Integrated proteomics and transcriptomics provide insights into molecular basis of ascidian metamorphosis

Shallow-water ascidians are invasive, fouling marine organisms that rapidly metamorphose from planktonic larvae to sessile forms. To gain insights into their environmental adaptability and develop methods for biofouling control, it is crucial to explore the molecular and cellular orchestration of metamorphosis. Here, we employed 4D label-free quantitative proteomics combined with transcriptomics to monitor protein and gene expression during ascidian Ciona metamorphosis across five post-embryonic stages. We identified a total of 6043 proteins. The temporal dynamics of protein and gene expression, along with differentially expressed proteins and genes, revealed biological processes associated with metamorphosis. We focused on phosphocreatine biosynthesis and protein secretion potentially involved in early metamorphosis, as well as cilium assembly/movement implicated in the regulation of juvenile physiology. We showed that several creatine kinases specifically expressed in larval tail muscles were up-regulated prior to metamorphosis, and phosphocreatine treatment significantly increased ATP levels and accelerated tail regression, suggesting that phosphocreatine shuttle system contributes to the initiation of metamorphosis. The secretory and extracellular matrix proteins up-regulated at pre-metamorphosis were revealed to be expressed by multiple tissues, including the nervous system, notochord, and epidermis; inhibition of the protein secretory pathway effectively reduced the proportion of larval adhesion and tail regression, highlighting the significance of extracellular proteins in larval settlement and metamorphosis. Moreover, the presence of systemic ciliary structures in various tissues/organs of juveniles supported the crucial role of cilium assembly/movement in the regulation of juvenile physiology. Overall, our study provides a valuable resource for investigating ascidian metamorphosis and contributes to a better understanding of its molecular basis.