Relationship Between Protein, MicroRNA Expression in Extracellular Vesicles and Rice Seed Vigor

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Oct 16

PMID 39408833

Authors

Rouxian Wu

Bingxian Chen

Junting Jia

Jun Liu

Affiliations

Soon will be listed here.

Abstract

Plant extracellular vesicles are non-self-replicating particles released by living plant cells and delimited by a lipid bilayer. They contain a large amount of lipids, RNA, and proteins. Seed vigor plays an important role in agricultural production and preservation of germplasm resources. Extracellular vesicles with cross-species communication with bioactive molecules can resist pathogens, exhibit anti-aging properties, and perform other functions; however, its potential influence on seed vigor has not been reported. In this study, rice seeds with different germination percentages were used to extract extracellular vesicles, endogenous proteins, and RNA. Protein qualitative identification and miRNA differential analysis were performed to analyze the regulatory mechanism of extracellular vesicles on seed vigor. Results: The profiles of four miRNA families were found to be significantly different: osa-miR164, osa-miR168, osa-miR166, and osa-miR159. Protein correlation analysis predicted that extracellular vesicles might mediate the synthesis of the seed cell wall; glyoxic acid cycle and tricarboxylic acid cycle; non-specific lipid transfer; mitochondrial quality control; and other biological processes to regulate rice seed viability. In addition, cupin protein, phospholipase D, aldehyde dehydrogenase, seven heat shock proteins (especially BiP1 and BiP2), protein disulfide isomerase-like (PDI), thioredoxin, calnexin and calreticulin, glutathione transferase, and other proteins found in extracellular vesicles were closely related to seed vigor. This provides a novel direction for the study of the regulation mechanism of seed vigor.

References

Todkar K, Chikhi L, Desjardins V, El-Mortada F, Pepin G, Germain M . Selective packaging of mitochondrial proteins into extracellular vesicles prevents the release of mitochondrial DAMPs. Nat Commun. 2021; 12(1):1971. PMC: 8009912. DOI: 10.1038/s41467-021-21984-w. View

Li Y, Guo L, Cui Y, Yan X, Ouyang J, Li S . Lipid transfer protein, OsLTPL18, is essential for grain weight and seed germination in rice. Gene. 2023; 883:147671. DOI: 10.1016/j.gene.2023.147671. View

Feng J, Xiu Q, Huang Y, Troyer Z, Li B, Zheng L . Plant-Derived Vesicle-Like Nanoparticles as Promising Biotherapeutic Tools: Present and Future. Adv Mater. 2023; 35(24):e2207826. DOI: 10.1002/adma.202207826. View

Saqib A, Scheller H, Fredslund F, Welner D . Molecular characteristics of plant UDP-arabinopyranose mutases. Glycobiology. 2019; 29(12):839-846. PMC: 6861824. DOI: 10.1093/glycob/cwz067. View

Li Q, Zhai W, Wei J, Jia Y . Rice lipid transfer protein, OsLTPL23, controls seed germination by regulating starch-sugar conversion and ABA homeostasis. Front Genet. 2023; 14:1111318. PMC: 9885049. DOI: 10.3389/fgene.2023.1111318. View

Zhuang X, Deng Z, Mu J, Zhang L, Yan J, Miller D . Ginger-derived nanoparticles protect against alcohol-induced liver damage. J Extracell Vesicles. 2015; 4:28713. PMC: 4662062. DOI: 10.3402/jev.v4.28713. View

Parkhey S, Naithani S, Keshavkant S . ROS production and lipid catabolism in desiccating Shorea robusta seeds during aging. Plant Physiol Biochem. 2012; 57:261-7. DOI: 10.1016/j.plaphy.2012.06.008. View

Lu D, Christopher D . Endoplasmic reticulum stress activates the expression of a sub-group of protein disulfide isomerase genes and AtbZIP60 modulates the response in Arabidopsis thaliana. Mol Genet Genomics. 2008; 280(3):199-210. DOI: 10.1007/s00438-008-0356-z. View

Zhou Y, Zhou S, Wang L, Wu D, Cheng H, Du X . miR164c and miR168a regulate seed vigor in rice. J Integr Plant Biol. 2019; 62(4):470-486. DOI: 10.1111/jipb.12792. View

10.

Wang S, He B, Wu H, Cai Q, Ramirez-Sanchez O, Abreu-Goodger C . Plant mRNAs move into a fungal pathogen via extracellular vesicles to reduce infection. Cell Host Microbe. 2023; 32(1):93-105.e6. PMC: 10872371. DOI: 10.1016/j.chom.2023.11.020. View

11.

Perut F, Roncuzzi L, Avnet S, Massa A, Zini N, Sabbadini S . Strawberry-Derived Exosome-Like Nanoparticles Prevent Oxidative Stress in Human Mesenchymal Stromal Cells. Biomolecules. 2021; 11(1). PMC: 7828105. DOI: 10.3390/biom11010087. View

12.

Ma X, Nicole M, Meteignier L, Hong N, Wang G, Moffett P . Different roles for RNA silencing and RNA processing components in virus recovery and virus-induced gene silencing in plants. J Exp Bot. 2014; 66(3):919-32. DOI: 10.1093/jxb/eru447. View

13.

Devaiah S, Pan X, Hong Y, Roth M, Welti R, Wang X . Enhancing seed quality and viability by suppressing phospholipase D in Arabidopsis. Plant J. 2007; 50(6):950-7. DOI: 10.1111/j.1365-313X.2007.03103.x. View

14.

van de Wakker S, Bauza-Martinez J, Rios Arceo C, Manjikian H, Snijders Blok C, Roefs M . Size matters: Functional differences of small extracellular vesicle subpopulations in cardiac repair responses. J Extracell Vesicles. 2024; 13(1):e12396. PMC: 10767609. DOI: 10.1002/jev2.12396. View

15.

Middleton H, Yergeau E, Monard C, Combier J, El Amrani A . Rhizospheric Plant-Microbe Interactions: miRNAs as a Key Mediator. Trends Plant Sci. 2020; 26(2):132-141. DOI: 10.1016/j.tplants.2020.09.005. View

16.

Voinnet O . Origin, biogenesis, and activity of plant microRNAs. Cell. 2009; 136(4):669-87. DOI: 10.1016/j.cell.2009.01.046. View

17.

Tang G . siRNA and miRNA: an insight into RISCs. Trends Biochem Sci. 2005; 30(2):106-14. DOI: 10.1016/j.tibs.2004.12.007. View

18.

Li Y, Wang Y, He Y, Ye T, Huang X, Wu H . Glutathionylation of a glycolytic enzyme promotes cell death and vigor loss during aging of elm seeds. Plant Physiol. 2024; 195(4):2596-2616. DOI: 10.1093/plphys/kiae197. View

19.

Macovei A, Tuteja N . microRNAs targeting DEAD-box helicases are involved in salinity stress response in rice (Oryza sativa L.). BMC Plant Biol. 2012; 12:183. PMC: 3502329. DOI: 10.1186/1471-2229-12-183. View

20.

Welsh J, Goberdhan D, ODriscoll L, Buzas E, Blenkiron C, Bussolati B . Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches. J Extracell Vesicles. 2024; 13(2):e12404. PMC: 10850029. DOI: 10.1002/jev2.12404. View