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Su X, Cui H, Zhang W. Copiotrophy in a Marine-Biofilm-Derived Roseobacteraceae Bacterium Can Be Supported by Amino Acid Metabolism and Thiosulfate Oxidation. Int J Mol Sci 2023; 24:ijms24108617. [PMID: 37239957 DOI: 10.3390/ijms24108617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023] Open
Abstract
Copiotrophic bacteria that respond rapidly to nutrient availability, particularly high concentrations of carbon sources, play indispensable roles in marine carbon cycling. However, the molecular and metabolic mechanisms governing their response to carbon concentration gradients are not well understood. Here, we focused on a new member of the family Roseobacteraceae isolated from coastal marine biofilms and explored the growth strategy at different carbon concentrations. When cultured in a carbon-rich medium, the bacterium grew to significantly higher cell densities than Ruegeria pomeroyi DSS-3, although there was no difference when cultured in media with reduced carbon. Genomic analysis showed that the bacterium utilized various pathways involved in biofilm formation, amino acid metabolism, and energy production via the oxidation of inorganic sulfur compounds. Transcriptomic analysis indicated that 28.4% of genes were regulated by carbon concentration, with increased carbon concentration inducing the expression of key enzymes in the EMP, ED, PP, and TCA cycles, genes responsible for the transformation of amino acids into TCA intermediates, as well as the sox genes for thiosulfate oxidation. Metabolomics showed that amino acid metabolism was enhanced and preferred in the presence of a high carbon concentration. Mutation of the sox genes decreased cell proton motive force when grown with amino acids and thiosulfate. In conclusion, we propose that copiotrophy in this Roseobacteraceae bacterium can be supported by amino acid metabolism and thiosulfate oxidation.
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Affiliation(s)
- Xiaoyan Su
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Han Cui
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Weipeng Zhang
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
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2
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Westermann LM, Lidbury ID, Li CY, Wang N, Murphy AR, Aguilo Ferretjans MDM, Quareshy M, Shanmugan M, Torcello-Requena A, Silvano E, Zhang YZ, Blindauer CA, Chen Y, Scanlan DJ. Bacterial catabolism of membrane phospholipids links marine biogeochemical cycles. SCIENCE ADVANCES 2023; 9:eadf5122. [PMID: 37126561 PMCID: PMC10132767 DOI: 10.1126/sciadv.adf5122] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
In marine systems, the availability of inorganic phosphate can limit primary production leading to bacterial and phytoplankton utilization of the plethora of organic forms available. Among these are phospholipids that form the lipid bilayer of all cells as well as released extracellular vesicles. However, information on phospholipid degradation is almost nonexistent despite their relevance for biogeochemical cycling. Here, we identify complete catabolic pathways for the degradation of the common phospholipid headgroups phosphocholine (PC) and phosphorylethanolamine (PE) in marine bacteria. Using Phaeobacter sp. MED193 as a model, we provide genetic and biochemical evidence that extracellular hydrolysis of phospholipids liberates the nitrogen-containing substrates ethanolamine and choline. Transporters for ethanolamine (EtoX) and choline (BetT) are ubiquitous and highly expressed in the global ocean throughout the water column, highlighting the importance of phospholipid and especially PE catabolism in situ. Thus, catabolic activation of the ethanolamine and choline degradation pathways, subsequent to phospholipid metabolism, specifically links, and hence unites, the phosphorus, nitrogen, and carbon cycles.
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Affiliation(s)
- Linda M. Westermann
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Ian D. E. A. Lidbury
- Molecular Microbiology: Biochemistry to Disease, School of Biosciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Chun-Yang Li
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
| | - Ning Wang
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Andrew R. J. Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | | | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Muralidharan Shanmugan
- Department of Chemistry and Photon Science Institute, The University of Manchester, Oxford Road, Manchester, M13 9PL, UK
| | | | - Eleonora Silvano
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Yu-Zhong Zhang
- College of Marine Life Sciences and Frontiers Science Center for Deep Ocean Multispheres and Earth System, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | | | - Yin Chen
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - David J. Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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3
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Zadjelovic V, Erni-Cassola G, Obrador-Viel T, Lester D, Eley Y, Gibson MI, Dorador C, Golyshin PN, Black S, Wellington EMH, Christie-Oleza JA. A mechanistic understanding of polyethylene biodegradation by the marine bacterium Alcanivorax. JOURNAL OF HAZARDOUS MATERIALS 2022; 436:129278. [PMID: 35739790 DOI: 10.1016/j.jhazmat.2022.129278] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 05/19/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Polyethylene (PE) is one of the most recalcitrant carbon-based synthetic materials produced and, currently, the most ubiquitous plastic pollutant found in nature. Over time, combined abiotic and biotic processes are thought to eventually breakdown PE. Despite limited evidence of biological PE degradation and speculation that hydrocarbon-degrading bacteria found within the plastisphere is an indication of biodegradation, there is no clear mechanistic understanding of the process. Here, using high-throughput proteomics, we investigated the molecular processes that take place in the hydrocarbon-degrading marine bacterium Alcanivorax sp. 24 when grown in the presence of low density PE (LDPE). As well as efficiently utilising and assimilating the leachate of weathered LDPE, the bacterium was able to reduce the molecular weight distribution (Mw from 122 to 83 kg/mol) and overall mass of pristine LDPE films (0.9 % after 34 days of incubation). Most interestingly, Alcanivorax acquired the isotopic signature of the pristine plastic and induced an extensive array of metabolic pathways for aliphatic compound degradation. Presumably, the primary biodegradation of LDPE by Alcanivorax sp. 24 is possible via the production of extracellular reactive oxygen species as observed both by the material's surface oxidation and the measurement of superoxide in the culture with LDPE. Our findings confirm that hydrocarbon-biodegrading bacteria within the plastisphere may in fact have a role in degrading PE.
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Affiliation(s)
- Vinko Zadjelovic
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK.
| | - Gabriel Erni-Cassola
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Program Man-Society-Environment (MGU), University of Basel, 4051 Basel, Switzerland
| | - Theo Obrador-Viel
- Department of Biology, University of the Balearic Islands, Palma 07122, Spain
| | - Daniel Lester
- Polymer Characterisation Research Technology Platform, University of Warwick, Coventry CV4 7AL, UK
| | - Yvette Eley
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, UK
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Coventry CV4 7AL, UK
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta, Universidad de Antofagasta, Chile; Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta Angamos 601, Antofagasta, Chile; Centre for Biotechnology & Bioengineering (CeBiB) Santiago, Chile
| | - Peter N Golyshin
- Centre for Environmental Biotechnology, School of Natural Sciences, Bangor University, Bangor LL57 2UW, UK
| | - Stuart Black
- Department of Geography and Environmental Science, University of Reading, UK
| | | | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK; Department of Biology, University of the Balearic Islands, Palma 07122, Spain.
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4
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A Novel Antimicrobial Metabolite Produced by Paenibacillus apiarius Isolated from Brackish Water of Lake Balkhash in Kazakhstan. Microorganisms 2022; 10:microorganisms10081519. [PMID: 36013937 PMCID: PMC9416454 DOI: 10.3390/microorganisms10081519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
Four aerobic bacteria with bacteriolytic capabilities were isolated from the brackish water site Strait Uzynaral of Lake Balkhash in Kazakhstan. The morphology and physiology of the bacterial isolates have subsequently been analyzed. Using matrix assisted laser desorption ionization-time of flight mass spectrum and partial 16S rRNA gene sequence analyses, three of the isolates have been identified as Pseudomonas veronii and one as Paenibacillus apiarius. We determined the capability of both species to lyse pre-grown cells of the Gram-negative strains Pseudomonas putida SBUG 24 and Escherichia coli SBUG 13 as well as the Gram-positive strains Micrococcus luteus SBUG 16 and Arthrobacter citreus SBUG 321 on solid media. The bacteriolysis process was analyzed by creating growth curves and electron micrographs of co-cultures with the bacteriolytic isolates and the lysis sensitive strain Arthrobacter citreus SBUG 321 in nutrient-poor liquid media. One metabolite of Paenibacillus apiarius was isolated and structurally characterized by various chemical structure determination methods. It is a novel antibiotic substance.
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5
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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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6
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Rangama S, Lidbury IDEA, Holden JM, Borsetto C, Murphy ARJ, Hawkey PM, Wellington EMH. Mechanisms Involved in the Active Secretion of CTX-M-15 β-Lactamase by Pathogenic Escherichia coli ST131. Antimicrob Agents Chemother 2021; 65:e0066321. [PMID: 34310213 PMCID: PMC8448145 DOI: 10.1128/aac.00663-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 07/19/2021] [Indexed: 11/20/2022] Open
Abstract
Infections caused by antimicrobial-resistant bacterial pathogens are fast becoming an important global health issue. Strains of Escherichia coli are common causal agents of urinary tract infection and can carry multiple resistance genes. This includes the gene blaCTX-M-15, which encodes an extended-spectrum beta-lactamase (ESBL). While studying antimicrobial resistance (AMR) in the environment, we isolated several strains of E. coli ST131 downstream of a wastewater treatment plan (WWTP) in a local river. These isolates were surviving in the river sediment, and characterization proved that a multiresistant phenotype was evident. Here, we show that E. coli strain 48 (river isolate ST131) provided a protective effect against a third-generation cephalosporin (cefotaxime) for susceptible E. coli strain 33 (river isolate ST3576) through secretion of a functional ESBL into the growth medium. Furthermore, extracellular ESBL activity was stable for at least 24 h after secretion. Proteomic and molecular genetic analyses identified CTX-M-15 as the major secreted ESBL responsible for the observed protective effect. In contrast to previous studies, outer membrane vesicles (OMVs) were not the route for CTX-M-15 secretion. Indeed, mutation of the type I secretion system led to a significant reduction in the growth of the ESBL-producing strain as well as a significantly reduced ability to confer protective effect. We speculate that CTX-M-15 secretion, mediated through active secretion using molecular machinery, provides a public goods service by facilitating the survival of otherwise susceptible bacteria in the presence of cefotaxime.
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Affiliation(s)
- Severine Rangama
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ian D. E. A. Lidbury
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Department of Animal and Plant Science, The University of Sheffield, Sheffield, United Kingdom
| | - Jennifer M. Holden
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Micropathology Ltd., University of Warwick Science Park, Coventry, United Kingdom
| | - Chiara Borsetto
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | | | - Peter M. Hawkey
- Institute of Microbiology and Infection, University of Birmingham, Edgbaston, United Kingdom
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7
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Wright RJ, Bosch R, Langille MGI, Gibson MI, Christie-Oleza JA. A multi-OMIC characterisation of biodegradation and microbial community succession within the PET plastisphere. MICROBIOME 2021; 9:141. [PMID: 34154652 PMCID: PMC8215760 DOI: 10.1186/s40168-021-01054-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Accepted: 03/19/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Plastics now pollute marine environments across the globe. On entering these environments, plastics are rapidly colonised by a diverse community of microorganisms termed the plastisphere. Members of the plastisphere have a myriad of diverse functions typically found in any biofilm but, additionally, a number of marine plastisphere studies have claimed the presence of plastic-biodegrading organisms, although with little mechanistic verification. Here, we obtained a microbial community from marine plastic debris and analysed the community succession across 6 weeks of incubation with different polyethylene terephthalate (PET) products as the sole carbon source, and further characterised the mechanisms involved in PET degradation by two bacterial isolates from the plastisphere. RESULTS We found that all communities differed significantly from the inoculum and were dominated by Gammaproteobacteria, i.e. Alteromonadaceae and Thalassospiraceae at early time points, Alcanivoraceae at later time points and Vibrionaceae throughout. The large number of encoded enzymes involved in PET degradation found in predicted metagenomes and the observation of polymer oxidation by FTIR analyses both suggested PET degradation was occurring. However, we were unable to detect intermediates of PET hydrolysis with metabolomic analyses, which may be attributed to their rapid depletion by the complex community. To further confirm the PET biodegrading potential within the plastisphere of marine plastic debris, we used a combined proteogenomic and metabolomic approach to characterise amorphous PET degradation by two novel marine isolates, Thioclava sp. BHET1 and Bacillus sp. BHET2. The identification of PET hydrolytic intermediates by metabolomics confirmed that both isolates were able to degrade PET. High-throughput proteomics revealed that whilst Thioclava sp. BHET1 used the degradation pathway identified in terrestrial environment counterparts, these were absent in Bacillus sp. BHET2, indicating that either the enzymes used by this bacterium share little homology with those characterised previously, or that this bacterium uses a novel pathway for PET degradation. CONCLUSIONS Overall, the results of our multi-OMIC characterisation of PET degradation provide a significant step forwards in our understanding of marine plastic degradation by bacterial isolates and communities and evidences the biodegrading potential extant in the plastisphere of marine plastic debris. Video abstract.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry, UK
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Rafael Bosch
- University of the Balearic Islands, Palma, Spain
- IMEDEA (CSIC-UIB), Esporles, Spain
| | - Morgan G. I. Langille
- Department of Pharmacology, Faculty of Medicine, Dalhousie University, Halifax, Canada
| | - Matthew I. Gibson
- Department of Chemistry, University of Warwick, Coventry, UK
- Medical School, University of Warwick, Coventry, UK
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry, UK
- University of the Balearic Islands, Palma, Spain
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8
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Ní Dhufaigh K, Botwright N, Dillon E, O’Connor I, MacCarthy E, Slattery O. Differential Exoproteome and Biochemical Characterisation of Neoparamoeba perurans. Microorganisms 2021; 9:microorganisms9061258. [PMID: 34207776 PMCID: PMC8226569 DOI: 10.3390/microorganisms9061258] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 06/01/2021] [Accepted: 06/04/2021] [Indexed: 12/17/2022] Open
Abstract
Infection with the protozoan ectoparasite Neoparamoeba perurans, the causative agent of AGD, remains a global threat to salmonid farming. This study aimed to analyse the exoproteome of both an attenuated and virulent N. perurans isolate using proteomics and cytotoxicity testing. A disproportionate presence of proteins from the co-cultured microbiota of N. perurans was revealed on searching an amalgamated database of bacterial, N. perurans and Amoebozoa proteins. LC-MS/MS identified 33 differentially expressed proteins, the majority of which were upregulated in the attenuated exoproteome. Proteins of putative interest found in both exoproteomes were maltoporin, ferrichrome-iron receptor, and putative ferric enterobactin receptor. Protease activity remained significantly elevated in the attenuated exoproteome compared with the virulent exoproteome. Similarly, the attenuated exoproteome had a significantly higher cytotoxic effect on rainbow trout gill cell line (RTgill W1) cells compared with the virulent exoproteome. The presence of a phosphatase and serine protease in the virulent exoproteome may facilitate AGD infection but do not appear to be key players in causing cytotoxicity. Altogether, this study reveals prolonged culture of N. perurans affects the exoproteome composition in favour of nutritional acquisition, and that the current culturing protocol for virulent N. perurans does not facilitate the secretion of virulence factors.
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Affiliation(s)
- Kerrie Ní Dhufaigh
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Co. Galway, H91 T8NW Eircode, Ireland; (I.O.); (E.M.)
- Correspondence:
| | - Natasha Botwright
- CSIRO Agriculture and Food, Livestock & Aquaculture, Queensland Biosciences Precinct, 306 Carmody Road, Brisbane, QLD 4067, Australia;
| | - Eugene Dillon
- Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Co. Dublin, D04 V1W8 Eircode, Ireland;
| | - Ian O’Connor
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Co. Galway, H91 T8NW Eircode, Ireland; (I.O.); (E.M.)
| | - Eugene MacCarthy
- Marine and Freshwater Research Centre, Galway-Mayo Institute of Technology, Co. Galway, H91 T8NW Eircode, Ireland; (I.O.); (E.M.)
| | - Orla Slattery
- Department of Biopharmaceutical and Medical Science, Galway-Mayo Institute of Technology, Co. Galway, H91 T8NW Eircode, Ireland;
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9
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Dedman CJ, King AM, Christie-Oleza JA, Davies GL. Environmentally relevant concentrations of titanium dioxide nanoparticles pose negligible risk to marine microbes. ENVIRONMENTAL SCIENCE. NANO 2021; 8:1236-1255. [PMID: 34046180 PMCID: PMC8136324 DOI: 10.1039/d0en00883d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 04/06/2021] [Indexed: 05/26/2023]
Abstract
Nano-sized titanium dioxide (nTiO2) represents the highest produced nanomaterial by mass worldwide and, due to its prevalent industrial and commercial use, it inevitably reaches the natural environment. Previous work has revealed a negative impact of nTiO2 upon marine phytoplankton growth, however, studies are typically carried out at concentrations far exceeding those measured and predicted to occur in the environment currently. Here, a series of experiments were carried out to assess the effects of both research-grade nTiO2 and nTiO2 extracted from consumer products upon the marine dominant cyanobacterium, Prochlorococcus, and natural marine communities at environmentally relevant and supra-environmental concentrations (i.e., 1 μg L-1 to 100 mg L-1). Cell declines observed in Prochlorococcus cultures were associated with the extensive aggregation behaviour of nTiO2 in saline media and the subsequent entrapment of microbial cells. Hence, higher concentrations of nTiO2 particles exerted a stronger decline of cyanobacterial populations. However, within natural oligotrophic seawater, cultures were able to recover over time as the nanoparticles aggregated out of solution after 72 h. Subsequent shotgun proteomic analysis of Prochlorococcus cultures exposed to environmentally relevant concentrations confirmed minimal molecular features of toxicity, suggesting that direct physical effects are responsible for short-term microbial population decline. In an additional experiment, the diversity and structure of natural marine microbial communities showed negligible variations when exposed to environmentally relevant nTiO2 concentrations (i.e., 25 μg L-1). As such, the environmental risk of nTiO2 towards marine microbial species appears low, however the potential for adverse effects in hotspots of contamination exists. In future, research must be extended to consider any effect of other components of nano-enabled product formulations upon nanomaterial fate and impact within the natural environment.
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Affiliation(s)
- Craig J Dedman
- School of Life Sciences, Gibbet Hill Campus, University of Warwick Coventry CV4 7AL UK
- Department of Chemistry, University of Warwick Gibbet Hill Coventry CV4 7EQ UK
| | - Aaron M King
- UCL Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, Gibbet Hill Campus, University of Warwick Coventry CV4 7AL UK
- Department of Biology, University of the Balearic Islands Ctra. Valldemossa, km 7.5 CP: 07122 Palma Spain
- IMEDEA (CSIC-UIB) CP: 07190 Esporles Spain
| | - Gemma-Louise Davies
- UCL Department of Chemistry, University College London 20 Gordon Street London WC1H 0AJ UK
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10
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Pili allow dominant marine cyanobacteria to avoid sinking and evade predation. Nat Commun 2021; 12:1857. [PMID: 33767153 PMCID: PMC7994388 DOI: 10.1038/s41467-021-22152-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 03/02/2021] [Indexed: 12/21/2022] Open
Abstract
How oligotrophic marine cyanobacteria position themselves in the water column is currently unknown. The current paradigm is that these organisms avoid sinking due to their reduced size and passive drift within currents. Here, we show that one in four picocyanobacteria encode a type IV pilus which allows these organisms to increase drag and remain suspended at optimal positions in the water column, as well as evade predation by grazers. The evolution of this sophisticated floatation mechanism in these purely planktonic streamlined microorganisms has important implications for our current understanding of microbial distribution in the oceans and predator-prey interactions which ultimately will need incorporating into future models of marine carbon flux dynamics.
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11
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Shropshire H, Jones RA, Aguilo-Ferretjans MM, Scanlan DJ, Chen Y. Proteomics insights into the Burkholderia cenocepacia phosphorus stress response. Environ Microbiol 2021; 23:5069-5086. [PMID: 33684254 DOI: 10.1111/1462-2920.15451] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 03/02/2021] [Indexed: 11/26/2022]
Abstract
The Burkholderia cepacia complex is a group of Burkholderia species that are opportunistic pathogens causing high mortality rates in patients with cystic fibrosis. An environmental stress often encountered by these soil-dwelling and pathogenic bacteria is phosphorus limitation, an essential element for cellular processes. Here, we describe cellular and extracellular proteins differentially regulated between phosphate-deplete (0 mM, no added phosphate) and phosphate-replete (1 mM) growth conditions using a comparative proteomics (LC-MS/MS) approach. We observed a total of 128 and 65 unique proteins were downregulated and upregulated respectively, in the B. cenocepacia proteome. Of those downregulated proteins, many have functions in amino acid transport/metabolism. We have identified 24 upregulated proteins that are directly/indirectly involved in inorganic phosphate or organic phosphorus acquisition. Also, proteins involved in virulence and antimicrobial resistance were differentially regulated, suggesting B. cenocepacia experiences a dramatic shift in metabolism under these stress conditions. Overall, this study provides a baseline for further research into the biology of Burkholderia in response to phosphorus stress.
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Affiliation(s)
- Holly Shropshire
- BBSRC Midlands Integrative Biosciences Training Partnership, University of Warwick, Coventry, CV4 7AL, UK.,School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Rebekah A Jones
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | - Yin Chen
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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12
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Chhun A, Sousoni D, Aguiló‐Ferretjans MDM, Song L, Corre C, Christie‐Oleza JA. Phytoplankton trigger the production of cryptic metabolites in the marine actinobacterium Salinispora tropica. Microb Biotechnol 2021; 14:291-306. [PMID: 33280260 PMCID: PMC7888443 DOI: 10.1111/1751-7915.13722] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/14/2020] [Indexed: 12/19/2022] Open
Abstract
Filamentous members of the phylum Actinobacteria are a remarkable source of natural products with pharmaceutical potential. The discovery of novel molecules from these organisms is, however, hindered because most of the biosynthetic gene clusters (BGCs) encoding these secondary metabolites are cryptic or silent and are referred to as orphan BGCs. While co-culture has proven to be a promising approach to unlock the biosynthetic potential of many microorganisms by activating the expression of these orphan BGCs, it still remains an underexplored technique. The marine actinobacterium Salinispora tropica, for instance, produces valuable compounds such as the anti-cancer molecule salinosporamide but half of its putative BGCs are still orphan. Although previous studies have used marine heterotrophs to induce orphan BGCs in Salinispora, its co-culture with marine phototrophs has yet to be investigated. Following the observation of an antimicrobial activity against a range of phytoplankton by S. tropica, we here report that the photosynthate released by photosynthetic primary producers influences its biosynthetic capacities with production of cryptic molecules and the activation of orphan BGCs. Our work, using an approach combining metabolomics and proteomics, pioneers the use of phototrophs as a promising strategy to accelerate the discovery of novel natural products from marine actinobacteria.
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Affiliation(s)
- Audam Chhun
- School of Life SciencesUniversity of WarwickCoventryUK
| | | | | | - Lijiang Song
- Department of ChemistryUniversity of WarwickCoventryUK
| | - Christophe Corre
- School of Life SciencesUniversity of WarwickCoventryUK
- Department of ChemistryUniversity of WarwickCoventryUK
| | - Joseph A. Christie‐Oleza
- School of Life SciencesUniversity of WarwickCoventryUK
- University of the Balearic IslandsPalmaSpain
- IMEDEA (CSIC‐UIB)EsporlesSpain
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13
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Helliwell KE, Harrison EL, Christie-Oleza JA, Rees AP, Kleiner FH, Gaikwad T, Downe J, Aguilo-Ferretjans MM, Al-Moosawi L, Brownlee C, Wheeler GL. A Novel Ca 2+ Signaling Pathway Coordinates Environmental Phosphorus Sensing and Nitrogen Metabolism in Marine Diatoms. Curr Biol 2020; 31:978-989.e4. [PMID: 33373640 DOI: 10.1016/j.cub.2020.11.073] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 10/26/2020] [Accepted: 11/30/2020] [Indexed: 10/22/2022]
Abstract
Diatoms are a diverse and globally important phytoplankton group, responsible for an estimated 20% of carbon fixation on Earth. They frequently form spatially extensive phytoplankton blooms, responding rapidly to increased availability of nutrients, including phosphorus (P) and nitrogen (N). Although it is well established that diatoms are common first responders to nutrient influxes in aquatic ecosystems, little is known of the sensory mechanisms that they employ for nutrient perception. Here, we show that P-limited diatoms use a Ca2+-dependent signaling pathway, not previously described in eukaryotes, to sense and respond to the critical macronutrient P. We demonstrate that P-Ca2+ signaling is conserved between a representative pennate (Phaeodactylum tricornutum) and centric (Thalassiosira pseudonana) diatom. Moreover, this pathway is ecologically relevant, being sensitive to sub-micromolar concentrations of inorganic phosphate and a range of environmentally abundant P forms. Notably, we show that diatom recovery from P limitation requires rapid and substantial increases in N assimilation and demonstrate that this process is dependent on P-Ca2+ signaling. P-Ca2+ signaling thus governs the capacity of diatoms to rapidly sense and respond to P resupply, mediating fundamental cross-talk between the vital nutrients P and N and maximizing diatom resource competition in regions of pulsed nutrient supply.
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Affiliation(s)
- Katherine E Helliwell
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK.
| | - Ellen L Harrison
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | - Andrew P Rees
- Plymouth Marine Laboratory, Plymouth, Devon PL1 3DH, UK
| | - Friedrich H Kleiner
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Trupti Gaikwad
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | - Joshua Downe
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
| | | | | | - Colin Brownlee
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK; School of Ocean and Earth Science, University of Southampton, Southampton SO14 3ZH, UK
| | - Glen L Wheeler
- Marine Biological Association, The Laboratory, Citadel Hill, Plymouth PL1 2PB, UK
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14
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Zadjelovic V, Chhun A, Quareshy M, Silvano E, Hernandez-Fernaud JR, Aguilo-Ferretjans MM, Bosch R, Dorador C, Gibson MI, Christie-Oleza JA. Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol 2020; 22:1356-1369. [PMID: 32079039 PMCID: PMC7187450 DOI: 10.1111/1462-2920.14947] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 02/18/2020] [Indexed: 12/31/2022]
Abstract
Pristine marine environments are highly oligotrophic ecosystems populated by well‐established specialized microbial communities. Nevertheless, during oil spills, low‐abundant hydrocarbonoclastic bacteria bloom and rapidly prevail over the marine microbiota. The genus Alcanivorax is one of the most abundant and well‐studied organisms for oil degradation. While highly successful under polluted conditions due to its specialized oil‐degrading metabolism, it is unknown how they persist in these environments during pristine conditions. Here, we show that part of the Alcanivorax genus, as well as oils, has an enormous potential for biodegrading aliphatic polyesters thanks to a unique and abundantly secreted alpha/beta hydrolase. The heterologous overexpression of this esterase proved a remarkable ability to hydrolyse both natural and synthetic polyesters. Our findings contribute to (i) better understand the ecology of Alcanivorax in its natural environment, where natural polyesters such as polyhydroxyalkanoates (PHA) are produced by a large fraction of the community and, hence, an accessible source of carbon and energy used by the organism in order to persist, (ii) highlight the potential of Alcanivorax to clear marine environments from polyester materials of anthropogenic origin as well as oils, and (iii) the discovery of a new versatile esterase with a high biotechnological potential.
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Affiliation(s)
| | - Audam Chhun
- School of Life Sciences, University of Warwick, Warwick, UK
| | - Mussa Quareshy
- School of Life Sciences, University of Warwick, Warwick, UK
| | | | - Juan R Hernandez-Fernaud
- School of Life Sciences, University of Warwick, Warwick, UK.,Unidad de investigación-HUC, La Laguna-Tenerife, Spain
| | - María M Aguilo-Ferretjans
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain
| | - Rafael Bosch
- Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Universidad de Antofagasta, Antofagasta, Chile.,Departamento de Biotecnología, Universidad de Antofagasta, Antofagasta, Chile.,Centre for Biotechnology & Bioengineering (CeBiB), Santiago, Chile
| | - Matthew I Gibson
- Department of Chemistry, University of Warwick, Warwick, UK.,Warwick Medical School, University of Warwick, Warwick, UK
| | - Joseph A Christie-Oleza
- School of Life Sciences, University of Warwick, Warwick, UK.,Department of Biology, University of the Balearic Islands, Spain.,IMEDEA (CSIC-UIB), Esporles, Spain
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15
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Wright RJ, Bosch R, Gibson MI, Christie-Oleza JA. Plasticizer Degradation by Marine Bacterial Isolates: A Proteogenomic and Metabolomic Characterization. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:2244-2256. [PMID: 31894974 PMCID: PMC7031849 DOI: 10.1021/acs.est.9b05228] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 12/30/2019] [Accepted: 01/02/2020] [Indexed: 05/19/2023]
Abstract
Many commercial plasticizers are toxic endocrine-disrupting chemicals that are added to plastics during manufacturing and may leach out once they reach the environment. Traditional phthalic acid ester plasticizers (PAEs), such as dibutyl phthalate (DBP) and bis(2-ethyl hexyl) phthalate (DEHP), are now increasingly being replaced with more environmentally friendly alternatives, such as acetyl tributyl citrate (ATBC). While the metabolic pathways for PAE degradation have been established in the terrestrial environment, to our knowledge, the mechanisms for ATBC biodegradation have not been identified previously and plasticizer degradation in the marine environment remains underexplored. From marine plastic debris, we enriched and isolated microbes able to grow using a range of plasticizers and, for the first time, identified the pathways used by two phylogenetically distinct bacteria to degrade three different plasticizers (i.e., DBP, DEHP, and ATBC) via a comprehensive proteogenomic and metabolomic approach. This integrated multi-OMIC study also revealed the different mechanisms used for ester side-chain removal from the different plasticizers (esterases and enzymes involved in the β-oxidation pathway) as well as the molecular response to deal with toxic intermediates, that is, phthalate, and the lower biodegrading potential detected for ATBC than for PAE plasticizers. This study highlights the metabolic potential that exists in the biofilms that colonize plastics-the Plastisphere-to effectively biodegrade plastic additives and flags the inherent importance of microbes in reducing plastic toxicity in the environment.
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Affiliation(s)
- Robyn J. Wright
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- School for Resource and Environmental Studies, Dalhousie University, Halifax B3H 4R2, Canada
- E-mail: (R.J.W.)
| | - Rafael Bosch
- University of the Balearic Islands, Palma 07122, Spain
- IMEDEA (CSIC-UIB), Esporles 07190, Spain
| | - Matthew I. Gibson
- Department
of Chemistry, University of Warwick, Coventry CV4 7AL, U.K.
- Medical School, University
of Warwick, Coventry CV4 7AL, U.K.
| | - Joseph A. Christie-Oleza
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, U.K.
- University of the Balearic Islands, Palma 07122, Spain
- IMEDEA (CSIC-UIB), Esporles 07190, Spain
- E-mail: (J.A.C.-O.)
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16
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Miura N, Motone K, Takagi T, Aburaya S, Watanabe S, Aoki W, Ueda M. Ruegeria sp. Strains Isolated from the Reef-Building Coral Galaxea fascicularis Inhibit Growth of the Temperature-Dependent Pathogen Vibrio coralliilyticus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2019; 21:1-8. [PMID: 30194504 DOI: 10.1007/s10126-018-9853-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Accepted: 08/23/2018] [Indexed: 06/08/2023]
Abstract
The coral microbiome has attracted increased attention because of its potential roles in host protection against deadly diseases. However, little is known about the role of coral-associated bacteria against the temperature-dependent opportunistic pathogen Vibrio coralliilyticus. In this study, we tested whether bacteria associated with the reef-building coral Galaxea fascicularis could inhibit the growth of V. coralliilyticus. Twenty-nine cultivable bacteria were successfully isolated from a healthy colony of G. fascicularis kept in an aquarium. Among the bacterial isolates, three Ruegeria sp. strains inhibited the growth of V. coralliilyticus P1 as a reference strain and Vibrio sp. isolated in this study. Ruegeria sp. strains were also detected from other G. fascicularis colonies in the aquarium and in previous field studies by 16S rRNA amplicon sequencing, suggesting that Ruegeria sp. strains are common among G. fascicularis colonies. These results illuminate the potential role of Ruegeria sp. in protecting corals against pathogenic Vibrio species.
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Affiliation(s)
- Natsuko Miura
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan.
- Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai, 599-8531, Japan.
| | - Keisuke Motone
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Toshiyuki Takagi
- Japan Society for the Promotion of Science, Tokyo, Japan
- Atmosphere and Ocean Research Institute, The University of Tokyo, Kashiwa, 277-8564, Japan
| | - Shunsuke Aburaya
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
- Japan Society for the Promotion of Science, Tokyo, Japan
| | - Sho Watanabe
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Wataru Aoki
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Mitsuyoshi Ueda
- Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
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17
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Matallana-Surget S, Werner J, Wattiez R, Lebaron K, Intertaglia L, Regan C, Morris J, Teeling H, Ferrer M, Golyshin PN, Gerogiorgis D, Reilly SI, Lebaron P. Proteogenomic Analysis of Epibacterium Mobile BBCC367, a Relevant Marine Bacterium Isolated From the South Pacific Ocean. Front Microbiol 2018; 9:3125. [PMID: 30622520 PMCID: PMC6308992 DOI: 10.3389/fmicb.2018.03125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Accepted: 12/03/2018] [Indexed: 12/16/2022] Open
Abstract
Epibacterium mobile BBCC367 is a marine bacterium that is common in coastal areas. It belongs to the Roseobacter clade, a widespread group in pelagic marine ecosystems. Species of the Roseobacter clade are regularly used as models to understand the evolution and physiological adaptability of generalist bacteria. E. mobile BBCC367 comprises two chromosomes and two plasmids. We used gel-free shotgun proteomics to assess its protein expression under 16 different conditions, including stress factors such as elevated temperature, nutrient limitation, high metal concentration, and UVB exposure. Comparison of the different conditions allowed us not only to retrieve almost 70% of the predicted proteins, but also to define three main protein assemblages: 584 essential core proteins, 2,144 facultative accessory proteins and 355 specific unique proteins. While the core proteome mainly exhibited proteins involved in essential functions to sustain life such as DNA, amino acids, carbohydrates, cofactors, vitamins and lipids metabolisms, the accessory and unique proteomes revealed a more specific adaptation with the expression of stress-related proteins, such as DNA repair proteins (accessory proteome), transcription regulators and a significant predominance of transporters (unique proteome). Our study provides insights into how E. mobile BBCC367 adapts to environmental changes and copes with diverse stresses.
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Affiliation(s)
- Sabine Matallana-Surget
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Johannes Werner
- Department of Biological Oceanography, Leibniz Institute of Baltic Sea Research, Rostock, Germany
| | - Ruddy Wattiez
- Department of Proteomics and Microbiology, Interdisciplinary Mass Spectrometry Center (CISMa), University of Mons, Mons, Belgium
| | - Karine Lebaron
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Laurent Intertaglia
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
| | - Callum Regan
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - James Morris
- Division of Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling, United Kingdom
| | - Hanno Teeling
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Manuel Ferrer
- Department of Applied Biocatalysis, Institute of Catalysis, CSIC, Madrid, Spain
| | - Peter N Golyshin
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Dimitrios Gerogiorgis
- Institute for Materials and Processes, School of Engineering, University of Edinburgh, The King's Buildings, Edinburgh, United Kingdom
| | - Simon I Reilly
- School of Natural Sciences, University of Bangor, Bangor, United Kingdom
| | - Philippe Lebaron
- Sorbonne Universites, UPMC Univ Paris 06, CNRS, Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls/Mer, France.,Sorbonne Universites, UPMC Univ Paris 06, CNRS, Observatoire Océanologique de Banyuls (OOB), Banyuls/Mer, France
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18
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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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19
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Kaur A, Hernandez-Fernaud JR, Aguilo-Ferretjans MDM, Wellington EM, Christie-Oleza JA. 100 Days of marine Synechococcus-Ruegeria pomeroyi interaction: A detailed analysis of the exoproteome. Environ Microbiol 2017; 20:785-799. [PMID: 29194907 PMCID: PMC5839243 DOI: 10.1111/1462-2920.14012] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/23/2017] [Indexed: 12/03/2022]
Abstract
Marine phototroph and heterotroph interactions are vital in maintaining the nutrient balance in the oceans as essential nutrients need to be rapidly cycled before sinking to aphotic layers. The aim of this study was to highlight the molecular mechanisms that drive these interactions. For this, we generated a detailed exoproteomic time‐course analysis of a 100‐day co‐culture between the model marine picocyanobacterium Synechococcus sp. WH7803 and the Roseobacter strain Ruegeria pomeroyi DSS‐3, both in nutrient‐enriched and natural oligotrophic seawater. The proteomic data showed a transition between the initial growth phase and stable‐state phase that, in the case of the heterotroph, was caused by a switch in motility attributed to organic matter availability. The phototroph adapted to seawater oligotrophy by reducing its selective leakiness, increasing the acquisition of essential nutrients and secreting conserved proteins of unknown function. We also report a surprisingly high abundance of extracellular superoxide dismutase produced by Synechococcus and a dynamic secretion of potential hydrolytic enzyme candidates used by the heterotroph to cleave organic groups and hydrolase polymeric organic matter produced by the cyanobacterium. The time course dataset we present here will become a reference for understanding the molecular processes underpinning marine phototroph‐heterotroph interactions.
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Affiliation(s)
- Amandeep Kaur
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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20
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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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21
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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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22
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Lidbury IDEA, Murphy ARJ, Scanlan DJ, Bending GD, Jones AME, Moore JD, Goodall A, Hammond JP, Wellington EMH. Comparative genomic, proteomic and exoproteomic analyses of three Pseudomonas strains reveals novel insights into the phosphorus scavenging capabilities of soil bacteria. Environ Microbiol 2016; 18:3535-3549. [PMID: 27233093 PMCID: PMC5082522 DOI: 10.1111/1462-2920.13390] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bacteria that inhabit the rhizosphere of agricultural crops can have a beneficial effect on crop growth. One such mechanism is the microbial-driven solubilization and remineralization of complex forms of phosphorus (P). It is known that bacteria secrete various phosphatases in response to low P conditions. However, our understanding of their global proteomic response to P stress is limited. Here, exoproteomic analysis of Pseudomonas putida BIRD-1 (BIRD-1), Pseudomonas fluorescens SBW25 and Pseudomonas stutzeri DSM4166 was performed in unison with whole-cell proteomic analysis of BIRD-1 grown under phosphate (Pi) replete and Pi deplete conditions. Comparative exoproteomics revealed marked heterogeneity in the exoproteomes of each Pseudomonas strain in response to Pi depletion. In addition to well-characterized members of the PHO regulon such as alkaline phosphatases, several proteins, previously not associated with the response to Pi depletion, were also identified. These included putative nucleases, phosphotriesterases, putative phosphonate transporters and outer membrane proteins. Moreover, in BIRD-1, mutagenesis of the master regulator, phoBR, led us to confirm the addition of several novel PHO-dependent proteins. Our data expands knowledge of the Pseudomonas PHO regulon, including species that are frequently used as bioinoculants, opening up the potential for more efficient and complete use of soil complexed P.
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Affiliation(s)
- Ian D E A Lidbury
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK.
| | - Andrew R J Murphy
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK
| | - Gary D Bending
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK
| | - Alexandra M E Jones
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK
| | - Jonathan D Moore
- The Genome Analysis Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Andrew Goodall
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, UK
| | - John P Hammond
- School of Agriculture, Policy, and Development, University of Reading, Earley Gate, Whiteknights, Reading, RG6 6AR, UK
- Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia
| | - Elizabeth M H Wellington
- School of Life Sciences, University of Warwick, Gibbet Hill Road, Coventry, West Midlands, CV4 7AL, UK
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23
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Zhang J, Yang MK, Zeng H, Ge F. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes. Mol Cell Proteomics 2016; 15:3529-3539. [PMID: 27630248 DOI: 10.1074/mcp.m116.060046] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Indexed: 11/06/2022] Open
Abstract
Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.
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Affiliation(s)
- Jia Zhang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Ming-Kun Yang
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Honghui Zeng
- §Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
| | - Feng Ge
- From the ‡Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; .,§Wuhan Branch, Supercomputing Center, Chinese Academy of Sciences, China
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Casas V, Vadillo S, San Juan C, Carrascal M, Abian J. The Exposed Proteomes of Brachyspira hyodysenteriae and B. pilosicoli. Front Microbiol 2016; 7:1103. [PMID: 27493641 PMCID: PMC4955376 DOI: 10.3389/fmicb.2016.01103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 07/01/2016] [Indexed: 11/13/2022] Open
Abstract
Brachyspira hyodysenteriae and Brachyspira pilosicoli are well-known intestinal pathogens in pigs. B. hyodysenteriae is the causative agent of swine dysentery, a disease with an important impact on pig production while B. pilosicoli is responsible of a milder diarrheal disease in these animals, porcine intestinal spirochetosis. Recent sequencing projects have provided information for the genome of these species facilitating the search of vaccine candidates using reverse vaccinology approaches. However, practically no experimental evidence exists of the actual gene products being expressed and of those proteins exposed on the cell surface or released to the cell media. Using a cell-shaving strategy and a shotgun proteomic approach we carried out a large-scale characterization of the exposed proteins on the bacterial surface in these species as well as of peptides and proteins in the extracellular medium. The study included three strains of B. hyodysenteriae and two strains of B. pilosicoli and involved 148 LC-MS/MS runs on a high resolution Orbitrap instrument. Overall, we provided evidence for more than 29,000 different peptides pointing to 1625 and 1338 different proteins in B. hyodysenteriae and B. pilosicoli, respectively. Many of the most abundant proteins detected corresponded to described virulence factors and vaccine candidates. The level of expression of these proteins, however, was different among species and strains, stressing the value of determining actual gene product levels as a complement of genomic-based approaches for vaccine design.
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Affiliation(s)
- Vanessa Casas
- Consejo Superior de Investigaciones Científicas/UAB Proteomics Laboratory, Instituto de Investigaciones Biomedicas de Barcelona-Consejo Superior de Investigaciones Científicas, Institut d'investigacions Biomèdiques August Pi i Sunyer Barcelona, Spain
| | - Santiago Vadillo
- Departamento Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura Cáceres, Spain
| | - Carlos San Juan
- Departamento Sanidad Animal, Facultad de Veterinaria, Universidad de Extremadura Cáceres, Spain
| | - Montserrat Carrascal
- Consejo Superior de Investigaciones Científicas/UAB Proteomics Laboratory, Instituto de Investigaciones Biomedicas de Barcelona-Consejo Superior de Investigaciones Científicas, Institut d'investigacions Biomèdiques August Pi i Sunyer Barcelona, Spain
| | - Joaquin Abian
- Consejo Superior de Investigaciones Científicas/UAB Proteomics Laboratory, Instituto de Investigaciones Biomedicas de Barcelona-Consejo Superior de Investigaciones Científicas, Institut d'investigacions Biomèdiques August Pi i Sunyer Barcelona, Spain
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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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Salt Stress Induced Changes in the Exoproteome of the Halotolerant Bacterium Tistlia consotensis Deciphered by Proteogenomics. PLoS One 2015; 10:e0135065. [PMID: 26287734 PMCID: PMC4545795 DOI: 10.1371/journal.pone.0135065] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Accepted: 07/16/2015] [Indexed: 11/19/2022] Open
Abstract
The ability of bacteria to adapt to external osmotic changes is fundamental for their survival. Halotolerant microorganisms, such as Tistlia consotensis, have to cope with continuous fluctuations in the salinity of their natural environments which require effective adaptation strategies against salt stress. Changes of extracellular protein profiles from Tistlia consotensis in conditions of low and high salinities were monitored by proteogenomics using a bacterial draft genome. At low salinity, we detected greater amounts of the HpnM protein which is involved in the biosynthesis of hopanoids. This may represent a novel, and previously unreported, strategy by halotolerant microorganisms to prevent the entry of water into the cell under conditions of low salinity. At high salinity, proteins associated with osmosensing, exclusion of Na+ and transport of compatible solutes, such as glycine betaine or proline are abundant. We also found that, probably in response to the high salt concentration, T. consotensis activated the synthesis of flagella and triggered a chemotactic response neither of which were observed at the salt concentration which is optimal for growth. Our study demonstrates that the exoproteome is an appropriate indicator of adaptive response of T. consotensis to changes in salinity because it allowed the identification of key proteins within its osmoadaptive mechanism that had not previously been detected in its cell proteome.
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Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes. ISME JOURNAL 2015; 10:21-9. [PMID: 26125681 DOI: 10.1038/ismej.2015.108] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 05/04/2015] [Accepted: 05/09/2015] [Indexed: 01/27/2023]
Abstract
The Geodermatophilaceae are unique model systems to study the ability to thrive on or within stones and their proteogenomes (referring to the whole protein arsenal encoded by the genome) could provide important insight into their adaptation mechanisms. Here we report the detailed comparative genome analysis of Blastococcus saxobsidens (Bs), Modestobacter marinus (Mm) and Geodermatophilus obscurus (Go) isolated respectively from the interior and the surface of calcarenite stones and from desert sandy soils. The genome-scale analysis of Bs, Mm and Go illustrates how adaptation to these niches can be achieved through various strategies including 'molecular tinkering/opportunism' as shown by the high proportion of lost, duplicated or horizontally transferred genes and ORFans. Using high-throughput discovery proteomics, the three proteomes under unstressed conditions were analyzed, highlighting the most abundant biomarkers and the main protein factors. Proteomic data corroborated previously demonstrated stone-related ecological distribution. For instance, these data showed starvation-inducible, biofilm-related and DNA-protection proteins as signatures of the microbes associated with the interior, surface and outside of stones, respectively.
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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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Christie-Oleza JA, Armengaud J, Guerin P, Scanlan DJ. Functional distinctness in the exoproteomes of marine Synechococcus. Environ Microbiol 2015; 17:3781-94. [PMID: 25727668 PMCID: PMC4949707 DOI: 10.1111/1462-2920.12822] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2015] [Accepted: 02/21/2015] [Indexed: 12/31/2022]
Abstract
The exported protein fraction of an organism may reflect its life strategy and, ultimately, the way it is perceived by the outside world. Bioinformatic prediction of the exported pan‐proteome of Prochlorococcus and Synechococcus lineages demonstrated that (i) this fraction of the encoded proteome had a much higher incidence of lineage‐specific proteins than the cytosolic fraction (57% and 73% homologue incidence respectively) and (ii) exported proteins are largely uncharacterized to date (54%) compared with proteins from the cytosolic fraction (35%). This suggests that the genomic and functional diversity of these organisms lies largely in the diverse pool of novel functions these organisms export to/through their membranes playing a key role in community diversification, e.g. for niche partitioning or evading predation. Experimental exoproteome analysis of marine Synechococcus showed transport systems for inorganic nutrients, an interesting array of strain‐specific exoproteins involved in mutualistic or hostile interactions (i.e. hemolysins, pilins, adhesins), and exoenzymes with a potential mixotrophic goal (i.e. exoproteases and chitinases). We also show how these organisms can remodel their exoproteome, i.e. by increasing the repertoire of interaction proteins when grown in the presence of a heterotroph or decrease exposure to prey when grown in the dark. Finally, our data indicate that heterotrophic bacteria can feed on the exoproteome of Synechococcus.
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Affiliation(s)
| | - Jean Armengaud
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - Philippe Guerin
- CEA, DSV, IBiTec-S, SPI, Li2D, Laboratory 'Technological Innovations for Detection and Diagnostic', Bagnols-sur-Cèze, F-30207, France
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
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Johnson-Rollings AS, Wright H, Masciandaro G, Macci C, Doni S, Calvo-Bado LA, Slade SE, Vallin Plou C, Wellington EMH. Exploring the functional soil-microbe interface and exoenzymes through soil metaexoproteomics. THE ISME JOURNAL 2014; 8:2148-50. [PMID: 25036924 PMCID: PMC4184004 DOI: 10.1038/ismej.2014.130] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/03/2014] [Indexed: 01/06/2023]
Abstract
Functionally important proteins at the interface of cell and soil are of potentially low abundance when compared with commonly recovered intracellular proteins. A novel approach was developed and used to extract the metaexoproteome, the subset of proteins found outside the cell, in the context of a soil enriched with the nitrogen-containing recalcitrant polymer chitin. The majority of proteins recovered was of bacterial origin and localized to the outer membrane or extracellular milieu. A wide variety of transporter proteins were identified, particularly those associated with amino-acid and phosphate uptake. The metaexoproteome extract retained chitinolytic activity and we were successful in detecting Nocardiopsis-like chitinases that correlated with the glycoside hydrolase family 18 (GH18) chi gene data and metataxonomic analysis. Nocardiopsis-like chitinases appeared to be solely responsible for chitinolytic activity in soil. This is the first study to detect and sequence bacterial exoenzymes with proven activity in the soil enzyme pool.
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Affiliation(s)
| | - Helena Wright
- School of Life Sciences, University of Warwick, Coventry, UK
| | | | - Cristina Macci
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | - Serena Doni
- Istituto per lo Studio degli Ecosistemi, CNR, Pisa, Italy
| | | | - Susan E Slade
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Carlos Vallin Plou
- Grupo de Biotecnología, CEIEB, IFAL, Universidad de La Habana, Havana, Cuba
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Durighello E, Christie-Oleza JA, Armengaud J. Assessing the exoproteome of marine bacteria, lesson from a RTX-toxin abundantly secreted by Phaeobacter strain DSM 17395. PLoS One 2014; 9:e89691. [PMID: 24586966 PMCID: PMC3933643 DOI: 10.1371/journal.pone.0089691] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 01/21/2014] [Indexed: 11/24/2022] Open
Abstract
Bacteria from the Roseobacter clade are abundant in surface marine ecosystems as over 10% of bacterial cells in the open ocean and 20% in coastal waters belong to this group. In order to document how these marine bacteria interact with their environment, we analyzed the exoproteome of Phaeobacter strain DSM 17395. We grew the strain in marine medium, collected the exoproteome and catalogued its content with high-throughput nanoLC-MS/MS shotgun proteomics. The major component represented 60% of the total protein content but was refractory to either classical proteomic identification or proteogenomics. We de novo sequenced this abundant protein with high-resolution tandem mass spectra which turned out being the 53 kDa RTX-toxin ZP_02147451. It comprised a peptidase M10 serralysin domain. We explained its recalcitrance to trypsin proteolysis and proteomic identification by its unusual low number of basic residues. We found this is a conserved trait in RTX-toxins from Roseobacter strains which probably explains their persistence in the harsh conditions around bacteria. Comprehensive analysis of exoproteomes from environmental bacteria should take into account this proteolytic recalcitrance.
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Affiliation(s)
- Emie Durighello
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
| | | | - Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, France
- * E-mail:
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Hartmann EM, Allain F, Gaillard JC, Pible O, Armengaud J. Taking the shortcut for high-throughput shotgun proteomic analysis of bacteria. Methods Mol Biol 2014; 1197:275-85. [PMID: 25172287 DOI: 10.1007/978-1-4939-1261-2_16] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Currently, proteomic tools are able to establish a complete list of the most abundant proteins present in a sample, providing the opportunity to study at high resolution the physiology of any bacteria for which the genome sequence is available. For a comprehensive list, proteins should be first resolved into fractions that are then proteolyzed by trypsin. The resulting peptide mixtures are analyzed by a high-throughput tandem mass spectrometer that records thousands of MS/MS spectra for each fraction. These spectra are then assigned to peptides, which are used as evidence of the existence of proteins. In addition to generating a list of protein identifications, this shortcut to proteomics uses the number of spectra recorded for each protein to quantify the observations. Here, we describe one of the most simple sample preparation methods for high-throughput proteomics of bacteria, as well as the subsequent data processing to extract quantitative information based on the spectral count approach.
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Vanden Bergh P, Heller M, Braga-Lagache S, Frey J. The Aeromonas salmonicida subsp. salmonicida exoproteome: global analysis, moonlighting proteins and putative antigens for vaccination against furunculosis. Proteome Sci 2013; 11:44. [PMID: 24127837 PMCID: PMC3826670 DOI: 10.1186/1477-5956-11-44] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Accepted: 10/04/2013] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Aeromonas salmonicida subsp. salmonicida, the etiologic agent of furunculosis, is a major pathogen of fisheries worldwide. Despite the identification of several virulence factors the pathogenesis is still poorly understood. We have used high-throughput proteomics to display the differences between in vitro secretome of A. salmonicida wild-type (wt, hypervirulent, JF5054) and T3SS-deficient (isogenic ΔascV, extremely low-virulent, JF2747) strains in exponential (GP) and stationary (SP) phases of growth. RESULTS Among the different experimental conditions we obtained semi-quantitative values for a total of 2136 A. salmonicida proteins. Proteins of specific A. salmonicida species were proportionally less detected than proteins common to the Aeromonas genus or those shared with other Aeromonas species, suggesting that in vitro growth did not induce the expression of these genes. Four detected proteins which are unidentified in the genome of reference strains of A. salmonicida were homologous to components of the conjugative T4SS of A. hydrophila pRA1 plasmid. Polypeptides of three proteins which are specific to the 01-B526 strain were also discovered. In supernatants (SNs), the number of detected proteins was higher in SP (326 for wt vs 329 for mutant) than in GP (275 for wt vs 263 for mutant). In pellets, the number of identified proteins (a total of 1536) was approximately the same between GP and SP. Numerous highly conserved cytoplasmic proteins were present in A. salmonicida SNs (mainly EF-Tu, EF-G, EF-P, EF-Ts, TypA, AlaS, ribosomal proteins, HtpG, DnaK, peptidyl-prolyl cis-trans isomerases, GAPDH, Enolase, FbaA, TpiA, Pgk, TktA, AckA, AcnB, Mdh, AhpC, Tpx, SodB and PNPase), and several evidences support the theory that their extracellular localization was not the result of cell lysis. According to the Cluster of Orthologous Groups classification, 29% of excreted proteins in A. salmonicida SNs were currently poorly characterized. CONCLUSIONS In this part of our work we elucidated the whole in vitro exoproteome of hypervirulent A. salmonicida subsp. salmonicida and showed the secretion of several highly conserved cytoplasmic proteins with putative moonlighting functions and roles in virulence. All together, our results offer new information about the pathogenesis of furunculosis and point out potential candidates for vaccine development.
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Affiliation(s)
- Philippe Vanden Bergh
- Institute of Veterinary Bacteriology, University of Bern, Länggassstrasse 122, P.O. Box 8466, 3001 Bern, Switzerland
| | - Manfred Heller
- Department of Clinical Research, University of Bern, P.O. Box 37, 3010 Bern, Switzerland
| | - Sophie Braga-Lagache
- Department of Clinical Research, University of Bern, P.O. Box 37, 3010 Bern, Switzerland
| | - Joachim Frey
- Institute of Veterinary Bacteriology, University of Bern, Länggassstrasse 122, P.O. Box 8466, 3001 Bern, Switzerland
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Armengaud J, Christie-Oleza JA, Clair G, Malard V, Duport C. Exoproteomics: exploring the world around biological systems. Expert Rev Proteomics 2013. [PMID: 23194272 DOI: 10.1586/epr.12.52] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The term 'exoproteome' describes the protein content that can be found in the extracellular proximity of a given biological system. These proteins arise from cellular secretion, other protein export mechanisms or cell lysis, but only the most stable proteins in this environment will remain in abundance. It has been shown that these proteins reflect the physiological state of the cells in a given condition and are indicators of how living systems interact with their environments. High-throughput proteomic approaches based on a shotgun strategy, and high-resolution mass spectrometers, have modified the authors' view of exoproteomes. In the present review, the authors describe how these new approaches should be exploited to obtain the maximum useful information from a sample, whatever its origin. The methodologies used for studying secretion from model cell lines derived from eukaryotic, multicellular organisms, virulence determinants of pathogens and environmental bacteria and their relationships with their habitats are illustrated with several examples. The implication of such data, in terms of proteogenomics and the discovery of novel protein functions, is discussed.
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Affiliation(s)
- Jean Armengaud
- CEA, DSV, IBEB, Lab Biochim System Perturb, Bagnols-sur-Cèze, F-30207, France.
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Slattery M, Ankisetty S, Corrales J, Marsh-Hunkin KE, Gochfeld DJ, Willett KL, Rimoldi JM. Marine proteomics: a critical assessment of an emerging technology. JOURNAL OF NATURAL PRODUCTS 2012; 75:1833-1877. [PMID: 23009278 DOI: 10.1021/np300366a] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The application of proteomics to marine sciences has increased in recent years because the proteome represents the interface between genotypic and phenotypic variability and, thus, corresponds to the broadest possible biomarker for eco-physiological responses and adaptations. Likewise, proteomics can provide important functional information regarding biosynthetic pathways, as well as insights into mechanism of action, of novel marine natural products. The goal of this review is to (1) explore the application of proteomics methodologies to marine systems, (2) assess the technical approaches that have been used, and (3) evaluate the pros and cons of this proteomic research, with the intent of providing a critical analysis of its future roles in marine sciences. To date, proteomics techniques have been utilized to investigate marine microbe, plant, invertebrate, and vertebrate physiology, developmental biology, seafood safety, susceptibility to disease, and responses to environmental change. However, marine proteomics studies often suffer from poor experimental design, sample processing/optimization difficulties, and data analysis/interpretation issues. Moreover, a major limitation is the lack of available annotated genomes and proteomes for most marine organisms, including several "model species". Even with these challenges in mind, there is no doubt that marine proteomics is a rapidly expanding and powerful integrative molecular research tool from which our knowledge of the marine environment, and the natural products from this resource, will be significantly expanded.
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Affiliation(s)
- Marc Slattery
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, USA.
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Christie-Oleza JA, Piña-Villalonga JM, Guerin P, Miotello G, Bosch R, Nogales B, Armengaud J. Shotgun nanoLC-MS/MS proteogenomics to document MALDI-TOF biomarkers for screening new members of theRuegeriagenus. Environ Microbiol 2012; 15:133-47. [DOI: 10.1111/j.1462-2920.2012.02812.x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Christie-Oleza JA, Miotello G, Armengaud J. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade. BMC Genomics 2012; 13:73. [PMID: 22336032 PMCID: PMC3305630 DOI: 10.1186/1471-2164-13-73] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 02/15/2012] [Indexed: 11/10/2022] Open
Abstract
Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs) that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera), we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase the reliability of the future annotation of marine bacterial genomes.
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Clair G, Armengaud J, Duport C. Restricting fermentative potential by proteome remodeling: an adaptive strategy evidenced in Bacillus cereus. Mol Cell Proteomics 2012; 11:M111.013102. [PMID: 22232490 DOI: 10.1074/mcp.m111.013102] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Pathogenesis hinges on successful colonization of the gastrointestinal (GI) tract by pathogenic facultative anaerobes. The GI tract is a carbohydrate-limited environment with varying oxygen availability and oxidoreduction potential (ORP). How pathogenic bacteria are able to adapt and grow in these varying conditions remains a key fundamental question. Here, we designed a system biology-inspired approach to pinpoint the key regulators allowing Bacillus cereus to survive and grow efficiently under low ORP anoxic conditions mimicking those encountered in the intestinal lumen. We assessed the proteome components using high throughput nanoLC-MS/MS techniques, reconstituted the main metabolic circuits, constructed ΔohrA and ΔohrR mutants, and analyzed the impacts of ohrA and ohrR disruptions by a novel round of shotgun proteomics. Our study revealed that OhrR and OhrA are crucial to the successful adaptation of B. cereus to the GI tract environment. Specifically, we showed that B. cereus restricts its fermentative growth under low ORP anaerobiosis and sustains efficient aerobic respiratory metabolism, motility, and stress response via OhrRA-dependent proteome remodeling. Finally, our results introduced a new adaptive strategy where facultative anaerobes prefer to restrict their fermentative potential for a long term benefit.
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Affiliation(s)
- Gérémy Clair
- Université d'Avignon et des Pays de Vaucluse, UMR408, Sécurité et Qualité des Produits d'Origine Végétale, F-84000 Avignon, France
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Christie-Oleza JA, Piña-Villalonga JM, Bosch R, Nogales B, Armengaud J. Comparative proteogenomics of twelve Roseobacter exoproteomes reveals different adaptive strategies among these marine bacteria. Mol Cell Proteomics 2011; 11:M111.013110. [PMID: 22122883 DOI: 10.1074/mcp.m111.013110] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Roseobacters are generalist bacteria abundantly found in the oceans. Because little is known on how marine microorganisms interact in association or competition, we focused our attention on the microbial exoproteome, a key component in their interaction with extracellular milieu. Here we present a comparative analysis of the theoretically encoded exoproteome of twelve members of the Roseobacter group validated by extensive comparative proteogenomics. In silico analysis revealed that 30% of the encoded proteome of these microorganisms could be exported. The ratio of the different protein categories varied in accordance to the ecological distinctness of each strain, a trait reinforced by quantitative proteomics data. Despite the interspecies variations found, the most abundantly detected proteins by shotgun proteomics were from transporter, adhesion, motility, and toxin-like protein categories, defining four different plausible adaptive strategies within the Roseobacter group. In some strains the toxin-secretion strategy was over-represented with repeats-in-toxin-like proteins. Our results show that exoproteomes strongly depend on bacterial trophic strategy and can slightly change because of culture conditions. Simulated natural conditions and the effect of the indigenous microbial community on the exoproteome of Ruegeria pomeroyi DSS-3 were also assayed. Interestingly, we observed a significant depletion of the toxin-like proteins usually secreted by R. pomeroyi DSS-3 when grown in presence of a natural community sampled from a Mediterranean Sea port. The significance of this specific fraction of the exoproteome is discussed.
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Analytical constraints for the analysis of human cell line secretomes by shotgun proteomics. J Proteomics 2011; 75:1043-54. [PMID: 22079246 DOI: 10.1016/j.jprot.2011.10.025] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2011] [Revised: 09/16/2011] [Accepted: 10/22/2011] [Indexed: 01/21/2023]
Abstract
Human cell line secretome represents a valuable source of therapeutic targets and candidate biomarkers. Secreted proteins found in biological fluids or culture media are by essence highly diluted. Secretome investigation with proteomic approaches is hardly compatible with the high content of proteins found in complete cell culture media. Therefore, many studies are currently done with media containing few or no protein. Such conditions may perturb cell metabolism and proliferation. Here, we compared seventeen different compositions of culture media for the human bronchial epithelial BEAS-2B cell line. Cell viability, proliferation rate and initial protein charge were systematically compared. We have shown that an important difficulty for the proteomic analysis is due to the presence of detergents such as Pluronic F-68 which hinders peptide mass spectrometry. The high glucose containing DMEM medium which is free of proteins was shown to preserve a good viability and proliferation of cells. With this conditioning medium, we identified 81 extracellular proteins in the secretome of BEAS-2B cells. Moreover, to illustrate this approach, we exposed BEAS-2B cells to a low toxic dose of CoCl(2,) and found 24 extracellular proteins modulated by cobalt. This study highlights the possible contribution of such proteomic approach in the field of toxicology.
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Christie-Oleza JA, Fernandez B, Nogales B, Bosch R, Armengaud J. Proteomic insights into the lifestyle of an environmentally relevant marine bacterium. ISME JOURNAL 2011; 6:124-35. [PMID: 21776030 DOI: 10.1038/ismej.2011.86] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In terms of lifestyle, free-living bacteria are classified as either oligotrophic/specialist or opportunist/generalist. Heterogeneous marine environments such as coastal waters favour the establishment of marine generalist bacteria, which code for a large pool of functions. This is basically foreseen to cope with the heterogeneity of organic matter supplied to these systems. Nevertheless, it is not known what fraction of a generalist proteome is needed for house-keeping functions or what fraction is modified to cope with environmental changes. Here, we used high-throughput proteomics to define the proteome of Ruegeria pomeroyi DSS-3, a model marine generalist bacterium of the Roseobacter clade. We evaluated its genome expression under several natural environmental conditions, revealing the versatility of the bacterium to adapt to anthropogenic influence, poor nutrient concentrations or the presence of the natural microbial community. We also assayed 30 different laboratory incubations to increase proteome coverage and to dig further into the functional genomics of the bacterium. We established its core proteome and the proteome devoted to adaptation to general cellular physiological variations (almost 50%). We suggest that the other half of its theoretical proteome is the opportunist genetic pool devoted exclusively to very specific environmental conditions.
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Utility of gel-free, label-free shotgun proteomics approaches to investigate microorganisms. Appl Microbiol Biotechnol 2011; 90:407-16. [DOI: 10.1007/s00253-011-3172-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Revised: 02/03/2011] [Accepted: 02/04/2011] [Indexed: 10/18/2022]
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Wilmes B, Kock H, Glagla S, Albrecht D, Voigt B, Markert S, Gardebrecht A, Bode R, Danchin A, Feller G, Hecker M, Schweder T. Cytoplasmic and periplasmic proteomic signatures of exponentially growing cells of the psychrophilic bacterium Pseudoalteromonas haloplanktis TAC125. Appl Environ Microbiol 2011; 77:1276-83. [PMID: 21183643 PMCID: PMC3067249 DOI: 10.1128/aem.01750-10] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Accepted: 12/13/2010] [Indexed: 11/20/2022] Open
Abstract
The psychrophilic model bacterium Pseudoalteromonas haloplanktis is characterized by remarkably fast growth rates under low-temperature conditions in a range from 5°C to 20°C. In this study the proteome of cellular compartments, the cytoplasm and periplasm, of P. haloplanktis strain TAC125 was analyzed under exponential growth conditions at a permissive temperature of 16°C. By means of two-dimensional protein gel electrophoresis and mass spectrometry, a first inventory of the most abundant cytoplasmic and periplasmic proteins expressed in a peptone-supplemented minimal medium was established. By this approach major enzymes of the amino acid catabolism of this marine bacterium could be functionally deduced. The cytoplasmic proteome showed a predominance of amino acid degradation pathways and tricarboxylic acid (TCA) cycle enzymes but also the protein synthesis machinery. Furthermore, high levels of cold acclimation and oxidative stress proteins could be detected at this moderate growth temperature. The periplasmic proteome was characterized by a significant abundance of transporters, especially of highly expressed putative TonB-dependent receptors. This high capacity for protein synthesis, efficient amino acid utilization, and substrate transport may contribute to the fast growth rates of the copiotrophic bacterium P. haloplanktis in its natural environments.
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Affiliation(s)
- Boris Wilmes
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Holger Kock
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Susanne Glagla
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Dirk Albrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Birgit Voigt
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Stephanie Markert
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antje Gardebrecht
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Rüdiger Bode
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Antoine Danchin
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Georges Feller
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Michael Hecker
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
| | - Thomas Schweder
- Institute of Marine Biotechnology, W. Rathenau Str. 49a, 17489 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Department of Pharmaceutical Biotechnology, F.-L. Jahn Str. 17, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Medical Faculty, Fleischmannstr. 8, 17475 Greifswald, Germany, University of Erlangen, Department of Microbiology, Staudtstr. 5, 91058 Erlangen, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, F.-L. Jahn Str. 15, 17487 Greifswald, Germany, Ernst Moritz Arndt University Greifswald, Institute of Microbiology, Department of Biochemistry, F. Hausdorff Str. 4, 17487 Greifswald, Germany, AMAbiotics, Genopole 1, 91030 Evry Cedex, France, University of Liège, Centre for Protein Engineering B6a, 4000 Liège, Belgium
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