Systematic characterization of extracellular vesicles from potato (Solanum tuberosum cv. Laura) roots and peels: biophysical properties and proteomic profiling

Gayandi Ekanayake; Johanna Piibor; Getnet Midekessa; Kasun Godakumara; Keerthie Dissanayake; Aneta Andronowska; Rajeev Bhat; Alireza Fazeli

doi:10.3389/fpls.2024.1477614

Systematic characterization of extracellular vesicles from potato (Solanum tuberosum cv. Laura) roots and peels: biophysical properties and proteomic profiling

Front Plant Sci. 2024 Nov 15:15:1477614. doi: 10.3389/fpls.2024.1477614. eCollection 2024.

Authors

Gayandi Ekanayake¹, Johanna Piibor¹, Getnet Midekessa^{1

2}, Kasun Godakumara¹, Keerthie Dissanayake^{2

3}, Aneta Andronowska⁴, Rajeev Bhat⁵, Alireza Fazeli^{1

2

6}

Affiliations

¹ Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia.
² Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.
³ Department of Anatomy, Faculty of Medicine, University of Peradeniya, Peradeniya, Sri Lanka.
⁴ Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland.
⁵ ERA-Chair for Food (By-) Products Valorisation Technologies (VALORTECH), Estonian University of Life Sciences, Tartu, Estonia.
⁶ Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, United Kingdom.

Abstract

Introduction: Extracellular vesicles (EVs) facilitate inter and intra-species/kingdom communication through biomolecule transfer, including proteins and small RNAs. Plant-derived EVs, a hot topic in the field, hold immense capability both as a potential biomarker to study plant physiology and as a biomaterial that can be mass-produced to be used in various industries ranging from cosmetics and food additives to biological pesticides. However, a systematic characterization of plant EVs is required to establish a foundation for further applications and studies.

Methods: In this study, EVs were enriched from hydroponically cultivated potato plants (Solanum tuberosum, cv. Laura). We isolated EVs from root exudates and the apoplastic wash of potato peels using vacuum infiltration. These EVs were then systematically characterized for their biophysical and chemical properties to compare with standard EV characteristics and to explore their roles in plant physiology.

Results: Biophysical and chemical analyses revealed morphological similarities between potato root and peel-derived EVs. The average diameter of root-derived EVs (164.6 ± 7.3 nm) was significantly larger than that of peel-derived EVs (132.2 ± 2.0 nm, p < 0.004). Liquid chromatography-mass spectrometry (LC-MS) demonstrated substantial protein enrichment in purified EVs compared to crude samples, with a 42% enrichment for root EVs and 25% for peel EVs. Only 11.8% of the identified proteins were common between root and peel EVs, with just 2% of significantly enriched proteins shared. Enriched pathways in both EV proteomes were associated with responses to biotic and abiotic stress, suggesting a defensive role of EVs in plants.

Discussion: With further experimentation to elucidate the specific methods of communication, these findings increase the details known about plant EVs in terms of their physical and chemical characteristics and their potential functions, aiding in sustainable agricultural waste utilization for large-scale EV production, aligning with the concept of "valorization".

Keywords: Solanum tuberosum; agricultural waste; plant biotic and abiotic stress; plant extracellular vesicles; proteomics; valorization; value addition and sustainability.

Associated data

figshare/10.6084/m9.figshare.25607601.v1

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The current project is funded by the COMBIVET ERA Chair project, which is funded by the European Union’s Horizon 2020 research and innovation program under grant agreement No 857418; VALORTECH ERA Chair, which is funded by the European Union’s Horizon 2020 research and innovation program under the grant agreement No 810630; and European Union through Horizon coordination and support actions under grant agreement No. 101079349 OH-Boost.