Strategies to investigate protein turnover with fluorescent protein reporters in eukaryotic organisms

Jonathan Trauth; Johannes Scheffer; Sophia Hasenjäger; Christof Taxis; Jonathan Trauth; Johannes Scheffer; Sophia Hasenjäger; Christof Taxis

doi:10.3934/biophy.2020008

AIMS Biophysics

2020, Volume 7, Issue 2: 90-118. doi: 10.3934/biophy.2020008

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Review Special Issues

Strategies to investigate protein turnover with fluorescent protein reporters in eukaryotic organisms

Molecular Genetics, Department of Biology, Philipps-University Marburg, Germany

Received: 26 February 2020 Accepted: 16 April 2020 Published: 23 April 2020

In higher eukaryotes, defects in regulated protein turnover are intimately linked to development of diseases and aging. Systematic investigation of proteostasis and protein degradation pathways is of high importance for understanding basic cellular events as well as developmental processes in higher organisms. Recently, novel fluorescent protein-based tools for monitoring protein degradation and mapping degradation pathways were described that facilitate this task. Here we give an overview of these tools and relate them to biophysical properties of fluorescent proteins. We focus on methods for the identification of degradation pathways, the discovery of novel degradation sequences, the investigation of proteome dynamics, and the characterization of protein stability. One can expect systematic application of these tools in the near future by systems biology approaches enhancing understanding of the ubiquitin-proteasome system from single protein degradation pathways to its influence on developmental processes.
- fluorescent protein,
- BFP,
- CFP,
- GFP,
- RFP,
- photoconvertible FP,
- fluorescent timer,
- tandem FP timer,
- proteasome,
- proteolysis,
- protein degradation,
- ubiquitin-proteasome system,
- ubiquitin,
- degron
Citation: Jonathan Trauth, Johannes Scheffer, Sophia Hasenjäger, Christof Taxis. Strategies to investigate protein turnover with fluorescent protein reporters in eukaryotic organisms[J]. AIMS Biophysics, 2020, 7(2): 90-118. doi: 10.3934/biophy.2020008

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Abstract

In higher eukaryotes, defects in regulated protein turnover are intimately linked to development of diseases and aging. Systematic investigation of proteostasis and protein degradation pathways is of high importance for understanding basic cellular events as well as developmental processes in higher organisms. Recently, novel fluorescent protein-based tools for monitoring protein degradation and mapping degradation pathways were described that facilitate this task. Here we give an overview of these tools and relate them to biophysical properties of fluorescent proteins. We focus on methods for the identification of degradation pathways, the discovery of novel degradation sequences, the investigation of proteome dynamics, and the characterization of protein stability. One can expect systematic application of these tools in the near future by systems biology approaches enhancing understanding of the ubiquitin-proteasome system from single protein degradation pathways to its influence on developmental processes.

Acknowledgments

The authors thank Alexander Monroe for critical reading of the manuscript. This work was supported by the Deutsche Forschungsgemeinschaft grant TA320-7-1 and the BMBF grant 031B0358A.

Conflict of interest

The authors declare no conflict of interest.

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