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Davis CN, Phillips H, Tomes JJ, Swain MT, Wilkinson TJ, Brophy PM, Morphew RM. The importance of extracellular vesicle purification for downstream analysis: A comparison of differential centrifugation and size exclusion chromatography for helminth pathogens. PLoS Negl Trop Dis 2019; 13:e0007191. [PMID: 30811394 PMCID: PMC6411213 DOI: 10.1371/journal.pntd.0007191] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 03/11/2019] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Robust protocols for the isolation of extracellular vesicles (EVs) from the rest of their excretory-secretory products are necessary for downstream studies and application development. The most widely used purification method of EVs for helminth pathogens is currently differential centrifugation (DC). In contrast, size exclusion chromatography (SEC) has been included in the purification pipeline for EVs from other pathogens, highlighting there is not an agreed research community 'gold standard' for EV isolation. In this case study, Fasciola hepatica from natural populations were cultured in order to collect EVs from culture media and evaluate a SEC or DC approach to pathogen helminth EV purification. METHODOLOGY/PRINCIPAL FINDINGS Transmission electron and atomic force microscopy demonstrated that EVs prepared by SEC were both smaller in size and less diverse than EV resolved by DC. Protein quantification and Western blotting further demonstrated that SEC purification realised a higher EV purity to free excretory-secretory protein (ESP) yield ratio compared to DC approaches as evident by the reduction of soluble free cathepsin L proteases in SEC EV preparations. Proteomic analysis further highlighted DC contamination from ESP as shown by an increased diversity of protein identifications and unique peptide hits in DC EVs as compared to SEC EVs. In addition, SEC purified EVs contained less tegumental based proteins than DC purified EVs. CONCLUSIONS/SIGNIFICANCE The data suggests that DC and SEC purification methods do not isolate equivalent EV population profiles and caution should be taken in the choice of EV purification utilised, with certain protocols for DC preparations including more free ES proteins and tegumental artefacts. We propose that SEC methods should be used for EV purification prior to downstream studies.
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Affiliation(s)
- Chelsea N. Davis
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Helen Phillips
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - John J. Tomes
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Martin T. Swain
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Toby J. Wilkinson
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Peter M. Brophy
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
| | - Russell M. Morphew
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, United Kingdom
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Sousa DM, Cunha NMFD, Silva DRD, Aragão PDTTDD, Aguiar MVDA, Lobo MDP, Moreira ACDOM, Cunha RMSD, Miranda RRCD, Bevilaqua CML. Differences in protein expression associated with ivermectin resistance in Caenorhabditis elegans. REVISTA BRASILEIRA DE PARASITOLOGIA VETERINARIA = BRAZILIAN JOURNAL OF VETERINARY PARASITOLOGY : ORGAO OFICIAL DO COLEGIO BRASILEIRO DE PARASITOLOGIA VETERINARIA 2019; 28:105-112. [PMID: 30916256 DOI: 10.1590/s1984-29612019013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 02/06/2019] [Indexed: 06/09/2023]
Abstract
The indiscriminate administration of synthetic anthelmintics such as ivermectin contributes to the selection of subpopulations capable of resisting the drugs' effects. To understand the mechanisms of ivermectin resistance in Caenorhabditis elegans, this study attempted to identify molecular targets. C. elegans lineages that were sensitive and resistant to ivermectin were used. Collected nematodes were added to an extraction buffer and macerated in liquid nitrogen for protein extraction. The extracted proteins were separated according to molecular weight by SDS-PAGE to verify their integrity. Subsequently, proteins from both lineages were separated using two-dimensional electrophoresis. The gels were analyzed and the relevant spots were excised and identified by mass spectrometry (NanoESI-Q-TOF and MASCOT®) and subsequently assessed by GO enrichment and STRING® analyses. The increased expression of proteins associated with high metabolic activity, such as ATP-2 and ENOL-1, which are responsible for ATP synthesis, was observed. Furthermore, proteins with involvement in mediating muscular function (MLC-1, ACT-1, and PDI-2), signaling (FAR-1 and FAR-2), and embryo development (VHA-2) were identified. Protein interaction analysis indicated that the majority of the identified proteins in the resistant lineages participated in the same reaction triggered by ivermectin.
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Affiliation(s)
- Dauana Mesquita Sousa
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
| | - Nivea Maria Ferreira da Cunha
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | - Deisianne Rodrigues da Silva
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | - Paulo de Tarso Teles Dourado de Aragão
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Programa de Pós-graduação em Biotecnologia, Universidade Federal do Ceará - UFC, Sobral, CE, Brasil
| | - Mônica Valéria de Almeida Aguiar
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | | | | | - Rodrigo Maranguape Silva da Cunha
- Laboratório de Biologia Molecular, Núcleo de Biotecnologia de Sobral, Universidade Estadual Vale do Acaraú - UVA, Sobral, CE, Brasil
| | | | - Claudia Maria Leal Bevilaqua
- Laboratório de Doenças Parasitárias, Programa de Pós-graduação em Ciências Veterinárias, Faculdade de Veterinária, Universidade Estadual do Ceará - UECE, Fortaleza, CE, Brasil
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Hart EH, Creevey CJ, Hitch T, Kingston-Smith AH. Meta-proteomics of rumen microbiota indicates niche compartmentalisation and functional dominance in a limited number of metabolic pathways between abundant bacteria. Sci Rep 2018; 8:10504. [PMID: 30002438 PMCID: PMC6043501 DOI: 10.1038/s41598-018-28827-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 06/29/2018] [Indexed: 11/17/2022] Open
Abstract
The rumen is a complex ecosystem. It is the primary site for microbial fermentation of ingested feed allowing conversion of a low nutritional feed source into high quality meat and milk products. However, digestive inefficiencies lead to production of high amounts of environmental pollutants; methane and nitrogenous waste. These inefficiencies could be overcome by development of forages which better match the requirements of the rumen microbial population. Although challenging, the application of meta-proteomics has potential for a more complete understanding of the rumen ecosystem than sequencing approaches alone. Here, we have implemented a meta-proteomic approach to determine the association between taxonomies of microbial sources of the most abundant proteins in the rumens of forage-fed dairy cows, with taxonomic abundances typical of those previously described by metagenomics. Reproducible proteome profiles were generated from rumen samples. The most highly abundant taxonomic phyla in the proteome were Bacteriodetes, Firmicutes and Proteobacteria, which corresponded with the most abundant taxonomic phyla determined from 16S rRNA studies. Meta-proteome data indicated differentiation between metabolic pathways of the most abundant phyla, which is in agreement with the concept of diversified niches within the rumen microbiota.
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Affiliation(s)
- E H Hart
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - C J Creevey
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - T Hitch
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK
| | - A H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth, SY23 3FG, UK.
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Emery DL, Hunt PW, Le Jambre LF. Haemonchus contortus: the then and now, and where to from here? Int J Parasitol 2016; 46:755-769. [DOI: 10.1016/j.ijpara.2016.07.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 07/20/2016] [Accepted: 07/22/2016] [Indexed: 12/16/2022]
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Hart EH, Onime LA, Davies TE, Morphew RM, Kingston-Smith AH. The effects of PPO activity on the proteome of ingested red clover and implications for improving the nutrition of grazing cattle. J Proteomics 2016; 141:67-76. [PMID: 27109346 PMCID: PMC4881418 DOI: 10.1016/j.jprot.2016.04.023] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Revised: 03/24/2016] [Accepted: 04/15/2016] [Indexed: 12/16/2022]
Abstract
UNLABELLED Increasing the rumen-stable protein content of feed would lead to improved nitrogen utilisation in cattle, and less nitrogenous waste. Red clover (Trifolium pratense L.) is a high protein ruminant feed containing high polyphenol oxidase (PPO) activity. PPO mediated protein-quinone binding has been linked to protecting plant proteins from proteolysis. To explore the mechanism underlying the effect of PPO on protein protection in fresh forage feeds, proteomic components of feed down-boli produced from wild-type red clover and a low PPO mutant, at point of ingestion and after 4h in vitro incubation with rumen inoculum were analysed. Significant differences in proteomic profiles between wild-type and mutant red clover were determined after 4h incubation, with over 50% less spots in mutant than wild-type proteomes, indicating decreased proteolysis in the latter. Protein identifications revealed preferentially retained proteins localised within the chloroplast, suggesting that PPO mediated protection in the wild-type operates due to the proximity of target proteins to the enzyme and substrates, either diffusing into this compartment from the vacuole or are present in the chloroplast. This increased understanding of protein targets of PPO indicates that wider exploitation of the trait could contribute to increased protein use efficiency in grazing cattle. BIOLOGICAL SIGNIFICANCE One of the main challenges for sustainable livestock farming is improving capture of dietary nitrogen by ruminants. Typically up to 70% of ingested protein-N is excreted representing a loss of productivity potential and a serious environmental problem in terms of nitrogenous pollution of lands and water. Identification of key characteristics of rumen-protected protein will deliver target traits for selection in forage breeding programmes. The chloroplastic enzyme PPO catalyzes the oxidation of phenols to quinones, which react with protein. Little is currently known about the intracellular protein targets of the products of PPO activity or the mechanism underlying protein complexing, including whether there is any specificity to the reaction. Here we have determined significant differences in the proteomes of freshly ingested down boli corresponding to the presence or absence of active PPO. These results show that in the presence of PPO the forage protein is less amenable to proteolysis and provide the novel information that the protected proteins are putatively chloroplastically located. These data also contribute to a growing evidence base that a chloroplastic PPO substrate exists in red clover in addition to the currently known vacuolar substrates.
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Affiliation(s)
- E H Hart
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - L A Onime
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - T E Davies
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - R M Morphew
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK
| | - A H Kingston-Smith
- Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Penglais, Aberystwyth SY23 3FG, UK.
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Husson SJ, Moyson S, Valkenborg D, Baggerman G, Mertens I. Proteomics applications in Caenorhabditis elegans research. Biochem Biophys Res Commun 2015; 468:519-24. [DOI: 10.1016/j.bbrc.2015.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 11/04/2015] [Indexed: 01/04/2023]
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