DUF642 proteins constitute a highly conserved family of proteins that are associated with the cell wall and are specific to spermatophytes. Transcriptome studies have suggested that members of this family are involved in seed development and germination processes. Previous in vitro studies have revealed that At4g32460- and At5g11420-encoded proteins interact with the catalytic domain of pectin methyl esterase 3 (AtPME3, which is encoded by At3g14310). PMEs play an important role in plant development, including seed germination. The aim of this study was to evaluate the function of the DUF642 gene At4g32460 during seed germination and plant development and to determine its relation to PME activity regulation. Our results indicated that the DUF642 proteins encoded by At4g32460 and At5g11420 could be positive regulators of PME activity during several developmental processes. Transgenic lines overexpressing these proteins showed increased PME activity during seed germination, and improved seed germination performance. In plants expressing At4g32460 antisense RNA, PME activity was decreased in the leaves, and the siliques were very short and contained no seeds. This phenotype was also present in the SALK_142260 and SALK_054867 lines for At4g32460. Our results suggested that the DUF642 family contributes to the complexity of the methylesterification process by participating in the fine regulation of pectin status during plant development.

Plant cell walls play a crucial role in plant development and evolution. This structure is primarily composed of proteins and polysaccharides, including cellulose, hemicellulose, and pectins. Homogalacturonan (HG), the most abundant pectin in the primary cell wall, is synthesized by α -1,4-D-GALACTURONOSYLTRANSFERASE (GAUT) enzymes, methylesterified, and subsequently secreted into the apoplast. The dynamics of pectin methylesterification is regulated by enzymes such as PECTIN METHYLESTERASES (PMEs) and PECTIN METHYLESTERASE INHIBITORS (PMEIs). Across plant evolution and development, different cell types display distinct domains of pectin methylesterification. The binding of de-methylesterified pectins to the Catharanthus roseus RECEPTOR-LIKE KINASE 1-LIKE (CrRLK1L) proteins and RAPID ALKALINIZATION FACTOR (RALF) peptides is involved in pectin signaling and cell wall integrity maintenance during developmental processes. While phylogenetic studies highlight molecular innovations in pectin metabolism, functional studies remain scarce outside of angiosperms. Furthermore, the explicit role of de-methylesterified pectin in coupling cell wall structure to intracellular signaling has only been demonstrated in angiosperms. Comparative functional studies addressing key evolutionary transitions will ultimately reveal how pectin metabolism has contributed to morphological innovations across plant evolution.