Deep quantitative proteomics of North American Pacific coast star tunicate (Botryllus schlosseri)

Dietmar Kültz, Alison M. Gardell, Anthony DeTomaso, Greg Stoney, Baruch Rinkevich, Yuval Rinkevich, Andy Qarri, Weizhen Dong, Brenda Luu, Mandy Lin

Research output: Contribution to journalArticlepeer-review

Abstract

Botryllus schlosseri, is a model marine invertebrate for studying immunity, regeneration, and stress-induced evolution. Conditions for validating its predicted proteome were optimized using nanoElute® 2 deep-coverage LCMS, revealing up to 4930 protein groups and 20,984 unique peptides per sample. Spectral libraries were generated and filtered to remove interferences, low-quality transitions, and only retain proteins with >3 unique peptides. The resulting DIA assay library enabled label-free quantitation of 3426 protein groups represented by 22,593 unique peptides. Quantitative comparisons of single systems from a laboratory-raised with two field-collected populations revealed (1) a more unique proteome in the laboratory-raised population, and (2) proteins with high/low individual variabilities in each population. DNA repair/replication, ion transport, and intracellular signaling processes were distinct in laboratory-cultured colonies. Spliceosome and Wnt signaling proteins were the least variable (highly functionally constrained) in all populations. In conclusion, we present the first colonial tunicate's deep quantitative proteome analysis, identifying functional protein clusters associated with laboratory conditions, different habitats, and strong versus relaxed abundance constraints. These results empower research on B. schlosseri with proteomics resources and enable quantitative molecular phenotyping of changes associated with transfer from in situ to ex situ and from in vivo to in vitro culture conditions.

Original languageEnglish
JournalProteomics
Early online date24 Feb 2024
DOIs
StateE-pub ahead of print - 24 Feb 2024
Externally publishedYes

Bibliographical note

Publisher Copyright:
© 2024 The Authors. Proteomics published by Wiley-VCH GmbH.

Keywords

  • data-independent acquisition
  • ecological proteomics
  • evolutionary proteomics
  • label-free protein quantitation
  • marine invertebrates
  • nanoElute® 2
  • spectral library
  • tunicates

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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