Transcriptomic and proteomic insights into the molecular mechanism underlying cell wall biosynthesis in Moso bamboo (Phyllostachys edulis)

KEY MESSAGE: This is the first integrated transcriptomic and proteomic atlas of Moso bamboo cell wall biosynthesis. The systems model revealed the cell wall biosynthesis network and hubs. PeCOBL1 overexpression enhanced cellulose synthesis in transgenic Arabidopsis. Moso bamboo (Phyllostachys edulis) grows rapidly and has unique physical and mechanical culm properties that depend on the cell wall. However, the molecular mechanisms underlying cell wall biosynthesis (CWB) in Moso bamboo remain unclear. In this study, microscopy showed that Moso bamboo protoplasts generated new cell walls within 120 h after transfer to a wall-regeneration medium. Integrated transcriptomic and proteomic analyses were used to elucidate the molecular basis of CWB at four time points (0, 24, 72, and 120 h). A total of 41,014 unigenes and 7454 proteins were identified, with significant differences in enriched Gene Ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways between differentially expressed genes (DEGs) and differentially abundant proteins reflecting temporal and spatial specificity at the transcript and protein levels. Integrated transcriptomic and proteomic analyses revealed that protoplast cell wall regeneration requires the coordinated regulation of gene expression, cytoskeletal guidance, and sufficient substrate supply. Based on systems evolutionary game networks, we constructed the multilayer, multiplex, and multiscale interactome network that regulates primary CWB in Moso bamboo protoplasts. In this network, six CWB-associated hub modules (M13, M15, M37, M104, M141, and M164) were identified. DEGs involved in signaling pathways served as the central regulators in this regulatory network. Of note, PeCOBL1 showed the strongest and most specific induction during protoplast regeneration, and overexpression of PeCOBL1 in transgenic Arabidopsis increased the leaf cellulose content and the relative crystallinity of cellulose. Overall, this study provides insights into the molecular mechanisms governing cell wall biosynthesis in Moso bamboo protoplasts and identifies candidate genes that may serve as valuable genetic resources for future breeding and improvement.