Article (Scientific journals)
Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms.
Lim, Hyobin Julianne; Yoon, Haejin; Kim, Hyeyeon et al.
2021In Frontiers in Cell and Developmental Biology, 9, p. 734950
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Keywords :
biogenesis; evolution; extracellular vesicle; network; purification
Abstract :
[en] Extracellular vesicles (EVs) are membranous structures containing bioactive molecules, secreted by most cells into the extracellular environment. EVs are classified by their biogenesis mechanisms into two major subtypes: ectosomes (enriched in large EVs; lEVs), budding directly from the plasma membrane, which is common in both prokaryotes and eukaryotes, and exosomes (enriched in small EVs; sEVs) generated through the multivesicular bodies via the endomembrane system, which is unique to eukaryotes. Even though recent proteomic analyses have identified key proteins associated with EV subtypes, there has been no systematic analysis, thus far, to support the general validity and utility of current EV subtype separation methods, still largely dependent on physical properties, such as vesicular size and sedimentation. Here, we classified human EV proteomic datasets into two main categories based on distinct centrifugation protocols commonly used for isolating sEV or lEV fractions. We found characteristic, evolutionarily conserved profiles of sEV and lEV proteins linked to their respective biogenetic origins. This may suggest that the evolutionary trajectory of vesicular proteins may result in a membership bias toward specific EV subtypes. Protein-protein interaction (PPI) network analysis showed that vesicular proteins formed distinct clusters with proteins in the same EV fraction, providing evidence for the existence of EV subtype-specific protein recruiters. Moreover, we identified functional modules enriched in each fraction, including multivesicular body sorting for sEV, and mitochondria cellular respiration for lEV proteins. Our analysis successfully captured novel features of EVs embedded in heterogeneous proteomics studies and suggests specific protein markers and signatures to be used as quality controllers in the isolation procedure for subtype-enriched EV fractions.
Disciplines :
Biochemistry, biophysics & molecular biology
Author, co-author :
Lim, Hyobin Julianne
Yoon, Haejin
Kim, Hyeyeon
Kang, Yun-Won
Kim, Ji-Eun
Kim, Oh Youn
Lee, Eun-Young
Twizere, Jean-Claude  ;  Université de Liège - ULiège > Département GxABT > Microbial, food and biobased technologies
Rak, Janusz
Kim, Dae-Kyum
Language :
English
Title :
Extracellular Vesicle Proteomes Shed Light on the Evolutionary, Interactive, and Functional Divergence of Their Biogenesis Mechanisms.
Publication date :
2021
Journal title :
Frontiers in Cell and Developmental Biology
eISSN :
2296-634X
Publisher :
Frontiers, Lausanne, Switzerland
Volume :
9
Pages :
734950
Peer reviewed :
Peer Reviewed verified by ORBi
Commentary :
Copyright © 2021 Lim, Yoon, Kim, Kang, Kim, Kim, Lee, Twizere, Rak and Kim.
Available on ORBi :
since 22 November 2021

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