMPL - at 0.44 and 1.11 μM). The percentage of free fatty acids (FFA) and PL of microalgae exposed to Co increased, whereas AMPL decreased in all concentrations tested. We were able to detect differences between the toxicity mechanisms of each metal, especially how Co interferes in the microalgae at a biochemical level. Furthermore, to the best of our knowledge, this is the first study reporting Co effects in lipid classes of a freshwater Chlorophyceae. The damage caused by Cd and Co may reach higher trophic levels, causing potential damage to the aquatic communities as microalgae are primary producers and the base of the food chain.
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Affiliation(s)
- Larissa Luiza Dos Reis
- Universidade Federal de São Carlos - UFSCar, Department of Hydrobiology, Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil; Post-Graduate Program in Ecology and Natural Resources (PPGERN), Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil.
| | - Lays de Oliveira Gonçalves Alho
- Universidade Federal de São Carlos - UFSCar, Department of Hydrobiology, Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil; Post-Graduate Program in Ecology and Natural Resources (PPGERN), Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil.
| | - Cínthia Bruno de Abreu
- Universidade Federal de São Carlos - UFSCar, Department of Hydrobiology, Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil; Post-Graduate Program in Ecology and Natural Resources (PPGERN), Universidade Federal de São Carlos (UFSCar), Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil.
| | - Maria da Graça Gama Melão
- Universidade Federal de São Carlos - UFSCar, Department of Hydrobiology, Rodovia Washington Luís, Km 235, Zip Code 13565-905, São Carlos, SP, Brazil.
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10
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Development of New Antiproliferative Compound against Human Tumor Cells from the Marine Microalgae Nannochloropsis gaditana by Applied Proteomics. Int J Mol Sci 2020; 22:ijms22010096. [PMID: 33374179 PMCID: PMC7795124 DOI: 10.3390/ijms22010096] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Revised: 12/15/2020] [Accepted: 12/22/2020] [Indexed: 12/18/2022] Open
Abstract
Proteomics is a crucial tool for unravelling the molecular dynamics of essential biological processes, becoming a pivotal technique for basic and applied research. Diverse bioinformatic tools are required to manage and explore the huge amount of information obtained from a single proteomics experiment. Thus, functional annotation and protein-protein interactions are evaluated in depth leading to the biological conclusions that best fit the proteomic response in the system under study. To gain insight into potential applications of the identified proteins, a novel approach named "Applied Proteomics" has been developed by comparing the obtained protein information with the existing patents database. The development of massive sequencing technology and mass spectrometry (MS/MS) improvements has allowed the application of proteomics nonmodel microorganisms, which have been deeply described as a novel source of metabolites. Between them, Nannochloropsis gaditana has been pointed out as an alternative source of biomolecules. Recently, our research group has reported the first complete proteome analysis of this microalga, which was analysed using the applied proteomics concept with the identification of 488 proteins with potential industrial applications. To validate our approach, we selected the UCA01 protein from the prohibitin family. The recombinant version of this protein showed antiproliferative activity against two tumor cell lines, Caco2 (colon adenocarcinoma) and HepG-2 (hepatocellular carcinoma), proving that proteome data have been transformed into relevant biotechnological information. From Nannochloropsis gaditana has been developed a new tool against cancer-the protein named UCA01. This protein has selective effects inhibiting the growth of tumor cells, but does not show any effect on control cells. This approach describes the first practical approach to transform proteome information in a potential industrial application, named "applied proteomics". It is based on a novel bioalgorithm, which is able to identify proteins with potential industrial applications. From hundreds of proteins described in the proteome of N. gaditana, the bioalgorithm identified over 400 proteins with potential uses; one of them was selected as UCA01, "in vitro" and its potential was demonstrated against cancer. This approach has great potential, but the applications are potentially numerous and undefined.
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Zeb L, Shafiq M, Chi ZY, Xiu ZL. Separation of microalgal docosahexaenoic acid-rich oils using a microwave-assisted three-phase partitioning system. Sep Purif Technol 2020. [DOI: 10.1016/j.seppur.2020.117441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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12
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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Fajardo C, Amil-Ruiz F, Fuentes-Almagro C, De Donato M, Martinez-Rodriguez G, Escobar-Niño A, Carrasco R, Mancera JM, Fernandez-Acero FJ. An “omic” approach to Pyrocystis lunula: New insights related with this bioluminescent dinoflagellate. J Proteomics 2019; 209:103502. [DOI: 10.1016/j.jprot.2019.103502] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 08/14/2019] [Accepted: 08/19/2019] [Indexed: 01/10/2023]
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14
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Salama ES, Govindwar SP, Khandare RV, Roh HS, Jeon BH, Li X. Can Omics Approaches Improve Microalgal Biofuels under Abiotic Stress? TRENDS IN PLANT SCIENCE 2019; 24:611-624. [PMID: 31085124 DOI: 10.1016/j.tplants.2019.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 03/27/2019] [Accepted: 04/11/2019] [Indexed: 06/09/2023]
Abstract
Microalgae hold the promise of an inexpensive and sustainable source of biofuels. The existing microalgal cultivation technologies need significant improvement to outcompete other biofuel sources such as terrestrial plants. Application of 'algomics' approaches under different abiotic stress conditions could be an effective strategy for optimization of microalgal growth and production of high-quality biofuels. In this review, we discuss the roles of omics in understanding genome structure and biocomponents metabolism in various microalgal species to optimize sustainable biofuel production. Application of individual and integrated omics revealed that genes and metabolic pathways of microalgae have been altered under multiple stress conditions, resulting in an increase in biocomponents, providing a research platform for expansion of genetic engineering studies in microalgal strains.
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Affiliation(s)
- El-Sayed Salama
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China; Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou 730000, Gansu Province, PR China
| | - Sanjay P Govindwar
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea
| | - Rahul V Khandare
- Amity Institute of Biotechnology, Amity University, Mumbai, 410206, India
| | - Hyun-Seog Roh
- Department of Environmental Engineering, Yonsei University, Wonju, Gangwon-do 220-710, South Korea
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul, 04763, South Korea.
| | - Xiangkai Li
- MOE, Key Laboratory of Cell Activities and Stress Adaptations, Lanzhou University, Lanzhou, 730000, Gansu Province, PR China.
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15
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Qiu C, He Y, Huang Z, Li S, Huang J, Wang M, Chen B. Lipid extraction from wet Nannochloropsis biomass via enzyme-assisted three phase partitioning. BIORESOURCE TECHNOLOGY 2019; 284:381-390. [PMID: 30959375 DOI: 10.1016/j.biortech.2019.03.148] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 03/28/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
A green and efficient enzyme assisted three phase partitioning (EA-TPP) process was firstly developed to extract microalgal lipids using wet Nannochloropsis sp. biomass. In the pretreatment of microalgal biomass by four hydrolytic enzymes, TPP obtained a higher TFAs lipid extraction efficiency by cellulase compared with the resting enzymes. After optimization by EA-TPP of the wet disrupted Nannochloropsis biomass (3 g), the maximum TFAs extraction yield (90.40%) was attained at 20% ammonium sulphate, 6-7 pH, 1:2 slurry/tert-butanol ratio and 70 °C for 2 h incubation time and two extraction cycles. Moreover, results also revealed that the lipidic species compositions of Nannochloropsis sp. biomass were greatly related with the EA-TPP parameters. In the laboratory scale for wet disrupted microalgae biomass, EA-TPP process achieved 88.70% TFAs extraction yield under the optimized conditions. In all, EA-TPP process could be a promising approach to extract microalgae lipids for food application using wet microalgae biomass.
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Affiliation(s)
- Changyang Qiu
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Yongjin He
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Key Laboratory of Feed Biotechnology, The Ministry of Agriculture of the People's Republic of China, Beijing 100081, China
| | - Zicheng Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Shaofeng Li
- College of Life Science, Fujian Normal University, Fuzhou 350117, China
| | - Jian Huang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Mingzi Wang
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China
| | - Bilian Chen
- College of Life Science, Fujian Normal University, Fuzhou 350117, China; Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350117, China.
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Improved Algal Toxicity Test System for Robust Omics-Driven Mode-of-Action Discovery in Chlamydomonas reinhardtii. Metabolites 2019; 9:metabo9050094. [PMID: 31083411 PMCID: PMC6572051 DOI: 10.3390/metabo9050094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 05/06/2019] [Accepted: 05/07/2019] [Indexed: 01/05/2023] Open
Abstract
Algae are key components of aquatic food chains. Consequently, they are internationally recognised test species for the environmental safety assessment of chemicals. However, existing algal toxicity test guidelines are not yet optimized to discover molecular modes of action, which require highly-replicated and carefully controlled experiments. Here, we set out to develop a robust, miniaturised and scalable Chlamydomonas reinhardtii toxicity testing approach tailored to meet these demands. We primarily investigated the benefits of synchronised cultures for molecular studies, and of exposure designs that restrict chemical volatilisation yet yield sufficient algal biomass for omics analyses. Flow cytometry and direct-infusion mass spectrometry metabolomics revealed significant and time-resolved changes in sample composition of synchronised cultures. Synchronised cultures in sealed glass vials achieved adequate growth rates at previously unachievably-high inoculation cell densities, with minimal pH drift and negligible chemical loss over 24-h exposures. Algal exposures to a volatile test compound (chlorobenzene) yielded relatively high reproducibility of metabolic phenotypes over experimental repeats. This experimental test system extends existing toxicity testing formats to allow highly-replicated, omics-driven, mode-of-action discovery.
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17
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Ivošević DeNardis N, Pečar Ilić J, Ružić I, Novosel N, Mišić Radić T, Weber A, Kasum D, Pavlinska Z, Balogh RK, Hajdu B, Marček Chorvátová A, Gyurcsik B. Algal cell response to laboratory-induced cadmium stress: a multimethod approach. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2019; 48:231-248. [PMID: 30806730 DOI: 10.1007/s00249-019-01347-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 01/07/2019] [Accepted: 02/06/2019] [Indexed: 02/05/2023]
Abstract
We examined the response of algal cells to laboratory-induced cadmium stress in terms of physiological activity, autonomous features (motility and fluorescence), adhesion dynamics, nanomechanical properties, and protein expression by employing a multimethod approach. We develop a methodology based on the generalized mathematical model to predict free cadmium concentrations in culture. We used algal cells of Dunaliella tertiolecta, which are widespread in marine and freshwater systems, as a model organism. Cell adaptation to cadmium stress is manifested through cell shape deterioration, slower motility, and an increase of physiological activity. No significant change in growth dynamics showed how cells adapt to stress by increasing active surface area against toxic cadmium in the culture. It was accompanied by an increase in green fluorescence (most likely associated with cadmium vesicular transport and/or beta-carotene production), while no change was observed in the red endogenous fluorescence (associated with chlorophyll). To maintain the same rate of chlorophyll emission, the cell adaptation response was manifested through increased expression of the identified chlorophyll-binding protein(s) that are important for photosynthesis. Since production of these proteins represents cell defence mechanisms, they may also signal the presence of toxic metal in seawater. Protein expression affects the cell surface properties and, therefore, the dynamics of the adhesion process. Cells behave stiffer under stress with cadmium, and thus, the initial attachment and deformation are slower. Physicochemical and structural characterizations of algal cell surfaces are of key importance to interpret, rationalize, and predict the behaviour and fate of the cell under stress in vivo.
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Affiliation(s)
- Nadica Ivošević DeNardis
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, 10000, Zagreb, Croatia.
| | - Jadranka Pečar Ilić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, 10000, Zagreb, Croatia
| | - Ivica Ružić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, 10000, Zagreb, Croatia
| | - Nives Novosel
- Department of Biology, Faculty of Science, University of Zagreb, Rooseveltov trg 6, 10000, Zagreb, Croatia
| | - Tea Mišić Radić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, 10000, Zagreb, Croatia
| | - Andreas Weber
- Department of Nanobiotechnology, Institute for Biophysics, University of Natural Resources and Life Sciences, Muthgasse 11, 1190, Vienna, Austria
| | - Damir Kasum
- Division for Marine and Environmental Research, Ruđer Bošković Institute, POB 180, 10000, Zagreb, Croatia
| | - Zuzana Pavlinska
- Department of Biophysics, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, nam. J Herdu 1, 91702, Trnava, Slovakia
- Department of Biophotonics, International Laser Centre, Ilkovičova 3, 84104, Bratislava, Slovakia
| | - Ria Katalin Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Bálint Hajdu
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
| | - Alžbeta Marček Chorvátová
- Department of Biophysics, Faculty of Natural Sciences, University of Ss. Cyril and Methodius, nam. J Herdu 1, 91702, Trnava, Slovakia
- Department of Biophotonics, International Laser Centre, Ilkovičova 3, 84104, Bratislava, Slovakia
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, 6720, Hungary
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18
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Differential hydrolysis of proteins of four microalgae by the digestive enzymes of gilthead sea bream and Senegalese sole. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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19
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Tse SPK, Lo SCL. Comparative proteomic studies of a Scrippsiella acuminata bloom with its laboratory-grown culture using a 15N-metabolic labeling approach. HARMFUL ALGAE 2017; 67:26-35. [PMID: 28755718 DOI: 10.1016/j.hal.2017.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 05/15/2017] [Accepted: 05/19/2017] [Indexed: 06/07/2023]
Abstract
Comparative proteomic analysis was carried out using cells isolated from a natural bloom of Scrippsiella acuminata (formerly Scrippsiella trochoidea) in the early bloom (EB) and late bloom (LB) stages as well as with laboratory-grown cultures of cells isolated from the bloom in early growth (EG) and late growth (LG) stages. For quantitative proteomics, LG cells were grown for 20 generations in the presence of 15N as a reference (i.e. common denominator) for all comparison. In comparisons with early growth laboratory grown cells (EG/LG), nearly 64% of proteins identified had similar abundance levels, with the remaining 36% mostly more abundant in EG cells. Calvin cycle, amino acid metabolism, chlorophyll biosynthesis and transcription/translation were among the up-regulated processes. Cells from the early bloom (EB/LG) had a greater abundance of transporters and enzymes related to light harvesting and oxidative phosphorylation, while the abundance of these proteins decreased in late bloom cells (LB/LG). All natural bloom samples showed either constant or lower abundance levels of enzymes involved in sugar synthesis and glycolytic pathways compared to laboratory grown cells. Our results represent the first examination of the proteomic changes in the development of a natural dinoflagellate bloom. Importantly, our results demonstrate that the proteome of cells grown in the laboratory is distinctively different from cells in a natural bloom.
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Affiliation(s)
- Sirius P K Tse
- Shenzhen Key Laboratory of Food Biological Safety Control, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region
| | - Samuel C L Lo
- Shenzhen Key Laboratory of Food Biological Safety Control, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region; Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hong Kong Special Administrative Region.
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20
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A Method for Microalgae Proteomics Analysis Based on Modified Filter-Aided Sample Preparation. Appl Biochem Biotechnol 2017; 183:923-930. [DOI: 10.1007/s12010-017-2473-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022]
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21
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Tran NAT, Padula MP, Evenhuis CR, Commault AS, Ralph PJ, Tamburic B. Proteomic and biophysical analyses reveal a metabolic shift in nitrogen deprived Nannochloropsis oculata. ALGAL RES 2016. [DOI: 10.1016/j.algal.2016.07.009] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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22
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Masoudzadeh N, Alidoust L, Samie N, Hajfarajollah H, Sharafi H, Modiri S, Zahiri HS, Vali H, Noghabi KA. Distinctive protein expression patterns of the strain Brevundimonas sp. ZF12 isolated from the aqueous zone containing high levels of radiation to cadmium-induced stress. J Biotechnol 2014; 186:49-57. [PMID: 24997353 DOI: 10.1016/j.jbiotec.2014.05.028] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Revised: 05/16/2014] [Accepted: 05/21/2014] [Indexed: 11/18/2022]
Abstract
In the current study, different protein expression profiles in a strain Brevundimonas sp. ZF12, isolated from the aqueous zone containing high levels of radiation, were characterized following exposure to cadmium (II) using a proteomic strategy. In order to gain a deeper understanding of the cellular events that allow this strain to survive and undergo cadmium adaptation and sorption, the strain was tested under three experimental conditions of 5, 10 and 30 ppm cadmium (II) ions stress. Two-dimensional polyacrylamide gel electrophoresis and mass spectrometry were used to identify the differentially expressed proteins under cadmium (II) stress. 20 differentially expressed spots were successfully identified by MS/MS analysis. These proteins are involved in DNA repair and protection, amino acid metabolism, nucleotide metabolism, energy homeostasis, oxidative stress response, redox homeostasis, protein folding and heat-shock response. The results obviously indicate that the ZF12 strain tends to endure the cadmium (II) stress conditions by modification in many aspects of its cellular physiology and metabolism.
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Affiliation(s)
- Nasrin Masoudzadeh
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Leila Alidoust
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Nima Samie
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hamidreza Hajfarajollah
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hakimeh Sharafi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Sima Modiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hossein Shahbani Zahiri
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran
| | - Hojatollah Vali
- Facility for Electron Microscopy Research, McGill University, 3640 Street, Montreal, Canada
| | - Kambiz Akbari Noghabi
- Division of Industrial & Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), P.O. Box 14155-6343, Tehran, Iran.
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Dupae J, Bohler S, Noben JP, Carpentier S, Vangronsveld J, Cuypers A. Problems inherent to a meta-analysis of proteomics data: a case study on the plants' response to Cd in different cultivation conditions. J Proteomics 2014; 108:30-54. [PMID: 24821411 DOI: 10.1016/j.jprot.2014.04.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2013] [Revised: 03/07/2014] [Accepted: 04/15/2014] [Indexed: 01/14/2023]
Abstract
UNLABELLED This meta-analysis focuses on plant-proteome responses to cadmium (Cd) stress. Initially, some general topics related to a proteomics meta-analysis are discussed: (1) obstacles encountered during data analysis, (2) a consensus in proteomic research, (3) validation and good reporting practices for protein identification and (4) guidelines for statistical analysis of differentially abundant proteins. In a second part, the Cd responses in leaves and roots obtained from a proteomics meta-analysis are discussed in (1) a time comparison (short versus long term exposure), and (2) a culture comparison (hydroponics versus soil cultivation). Data of the meta-analysis confirmed the existence of an initial alarm phase upon Cd exposure. Whereas no metabolic equilibrium is established in hydroponically exposed plants, an equilibrium seems to be manifested in roots of plants grown in Cd-contaminated soil after long term exposure. In leaves, the carbohydrate metabolism is primarily affected independent of the exposure time and the cultivation method. In addition, a metabolic shift from CO2-fixation towards respiration is manifested, independent of the cultivation system. Finally, some ideas for the improvement of proteomics setups and for comparisons between studies are discussed. BIOLOGICAL SIGNIFICANCE This meta-analysis focuses on the plant responses to Cd stress in leaves and roots at the proteome level. This meta-analysis points out the encountered obstacles when performing a proteomics meta-analysis related to inherent technologies, but also related to experimental setups. Furthermore, the question is addressed whether an extrapolation of results obtained in hydroponic cultivation towards soil-grown plants is possible.
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Affiliation(s)
- Joke Dupae
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sacha Bohler
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Jean-Paul Noben
- Biomedical Institute, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Sebastien Carpentier
- Afdeling Plantenbiotechniek, Catholic University Leuven, Willem de Croylaan 42 - bus 2455, 3001 Leuven, Belgium.
| | - Jaco Vangronsveld
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
| | - Ann Cuypers
- Environmental Biology, Hasselt University, Agoralaan - Gebouw D, 3590 Diepenbeek, Belgium.
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Rotini A, Anello L, Bernardo MD, Giallongo A, Valiante L, Migliore L. Comparative analysis of bed density, total phenol content and protein expression pattern in <i>Posidonia oceanica</i> (L.) Delile. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/oje.2013.36050] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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25
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Ling XP, Lu YH, Huang HQ. Differential protein profile in zebrafish (Danio rerio) brain under the joint exposure of methyl parathion and cadmium. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2012; 19:3925-3941. [PMID: 22767353 DOI: 10.1007/s11356-012-1037-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2011] [Accepted: 06/11/2012] [Indexed: 06/01/2023]
Abstract
As different chemicals, methyl parathion (MP) and cadmium (Cd) can induce neurotoxicity on the brain of aquatic ecosystems. This study aims to explore the differential expression proteins in the brain induced by their joint stress and their joint effects, which are poorly reported, and devotes finding novel biomarkers for monitoring their contamination in water and assessing their neurological effects. The bioaccumulation of MP and Cd in tissues after 96 h of exposure was first analyzed by GC and inductively coupled plasma-MS to provide insights into the interaction. Protein profile changes in the brains of the zebrafish (Danio rerio) exposed to MP and Cd were further investigated using the proteomic approach. The correlation of gene expression on the transcription level of mRNA and the translation level of protein was examined by real-time quantitative PCR and Western blotting analysis. It showed that Cd and MP have an interaction on their bioaccumulation, which suggests that their joint effect over 96 h might be antagonistic. Proteomics revealed that 22 protein spots changed their expression levels under stress, of which 16 proteins were identified using MS. These proteins were involved in oxidation/reduction, metabolism, energy production, receptor activity, and cytoskeleton assembly. Among them, five proteins with a remarkable abundance change are significantly suggested to play important roles in the joint effect. This work demonstrates that there exists an interaction between MP and Cd toxicities, which may aid in our understanding of the mechanism of neurotoxicity induced by joint stress. The results may also provide the possibility of the establishment of candidate biomarkers for monitoring MP and Cd contamination in water.
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Affiliation(s)
- Xue-Ping Ling
- Department of Chemical Biology, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, China,
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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27
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Differential protein expression associated with heat stress in Antarctic microalga. BIOCHIP JOURNAL 2012. [DOI: 10.1007/s13206-012-6310-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Rodrigues PM, Silva TS, Dias J, Jessen F. PROTEOMICS in aquaculture: applications and trends. J Proteomics 2012; 75:4325-45. [PMID: 22498885 DOI: 10.1016/j.jprot.2012.03.042] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2011] [Revised: 03/18/2012] [Accepted: 03/24/2012] [Indexed: 01/15/2023]
Abstract
Over the last forty years global aquaculture presented a growth rate of 6.9% per annum with an amazing production of 52.5 million tonnes in 2008, and a contribution of 43% of aquatic animal food for human consumption. In order to meet the world's health requirements of fish protein, a continuous growth in production is still expected for decades to come. Aquaculture is, though, a very competitive market, and a global awareness regarding the use of scientific knowledge and emerging technologies to obtain a better farmed organism through a sustainable production has enhanced the importance of proteomics in seafood biology research. Proteomics, as a powerful comparative tool, has therefore been increasingly used over the last decade to address different questions in aquaculture, regarding welfare, nutrition, health, quality, and safety. In this paper we will give an overview of these biological questions and the role of proteomics in their investigation, outlining the advantages, disadvantages and future challenges. A brief description of the proteomics technical approaches will be presented. Special focus will be on the latest trends related to the aquaculture production of fish with defined nutritional, health or quality properties for functional foods and the integration of proteomics techniques in addressing this challenging issue.
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Affiliation(s)
- Pedro M Rodrigues
- Centro de Ciências do Mar do Algarve (CCMar), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal.
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Pan K, Qin J, Li S, Dai W, Zhu B, Jin Y, Yu W, Yang G, Li D. NUCLEAR MONOPLOIDY AND ASEXUAL PROPAGATION OF NANNOCHLOROPSIS OCEANICA (EUSTIGMATOPHYCEAE) AS REVEALED BY ITS GENOME SEQUENCE(1). JOURNAL OF PHYCOLOGY 2011; 47:1425-1432. [PMID: 27020366 DOI: 10.1111/j.1529-8817.2011.01057.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Species in genus Nannochloropsis are promising candidates for both biofuel and biomass production due to their ability to accumulate rich fatty acids and grow fast; however, their sexual reproduction has not been studied. It is clear that the construction of their metabolic pathways, such as that of polyunsaturated fatty acid (PUFA) biosynthesis, and understanding of their biological characteristics, such as nuclear ploidy and reproductive strategy, will certainly facilitate their genetic improvement through gene engineering and mutation and clonal expansion. In this study, the genome of N. oceanica S. Suda et Miyashita was sequenced with the next-generation Illumina GA sequencing technologies. The genome was ∼30 Mb in size, which contained 11,129 protein-encoding genes. Of them, 59.65% were annotated by aligning with those in diverse protein databases, and 29.68% were assigned at least one function described in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. Less frequent polymorphic nucleotides (one in 22.06 kb) and the obvious deviation from 1:1 (major:minor, minor ≥10) expectation indicated the nuclear monoploidy of N. oceanica. The lack of the majority of meiosis-specific proteins implied the asexual reproduction of this alga. In combination, the nuclear monoploidy and asexual propagation led us to favor the hypothesis that N. oceanica was a premeiotic or ameiotic alga. In addition, sequence similarity-based searching identified the elongase- and desaturase-encoding genes involved in the biosynthesis of long-chain PUFAs, which provided the genetic basis of its rich content of eicosapentaenoic acid (EPA). The functional genes and their metabolic pathways profiled against its genome sequence will facilitate its integrative investigations.
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Affiliation(s)
- Kehou Pan
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Junjie Qin
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Si Li
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Wenkui Dai
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Baohua Zhu
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Yuanchun Jin
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Wengong Yu
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Guanpin Yang
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
| | - Dongfang Li
- Key Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, China Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China Graduate University of Chinese Academy of Sciences, Beijing 100049, China Beijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaKey Laboratory of Mariculture of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, ChinaCollege of Medicine and Drugs, Ocean University of China, Qingdao 266003, ChinaKey Laboratory of Marine Genetics and Breeding of Chinese Ministry of Education, Ocean University of China, Qingdao 266003, ChinaBeijing Genomics Institute (BGI) at Shenzhen, Shenzhen 518083, China
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Examination of triacylglycerol biosynthetic pathways via de novo transcriptomic and proteomic analyses in an unsequenced microalga. PLoS One 2011; 6:e25851. [PMID: 22043295 PMCID: PMC3197185 DOI: 10.1371/journal.pone.0025851] [Citation(s) in RCA: 186] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2011] [Accepted: 09/12/2011] [Indexed: 11/19/2022] Open
Abstract
Biofuels derived from algal lipids represent an opportunity to dramatically impact the global energy demand for transportation fuels. Systems biology analyses of oleaginous algae could greatly accelerate the commercialization of algal-derived biofuels by elucidating the key components involved in lipid productivity and leading to the initiation of hypothesis-driven strain-improvement strategies. However, higher-level systems biology analyses, such as transcriptomics and proteomics, are highly dependent upon available genomic sequence data, and the lack of these data has hindered the pursuit of such analyses for many oleaginous microalgae. In order to examine the triacylglycerol biosynthetic pathway in the unsequenced oleaginous microalga, Chlorella vulgaris, we have established a strategy with which to bypass the necessity for genomic sequence information by using the transcriptome as a guide. Our results indicate an upregulation of both fatty acid and triacylglycerol biosynthetic machinery under oil-accumulating conditions, and demonstrate the utility of a de novo assembled transcriptome as a search model for proteomic analysis of an unsequenced microalga.
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31
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Jeon YM, Son BS, Lee MY. Proteomic identification of the differentially expressed proteins in human lung epithelial cells by airborne particulate matter. J Appl Toxicol 2011; 31:45-52. [PMID: 20658469 DOI: 10.1002/jat.1566] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Exposure to airborne PM₁₀, particulate matter with a median aerodynamic diameter of less than 10 µm, is known to be associated with a number of adverse health effects. To gain a better understanding of the cytotoxic mechanism and to develop protein biomarker candidates for PM₁₀-induced toxicity, proteomic analyses were performed in human lung epithelial cells. Two-dimensional gel electrophoresis (2-DE) was followed by matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to analyze the proteins differentially expressed by exposure to PM₁₀. Analysis of 2-DE gels revealed more than 1270 protein spots in the cells, of which 36 showed changes of more than 2-fold on exposure to PM₁₀ (up-regulation, n = 6; down-regulation, n = 30). The glycolytic enzyme pyruvate kinase, which also plays a role in tumor metabolism, showed a marked increase in expression, whereas the cytoskeleton-related vinculin and anti-inflammatory annexin 1 showed marked decreases in expression.
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Affiliation(s)
- Yu Mi Jeon
- Department of Medical Biotechnology, SoonChunHyang University, Asan, Chungnam 336-600, Republic of Korea
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32
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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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33
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Dorts J, Kestemont P, Dieu M, Raes M, Silvestre F. Proteomic Response to Sublethal Cadmium Exposure in a Sentinel Fish Species, Cottus gobio. J Proteome Res 2010; 10:470-8. [DOI: 10.1021/pr100650z] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Jennifer Dorts
- Unité de Recherche en Biologie des Organismes (URBO), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium, and Unité de Recherche en Biologie Cellulaire (URBC), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Patrick Kestemont
- Unité de Recherche en Biologie des Organismes (URBO), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium, and Unité de Recherche en Biologie Cellulaire (URBC), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Marc Dieu
- Unité de Recherche en Biologie des Organismes (URBO), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium, and Unité de Recherche en Biologie Cellulaire (URBC), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Martine Raes
- Unité de Recherche en Biologie des Organismes (URBO), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium, and Unité de Recherche en Biologie Cellulaire (URBC), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium
| | - Frédéric Silvestre
- Unité de Recherche en Biologie des Organismes (URBO), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium, and Unité de Recherche en Biologie Cellulaire (URBC), The University of Namur (FUNDP), Rue de Bruxelles 61, B-5000, Namur, Belgium
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Lacerda CMR, Reardon KF. Environmental proteomics: applications of proteome profiling in environmental microbiology and biotechnology. BRIEFINGS IN FUNCTIONAL GENOMICS AND PROTEOMICS 2009; 8:75-87. [PMID: 19279070 DOI: 10.1093/bfgp/elp005] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
In this review, we present the use of proteomics to advance knowledge in the field of environmental biotechnology, including studies of bacterial physiology, metabolism and ecology. Bacteria are widely applied in environmental biotechnology for their ability to catalyze dehalogenation, methanogenesis, denitrification and sulfate reduction, among others. Their tolerance to radiation and toxic compounds is also of importance. Proteomics has an important role in helping uncover the pathways behind these cellular processes. Environmental samples are often highly complex, which makes proteome studies in this field especially challenging. Some of these challenges are the lack of genome sequences for the vast majority of environmental bacteria, difficulties in isolating bacteria and proteins from certain environments, and the presence of complex microbial communities. Despite these challenges, proteomics offers a unique dynamic view into cellular function. We present examples of environmental proteomics of model organisms, and then discuss metaproteomics (microbial community proteomics), which has the potential to provide insights into the function of a community without isolating organisms. Finally, the environmental proteomics literature is summarized as it pertains to the specific application areas of wastewater treatment, metabolic engineering, microbial ecology and environmental stress responses.
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Affiliation(s)
- Carla M R Lacerda
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, CO 80523-1370, USA
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Contreras L, Ritter A, Dennett G, Boehmwald F, Guitton N, Pineau C, Moenne A, Potin P, Correa JA. TWO-DIMENSIONAL GEL ELECTROPHORESIS ANALYSIS OF BROWN ALGAL PROTEIN EXTRACTS(1). JOURNAL OF PHYCOLOGY 2008; 44:1315-1321. [PMID: 27041728 DOI: 10.1111/j.1529-8817.2008.00575.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
High-quality protein extracts are required for proteomic studies, a field that is poorly developed for marine macroalgae. A reliable phenol extraction protocol using Scytosiphon gracilis Kogame and Ectocarpus siliculosus (Dillwyn) Lyngb. (Phaeophyceae) as algal models resulted in high-quality protein extracts. The performance of the new protocol was tested against four methods available for vascular plants and a seaweed. The protocol, which includes an initial step to remove salts from the algal tissues, allowed the use of highly resolving two-dimensional gel electrophoresis (2-DE) protein analyses, providing the opportunity to unravel potentially novel physiological processes unique to this group of marine organisms.
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Affiliation(s)
- Loretto Contreras
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Andrés Ritter
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Geraldine Dennett
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Freddy Boehmwald
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Nathalie Guitton
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Charles Pineau
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alejandra Moenne
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Philippe Potin
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Juan A Correa
- Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile Center for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile CNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, ChileDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, Chile High-Throughput Proteomics Platform OUEST-genopole®, UPRES JE 2459, INSERM, U625, Campus de Beaulieu F-35042, FranceDepartamento de Biología, Facultad de Química y Biología, Universidad de Santiago, Santiago, ChileCNRS, Université Pierre et Marie Curie, UMR 7139, Station Biologique, Roscoff, FranceCenter for Advanced Studies in Ecology & Biodiversity, Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
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Poynton HC, Wintz H, Vulpe CD. Progress in ecotoxicogenomics for environmental monitoring, mode of action, and toxicant identification. COMPARATIVE TOXICOGENOMICS 2008. [DOI: 10.1016/s1872-2423(08)00002-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Abstract
Within the growing body of proteomics studies, issues addressing problems of ecotoxicology are on the rise. Generally speaking, ecotoxicology uses quantitative expression changes of distinct proteins known to be involved in toxicological responses as biomarkers. Unlike these directed approaches, proteomics examines how multiple expression changes are associated with a contamination that is suspected to be detrimental. Consequently, proteins involved in toxicological responses that have not been described previously may be revealed. Following identification of key proteins indicating exposure or effect, proteomics can potentially be employed in environmental risk assessment. To this end, bioinformatics may unveil protein patterns specific to an environmental stress that would constitute a classifier able to distinguish an exposure from a control state. The combined use of sets of marker proteins associated with a given pollution impact may prove to be more reliable, as they are based not only on a few unique markers which are measured independently, but reflect the complexity of a toxicological response. Such a proteomic pattern might also integrate some of the already established biomarkers of environmental toxicity. Proteomics applications in ecotoxicology may also comprise functional examination of known classes of proteins, such as glutathione transferases or metallothioneins, to elucidate their toxicological responses.
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Affiliation(s)
- Tiphaine Monsinjon
- Laboratoire d'Ecotoxicologie - Milieux Aquatiques, Université du Havre, Le Havre, France
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Ahsan N, Lee SH, Lee DG, Lee H, Lee SW, Bahk JD, Lee BH. Physiological and protein profiles alternation of germinating rice seedlings exposed to acute cadmium toxicity. C R Biol 2007; 330:735-46. [PMID: 17905393 DOI: 10.1016/j.crvi.2007.08.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Revised: 05/25/2007] [Accepted: 08/02/2007] [Indexed: 11/16/2022]
Abstract
Seed germination is a complex physiological process in plants that can be affected severely by heavy metals. The interference of germination by cadmium stress has not been well documented at the proteomic level. In the present study, in order to investigate the protein profile alternations during the germination stage following exposure to cadmium, a proteomic approach has been adopted in combination with morphological and physiological parameters. Seeds were exposed with a wide range of cadmium between 0.2 and 1.0 mM. Increases of cadmium concentration in the medium resulted in increased cadmium accumulation in seeds and TBARS content, whereas germination rate, shoot elongation, biomass, and water content were decreased significantly. Temporal changes of the total proteins were investigated by two-dimensional electrophoresis (2-DE). Twenty-one proteins were identified using MALDI-TOF mass spectrometry, which were upregulated at least 1.5-fold in response to cadmium stress. The identified proteins are involved in several processes, including defense and detoxification, antioxidant, protein biosynthesis, and germination processes. The identification of these proteins in the cadmium stress response provides new insight that can lead to a better understanding of the molecular basis of heavy metal responses of seeds at the germination stage.
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Affiliation(s)
- Nagib Ahsan
- Division of Applied Life Sciences (BK21 & EB-NCRC), Gyeongsang National University, Jinju 660-701, Republic of Korea
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Monsinjon T, Andersen OK, Leboulenger F, Knigge T. Data processing and classification analysis of proteomic changes: a case study of oil pollution in the mussel, Mytilus edulis. Proteome Sci 2006; 4:17. [PMID: 16970821 PMCID: PMC1592071 DOI: 10.1186/1477-5956-4-17] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2006] [Accepted: 09/13/2006] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Proteomics may help to detect subtle pollution-related changes, such as responses to mixture pollution at low concentrations, where clear signs of toxicity are absent. The challenges associated with the analysis of large-scale multivariate proteomic datasets have been widely discussed in medical research and biomarker discovery. This concept has been introduced to ecotoxicology only recently, so data processing and classification analysis need to be refined before they can be readily applied in biomarker discovery and monitoring studies. RESULTS Data sets obtained from a case study of oil pollution in the Blue mussel were investigated for differential protein expression by retentate chromatography-mass spectrometry and decision tree classification. Different tissues and different settings were used to evaluate classifiers towards their discriminatory power. It was found that, due the intrinsic variability of the data sets, reliable classification of unknown samples could only be achieved on a broad statistical basis (n > 60) with the observed expression changes comprising high statistical significance and sufficient amplitude. The application of stringent criteria to guard against overfitting of the models eventually allowed satisfactory classification for only one of the investigated data sets and settings. CONCLUSION Machine learning techniques provide a promising approach to process and extract informative expression signatures from high-dimensional mass-spectrometry data. Even though characterisation of the proteins forming the expression signatures would be ideal, knowledge of the specific proteins is not mandatory for effective class discrimination. This may constitute a new biomarker approach in ecotoxicology, where working with organisms, which do not have sequenced genomes render protein identification by database searching problematic. However, data processing has to be critically evaluated and statistical constraints have to be considered before supervised classification algorithms are employed.
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Affiliation(s)
- Tiphaine Monsinjon
- IRIS – International Research Institute of Stavanger AS, Randaberg, Norway
- Laboratoire d'Ecotoxicologie – Milieux Aquatiques, Université du Havre, Le Havre, France
| | - Odd Ketil Andersen
- IRIS – International Research Institute of Stavanger AS, Randaberg, Norway
| | - François Leboulenger
- Laboratoire d'Ecotoxicologie – Milieux Aquatiques, Université du Havre, Le Havre, France
| | - Thomas Knigge
- IRIS – International Research Institute of Stavanger AS, Randaberg, Norway
- Laboratoire d'Ecotoxicologie – Milieux Aquatiques, Université du Havre, Le Havre, France
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Kim CI, Lee SH, Seong GJ, Kim YH, Lee MY. Nuclear translocation and overexpression of GAPDH by the hyper-pressure in retinal ganglion cell. Biochem Biophys Res Commun 2006; 341:1237-43. [PMID: 16469296 DOI: 10.1016/j.bbrc.2006.01.087] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2006] [Accepted: 01/13/2006] [Indexed: 01/12/2023]
Abstract
To investigate the effect of hyper-pressure on retinal ganglion cells (RGC-5), RGC-5 cells were exposed to an ambient hydrostatic pressure of 100 mmHg. Upon treatment, the proliferation of RGC-5 cells was inhibited and neuronal apoptosis was detected by specific apoptosis marker TUNEL (terminal deoxynucleotidyl transferase dUTP nick-end labeling). To probe into the mechanism mediating the apoptosis of RGC-5 cells in 100 mmHg, protein profile alterations following hyper-pressure treatment were examined using two-dimensional gel electrophoresis (2-DE) followed by MALDI-TOF. Out of the 400 protein spots of RGC-5 cells detected on 2-DE gels, 37 differentially expressed protein spots were further identified using in gel tryptic digestion and mass spectrometry. Among these proteins, glyceraldehyde-3-phosphate-dehydrogenase (GAPDH) was significantly expressed 10 times more in 100 mmHg than in normal pressure. The accumulation of GAPDH in the nucleus and its translocation from the cytosol to the nucleus in 100 mmHg were observed using a microscope. These results suggest that the hyper-pressure-induced apoptosis in RGC-5 cells may be involved with not only the increase of GAPDH expression, but also the accumulation and the translocalization of GAPDH to the nucleus.
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Affiliation(s)
- Choong-Il Kim
- Division of Life Science, Soonchunhyang University, Asan, Chungnam, Republic of Korea
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