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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2023
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.
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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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