Proteomics-based multi-omics identifies the roadmap of transcription-translation-protein dynamics in planarian regeneration

Identifying regulators for tissue regeneration is fundamental for regenerative biology. While transcription dynamics control planarian regeneration initiation, how protein machinery controls regeneration remains unclear, as transcript levels often fail to predict protein abundance. To address this gap, we performed mass-spectrometry-based proteomic analyses of the planarian Schmidtea mediterranea, establishing a spectral library covering ∼10,000 proteins, and employed quantitative approaches to measure proteome dynamics during regeneration. Our study identified upregulated ribosomal proteins, which were supported by ribosome profiling sequencing (Ribo-seq). Combining RNA sequencing (RNA-seq) and Ribo-seq analyses categorized the increased protein abundance into regulatory modes at transcriptional, translational, and protein stability levels. Functional examination identified 25 proteins essential for planarian regeneration. Troponin T was identified as a regulator of regeneration initiation, showing increased protein abundance before upregulation at transcriptional and translational levels, suggesting a regulation of protein stability. In summary, our study demonstrates previously unexplored ribosome-mediated and transcription-independent protein machinery essential for planarian regeneration initiation.