Regulation of early-stage tomato fruit growth by the splicing factor RS2Z36

Fruit size and shape are determined by cell division and expansion. In tomato, the model plant for fleshy fruit development, both processes are associated with changes in gene expression, including transcription and RNA processing. While several transcription factors have been identified as regulators of genes involved in fruit development, the contribution of splicing regulators remains unknown. Profiling of RNA splicing-related genes revealed stage-preferential expression of several factors, including RS2Z36, a serine/arginine-rich splicing factor highly expressed during the early stages of fruit development. Mutations in RS2Z36 lead to smaller ellipsoid fruits than the wild type, with histological analysis showing elongated pericarp cells in the ovaries along the longitudinal axis. RNA-seq analysis uncovered numerous alternatively spliced genes involved in different biological processes. Complementary proteome analysis identified proteins with altered abundance and peptides corresponding to novel RNA splice isoforms, underscoring the role of RS2Z36 in shaping both transcriptome and proteome diversity. Immunofluorescence screening of cell wall proteins further demonstrated an increased abundance of LM6-recognized arabinan epitopes of rhamnogalacturonan-I pectins and arabinogalactan protein (AGP) epitopes in rs2z36.1 pericarp cells compared to the wild type. These findings highlight RS2Z36 as a critical regulator of alternative splicing, impacting fruit development through diverse transcriptome and proteome changes.