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Fluorescence Labeling to Visualize Low-Expressed Proteins in Zebrafish

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Time-Resolved Proteomic Analysis in Zebrafish Using Bioorthogonal Noncanonical Amino Acid Tagging.

Sophie E Miller¹, Ting-Yu Wang², Baiyi Quan²

¹Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States.

Journal of Proteome Research

|April 14, 2026

Summary

This summary is machine-generated.

Bioorthogonal noncanonical amino acid tagging (BONCAT) enables time-resolved proteomic analysis in zebrafish. This method sensitively detects transient protein synthesis changes, like those induced by heat shock, offering new insights into development and stress responses.

Keywords:

BONCAT click chemistry heat shock larval zebrafish noncanonical amino acid tagging protein synthesis proteomics

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Area of Science:

Proteomics
Molecular Biology
Zebrafish Model Organism

Background:

Tracking dynamic proteomic changes is difficult.
Bioorthogonal noncanonical amino acid tagging (BONCAT) allows targeted protein identification within specific timeframes.

Purpose of the Study:

To establish and validate BONCAT for time-resolved proteomic analysis in larval zebrafish.
To investigate proteomic alterations during heat shock response in zebrafish.

Main Methods:

Utilized BONCAT with azidohomoalanine labeling in larval zebrafish.
Enriched and identified labeled proteins using mass spectrometry.
Performed gene set enrichment analysis on BONCAT and whole lysate samples.

Main Results:

Successfully detected azidohomoalanine-labeled proteins with high signal-to-noise ratio after short labeling periods (12h).
BONCAT demonstrated higher sensitivity in detecting heat shock-induced protein synthesis compared to global proteomics.
Identified proteins involved in stress response, lipid metabolism, and neural regulation beyond canonical heat shock proteins.

Conclusions:

BONCAT is a powerful tool for time-resolved proteomic studies in zebrafish.
This technique can reveal transient molecular responses masked in global proteomic analyses.
BONCAT provides novel insights into zebrafish development, stress responses, and behavior.