Epigenetic modification of a pectin methylesterase gene activates apoplastic iron reutilization in tomato roots

Abstract

Iron (Fe) distribution and reutilization are crucial for maintaining Fe homeostasis in plants. Here, we demonstrate that the tomato (Solanum lycopersicum) Colorless non-ripening (Cnr) epimutant exhibits increased Fe retention in cell wall pectin due to an increase in pectin methylesterase (PME) activity. This ultimately leads to Fe deficiency responses even under Fe-sufficient conditions when compared to the wild type (WT). Whole-genome bisulfite sequencing revealed that modifications to cell wall-related genes, especially CG hypermethylation in the intron region of PECTIN METHYLESTERASE53 (SlPME53), are involved in the Cnr response to Fe deficiency. When this intron hypermethylation of SlPME53 was artificially induced in WT, we found that elevated SlPME53 expression was accompanied by increased PME activity and increased pectin-Fe retention. The manipulation of SlPME53, either through overexpression in WT or knockdown in Cnr, influenced levels of pectin methylesterification and accumulation of apoplast Fe in roots. Moreover, CG hypermethylation mediated by METHYLTRANSFERASE1 (SlMET1) increased SlPME53 transcript abundance, resulting in greater PME activity and higher Fe retention in cell wall pectin. Therefore, we conclude that the Cnr mutation epigenetically modulates SlPME53 expression by SlMET1-mediated CG hypermethylation, and thus the capacity of the apoplastic Fe pool, creating opportunities for genetic improvement of crop mineral nutrition.

Epigenetic insights into an epimutant colorless non-ripening: from fruit ripening to stress responses

“…Additionally, SlymiR157 targets SlSPL-CNR expression for mRNA degradation, consequently releasing SlbHLH101 expression to facilitate Fe-deficient responses ( Zhu et al., 2022 ). Furthermore, SlMET1-dependent CG hypermethylation of the SlPME53 ( PECTIN METHYLESTERASE53 ) intron induces its expression, regulating apoplastic Fe reutilization in the Cnr epimutant ( Zhu et al., 2024 ). In summary, the retention of Fe in the apoplast and its uptake into the cytoplasm contribute to the constitutive Fe-deficient response of Cnr under Fe-sufficient conditions.…”

“…(2022) , and Zhu et al. (2022 , 2024 ). SlMET1: METHYLTRANSFERASE1; SlbHLH101: BASIC HELIX-LOOP-HELIX101; SlPME53: PECTIN METHYLESTERASE53.…”

“…Furthermore, the methylome pattern of Cnr appears to vary depending on organ type or developmental stages, as evidenced by disparities between Cnr fruits and roots in bisulfite sequencing data ( Zhu et al., 2024 ). Considering these observations alongside the diverse effects of Cnr on fruit ripening, leaf cell death, and root responses to abiotic stress, it is imperative to account for tissue-specific effects when evaluating the pleiotropic effects of Cnr .…”