Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea

Andrea Pagano; Carolina Gomes; Evy Timmerman; Paweł Sulima; Jerzy Andrzej Przyborowski; Dariusz Kruszka; Francis Impens; Jorge Almiro Pinto Paiva

doi:10.3389/fpls.2023.1304327

Revealing the transitory and local effect of zebularine on development and on proteome dynamics of Salix purpurea

Front Plant Sci. 2024 Jan 17:14:1304327. doi: 10.3389/fpls.2023.1304327. eCollection 2023.

Authors

Andrea Pagano¹, Carolina Gomes¹, Evy Timmerman^{2

3

4}, Paweł Sulima⁵, Jerzy Andrzej Przyborowski⁵, Dariusz Kruszka¹, Francis Impens^{2

3

4}, Jorge Almiro Pinto Paiva¹

Affiliations

¹ Department of Integrative Plant Biology, Institute of Plant Genetics, Polish Academy of Sciences, Poznań, Poland.
² VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
³ Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
⁴ VIB Proteomics Core, Ghent, Belgium.
⁵ Department of Genetics, Plant Breeding and Bioresource Engineering, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.

Abstract

Introduction: DNA methylation plays major roles in the epigenetic regulation of gene expression, transposon and transcriptional silencing, and DNA repair, with implications in developmental processes and phenotypic plasticity. Relevantly for woody species, DNA methylation constitutes a regulative layer in cell wall dynamics associated with xylogenesis. The use of methyltransferase and/or demethylase inhibitors has been proven informative to shed light on the methylome dynamics behind the regulation of these processes.

Methods: The present work employs the cytidine analog zebularine to inhibit DNA methyltransferases and induce DNA hypomethylation in Salix purpurea plantlets grown in vitro and in soil. An integrative approach was adopted to highlight the effects of zebularine on proteomic dynamics, revealing age-specific (3 weeks of in vitro culture and 1 month of growth in soil) and tissue-specific (stem and root) effects.

Results and discussion: After 3 weeks of recovery from zebularine treatment, a decrease of 5-mC levels was observed in different genomic contexts in the roots of explants that were exposed to zebularine, whereas a functionally heterogeneous subset of protein entries was differentially accumulated in stem samples, including entries related to cell wall biosynthesis, tissue morphogenesis, and hormonal regulation. Significant proteomic remodeling was revealed in the development from in vitro to in-soil culture, but no significant changes in 5-mC levels were observed. The identification of tissue-specific proteomic hallmarks in combination with hypomethylating agents provides new insights into the role of DNA methylation and proteome in early plant development in willow species. Proteomic data are available via ProteomeXchange with identifier PXD045653. WGBS data are available under BioProject accession PRJNA889596.

Keywords: DNA methylation; cytidine analogue; plant development; proteomic; purple willow.

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. The authors thank the support by the National Science Centre, Poland, NCN project Sonata-bis grant number UMO-2015/18/E/NZ2/00694 (PurpleWalls Project) and by by the European Proteomics Infrastructure Consortium (EPIC-XS) (Project PRC-4969). JAPP thanks the contract funded by FP7-ERAChairs-PilotCall-2013 grant BIO-TALENT number 621321. AP thanks the Erasmus+ Program of the European Union and the IUSS (University School for Advanced Studies) of Pavia. AP and CG thank the PostDoctoral and PhD fellowship in the frame of the PurpleWalls Project. Preparing of plant material used in this study was supported by University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Genetics, Plant Breeding and Bioresource Engineering (grant No. 538 30.610.007-110).