This study conducted a systematic identification and functional analysis of the SlACX gene family in Solanum lycopersicum. Through genome-wide screening, a total of six SlACX members were identified, and their encoded proteins showed significant differences in physicochemical properties, suggesting potential functional differentiation. Analysis of gene structure and conserved motifs revealed that SlACXs were highly conserved in evolution, but the cis-acting elements in the promoter region were rich and diverse, suggesting that they may integrate multiple signaling pathways. Chromosomal localization and collinearity analysis revealed that gene replication events were the main driving force for family expansion, and there were key interspecific collinearity blocks with Arabidopsis thaliana and Glycine max. Expression analysis showed that SlACXs exhibited remarkable tissue specificity and strong temporal dynamic response patterns to UV, dark, ABA, MeJA, and various abiotic stresses (cold, heat, H₂O₂, PEG, and NaCl). Several genes (such as SlACX1, SlACX3, SlACX4, and SlACX5) exhibited consistently high expression levels under various stress conditions, underscoring their potential role as central regulatory hubs.

Pyruvate decarboxylase (PDC) is an intracellular non-oxidizing enzyme that relies on thiamine pyrophosphate (TPP), which is important for plant survival under anaerobic conditions and increasingly recognized for its role in broader stress reaction. However, the PDC gene family of tomato (Solanum lycopersicum), an important waterlogging-sensitive agricultural product, has not yet been discovered. In this study, eight SlPDC genes were discovered within the tomato genome. Gene structure analysis revealed that SlPDC members exhibited varying intron–exon configurations, with SlPDC8 possessing the most complex structure containing seven introns. Promoter analysis revealed a multitude of cis-acting elements responsive to light, hormones, and various stresses. Particularly, the promoter of SlPDC8 contains both ABRE and TGACG/CGTCA-motif. Tissue-specific expression profiles showed that SlPDC8 was mainly highly expressed in the roots. Expression profiling demonstrated that SlPDC genes respond divergently to different abiotic stresses, including salt, hydrogen peroxide (H₂O₂), drought, waterlogging, cold, heat, darkness, and UV radiation stresses. Notably, SlPDC1, SlPDC7, and SlPDC8 were significantly upregulated by waterlogging, with SlPDC8 showing the most robust induction. Functional validation through VIGS proved that SlPDC8-silenced plants exhibited significantly impaired growth, decreased photosynthetic pigment content, severe leaf wilting, and poor root development under waterlogging conditions compared to control plants. Furthermore, silencing SlPDC8 led to increased malondialdehyde (MDA) levels and decreased antioxidant enzyme activities, indicating heightened oxidative damage under waterlogging stress. We conclusively demonstrate that SlPDC8 plays a critical positive regulatory role in waterlogging tolerance by maintaining cellular homeostasis and enhancing antioxidant capacity.

Salinity is an abiotic constraint that limits the growth and productivity of tomato (Solanum lycopersicum L.). However, the role of small ubiquitin-like modifier (SUMO) E3 ligases (SIZs) in the salt stress response in tomato remains unknown. Here, a genome-wide analysis identified four SIZ-type genes in tomato, designated SlSIZ1–SlSIZ4. Gene structure and conserved motif analyses revealed the canonical SAP (SAF-A/B, Acinus, and PIAS) domain and the SP-RING (Siz/PIAS RING finger) domain in all SlSIZ proteins. Phylogenetic analysis grouped SIZ proteins from tomato and representative plant species into five major groups (A–E), with SlSIZ members distributed across distinct clades, and members within each clade shared conserved gene structures. Online transcriptome data and our qRT-PCR analyses showed that SlSIZ4 was highly expressed in leaves, flowers, and fruits, whereas SlSIZ1 showed broad expression, with relatively higher levels in roots, flowers, and multiple fruit stages. Under salt stress, abscisic acid (ABA), and methyl jasmonate (MeJA) treatments, the expression of SlSIZ1 and SlSIZ4 was strongly induced, whereas the expression of SlSIZ2 and SlSIZ3 was rarely promoted. In addition, virus-induced gene silencing (VIGS) of SlSIZ1 and SlSIZ4 markedly reduced salt tolerance of tomato seedlings, as reflected by growth inhibition, chlorophyll loss, increased reactive oxygen species (ROS), reduced proline accumulation, and diminished antioxidant gene expressions. Collectively, these findings identify SlSIZ1 and SlSIZ4 as positive regulators of salt stress tolerance in tomato and provide a framework for further dissection of the SlSIZ gene family.