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Zhu H, Jiang S, Zhou W, Chi H, Sun J, Shi J, Zhang Z, Chang L, Yu L, Zhang L, Lyu Z, Xu P, Zhang Y. Ac-LysargiNase efficiently helps genome reannotation of Mycolicibacterium smegmatis MC2 155. J Proteomics 2022; 264:104622. [DOI: 10.1016/j.jprot.2022.104622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 10/18/2022]
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2
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Pujic P, Alloisio N, Miotello G, Armengaud J, Abrouk D, Fournier P, Normand P. The Proteogenome of Symbiotic Frankia alni in Alnus glutinosa Nodules. Microorganisms 2022; 10:microorganisms10030651. [PMID: 35336227 PMCID: PMC8951365 DOI: 10.3390/microorganisms10030651] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 03/14/2022] [Accepted: 03/15/2022] [Indexed: 02/05/2023] Open
Abstract
Omics are the most promising approaches to investigate microbes for which no genetic tools exist such as the nitrogen-fixing symbiotic Frankia. A proteogenomic analysis of symbiotic Frankia alni was done by comparing those proteins more and less abundant in Alnus glutinosa nodules relative to N2-fixing pure cultures with propionate as the carbon source. There were 250 proteins that were significantly overabundant in nodules at a fold change (FC) ≥ 2 threshold, and 1429 with the same characteristics in in vitro nitrogen-fixing pure culture. Nitrogenase, SuF (Fe–Su biogenesis) and hopanoid lipids synthesis determinants were the most overabundant proteins in symbiosis. Nitrogenase was found to constitute 3% of all Frankia proteins in nodules. Sod (superoxide dismutase) was overabundant, indicating a continued oxidative stress, while Kats (catalase) were not. Several transporters were overabundant including one for dicarboxylates and one for branched amino acids. The present results confirm the centrality of nitrogenase in the actinorhizal symbiosis.
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Affiliation(s)
- Petar Pujic
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
| | - Nicole Alloisio
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Guylaine Miotello
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Jean Armengaud
- Département Médicaments et Technologies pour la Santé (DMTS), CEA, INRAE, Université Paris-Saclay, SPI, 30200 Bagnols sur Cèze, France; (G.M.); (J.A.)
| | - Danis Abrouk
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Pascale Fournier
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
| | - Philippe Normand
- Ecologie Microbienne, CNRS, UMR5557, Université Lyon 1, Université de Lyon; INRA, UMR1418, 7330 Villeurbanne, France; (N.A.); (D.A.); (P.F.)
- Correspondence: (P.P.); (P.N.)
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3
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Xie ZX, He YB, Zhang SF, Lin L, Wang MH, Wang DZ. Metaexoproteomics Reveals Microbial Behavior in the Ocean's Interior. Front Microbiol 2022; 13:749874. [PMID: 35250917 PMCID: PMC8889253 DOI: 10.3389/fmicb.2022.749874] [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: 07/30/2021] [Accepted: 01/10/2022] [Indexed: 11/13/2022] Open
Abstract
The proteins present in the extracellular environment of cells, named the "exoproteome," are critical for microbial survival, growth, and interaction with their surroundings. However, little is known about microbial exoproteomes in natural marine environments. Here, we used a metaproteomic approach to characterize the exoprotein profiles (10 kDa-0.2 μm) throughout a water column in the South China Sea. Viruses, together with Alpha- and Gammaproteobacteria were the predominant contributors. However, the exoprotein-producing microbial communities varied with depth: SAR11 in the shallow waters, Pseudomonadales and Nitrososphaeria in the mesopelagic layer, and Alteromonadales, Rhizobiales, and Betaproteobacteria in the bathypelagic layer. Besides viral and unknown proteins, diverse transporters contributed substantially to the exoproteomes and varied vertically in their microbial origins, but presented similar patterns in their predicted substrate identities throughout the water column. Other microbial metabolic processes subject to vertical zonation included proteolysis, the oxidation of ammonia, nitrite and carbon monoxide, C1 metabolism, and the degradation of sulfur-containing dissolved organic matter (DOM). Our metaexoproteomic study provides insights into the depth-variable trends in the in situ ecological traits of the marine microbial community hidden in the non-cellular world, including nutrient cycling, niche partitioning and DOM remineralization.
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Affiliation(s)
- Zhang-Xian Xie
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China.,College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai, China
| | | | - Shu-Feng Zhang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Lin Lin
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai, China
| | - Ming-Hua Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China
| | - Da-Zhi Wang
- State Key Laboratory of Marine Environmental Science/College of the Environment and Ecology, Xiamen University, Xiamen, China.,Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Sun Yat-sen University, Zhuhai, China
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4
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Cárdenas A, Neave MJ, Haroon MF, Pogoreutz C, Rädecker N, Wild C, Gärdes A, Voolstra CR. Excess labile carbon promotes the expression of virulence factors in coral reef bacterioplankton. ISME JOURNAL 2017; 12:59-76. [PMID: 28895945 PMCID: PMC5739002 DOI: 10.1038/ismej.2017.142] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 07/23/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023]
Abstract
Coastal pollution and algal cover are increasing on many coral reefs, resulting in higher dissolved organic carbon (DOC) concentrations. High DOC concentrations strongly affect microbial activity in reef waters and select for copiotrophic, often potentially virulent microbial populations. High DOC concentrations on coral reefs are also hypothesized to be a determinant for switching microbial lifestyles from commensal to pathogenic, thereby contributing to coral reef degradation, but evidence is missing. In this study, we conducted ex situ incubations to assess gene expression of planktonic microbial populations under elevated concentrations of naturally abundant monosaccharides (glucose, galactose, mannose, and xylose) in algal exudates and sewage inflows. We assembled 27 near-complete (>70%) microbial genomes through metagenomic sequencing and determined associated expression patterns through metatranscriptomic sequencing. Differential gene expression analysis revealed a shift in the central carbohydrate metabolism and the induction of metalloproteases, siderophores, and toxins in Alteromonas, Erythrobacter, Oceanicola, and Alcanivorax populations. Sugar-specific induction of virulence factors suggests a mechanistic link for the switch from a commensal to a pathogenic lifestyle, particularly relevant during increased algal cover and human-derived pollution on coral reefs. Although an explicit test remains to be performed, our data support the hypothesis that increased availability of specific sugars changes net microbial community activity in ways that increase the emergence and abundance of opportunistic pathogens, potentially contributing to coral reef degradation.
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Affiliation(s)
- Anny Cárdenas
- Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany.,Max Plank Institute for Marine Microbiology, Bremen, Germany.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Matthew J Neave
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Mohamed Fauzi Haroon
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Claudia Pogoreutz
- Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany.,Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Germany
| | - Nils Rädecker
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.,Marine Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Germany
| | - Christian Wild
- Marine Ecology Group, Faculty of Biology and Chemistry, University of Bremen, Germany
| | - Astrid Gärdes
- Leibniz Center for Tropical Marine Ecology (ZMT), Bremen, Germany
| | - Christian R Voolstra
- Red Sea Research Center, Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
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5
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Gardiner M, Bournazos AM, Maturana-Martinez C, Zhong L, Egan S. Exoproteome Analysis of the Seaweed Pathogen Nautella italica R11 Reveals Temperature-Dependent Regulation of RTX-Like Proteins. Front Microbiol 2017; 8:1203. [PMID: 28706511 PMCID: PMC5489592 DOI: 10.3389/fmicb.2017.01203] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Accepted: 06/13/2017] [Indexed: 12/29/2022] Open
Abstract
Climate fluctuations have been linked to an increased prevalence of disease in seaweeds, including the red alga Delisea pulchra, which is susceptible to a bleaching disease caused by the bacterium Nautella italica R11 under elevated seawater temperatures. To further investigate the role of temperature in the induction of disease by N. italica R11, we assessed the effect of temperature on the expression of the extracellular proteome (exoproteome) in this bacterium. Label-free quantitative mass spectrometry was used to identify 207 proteins secreted into supernatant fraction, which is equivalent to 5% of the protein coding genes in the N. italica R11 genome. Comparative analysis demonstrated that expression of over 30% of the N. italica R11 exoproteome is affected by temperature. The temperature-dependent proteins include traits that could facilitate the ATP-dependent transport of amino acid and carbohydrate, as well as several uncharacterized proteins. Further, potential virulence determinants, including two RTX-like proteins, exhibited significantly higher expression in the exoproteome at the disease inducing temperature of 24°C relative to non-inducing temperature (16°C). This is the first study to demonstrate that temperature has an influence exoproteome expression in a macroalgal pathogen. The results have revealed several temperature regulated candidate virulence factors that may have a role in macroalgal colonization and invasion at elevated sea-surface temperatures, including novel RTX-like proteins.
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Affiliation(s)
- Melissa Gardiner
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Adam M Bournazos
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Claudia Maturana-Martinez
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
| | - Ling Zhong
- Bioanalytical Mass Spectrometry Facility, Mark Wainwright Analytical Centre, The University of New South Wales, SydneyNSW, Australia
| | - Suhelen Egan
- School of Biological Earth and Environmental Sciences-Centre for Marine Bio-Innovation, The University of New South Wales, Sydney,NSW, Australia
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6
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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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7
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Christie-Oleza JA, Armengaud J. Proteomics of theRoseobacterclade, a window to the marine microbiology landscape. Proteomics 2015; 15:3928-42. [DOI: 10.1002/pmic.201500222] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Revised: 08/24/2015] [Accepted: 09/22/2015] [Indexed: 11/07/2022]
Affiliation(s)
| | - Jean Armengaud
- CEA; DSV; IBiTec-S; SPI; Li2D; Laboratory “Innovative Technologies for Detection and Diagnostics”; Bagnols-sur-Cèze France
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8
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Christie-Oleza JA, Scanlan DJ, Armengaud J. "You produce while I clean up", a strategy revealed by exoproteomics during Synechococcus-Roseobacter interactions. Proteomics 2015; 15:3454-62. [PMID: 25728650 PMCID: PMC4949626 DOI: 10.1002/pmic.201400562] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2014] [Revised: 01/15/2015] [Accepted: 02/24/2015] [Indexed: 11/06/2022]
Abstract
Most of the energy that is introduced into the oceans by photosynthetic primary producers is in the form of organic matter that then sustains the rest of the food web, from micro to macro-organisms. However, it is the interactions between phototrophs and heterotrophs that are vital to maintaining the nutrient balance of marine microbiomes that ultimately feed these higher trophic levels. The primary produced organic matter is mostly remineralized by heterotrophic microorganisms but, because most of the oceanic dissolved organic matter is in the form of biopolymers, and microbial membrane transport systems operate with molecules <0.6 kDa, it must be hydrolyzed outside the cell before a microorganism can acquire it. As a simili of the marine microbiome, we analyzed, using state-of-the-art proteomics, the exoproteomes obtained from synthetic communities combining specific Roseobacter (Ruegeria pomeroyi DSS-3, Roseobacter denitrificans OCh114, and Dinoroseobacter shibae DFL-12) and Synechococcus strains (WH7803 and WH8102). This approach identified the repertoire of hydrolytic enzymes secreted by Roseobacter, opening up the black box of heterotrophic transformation/remineralization of biopolymers generated by marine phytoplankton. As well as highlighting interesting exoenzymes this strategy also allowed us to infer clues on the molecular basis of niche partitioning.
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Affiliation(s)
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory "Technological Innovations for Detection and Diagnostic", Bagnols-sur-Cèze, France
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9
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Riedel T, Spring S, Fiebig A, Scheuner C, Petersen J, Göker M, Klenk HP. Genome sequence of the Roseovarius mucosus type strain (DSM 17069(T)), a bacteriochlorophyll a-containing representative of the marine Roseobacter group isolated from the dinoflagellate Alexandrium ostenfeldii. Stand Genomic Sci 2015; 10:17. [PMID: 26203330 PMCID: PMC4511512 DOI: 10.1186/1944-3277-10-17] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 12/10/2014] [Indexed: 02/01/2023] Open
Abstract
Roseovarius mucosus Biebl et al. 2005 is a bacteriochlorophyll a-producing representative of the marine Roseobacter group within the alphaproteobacterial family Rhodobacteraceae, which was isolated from the dinoflagellate Alexandrium ostenfeldii. The marine Roseobacter group was found to be abundant in the ocean and plays an important role for global and biogeochemical processes. Here we describe the features of the R. mucosus strain DFL-24(T) together with its genome sequence and annotation generated from a culture of DSM 17069(T). The 4,247,724 bp containing genome sequence encodes 4,194 protein-coding genes and 57 RNA genes. In addition to the presence of four plasmids, genome analysis revealed the presence of genes associated with host colonization, DMSP utilization, cytotoxins, and quorum sensing that could play a role in the interrelationship of R. mucosus with the dinoflagellate A. ostenfeldii and other marine organisms. Furthermore, the genome encodes genes associated with mixotrophic growth, where both reduced inorganic compounds for lithotrophic growth and a photoheterotrophic lifestyle using light as additional energy source could be used.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Stefan Spring
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Anne Fiebig
- Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Carmen Scheuner
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Jörn Petersen
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Markus Göker
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Hans-Peter Klenk
- Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
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10
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Hartmann EM, Durighello E, Pible O, Nogales B, Beltrametti F, Bosch R, Christie-Oleza JA, Armengaud J. Proteomics meets blue biotechnology: a wealth of novelties and opportunities. Mar Genomics 2014; 17:35-42. [PMID: 24780860 DOI: 10.1016/j.margen.2014.04.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2014] [Revised: 04/11/2014] [Accepted: 04/12/2014] [Indexed: 10/25/2022]
Abstract
Blue biotechnology, in which aquatic environments provide the inspiration for various products such as food additives, aquaculture, biosensors, green chemistry, bioenergy, and pharmaceuticals, holds enormous promise. Large-scale efforts to sequence aquatic genomes and metagenomes, as well as campaigns to isolate new organisms and culture-based screenings, are helping to push the boundaries of known organisms. Mass spectrometry-based proteomics can complement 16S gene sequencing in the effort to discover new organisms of potential relevance to blue biotechnology by facilitating the rapid screening of microbial isolates and by providing in depth profiles of the proteomes and metaproteomes of marine organisms, both model cultivable isolates and, more recently, exotic non-cultivable species and communities. Proteomics has already contributed to blue biotechnology by identifying aquatic proteins with potential applications to food fermentation, the textile industry, and biomedical drug development. In this review, we discuss historical developments in blue biotechnology, the current limitations to the known marine biosphere, and the ways in which mass spectrometry can expand that knowledge. We further speculate about directions that research in blue biotechnology will take given current and near-future technological advancements in mass spectrometry.
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Affiliation(s)
- Erica M Hartmann
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Olivier Pible
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France
| | - Balbina Nogales
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | | | - Rafael Bosch
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry CV47AL, United Kingdom
| | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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