Abstract
BACKGROUND: Phosphorylation is one of the most common post-translational modifications and is central to many cellular signaling events; however, little is currently known about the phosphorylation landscape during somatic embryogenesis (SE) for plant regeneration. RESULTS: Here, we systematically analyzed the phosphoproteomic profile of three typical developmentally staged cultures of SE, non-embryogenic calli (NEC), primary embryogenic calli (PEC), and globular embryos (GE), in cotton (Gossypium hirsutum L.), the pioneer crop for genetic biotechnology applications. Our data revealed a total of 6301 quantifiable phosphorylation sites in 2627 quantifiable phosphoproteins from 5548 modified peptides, of which 1105 phosphoproteins (2147 sites) were differentially phosphorylated. Functional enrichment analyses revealed that differentially regulated phosphoproteins (DRPPs) were significantly enriched in DNA mismatch repair and peroxisome during callus embryogenic differentiation (PEC vs. NEC) and somatic embryo initiation (GE vs. PEC), respectively. Notably, six dynamic trajectory patterns of DRPP enrichment were observed. In addition, preferentially activated DRPPs with specific phosphorylation patterns were identified at different developmental stages. These DRPPs were mainly involved in hormone-responsive and photosystem events during initiation of plant regeneration. CONCLUSIONS: Overall, this study identified a series of potential phosphoproteins responsible for SE trans-differentiation and plant regeneration, providing a valuable resource and molecular basis for understanding the regulatory pathways underlying cell totipotency at the post-translational modification level.