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Updated: Apr 4, 2026

In Vivo Biosensor Tracks Non-apoptotic Caspase Activity in Drosophila

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Proteomic mapping in live Drosophila tissues using an engineered ascorbate peroxidase.

Chiao-Lin Chen¹, Yanhui Hu², Namrata D Udeshi³

¹Department of Genetics, Harvard Medical School, Boston, MA 02115; clchen@genetics.med.harvard.edu perrimon@receptor.med.harvard.edu.

Proceedings of the National Academy of Sciences of the United States of America

|September 13, 2015

Summary

Researchers developed a new proteomic mapping platform using ascorbate peroxidase (APEX) in live Drosophila tissues. This method effectively identifies proteins within subcellular compartments, aiding the study of cellular organization and protein interactions.

Keywords:

APEX Drosophila proteomics

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Area of Science:

Cell Biology
Proteomics
Biochemistry

Background:

Understanding cellular organization requires characterizing organelle and subcellular proteomes.
Identifying protein complexes and interaction networks is crucial for cellular function.
Existing methods may have limitations in live-cell, in-situ proteomic analysis.

Purpose of the Study:

To establish a proteomic mapping platform in live Drosophila tissues using engineered ascorbate peroxidase (APEX).
To demonstrate the efficacy of APEX labeling for characterizing subcellular proteomes in various fly tissues and compartments.
To create a comprehensive database of Drosophila mitochondrial proteins with subcompartmental annotation.

Main Methods:

Utilized an engineered ascorbate peroxidase (APEX) enzyme for proximity-dependent biotinylation of endogenous proteins in live Drosophila tissues.
Activated APEX to catalyze biotinylation, followed by isolation and identification of labeled proteins using mass spectrometry.
Developed the "MitoMax" database to inventory and annotate Drosophila mitochondrial proteins.

Main Results:

APEX labeling was demonstrated to be effective across multiple Drosophila tissues and for different subcellular compartments.
The mitochondrial matrix proteome of Drosophila muscle was successfully mapped, showcasing APEX's capability.
The "MitoMax" database provides valuable subcompartmental annotation for Drosophila mitochondrial proteins.

Conclusions:

APEX labeling in live Drosophila tissues offers a powerful approach for characterizing organelle proteomes.
This platform enables the study of specific cell types within different physiological conditions.
The developed methodology and database advance the understanding of cellular organization and protein interactions.