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Proteome analysis refines molecular processes underlying metamorphosis in the ascidian Ciona intestinalis.

Overview

Authors: Daniele Capitanio1, Silvia Mercurio2, Ettore Mosca3, Cristina Battaglia4, Marco Venturin4, Roberta Pennati2
ORCID iDs: Daniele Capitanio, Silvia Mercurio, Ettore Mosca, Cristina Battaglia, Marco Venturin, Roberta Pennati
  1. Department of Biomedical Sciences for Health, Università degli Studi di Milano, Milan, Italy
  2. Department of Environmental Science and Policy, Università degli Studi di Milano, Milan, Italy
  3. Institute of Biomedical Technologies, National Research Council, Segrate, Italy
  4. Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Milan, Italy
Institutions: University of Milan (Italy); Institute of Biomedical Technologies (Italy); National Research Council (Italy)
Journal: PloS one, volume 21, issue 6, article e0350646
Dates: received 15 January 2026; accepted 16 May 2026; published online 1 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pone.0350646 · PMID 42224304 · PMCID PMC13225635 · OpenAlex W7163050077
Open access: gold, a free copy (OpenAlex)
Status: data only
Categories: genetics / omics (modality), cellular / molecular (subfield)
Methods: Statistics, Preprocessing, Graphs
MeSH: Ciona intestinalis*, Metamorphosis, Biological*, Proteome*, Proteomics*, Animals, Central Nervous System, Larva (* major topic)
Journal subjects: Biology and Life Sciences, Developmental Biology, Life Cycles, Larvae, Biochemistry, Proteins, Protein Domains, Metamorphosis, Organisms, Eukaryota, Animals, Sea Squirts, Zoology, Molecular Biology, Molecular Biology Techniques, Molecular Biology Assays and Analysis Techniques, Gene Expression and Vector Techniques, Protein Expression, Research and Analysis Methods, Physiology, Biological Locomotion, Swimming, Computer and Information Sciences, Network Analysis, Cell Biology, Cellular Structures and Organelles, Cytoskeleton
Topic: Marine Ecology and Invasive Species (Global and Planetary Change, Environmental Science), according to OpenAlex
Funding: ‘Piano Sviluppo Unimi - Linea 3 - Bando SoE’ Grant, University of Milan (RV_PSR_SOE_2020_RPENN); PRIN2022 Grant, Italian Ministry of University and Research (2022SF7HY9)
Citations: not cited yet (Europe PMC); 70 references in the paper

Abstract

Tunicates, including ascidians, are recognized as the true ‘sister group’ of vertebrates and are emerging as models to study larval and post-larval development, including degeneration of central nervous system (CNS), in chordates. Ascidian larvae have the typical chordate body plan that includes a dorsal neural tube. During their metamorphosis, a deep tissue reorganization takes place, with some tissues that degenerate while others develop to become functional during the adult life. The larval CNS also degenerates, and most neurons disappear, making room for the formation of adult CNS. The genome of the ascidian Ciona intestinalis has been sequenced and annotated, with several CNS specific genes that have been characterized. These features make ascidian metamorphosis a good model to study the mechanisms underlying physiological CNS degeneration. To shed light on the molecular determinants of C. intestinalis metamorphosis, we analyzed the proteome at three stages of development: swimming larva (SwL, Hotta stage 28), settled larva (SetL, Hotta stage 32) and metamorphosing larva (MetL, Hotta stage 34). A total of 405 modulated proteins were identified by mass spectrometry by comparing the three stages. Enrichment and network analysis showed the involvement of several processes/pathways, including autophagy and mTOR pathways, and actin cytoskeleton organization and remodeling among the most significant ones. This study helps to elucidate the molecular processes underlying ascidian metamorphosis and provides insight into mechanisms of physiological neurodegeneration in ascidians.

Reproduced under the paper's license (CC BY), from the paper cited above.

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Data

Datasets cited

Data Availability

The data supporting the findings of this study are available within the article and its supplemental data. Raw data that support the findings of this study are openly available in the UNIMI Dataverse repository with persistent identifier number: doi.org/10.13130/RD_UNIMI/K091MC, reference name “SEED_IMPATTO_PROGETTO”.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

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Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 6 authors, 7 MeSH terms, 2 funders, 68 references.

Cite

This paper

Capitanio, D., Mercurio, S., Mosca, E., Battaglia, C., Venturin, M., & Pennati, R. (2026). Proteome analysis refines molecular processes underlying metamorphosis in the ascidian Ciona intestinalis. PloS one, 21(6), e0350646. https://doi.org/10.1371/journal.pone.0350646

BibTeX

@article{capitanio2026proteome,
author = {Capitanio, Daniele and Mercurio, Silvia and Mosca, Ettore and Battaglia, Cristina and Venturin, Marco and Pennati, Roberta},
title = {{Proteome analysis refines molecular processes underlying metamorphosis in the ascidian Ciona intestinalis}},
journal = {PloS one},
year = {2026},
month = jun,
volume = {21},
number = {6},
pages = {e0350646},
publisher = {PLOS},
issn = {1932-6203},
doi = {10.1371/journal.pone.0350646},
url = {https://doi.org/10.1371/journal.pone.0350646},
pmid = {42224304},
pmcid = {PMC13225635}
}

RIS

TY - JOUR
AU - Capitanio, Daniele
AU - Mercurio, Silvia
AU - Mosca, Ettore
AU - Battaglia, Cristina
AU - Venturin, Marco
AU - Pennati, Roberta
TI - Proteome analysis refines molecular processes underlying metamorphosis in the ascidian Ciona intestinalis
T2 - PloS one
J2 - PLoS One
PY - 2026
DA - 2026/06/01
VL - 21
IS - 6
SP - e0350646
SN - 1932-6203
PB - PLOS
DO - 10.1371/journal.pone.0350646
UR - https://doi.org/10.1371/journal.pone.0350646
LA - en
ER -

CSL-JSON

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