2025 Hyper Recent •CC0 1.0 Universal

This work is dedicated to the public domain. No rights reserved.

Access Preprint From Server
September 2nd, 2025
Version: 3
Department of Pharmacology, School of Medicine, Universidad Autonoma de Madrid
molecular biology
bioRxiv

A compendium of bona fide reference markers for genuine plant-derived extracellular vesicles and their degree of phylogenetic conservation

Rodriguez de Lope, M. M.Open in Google Scholar•Sanchez-Pajares, I. R.Open in Google Scholar•Herranz, E.Open in Google Scholar•Lopez-Vazquez, C. M.Open in Google Scholar•Gonzalez-Moro, A.Open in Google Scholar•Rivera-Tenorio, A.Open in Google Scholar•Gonzalez-Sanz, C.Open in Google Scholar•Sacristan, S.Open in Google Scholar•Chicano-Galvez, E.Open in Google Scholar•de la Cuesta, F.Open in Google Scholar

Although the field of plant EVs (PEVs) is experiencing exponential growth, rigorous characterisation complying with MISEV guidelines has not been yet implemented due to the lack of bona fide reference markers. In this work, we have paved the way for the standardisation of PEV markers, providing the most profound proteomic data so far from apoplastic washing fluid-EVs, a sample enriched in genuine extracellular vesicles from plant tissue of two reference plant species: Arabidopsis thaliana (Arath-EVs) and Brassica oleracea (Braol-EVs). Besides, we analysed the protein content of the soluble fraction of the apoplast and calculated the enrichment of the potential markers studied in EVs. Additionally, we have conducted an exhaustive analysis of the proteomic data available so far from genuine EVs from any plant species, evaluating current potential markers, together with those found in our proteomic analyses. Our results provide evidence supporting the potential use of the following families as PEV markers: aquaporins, vacuolar-type ATPase complex subunits, some fasciclin-like arabinogalactan proteins (FLAs), tetraspanins, syntaxins, germin-like proteins and calreticulins. Next, we analysed the presence of orthologues and their degree of conservation throughout plant taxa, as well as in 2 reference species from the animal kingdom: human and mouse. Their degree of conservation was compared with that of current animal EV: CD63, CD81 and CD9. Among the protein families with potential to be used as PEV markers, 2 were found to be plant-specific: FLAs and germin-like proteins. On the other hand, aquaporins and vacuolar-type ATPase complex subunits showed the greatest degree of conservation across plant and animal kingdoms. Our results provide key insights on several aspects of classical and novel protein identity markers for PEVs to assist in the selection of the best candidates for standardisation: 1) species-specific abundance, 2) specificity for PEVs, and 3) conservation and plant specificity.

Similar Papers

bioRxiv
Fri Sep 05 2025
Cross-platform digital PCR evaluation of bovine papilloma virus quantification: introducing PCR-ValiPal for Standardized guided assay validation
Digital Polymerase chain reaction (dPCR) enables precise and absolute quantification of nucleic acids by partitioning samples into thousands of individual PCR micro-reactions. While it minimizes the need for standard curves and enhances reproducibility compared to qPCR, thorough assay validation remains crucial. We introduce PCR-ValiPal, a user-friendly web application that standardizes dPCR assay...
Gleerup, D.
•
Vynck, M.
•
Gysens, L.
•
De Baere, C.
...•
De Spiegelaere, W.
bioRxiv
Fri Sep 05 2025
Pivotal role of Disrupted-in-Schizophrenia 1 (DISC1) in cardiac resilience to ischemic stress
Molecular targets that contribute to post-myocardial infarction heart failure remains elusive. Here we studied the global transcriptional landscape of human inducible pluripotent stem cell-derived cardiomyocytes under simulated ischemia at the whole genome level in an unbiased manner. Unexpectedly, we identified Disrupted in Schizophrenia 1 (DISC1), which has been almost exlusively studied in neur...
Gurdeep Marwahra, G.
•
Pinho, M. J.
•
Scrimgeour, N. R.
•
Slagsvold, K. H.
...•
Hoydal, M. A.
bioRxiv
Fri Sep 05 2025
P53 supresses transcription of the p300-E2F1-dependent gene subset by maintaining KDM5B associated with gene promoters
p53 is a transcription activator or repressor that acts mainly by having direct control over the expression of CDK inhibitor - p21 in response to DNA damage. In this study, molecular evidence was provided for the occurrence of p53 at the subset of E2F1-driven promoters and their suppression, despite the co-occurrence of p53 with p300. P53 repressed promoters were characterized by relatively high n...
Gronkowska, K.
•
Kolacz-Milewska, K.
•
Michlewska, S.
•
Robaszkiewicz, A.
bioRxiv
Fri Sep 05 2025
TRAF6 integrates innate immune signals to regulate glucose homeostasis via Parkin-dependent and -independent mitophagy
Activation of innate immune signaling occurs during the progression of immunometabolic diseases, including type 2 diabetes (T2D), yet the impact of innate immune signaling on glucose homeostasis is controversial. Here, we report that the E3 ubiquitin ligase TRAF6 integrates innate immune signals following diet-induced obesity to promote glucose homeostasis through the induction of mitophagy. Where...
Levi-DAncona, E.
•
Walker, E. M.
•
Zhu, J.
•
Deng, Y.
...•
Soleimanpour, S. A.
bioRxiv
Thu Sep 04 2025
NRDE2 Interacts with an Early Transcription Elongation Complex and Widely Impacts Gene Expression
NRDE2 is a highly conserved protein that is implicated in post-transcriptional gene silencing in S. pombe and C. elegans while in mammals, it has been shown to modulate splicing. To determine whether NRDE2 may be implicated in other processes in humans, we performed tandem affinity purification followed by proteomic analysis of NRDE2 from nuclear extracts in HEK293T and HeLa cells. Our data show t...
Srbic, M.
•
Belhaouari, C.
•
Raffel, R.
•
Lemaire, L.
...•
Kiernan, R.
bioRxiv
Thu Sep 04 2025
Investigating the role of melatonin in bipolar disorder using transcriptomics
Melatonin may be a potential therapeutic target for bipolar disorder (BD) treatment; however, its role in BD pathophysiology remains poorly understood. This study aimed to investigate the therapeutic and mechanistic role of melatonin in BD using transcriptomics. RNA sequencing (RNAseq) data from 216 post-mortem dorsolateral prefrontal cortex samples (156 controls, 60 BD) were used to generate gene...
Macpherson, H. K.
•
Truong, T. T. T.
•
Berk, M.
•
Walder, K. R. K.
•
Tye, S. J.
bioRxiv
Thu Sep 04 2025
Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries
Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers a cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection of rare, cryptic, and elusive species from environmental samples. However, limited access to genomic technologies restricts the application of eDNA metabarcoding in highly biodiverse remote r...
Gygax, D.
•
Ramirez, S.
•
Chibesa, M.
•
Simpamba, T.
...•
Urban, L.
bioRxiv
Thu Sep 04 2025
Evaluation of nanopore sequencing for increasing accessibility of eDNA studies in biodiverse countries
Biodiversity loss is a global challenge of the 21st century. Environmental DNA (eDNA)-based metabarcoding offers a cost- and time-efficient alternative to conventional biodiversity surveys, enabling detection of rare, cryptic, and elusive species from environmental samples. However, limited access to genomic technologies restricts the application of eDNA metabarcoding in highly biodiverse remote r...
Gygax, D.
•
Ramirez, S.
•
Chibesa, M.
•
Simpamba, T.
...•
Urban, L.
bioRxiv
Thu Sep 04 2025
Transmission potential of Culex and Aedes species for Madariaga virus, a member of the eastern equine encephalitis virus complex
Madariaga virus (MADV), widely distributed in Latin America, can cause severe disease in humans and equids, yet, key aspects of its transmission cycle remain unclear. To identify mosquitoes that could act as MADV vectors, we assessed the vector competence of Aedes aegypti, Ae. albopictus, Ae. taeniorhynchus, Culex tarsalis, Cx. coronator, and Cx. quinquefasciatus, following oral exposure to MADV i...
Carvalho-Leandro, D. d.
•
Ferreira, F. C.
•
Santos, N. F.
•
Sames, W. J.
...•
Magalhaes, T.
bioRxiv
Thu Sep 04 2025
Fluctuations in AAV genome quantification via digital PCR affected by heat-based virion lysis
Adeno-associated virus (AAV) vectors are central to gene therapy, making precise genome quantification essential for product quality and dose determination. We systematically assessed digital PCR (dPCR) on the QIAcuity platform to quantify recombinant AAV2 and AAV8 genomes, examining how assay design, amplicon length, and heat-based sample preparation affect results. Across multiple genomic target...
Govorov, A.
•
Trajkovski, F.
•
Wagner, N.
•
Klughertz, L.
...•
Hertel, R.