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Faugere J, Brunet TA, Clément Y, Espeyte A, Geffard O, Lemoine J, Chaumot A, Degli-Esposti D, Ayciriex S, Salvador A. Development of a multi-omics extraction method for ecotoxicology: investigation of the reproductive cycle of Gammarus fossarum. Talanta 2023; 253:123806. [PMID: 36113334 DOI: 10.1016/j.talanta.2022.123806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 07/24/2022] [Accepted: 07/29/2022] [Indexed: 12/13/2022]
Abstract
Omics study exemplified by proteomics, lipidomics or metabolomics, provides the opportunity to get insight of the molecular modifications occurring in living organisms in response to contaminants or in different physiological conditions. However, individual omics discloses only a single layer of information leading to a partial image of the biological complexity. Multiplication of samples preparation and processing can generate analytical variations resulting from several extractions and instrumental runs. To get all the -omics information at the proteins, metabolites and lipids level coming from a unique sample, a specific sample preparation must be optimized. In this study, we streamlined a biphasic extraction procedure based on a MTBE/Methanol mixture to provide the simultaneous extraction of polar (proteins, metabolites) and apolar compounds (lipids) for multi-omics analyses from a unique biological sample by a liquid chromatography (LC)/mass spectrometry (MS)/MS-based targeted approach. We applied the methodology for the study of female amphipod Gammarus fossarum during the reproductive cycle. Multivariate data analyses including Partial Least Squares Discriminant Analysis and multiple factor analysis were applied for the integration of the multi-omics data sets and highlighted molecular signatures, specific to the different stages.
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Affiliation(s)
- Julien Faugere
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Thomas Alexandre Brunet
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Yohann Clément
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Anabelle Espeyte
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Olivier Geffard
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | - Jérôme Lemoine
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Chaumot
- INRAE, UR RiverLy, Laboratoire D'écotoxicologie, F-69625, Villeurbanne, France
| | | | - Sophie Ayciriex
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France
| | - Arnaud Salvador
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques, CNRS UMR 5280, 5 Rue de La Doua, F-69100, Villeurbanne, France.
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Gregersen Echers S, Abdul-Khalek N, Mikkelsen RK, Holdt SL, Jacobsen C, Hansen EB, Olsen TH, Sejberg JJ, Overgaard MT. Is Gigartina a potential source of food protein and functional peptide-based ingredients? Evaluating an industrial, pilot-scale extract by proteomics and bioinformatics. FUTURE FOODS 2022. [DOI: 10.1016/j.fufo.2022.100189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
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3
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Zhao S, Pan C, Zhao J, Du H, Li M, Yu H, Chen X. Quantitative proteomic analysis of the microbial degradation of 3-aminobenzoic acid by Comamonas sp. QT12. Sci Rep 2022; 12:17609. [PMID: 36266292 PMCID: PMC9584955 DOI: 10.1038/s41598-022-17570-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 07/27/2022] [Indexed: 01/13/2023] Open
Abstract
A mab cluster associated with 3-aminobenzoic acid (3AB) degradation was identified in Comamonas sp. QT12. However, the cellular response of Comamonas sp. QT12 to 3-aminobenzoic acid remains unclear. In this study, label-free quantitative proteome analysis based on LC-MS/MS was used to study the protein expression difference of strain QT12 under the condition of using 3AB (3AB) and citric acid/ammonium chloride as substrates (3ABCon). A total of 2068 proteins were identified, of which 239 were significantly up-regulated in 3AB group, 124 were significantly down-regulated in 3AB group, 624 were expressed only in 3AB group, and 216 were expressed only in 3ABCon group in 3AB group. KEGG pathway analysis found that 83 pathways were up-regulated and 49 pathways were down-regulated, In GO analysis, 315 paths were up-regulated and 156 paths were down-regulated. There were 6 genes in the mab cluster that were only detected in the 3AB group.The mab cluster was found to be related to degradation of 3AB. By knockout, it was found that the growth rate of the mutant △orf7 and △orf9 were slowed down. HPLC results showed that the mutant △orf7 and △orf9 could still degrade 3AB, it was found that orf7, orf9 were not key genes about 3AB degradation and they could be replaced by other genes in strain QT12. These findings improve our understanding of the molecular mechanisms underlying the cellular response of 3AB degradation in Comamonas bacterium.
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Affiliation(s)
- Shuxue Zhao
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China ,grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Chao Pan
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
| | - Junxing Zhao
- Qingdao Water Administration Bureau, Qingdao, 266071 China
| | - Haiyan Du
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Min Li
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Hao Yu
- grid.412608.90000 0000 9526 6338Shandong Provincial Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, 700 Changcheng Road, Chengyang District, Qingdao, 266109 Shandong Province People’s Republic of China
| | - Xi Chen
- grid.4422.00000 0001 2152 3263College of Marine Life Sciences, Ocean University of China, Qingdao, 266100 China
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Pinel-Cabello M, Chapon V, Ruiz-Fresneda MA, Alpha-Bazin B, Berthomieu C, Armengaud J, Merroun ML. Delineation of cellular stages and identification of key proteins for reduction and biotransformation of Se(IV) by Stenotrophomonas bentonitica BII-R7. JOURNAL OF HAZARDOUS MATERIALS 2021; 418:126150. [PMID: 34111750 DOI: 10.1016/j.jhazmat.2021.126150] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 04/30/2021] [Accepted: 05/14/2021] [Indexed: 06/12/2023]
Abstract
The widespread use of selenium (Se) in technological applications (e.g., solar cells and electronic devices) has led to an accumulation of this metalloid in the environment to toxic levels. The newly described bacterial strain Stenotrophomonas bentonitica BII-R7 has been demonstrated to reduce mobile Se(IV) to Se(0)-nanoparticles (Se(0)NPs) and volatile species. Amorphous Se-nanospheres are reported to aggregate to form crystalline nanostructures and trigonal selenium. We investigated the molecular mechanisms underlying the biotransformation of Se(IV) to less toxic forms using differential shotgun proteomics analysis of S. bentonitica BII-R7 grown with or without sodium selenite for three different time-points. Results showed an increase in the abundance of several proteins involved in Se(IV) reduction and stabilization of Se(0)NPs, such as glutathione reductase, in bacteria grown with Se(IV), in addition to many proteins with transport functions, including RND (resistance-nodulation-division) systems, possibly facilitating Se uptake. Notably proteins involved in oxidative stress defense (e.g., catalase/peroxidase HPI) were also induced by Se exposure. Electron microscopy analyses confirmed the biotransformation of amorphous nanospheres to trigonal Se. Overall, our results highlight the potential of S. bentonitica in reducing the bioavailability of Se, which provides a basis both for the development of bioremediation strategies and the eco-friendly synthesis of biotechnological nanomaterials.
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Affiliation(s)
- M Pinel-Cabello
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain.
| | - V Chapon
- CEA, CNRS, Aix-Marseille Université, BIAM, IPM, 13108 Saint-Paul-lez-Durance, France
| | - M A Ruiz-Fresneda
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
| | - B Alpha-Bazin
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols sur Cèze, France
| | - C Berthomieu
- CEA, CNRS, Aix-Marseille Université, BIAM, IPM, 13108 Saint-Paul-lez-Durance, France
| | - J Armengaud
- Université Paris-Saclay, CEA, INRAE, Département Médicaments et Technologies pour la Santé (DMTS), SPI, 30200 Bagnols sur Cèze, France
| | - M L Merroun
- Department of Microbiology, University of Granada, Campus Fuentenueva s/n, 18071 Granada, Spain
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Zhao S, Chen X, Sun Q, Wang F, Hu C, Guo L, Bai J, Yu H. Label-Free Quantitative Proteomic Analysis of the Global Response to Indole-3-Acetic Acid in Newly Isolated Pseudomonas sp. Strain LY1. Front Microbiol 2021; 12:694874. [PMID: 34447357 PMCID: PMC8383072 DOI: 10.3389/fmicb.2021.694874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
Abstract
Indole-3-acetic acid (IAA), known as a common plant hormone, is one of the most distributed indole derivatives in the environment, but the degradation mechanism and cellular response network to IAA degradation are still not very clear. The objective of this study was to elucidate the molecular mechanisms of IAA degradation at the protein level by a newly isolated strain Pseudomonas sp. LY1. Label-free quantitative proteomic analysis of strain LY1 cultivated with IAA or citrate/NH4Cl was applied. A total of 2,604 proteins were identified, and 227 proteins have differential abundances in the presence of IAA, including 97 highly abundant proteins and 130 less abundant proteins. Based on the proteomic analysis an IAA degrading (iad) gene cluster in strain LY1 containing IAA transformation genes (organized as iadHABICDEFG), genes of the β-ketoadipate pathway for catechol and protocatechuate degradation (catBCA and pcaABCDEF) were identified. The iadA, iadB, and iadE-disrupted mutants lost the ability to grow on IAA, which confirmed the role of the iad cluster in IAA degradation. Degradation intermediates were analyzed by HPLC, LC-MS, and GC-MS analysis. Proteomic analysis and identified products suggested that multiple degradation pathways existed in strain LY1. IAA was initially transformed to dioxindole-3-acetic acid, which was further transformed to isatin. Isatin was then transformed to isatinic acid or catechol. An in-depth data analysis suggested oxidative stress in strain LY1 during IAA degradation, and the abundance of a series of proteins was upregulated to respond to the stress, including reaction oxygen species (ROS) scavenging, protein repair, fatty acid synthesis, RNA protection, signal transduction, chemotaxis, and several membrane transporters. The findings firstly explained the adaptation mechanism of bacteria to IAA degradation.
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Affiliation(s)
- Shuxue Zhao
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Xi Chen
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Qianshu Sun
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China.,Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Fei Wang
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Chunhui Hu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lizhong Guo
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Jie Bai
- College of Environmental Science and Engineering, Ocean University of China, Qingdao, China
| | - Hao Yu
- Shandong Province Key Laboratory of Applied Mycology, School of Life Sciences, Qingdao Agricultural University, Qingdao, China
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Olaya-Abril A, Hidalgo-Carrillo J, Luque-Almagro VM, Fuentes-Almagro C, Urbano FJ, Moreno-Vivián C, Richardson DJ, Roldán MD. Effect of pH on the denitrification proteome of the soil bacterium Paracoccus denitrificans PD1222. Sci Rep 2021; 11:17276. [PMID: 34446760 PMCID: PMC8390676 DOI: 10.1038/s41598-021-96559-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 07/23/2021] [Indexed: 11/25/2022] Open
Abstract
Denitrification is a respiratory process by which nitrate is reduced to dinitrogen. Incomplete denitrification results in the emission of the greenhouse gas nitrous oxide and this is potentiated in acidic soils, which display reduced denitrification rates and high N2O/N2 ratios compared to alkaline soils. In this work, impact of pH on the proteome of the soil denitrifying bacterium Paracoccus denitrificans PD1222 was analysed with nitrate as sole energy and nitrogen source under anaerobic conditions at pH ranging from 6.5 to 7.5. Quantitative proteomic analysis revealed that the highest difference in protein representation was observed when the proteome at pH 6.5 was compared to the reference proteome at pH 7.2. However, this difference in the extracellular pH was not enough to produce modification of intracellular pH, which was maintained at 6.5 ± 0.1. The biosynthetic pathways of several cofactors relevant for denitrification and nitrogen assimilation like cobalamin, riboflavin, molybdopterin and nicotinamide were negatively affected at pH 6.5. In addition, peptide representation of reductases involved in nitrate assimilation and denitrification were reduced at pH 6.5. Data highlight the strong negative impact of pH on NosZ synthesis and intracellular copper content, thus impairing active NosZ assembly and, in turn, leading to elevated nitrous oxide emissions.
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Affiliation(s)
- Alfonso Olaya-Abril
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Jesús Hidalgo-Carrillo
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Víctor M Luque-Almagro
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - Carlos Fuentes-Almagro
- Servicio Central de Apoyo a la Investigación (SCAI), Unidad de Proteómica, Universidad de Córdoba, Campus de Rabanales, 14071, Córdoba, Spain
| | - Francisco J Urbano
- Departamento de Química Orgánica, Universidad de Córdoba, Edificio Marie Curie, Campus de Rabanales, 14071, Córdoba, Spain
| | - Conrado Moreno-Vivián
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain
| | - David J Richardson
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - María Dolores Roldán
- Departamento de Bioquímica y Biología Molecular, Universidad de Córdoba, Edificio Severo Ochoa, 1ª planta, Campus de Rabanales, 14071, Córdoba, Spain.
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Mappa C, Pible O, Armengaud J, Alpha-Bazin B. Assessing the ratio of Bacillus spores and vegetative cells by shotgun proteomics. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:25107-25115. [PMID: 30302730 DOI: 10.1007/s11356-018-3341-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/26/2018] [Indexed: 06/08/2023]
Abstract
Mass spectrometry for rapid identification of microorganisms is expanding over the last years because this approach is quick. This methodology provides a decisive interest to fight against bioterrorism as it is applicable whatever the pathogen to be considered and often allows subtyping which may be crucial for confirming a massive and widespread attack with biological agents. Here, we present a methodology based on next-generation proteomics and tandem mass spectrometry for discovering numerous protein biomarkers allowing the discrimination of spores and vegetative cells of Bacillus atrophaeus, a biowarfare simulant. We propose a global quantitative evaluation of the two groups of discriminant biomarkers based on their aggregated normalized spectral abundance factors.
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Affiliation(s)
- Charlotte Mappa
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207, Bagnols sur Cèze, France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207, Bagnols sur Cèze, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207, Bagnols sur Cèze, France.
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, 30207, Bagnols sur Cèze, France
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Can Proteomics Be Considered as a Valuable Tool to Assess the Toxicity of Nanoparticles in Marine Bivalves? JOURNAL OF MARINE SCIENCE AND ENGINEERING 2020. [DOI: 10.3390/jmse8121033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Exposure to nanoparticles (NPs) has been identified as a major concern for marine ecosystems. Because of their peculiar physico-chemical features, NPs are accumulated in marine organisms, which suffer a variety of adverse effects. In particular, bivalve mollusks represent a unique target for NPs, mainly because they are suspension-feeders with highly developed processes for cellular internalization of nano- and micrometric particles. Several studies have demonstrated that the uptake and the accumulation of NPs can induce sub-lethal effects towards marine bivalves. However, to understand the real risk of NP exposures the application of the so-called “omics” techniques (e.g., proteomics, genomics, metabolomics, lipidomics) has been suggested. In particular, proteomics has been used to study the effects of NPs and their mechanism(s) of action in marine bivalves, but to date its application is still limited. The present review aims at summarizing the state of the art concerning the application of proteomics as a tool to investigate the effects of nanoparticles on the proteome of marine bivalves, and to critically discuss the advantages and limitations of proteomics in this field of research. Relying on results obtained by studies that applied proteomics on bivalve tissues, proteomics application needs to be considered cautiously as a promising and valuable tool to shed light on toxicity and mechanism(s) of action of NPs. Although on one hand, the analysis of the current literature demonstrated undeniable strengths, potentiality and reliability of proteomics, on the other hand a number of limitations suggest that some gaps of knowledge need to be bridged, and methodological and technical improvements are necessary before proteomics can be readily and routinely applied to nanotoxicology studies.
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Torson AS, Dong YW, Sinclair BJ. Help, there are ‘omics’ in my comparative physiology! J Exp Biol 2020; 223:223/24/jeb191262. [DOI: 10.1242/jeb.191262] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Abstract
‘Omics’ methods, such as transcriptomics, proteomics, lipidomics or metabolomics, yield simultaneous measurements of many related molecules in a sample. These approaches have opened new opportunities to generate and test hypotheses about the mechanisms underlying biochemical and physiological phenotypes. In this Commentary, we discuss general approaches and considerations for successfully integrating omics into comparative physiology. The choice of omics approach will be guided by the availability of existing resources and the time scale of the process being studied. We discuss the use of whole-organism extracts (common in omics experiments on small invertebrates) because such an approach may mask underlying physiological mechanisms, and we consider the advantages and disadvantages of pooling samples within biological replicates. These methods can bring analytical challenges, so we describe the most easily analyzed omics experimental designs. We address the propensity of omics studies to digress into ‘fishing expeditions’ and show how omics can be used within the hypothetico-deductive framework. With this Commentary, we hope to provide a roadmap that will help newcomers approach omics in comparative physiology while avoiding some of the potential pitfalls, which include ambiguous experiments, long lists of candidate molecules and vague conclusions.
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Affiliation(s)
- Alex S. Torson
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
| | - Yun-wei Dong
- The Key Laboratory of Mariculture, Ministry of Education, Fisheries College, Ocean University of China, Qingdao 266003, PR China
| | - Brent J. Sinclair
- Department of Biology, The University of Western Ontario, London, ON N6A 5B7, Canada
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10
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López-Pedrouso M, Varela Z, Franco D, Fernández JA, Aboal JR. Can proteomics contribute to biomonitoring of aquatic pollution? A critical review. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 267:115473. [PMID: 32882465 DOI: 10.1016/j.envpol.2020.115473] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 08/14/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Aquatic pollution is one of the greatest environmental problems, and therefore its control represents one of the major challenges in this century. In recent years, proteomics has emerged as a powerful tool for searching protein biomarkers in the field of pollution biomonitoring. For biomonitoring marine contamination, there is a consensus that bivalves are preferred organisms to assess organic and inorganic pollutants. Thus, the bivalve proteome was intensively studied, particularly the mussel. It is well documented that heavy metal pollution and organic chemicals altered the structural proteins causing degradation of tissues of molluscs. Also, it is well known that proteins involved in stress oxidative such as glutathione and enzymes as catalase, superoxide dismutase or peroxisomes are overexpressed in response to contaminants. Additionally, using bivalves, other groups of proteins proposed as pollution biomarkers are the metabolic proteins. Even though other marine species are used to monitor the pollution, the presence of proteomic tools in these studies is scarce. Concerning freshwater pollution field, a great variety of animal species (fish and crustaceans) are used as biomonitors in proteomics studies compared to plants that are scarcely analysed. In fish species, proteins involved in stress oxidative such as heat shock family or proteins from lipid and carbohydrate metabolism were proposed as candidate biomarkers. On the contrary, for crustaceans there is a lack of proteomic studies individually assessing the contaminants. Novel scenarios, including emerging contaminants and new threats, will require proteomic technology for a systematic search of protein biomarkers and a greater knowledge at molecular level of those cellular pathways induced by contamination.
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Affiliation(s)
- M López-Pedrouso
- Department of Zoology, Genetics and Physical Anthropology, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain.
| | - Z Varela
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
| | - D Franco
- Centro Tecnológico de La Carne de Galicia, Rúa Galicia Nº 4, Parque Tecnológico de Galicia, San Cibrao Das Viñas, 32900, Ourense, Spain
| | - J A Fernández
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
| | - J R Aboal
- CRETUS Institute, Department of Functional Biology, Ecology Unit, University of Santiago de Compostela, Santiago de Compostela, 15872, A Coruña, Spain
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Hayoun K, Pible O, Petit P, Allain F, Jouffret V, Culotta K, Rivasseau C, Armengaud J, Alpha-Bazin B. Proteotyping Environmental Microorganisms by Phylopeptidomics: Case Study Screening Water from a Radioactive Material Storage Pool. Microorganisms 2020; 8:E1525. [PMID: 33020444 PMCID: PMC7599590 DOI: 10.3390/microorganisms8101525] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Revised: 09/30/2020] [Accepted: 10/01/2020] [Indexed: 02/07/2023] Open
Abstract
The microbial diversity encompassed by the environmental biosphere is largely unexplored, although it represents an extensive source of new knowledge and potentially of novel enzymatic catalysts for biotechnological applications. To determine the taxonomy of microorganisms, proteotyping by tandem mass spectrometry has proved its efficiency. Its latest extension, phylopeptidomics, adds a biomass quantitation perspective for mixtures of microorganisms. Here, we present an application of phylopeptidomics to rapidly and sensitively screen microorganisms sampled from an industrial environment, i.e., a pool where radioactive material is stored. The power of this methodology is demonstrated through the identification of both prokaryotes and eukaryotes, whether as pure isolates or present as mixtures or consortia. In this study, we established accurate taxonomical identification of environmental prokaryotes belonging to the Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria phyla, as well as eukaryotes from the Ascomycota phylum. The results presented illustrate the potential of tandem mass spectrometry proteotyping, in particular phylopeptidomics, to screen for and rapidly identify microorganisms.
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Affiliation(s)
- Karim Hayoun
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Université de Montpellier, F-30207 Bagnols-sur-Cèze, France
| | - Olivier Pible
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
| | - Pauline Petit
- CEA, CNRS, INRA, Université Grenoble Alpes, Institut de Biosciences et Biotechnologies de Grenoble, UMR5168, F-38000 Grenoble, France;
| | - François Allain
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
| | - Virginie Jouffret
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
| | - Karen Culotta
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
| | - Corinne Rivasseau
- CEA-Saclay, DRF/Joliot/SB2SM/BBC, I2BC, 91191 Gif-sur-Yvette, France;
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
| | - Béatrice Alpha-Bazin
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, SPI, Université Paris Saclay, F-30200 Bagnols-sur-Cèze, France; (K.H.); (O.P.); (F.A.); (V.J.); (K.C.); (B.A.-B.)
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12
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FoodOmics as a new frontier to reveal microbial community and metabolic processes occurring on table olives fermentation. Food Microbiol 2020; 92:103606. [PMID: 32950142 DOI: 10.1016/j.fm.2020.103606] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 07/22/2020] [Accepted: 07/22/2020] [Indexed: 01/18/2023]
Abstract
Table olives are considered the most widespread fermented food in the Mediterranean area and their consumption is expanding all over the world. This fermented vegetable can be considered as a natural functional food thanks to their high nutritional value and high content of bioactive compounds that contribute to the health and well-being of consumers. The presence of bioactive compounds is strongly influenced by a complex microbial consortium, traditionally exploited through culture-dependent approaches. Recently, the rapid spread of omics technologies has represented an important challenge to better understand the function, the adaptation and the exploitation of microbial diversity in different complex ecosystems, such as table olives. This review provides an overview of the potentiality of omics technologies to in depth investigate the microbial composition and the metabolic processes that drive the table olives fermentation, affecting both sensorial profile and safety properties of the final product. Finally, the review points out the role of omics approaches to raise at higher sophisticated level the investigations on microbial, gene, protein, and metabolite, with huge potential for the integration of table olives composition with functional assessments.
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13
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High-throughput proteotyping of bacterial isolates by double barrel chromatography-tandem mass spectrometry based on microplate paramagnetic beads and phylopeptidomics. J Proteomics 2020; 226:103887. [PMID: 32619772 DOI: 10.1016/j.jprot.2020.103887] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/19/2020] [Accepted: 06/25/2020] [Indexed: 12/18/2022]
Abstract
Tandem mass spectrometry-based proteotyping of microorganisms presents several advantages over whole-cell MALDI-TOF mass spectrometry: because a larger number of signals are recorded with better accuracy and precision, the approach allows for the identification of microorganisms at more resolved taxonomic levels, and can easily manage complex samples. Additionally, the use of SP3 paramagnetic beads for cell lysis and protein cleanup simplifies sample preparation for proteotyping. Based on these features, we have developed and tested a 96-well plate platform for high-throughput proteotyping of a large variety of bacteria. We evaluated the performance of the platform in terms of bacterial load and found no cross-contamination between wells. Likewise, phylopeptidomics analysis revealed no alteration in the relative quantifications of microorganisms. Finally, we applied this new format for rapid proteotyping of a large set of dental isolates using double-barrel chromatography coupled to tandem mass spectrometry, which maximizes the number of spectra per unit of time. The procedure allowed us to establish whether these isolates were pure strains or mixtures of strains and to identify the microorganisms at the most resolved taxonomic level. SIGNIFICANCE: The rapid and accurate identification of microorganisms is a clinical priority in medical diagnostics; however, specimens containing mixtures of microorganisms are difficult to analyze and the procedure is time-consuming. Tandem mass spectrometry proteotyping allows the fast identification of complex mixtures of microorganisms, known or unknown, and can also establish the biomass ratio of each component. We describe here a new workflow for preparing microbial samples in a 96-well-plate format for tandem mass spectrometry proteotyping and document its advantages and limitations. We demonstrate that this new format coupled to a highly efficient double-barrel LC-MS/MS system allows proteotyping of 96 isolates in 55 h.
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14
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Kucharzyk KH, Meisel JE, Kara-Murdoch F, Murdoch RW, Higgins SA, Vainberg S, Bartling CM, Mullins L, Hatzinger PB, Löffler FE. Metagenome-Guided Proteomic Quantification of Reductive Dehalogenases in the Dehalococcoides mccartyi-Containing Consortium SDC-9. J Proteome Res 2020; 19:1812-1823. [PMID: 32135063 DOI: 10.1021/acs.jproteome.0c00072] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
At groundwater sites contaminated with chlorinated ethenes, fermentable substrates are often added to promote reductive dehalogenation by indigenous or augmented microorganisms. Contemporary bioremediation performance monitoring relies on nucleic acid biomarkers of key organohalide-respiring bacteria, such as Dehalococcoides mccartyi (Dhc). Metagenome sequencing of the commercial, Dhc-containing consortium, SDC-9, identified 12 reductive dehalogenase (RDase) genes, including pceA (two copies), vcrA, and tceA, and allowed for specific detection and quantification of RDase peptides using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). Shotgun (i.e., untargeted) proteomics applied to the SDC-9 consortium grown with tetrachloroethene (PCE) and lactate identified 143 RDase peptides, and 36 distinct peptides that covered greater than 99% of the protein-coding sequences of the PceA, TceA, and VcrA RDases. Quantification of RDase peptides using multiple reaction monitoring (MRM) assays with 13C-/15N-labeled peptides determined 1.8 × 103 TceA and 1.2 × 102 VcrA RDase molecules per Dhc cell. The MRM mass spectrometry approach allowed for sensitive detection and accurate quantification of relevant Dhc RDases and has potential utility in bioremediation monitoring regimes.
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Affiliation(s)
| | - Jayda E Meisel
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Fadime Kara-Murdoch
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States
| | - Robert W Murdoch
- Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
| | - Steven A Higgins
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States
| | - Simon Vainberg
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Craig M Bartling
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Larry Mullins
- Battelle Memorial Institute, 505 King Avenue, Columbus, Ohio 43201, United States
| | - Paul B Hatzinger
- APTIM, Biotechnology Development and Applications Group, 17 Princess Road, Lawrenceville, New Jersey 08648, United States
| | - Frank E Löffler
- Department of Microbiology, University of Tennessee, 1311 Cumberland Avenue, Knoxville, Tennessee 37996, United States.,Center for Environmental Biotechnology, University of Tennessee, 1416 Circle Drive, Knoxville, Tennessee 37996, United States.,Department of Civil and Environmental Engineering, University of Tennessee, 851 Neyland Drive, Knoxville, Tennessee 37996, United States.,Department of Biosystems Engineering and Soil Science University of Tennessee, 2506 E. J. Chapman Drive, Knoxville, Tennessee 37996, United States.,Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, United States
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15
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Giovanella P, Vieira GAL, Ramos Otero IV, Pais Pellizzer E, de Jesus Fontes B, Sette LD. Metal and organic pollutants bioremediation by extremophile microorganisms. JOURNAL OF HAZARDOUS MATERIALS 2020; 382:121024. [PMID: 31541933 DOI: 10.1016/j.jhazmat.2019.121024] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 07/17/2019] [Accepted: 08/14/2019] [Indexed: 06/10/2023]
Abstract
Extremophiles comprise microorganisms that are able to grow and thrive in extreme environments, including in an acidic or alkaline pH, high or low temperatures, high concentrations of pollutants, and salts, among others. These organisms are promising for environmental biotechnology due to their unique physiological and enzymatic characteristics, which allow them to survive in harsh environments. Due to the stability and persistence of these microorganisms under adverse environmental conditions, they can be used for the bioremediation of environments contaminated with extremely recalcitrant pollutants. Here, we provide an overview of extremophiles and the role of "omics" in the field of bioremediation of environmental pollutants, including hydrocarbons, textile dyes and metals.
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Affiliation(s)
- Patricia Giovanella
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
| | - Gabriela A L Vieira
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Igor V Ramos Otero
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Elisa Pais Pellizzer
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Bruno de Jesus Fontes
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil
| | - Lara D Sette
- Departamento de Bioquímica e Microbiologia, Instituto de Biociências, Universidade Estadual Paulista Júlio de Mesquita Filho, Rio Claro, SP, Brazil.
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16
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Duport C, Alpha-Bazin B, Armengaud J. Advanced Proteomics as a Powerful Tool for Studying Toxins of Human Bacterial Pathogens. Toxins (Basel) 2019; 11:toxins11100576. [PMID: 31590258 PMCID: PMC6832400 DOI: 10.3390/toxins11100576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/27/2019] [Accepted: 09/30/2019] [Indexed: 12/15/2022] Open
Abstract
Exotoxins contribute to the infectious processes of many bacterial pathogens, mainly by causing host tissue damages. The production of exotoxins varies according to the bacterial species. Recent advances in proteomics revealed that pathogenic bacteria are capable of simultaneously producing more than a dozen exotoxins. Interestingly, these toxins may be subject to post-transcriptional modifications in response to environmental conditions. In this review, we give an outline of different bacterial exotoxins and their mechanism of action. We also report how proteomics contributed to immense progress in the study of toxinogenic potential of pathogenic bacteria over the last two decades.
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Affiliation(s)
- Catherine Duport
- SQPOV, UMR0408, Avignon Université, INRA, F-84914 Avignon, France
- Correspondence:
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France; (B.A.-B.); (J.A.)
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17
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Hayoun K, Gouveia D, Grenga L, Pible O, Armengaud J, Alpha-Bazin B. Evaluation of Sample Preparation Methods for Fast Proteotyping of Microorganisms by Tandem Mass Spectrometry. Front Microbiol 2019; 10:1985. [PMID: 31555227 PMCID: PMC6742703 DOI: 10.3389/fmicb.2019.01985] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 08/13/2019] [Indexed: 12/13/2022] Open
Abstract
Tandem mass spectrometry-based proteotyping allows characterizing microorganisms in terms of taxonomy and is becoming an important tool for investigating microbial diversity from several ecosystems. Fast and automatable sample preparation for obtaining peptide pools amenable to tandem mass spectrometry is necessary for enabling proteotyping as a high-throughput method. First, the protocol to increase the yield of lysis of several representative bacterial and eukaryotic microorganisms was optimized by using a long and drastic bead-beating setting with 0.1 mm silica beads, 0.1 and 0.5 mm glass beads, in presence of detergents. Then, three different methods to obtain greater digestion yield from these extracts were tested and optimized for improve efficiency and reduce application time: denaturing electrophoresis of proteins and in-gel proteolysis, suspension-trapping filter-based approach (S-Trap) and, solid-phase-enhanced sample preparation named SP3. The latter method outperforms the other two in terms of speed and delivers also more peptides and proteins than with the in-gel proteolysis (2.2 fold for both) and S-trap approaches (1.3 and 1.2 fold, respectively). Thus, SP3 directly improves tandem mass spectrometry proteotyping.
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Affiliation(s)
| | | | | | | | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la Détection et le Diagnostic, Service de Pharmacologie et Immunoanalyse, CEA, INRA, Bagnols-sur-Cèze, France
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18
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Yu X, Wang Y, Kohnen MV, Piao M, Tu M, Gao Y, Lin C, Zuo Z, Gu L. Large Scale Profiling of Protein Isoforms Using Label-Free Quantitative Proteomics Revealed the Regulation of Nonsense-Mediated Decay in Moso Bamboo ( Phyllostachys edulis). Cells 2019; 8:E744. [PMID: 31330982 PMCID: PMC6678154 DOI: 10.3390/cells8070744] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Revised: 07/12/2019] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
Moso bamboo is an important forest species with a variety of ecological, economic, and cultural values. However, the gene annotation information of moso bamboo is only based on the transcriptome sequencing, lacking the evidence of proteome. The lignification and fiber in moso bamboo leads to a difficulty in the extraction of protein using conventional methods, which seriously hinders research on the proteomics of moso bamboo. The purpose of this study is to establish efficient methods for extracting the total proteins from moso bamboo for following mass spectrometry-based quantitative proteome identification. Here, we have successfully established a set of efficient methods for extracting total proteins of moso bamboo followed by mass spectrometry-based label-free quantitative proteome identification, which further improved the protein annotation of moso bamboo genes. In this study, 10,376 predicted coding genes were confirmed by quantitative proteomics, accounting for 35.8% of all annotated protein-coding genes. Proteome analysis also revealed the protein-coding potential of 1015 predicted long noncoding RNA (lncRNA), accounting for 51.03% of annotated lncRNAs. Thus, mass spectrometry-based proteomics provides a reliable method for gene annotation. Especially, quantitative proteomics revealed the translation patterns of proteins in moso bamboo. In addition, the 3284 transcript isoforms from 2663 genes identified by Pacific BioSciences (PacBio) single-molecule real-time long-read isoform sequencing (Iso-Seq) was confirmed on the protein level by mass spectrometry. Furthermore, domain analysis of mass spectrometry-identified proteins encoded in the same genomic locus revealed variations in domain composition pointing towards a functional diversification of protein isoform. Finally, we found that part transcripts targeted by nonsense-mediated mRNA decay (NMD) could also be translated into proteins. In summary, proteomic analysis in this study improves the proteomics-assisted genome annotation of moso bamboo and is valuable to the large-scale research of functional genomics in moso bamboo. In summary, this study provided a theoretical basis and technical support for directional gene function analysis at the proteomics level in moso bamboo.
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Affiliation(s)
- Xiaolan Yu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongsheng Wang
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Markus V Kohnen
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Mingxin Piao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun 130062, China
| | - Min Tu
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yubang Gao
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Chentao Lin
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Department of Molecular, Cell & Developmental Biology, University of California, Los Angeles, CA 90095, USA
| | - Zecheng Zuo
- Basic Forestry and Proteomics Research Center, College of Life Science, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
- Jilin Province Engineering Laboratory of Plant Genetic Improvement, College of Plant Science, Jilin University, 5333 Xi'an Road, Changchun 130062, China.
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of forestry, Fujian Agriculture and Forestry University, Fuzhou 350002, China.
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19
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Freitas AC, Gomes AM. Analytical approaches for proteomics and lipidomics of arsenic in algae. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/bs.coac.2019.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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20
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Dialogue on the nomenclature and classification of prokaryotes. Syst Appl Microbiol 2019; 42:5-14. [DOI: 10.1016/j.syapm.2018.07.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/08/2018] [Accepted: 07/03/2018] [Indexed: 12/16/2022]
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21
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Orellana R, Macaya C, Bravo G, Dorochesi F, Cumsille A, Valencia R, Rojas C, Seeger M. Living at the Frontiers of Life: Extremophiles in Chile and Their Potential for Bioremediation. Front Microbiol 2018; 9:2309. [PMID: 30425685 PMCID: PMC6218600 DOI: 10.3389/fmicb.2018.02309] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 09/10/2018] [Indexed: 11/19/2022] Open
Abstract
Extremophiles are organisms capable of adjust, survive or thrive in hostile habitats that were previously thought to be adverse or lethal for life. Chile gathers a wide range of extreme environments: salars, geothermal springs, and geysers located at Altiplano and Atacama Desert, salars and cold mountains in Central Chile, and ice fields, cold lakes and fjords, and geothermal sites in Patagonia and Antarctica. The aims of this review are to describe extremophiles that inhabit main extreme biotopes in Chile, and their molecular and physiological capabilities that may be advantageous for bioremediation processes. After briefly describing the main ecological niches of extremophiles along Chilean territory, this review is focused on the microbial diversity and composition of these biotopes microbiomes. Extremophiles have been isolated in diverse zones in Chile that possess extreme conditions such as Altiplano, Atacama Desert, Central Chile, Patagonia, and Antarctica. Interesting extremophiles from Chile with potential biotechnological applications include thermophiles (e.g., Methanofollis tationis from Tatio Geyser), acidophiles (e.g., Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum from Atacama Desert and Central Chile copper ores), halophiles (e.g., Shewanella sp. Asc-3 from Altiplano, Streptomyces sp. HKF-8 from Patagonia), alkaliphiles (Exiguobacterium sp. SH31 from Altiplano), xerotolerant bacteria (S. atacamensis from Atacama Desert), UV- and Gamma-resistant bacteria (Deinococcus peraridilitoris from Atacama Desert) and psychrophiles (e.g., Pseudomonas putida ATH-43 from Antarctica). The molecular and physiological properties of diverse extremophiles from Chile and their application in bioremediation or waste treatments are further discussed. Interestingly, the remarkable adaptative capabilities of extremophiles convert them into an attractive source of catalysts for bioremediation and industrial processes.
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Affiliation(s)
- Roberto Orellana
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
- Departamento de Biología, Facultad de Ciencias Naturales y Exactas, Universidad de Playa Ancha, Valparaíso, Chile
| | - Constanza Macaya
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Guillermo Bravo
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Flavia Dorochesi
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Andrés Cumsille
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Ricardo Valencia
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Claudia Rojas
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
| | - Michael Seeger
- Laboratorio de Microbiología Molecular y Biotecnología Ambiental, Departamento de Química and Centro de Biotecnología Daniel Alkalay Lowitt, Universidad Técnica Federico Santa María, Valparaíso, Chile
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22
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Thiaucourt F, Pible O, Miotello G, Nwankpa N, Armengaud J. Improving Quality Control of Contagious Caprine Pleuropneumonia Vaccine with Tandem Mass Spectrometry. Proteomics 2018; 18:e1800088. [PMID: 29911326 DOI: 10.1002/pmic.201800088] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/16/2018] [Indexed: 01/20/2023]
Abstract
Vaccines to protect livestock against contagious caprine pleuropneumonia (CCPP) consist of inactivated, adjuvanted antigens. Quality control of these vaccines is challenging as total protein quantification provides no indication of protein identity or purity, and culture is not an option. Here, a tandem mass spectrometry approach is used to identify the mycoplasma antigen contained in reference samples and in commercial CCPP vaccines. By the same approach, the relative amounts of mycoplasma antigen and residual proteins originating from the production medium are determined. Mass spectrometry allows easy and rapid identification of the peptides present in the vaccine samples. Alongside the most probable mycoplasma species effectively present in the vaccines, a very high proportion of peptides from medium constituents are detected in the commercial vaccines tested.
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Affiliation(s)
- François Thiaucourt
- Agricultural Resesarch Center for Intemational Development(CIRAD) CIRAD, UMR ASTRE, F-34398 Montpellier, France ASTRE, CIRAD, INRA, Univ Montpellier, Montpellier, France
| | - Olivier Pible
- Laboratoire Innovations Technologiques pour la détection et le diagnostic (Li2D), Service de Pharmacologie et Immunoanalyses (SPI), CEA INRA, F-30207 Bagnols sur Cèze, France
| | - Guylaine Miotello
- Laboratoire Innovations Technologiques pour la détection et le diagnostic (Li2D), Service de Pharmacologie et Immunoanalyses (SPI), CEA INRA, F-30207 Bagnols sur Cèze, France
| | - Nick Nwankpa
- Pan African Veterinary Vaccine Center, African Union Commission, 1746 Debre Zeit, Ethiopia
| | - Jean Armengaud
- Laboratoire Innovations Technologiques pour la détection et le diagnostic (Li2D), Service de Pharmacologie et Immunoanalyses (SPI), CEA INRA, F-30207 Bagnols sur Cèze, France
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23
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Sandrin TR, Demirev PA. Characterization of microbial mixtures by mass spectrometry. MASS SPECTROMETRY REVIEWS 2018; 37:321-349. [PMID: 28509357 DOI: 10.1002/mas.21534] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Revised: 03/09/2017] [Accepted: 03/09/2017] [Indexed: 05/27/2023]
Abstract
MS applications in microbiology have increased significantly in the past 10 years, due in part to the proliferation of regulator-approved commercial MALDI MS platforms for rapid identification of clinical infections. In parallel, with the expansion of MS technologies in the "omics" fields, novel MS-based research efforts to characterize organismal as well as environmental microbiomes have emerged. Successful characterization of microorganisms found in complex mixtures of other organisms remains a major challenge for researchers and clinicians alike. Here, we review recent MS advances toward addressing that challenge. These include sample preparation methods and protocols, and established, for example, MALDI, as well as newer, for example, atmospheric pressure ionization (API) techniques. MALDI mass spectra of intact cells contain predominantly information on the highly expressed house-keeping proteins used as biomarkers. The API methods are applicable for small biomolecule analysis, for example, phospholipids and lipopeptides, and facilitate species differentiation. MS hardware and techniques, for example, tandem MS, including diverse ion source/mass analyzer combinations are discussed. Relevant examples for microbial mixture characterization utilizing these combinations are provided. Chemometrics and bioinformatics methods and algorithms, including those applied to large scale MS data acquisition in microbial metaproteomics and MS imaging of biofilms, are highlighted. Select MS applications for polymicrobial culture analysis in environmental and clinical microbiology are reviewed as well.
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Affiliation(s)
- Todd R Sandrin
- School of Mathematical and Natural Sciences, Arizona State University, Phoenix, Arizona
| | - Plamen A Demirev
- Applied Physics Laboratory, Johns Hopkins University, Laurel, Maryland
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Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA. Population Genomics: Advancing Understanding of Nature. POPULATION GENOMICS 2018. [DOI: 10.1007/13836_2018_60] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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25
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Gallois N, Alpha-Bazin B, Ortet P, Barakat M, Piette L, Long J, Berthomieu C, Armengaud J, Chapon V. Proteogenomic insights into uranium tolerance of a Chernobyl's Microbacterium bacterial isolate. J Proteomics 2017; 177:148-157. [PMID: 29223802 DOI: 10.1016/j.jprot.2017.11.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 11/15/2017] [Accepted: 11/27/2017] [Indexed: 10/18/2022]
Abstract
Microbacterium oleivorans A9 is a uranium-tolerant actinobacteria isolated from the trench T22 located near the Chernobyl nuclear power plant. This site is contaminated with different radionuclides including uranium. To observe the molecular changes at the proteome level occurring in this strain upon uranyl exposure and understand molecular mechanisms explaining its uranium tolerance, we established its draft genome and used this raw information to perform an in-depth proteogenomics study. High-throughput proteomics were performed on cells exposed or not to 10μM uranyl nitrate sampled at three previously identified phases of uranyl tolerance. We experimentally detected and annotated 1532 proteins and highlighted a total of 591 proteins for which abundances were significantly differing between conditions. Notably, proteins involved in phosphate and iron metabolisms show high dynamics. A large ratio of proteins more abundant upon uranyl stress, are distant from functionally-annotated known proteins, highlighting the lack of fundamental knowledge regarding numerous key molecular players from soil bacteria. BIOLOGICAL SIGNIFICANCE Microbacterium oleivorans A9 is an interesting environmental model to understand biological processes engaged in tolerance to radionuclides. Using an innovative proteogenomics approach, we explored its molecular mechanisms involved in uranium tolerance. We sequenced its genome, interpreted high-throughput proteomic data against a six-reading frame ORF database deduced from the draft genome, annotated the identified proteins and compared protein abundances from cells exposed or not to uranyl stress after a cascade search. These data show that a complex cellular response to uranium occurs in Microbacterium oleivorans A9, where one third of the experimental proteome is modified. In particular, the uranyl stress perturbed the phosphate and iron metabolic pathways. Furthermore, several transporters have been identified to be specifically associated to uranyl stress, paving the way to the development of biotechnological tools for uranium decontamination.
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Affiliation(s)
- Nicolas Gallois
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Béatrice Alpha-Bazin
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France
| | - Philippe Ortet
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Mohamed Barakat
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Laurie Piette
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Justine Long
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire d'écologie microbienne de la rhizosphère et d'environnements extrêmes, 13108 Saint-Paul-lez-Durance, France
| | - Catherine Berthomieu
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
| | - Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D), Service de Pharmacologie et Immunoanalyse (SPI), CEA, INRA, F-30207 Bagnols sur Cèze, France.
| | - Virginie Chapon
- CEA, CNRS, Aix-Marseille Université, UMR 7265 Biologie Végétale et Microbiologie Environnementales, Laboratoire des Interactions Protéine Métal, 13108 Saint-Paul-lez-Durance, France
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26
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Armengaud J, Pible O, Gaillard JC, Cian A, Gantois N, Tan KSW, Chabé M, Viscogliosi E. Proteogenomic Insights into the Intestinal Parasite Blastocystis
sp. Subtype 4 Isolate WR1. Proteomics 2017; 17. [DOI: 10.1002/pmic.201700211] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Revised: 08/09/2017] [Indexed: 12/15/2022]
Affiliation(s)
- Jean Armengaud
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D); Service de Pharmacologie et Immunoanalyse (SPI); CEA, INRA; Gif-Sur-Yvette France
| | - Olivier Pible
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D); Service de Pharmacologie et Immunoanalyse (SPI); CEA, INRA; Gif-Sur-Yvette France
| | - Jean-Charles Gaillard
- Laboratoire Innovations technologiques pour la Détection et le Diagnostic (Li2D); Service de Pharmacologie et Immunoanalyse (SPI); CEA, INRA; Gif-Sur-Yvette France
| | - Amandine Cian
- Université de Lille; CNRS, Inserm, CHU Lille; Institut Pasteur de Lille; U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille; 1 rue du Professeur Calmette, Lille, France
| | - Nausicaa Gantois
- Université de Lille; CNRS, Inserm, CHU Lille; Institut Pasteur de Lille; U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille; 1 rue du Professeur Calmette, Lille, France
| | - Kevin S. W. Tan
- Laboratory of Molecular and Cellular Parasitology; Department of Microbiology and Immunology; Yong Loo Lin School of Medicine; National University of Singapore; Singapore Singapore
| | - Magali Chabé
- Université de Lille; CNRS, Inserm, CHU Lille; Institut Pasteur de Lille; U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille; 1 rue du Professeur Calmette, Lille, France
| | - Eric Viscogliosi
- Université de Lille; CNRS, Inserm, CHU Lille; Institut Pasteur de Lille; U1019-UMR 8204-CIIL-Centre d'Infection et d'Immunité de Lille; 1 rue du Professeur Calmette, Lille, France
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27
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Armengaud J. Striking against bioterrorism with advanced proteomics and reference methods. Proteomics 2017; 17. [PMID: 27928908 DOI: 10.1002/pmic.201600412] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Revised: 11/29/2016] [Accepted: 12/01/2016] [Indexed: 02/02/2023]
Abstract
The intentional use by terrorists of biological toxins as weapons has been of great concern for many years. Among the numerous toxins produced by plants, animals, algae, fungi, and bacteria, ricin is one of the most scrutinized by the media because it has already been used in biocrimes and acts of bioterrorism. Improving the analytical toolbox of national authorities to monitor these potential bioweapons all at once is of the utmost interest. MS/MS allows their absolute quantitation and exhibits advantageous sensitivity, discriminative power, multiplexing possibilities, and speed. In this issue of Proteomics, Gilquin et al. (Proteomics 2017, 17, 1600357) present a robust multiplex assay to quantify a set of eight toxins in the presence of a complex food matrix. This MS/MS reference method is based on scheduled SRM and high-quality standards consisting of isotopically labeled versions of these toxins. Their results demonstrate robust reliability based on rather loose scheduling of SRM transitions and good sensitivity for the eight toxins, lower than their oral median lethal doses. In the face of an increased threat from terrorism, relevant reference assays based on advanced proteomics and high-quality companion toxin standards are reliable and firm answers.
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Affiliation(s)
- Jean Armengaud
- CEA, DRF, IBiTec-S, SPI, Li2D, Laboratory "Innovative technologies for Detection and Diagnostics", Bagnols-sur-Cèze, France
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28
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Low CF, Rozaini MZH, Musa N, Syarul Nataqain B. Current knowledge of metabolomic approach in infectious fish disease studies. JOURNAL OF FISH DISEASES 2017; 40:1267-1277. [PMID: 28252175 DOI: 10.1111/jfd.12610] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 05/20/2023]
Abstract
The approaches of transcriptomic and proteomic have been widely used to study host-pathogen interactions in fish diseases, and this is comparable to the recently emerging application of metabolomic in elucidating disease-resistant mechanisms in fish that gives new insight into potential therapeutic strategies to improve fish health. Metabolomic is defined as the large-scale study of all metabolites within an organism and represents the frontline in the 'omics' approaches, providing direct information on the metabolic responses and perturbations in metabolic pathways. In this review, the current research in infectious fish diseases using metabolomic approach will be summarized. The metabolomic approach in economically important fish infected with viruses, bacteria and nematodes will also be discussed. The potential of the metabolomic approach for management of these infectious diseases as well as the challenges and the limitations of metabolomic in fish disease studies will be explored. Current review highlights the impacts of metabolomic studies in infectious fish diseases, which proposed the potential of new therapeutic strategies to enhance disease resistance in fish.
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Affiliation(s)
- C-F Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - M Z H Rozaini
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - N Musa
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - B Syarul Nataqain
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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29
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Chen G, Chen C, Lei Z. Meta-omics insights in the microbial community profiling and functional characterization of fermented foods. Trends Food Sci Technol 2017. [DOI: 10.1016/j.tifs.2017.05.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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30
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31
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Exoproteomics of Pathogens: Analysis of Toxins and Other Virulence Factors by Proteomics. Methods Enzymol 2017; 586:211-227. [PMID: 28137564 DOI: 10.1016/bs.mie.2016.09.033] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
Pathogens are known to release in their environment a large range of toxins and other virulence factors. Their pathogenicity relies on this arsenal of exoproteins and their orchestrated release upon changing environmental conditions. Exoproteomics aims at describing and quantifying the proteins found outside of the cells, thus takes advantage of the most recent methodologies of next-generation proteomics. This approach has been applied with great success to a variety of pathogens increasing the fundamental knowledge on pathogenicity. In this chapter, we describe how the exoproteome should be prepared and handled for high-throughput identification of exoproteins and their quantitation by label-free shotgun proteomics. We also mentioned some bioinformatics tools for extracting information such as toxin similarity search.
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Abstract
Omics approaches have become popular in biology as powerful discovery tools, and currently gain in interest for diagnostic applications. Establishing the accurate genome sequence of any organism is easy, but the outcome of its annotation by means of automatic pipelines remains imprecise. Some protein-encoding genes may be missed as soon as they are specific and poorly conserved in a given taxon, while important to explain the specific traits of the organism. Translational starts are also poorly predicted in a relatively important number of cases, thus impacting the protein sequence database used in proteomics, comparative genomics, and systems biology. The use of high-throughput proteomics data to improve genome annotation is an attractive option to obtain a more comprehensive molecular picture of a given organism. Here, protocols for reannotating prokaryote genomes are described based on shotgun proteomics and derivatization of protein N-termini with a positively charged reagent coupled to high-resolution tandem mass spectrometry.
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