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Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles
Bacterial extracellular vesicles (EVs) are natural lipidic nanoparticles implicated in intercellular communication. Although EV research focused mainly on pathogens, the interest in probiotic-derived EVs is now rising. One example is Propionibacterium freudenreichii, which produces EVs with anti-inf...
Autores principales: | , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10265600/ https://www.ncbi.nlm.nih.gov/pubmed/37324655 http://dx.doi.org/10.1093/femsml/uqad029 |
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author | Rodovalho, Vinícius de Rezende da Luz, Brenda Silva Rosa Nicolas, Aurélie Jardin, Julien Briard-Bion, Valérie Folador, Edson Luiz Santos, Anderson Rodrigues Jan, Gwénaël Loir, Yves Le Azevedo, Vasco Ariston de Carvalho Guédon, Éric |
author_facet | Rodovalho, Vinícius de Rezende da Luz, Brenda Silva Rosa Nicolas, Aurélie Jardin, Julien Briard-Bion, Valérie Folador, Edson Luiz Santos, Anderson Rodrigues Jan, Gwénaël Loir, Yves Le Azevedo, Vasco Ariston de Carvalho Guédon, Éric |
author_sort | Rodovalho, Vinícius de Rezende |
collection | PubMed |
description | Bacterial extracellular vesicles (EVs) are natural lipidic nanoparticles implicated in intercellular communication. Although EV research focused mainly on pathogens, the interest in probiotic-derived EVs is now rising. One example is Propionibacterium freudenreichii, which produces EVs with anti-inflammatory effects on human epithelial cells. Our previous study with P. freudenreichii showed that EVs purified by size exclusion chromatography (SEC) displayed variations in protein content according to bacterial growth conditions. Considering these content variations, we hypothesized that a comparative proteomic analysis of EVs recovered in different conditions would elucidate whether a representative vesicular proteome existed, possibly providing a robust proteome dataset for further analysis. Therefore, P. freudenreichii was grown in two culture media, and EVs were purified by sucrose density gradient ultracentrifugation (UC). Microscopic and size characterization confirmed EV purification, while shotgun proteomics unveiled that they carried a diverse set of proteins. A comparative analysis of the protein content of UC- and SEC-derived EVs, isolated from cultures either in UF (cow milk ultrafiltrate medium) or YEL (laboratory yeast extract lactate medium), showed that EVs from all these conditions shared 308 proteins. This EV core proteome was notably enriched in proteins related to immunomodulation. Moreover, it showed distinctive features, including highly interacting proteins, compositional biases for some specific amino acids, and other biochemical parameters. Overall, this work broadens the toolset for the purification of P. freudenreichii-derived EVs, identifies a representative vesicular proteome, and enumerates conserved features in vesicular proteins. These results hold the potential for providing candidate biomarkers of purification quality, and insights into the mechanisms of EV biogenesis and cargo sorting. |
format | Online Article Text |
id | pubmed-10265600 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-102656002023-06-15 Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles Rodovalho, Vinícius de Rezende da Luz, Brenda Silva Rosa Nicolas, Aurélie Jardin, Julien Briard-Bion, Valérie Folador, Edson Luiz Santos, Anderson Rodrigues Jan, Gwénaël Loir, Yves Le Azevedo, Vasco Ariston de Carvalho Guédon, Éric Microlife Research Article Bacterial extracellular vesicles (EVs) are natural lipidic nanoparticles implicated in intercellular communication. Although EV research focused mainly on pathogens, the interest in probiotic-derived EVs is now rising. One example is Propionibacterium freudenreichii, which produces EVs with anti-inflammatory effects on human epithelial cells. Our previous study with P. freudenreichii showed that EVs purified by size exclusion chromatography (SEC) displayed variations in protein content according to bacterial growth conditions. Considering these content variations, we hypothesized that a comparative proteomic analysis of EVs recovered in different conditions would elucidate whether a representative vesicular proteome existed, possibly providing a robust proteome dataset for further analysis. Therefore, P. freudenreichii was grown in two culture media, and EVs were purified by sucrose density gradient ultracentrifugation (UC). Microscopic and size characterization confirmed EV purification, while shotgun proteomics unveiled that they carried a diverse set of proteins. A comparative analysis of the protein content of UC- and SEC-derived EVs, isolated from cultures either in UF (cow milk ultrafiltrate medium) or YEL (laboratory yeast extract lactate medium), showed that EVs from all these conditions shared 308 proteins. This EV core proteome was notably enriched in proteins related to immunomodulation. Moreover, it showed distinctive features, including highly interacting proteins, compositional biases for some specific amino acids, and other biochemical parameters. Overall, this work broadens the toolset for the purification of P. freudenreichii-derived EVs, identifies a representative vesicular proteome, and enumerates conserved features in vesicular proteins. These results hold the potential for providing candidate biomarkers of purification quality, and insights into the mechanisms of EV biogenesis and cargo sorting. Oxford University Press 2023-06-02 /pmc/articles/PMC10265600/ /pubmed/37324655 http://dx.doi.org/10.1093/femsml/uqad029 Text en © The Author(s) 2023. Published by Oxford University Press on behalf of FEMS. https://creativecommons.org/licenses/by-nc/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (https://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Research Article Rodovalho, Vinícius de Rezende da Luz, Brenda Silva Rosa Nicolas, Aurélie Jardin, Julien Briard-Bion, Valérie Folador, Edson Luiz Santos, Anderson Rodrigues Jan, Gwénaël Loir, Yves Le Azevedo, Vasco Ariston de Carvalho Guédon, Éric Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title | Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title_full | Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title_fullStr | Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title_full_unstemmed | Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title_short | Different culture media and purification methods unveil the core proteome of Propionibacterium freudenreichii-derived extracellular vesicles |
title_sort | different culture media and purification methods unveil the core proteome of propionibacterium freudenreichii-derived extracellular vesicles |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10265600/ https://www.ncbi.nlm.nih.gov/pubmed/37324655 http://dx.doi.org/10.1093/femsml/uqad029 |
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