Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems

Sailasree Rajalekshmi; Kizhakke Mattada Sathyan

doi:10.1002/bies.70075

journal article Oct 05, 2025

Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems

Sailasree Rajalekshmi Kizhakke Mattada Sathyan

BioEssays Vol. 47 No. 12 · Wiley

View at Publisher Save 10.1002/bies.70075

Abstract

ABSTRACT
Conditional degron approaches for acute and reversible protein depletion have become standard tools for studying gene function in cells and model organisms. Traditional gene perturbation methods have advanced gene function studies but are limited by slow kinetics, potential irreversibility, and lethality when targeting essential genes. To overcome these limitations, tag‐based and antibody‐based direct protein degradation technologies have been developed. These direct protein degradation systems utilize endogenous protein degradation pathways to achieve rapid and reversible protein depletion. When combined with genome editing, these systems provide precise temporal—and in some cases, spatial—control over endogenous protein expression. In this review, we will discuss the current status of tag‐based and antibody‐based direct protein degron technologies. We aim to provide a comprehensive guide for selecting these tools, highlighting their context‐dependent applications and potential improvements to enhance efficiency and reliability.

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References

156

[1]

The Sequence of the Human Genome

J. Craig Venter, Mark D. Adams, Eugene W. Myers et al.

Science 10.1126/science.1058040

[2]

The complete sequence of a human genome

Sergey Nurk, Sergey Koren, Arang Rhie et al.

Science 10.1126/science.abj6987

[3]

An integrated encyclopedia of DNA elements in the human genome

Nature 10.1038/nature11247

[4]

The Ensembl genome database project

T. Hubbard

Nucleic Acids Research 10.1093/nar/30.1.38

[5]

10.1093/nar/gkae1078

[6]

10.1038/s41586-023-06490-x

[7]

10.1093/nar/gky587

[8]

10.1038/s41586-024-08243-w

[9]

Too many roads not taken

Aled M. Edwards, Ruth Isserlin, Gary D. Bader et al.

Nature 10.1038/470163a

[10]

Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans

Andrew Fire, SiQun Xu, Mary K. Montgomery et al.

Nature 10.1038/35888

[11]

10.1038/323445a0

[12]

10.1038/330576a0

[13]

10.1016/0092-8674(87)90646-5

[14]

10.1126/science.2660260

[15]

10.1016/j.cell.2017.07.005

[16]

10.1016/j.cell.2017.06.010

[17]

10.1016/j.cell.2022.10.017

[18]

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

Fiona M. Behan, Francesco Iorio, Gabriele Picco et al.

Nature 10.1038/s41586-019-1103-9

[19]

10.1016/j.cell.2015.11.062

[20]

10.1038/s41573-024-00912-9

[21]

10.1038/s41573-019-0017-4

[22]

Identification and characterization of essential genes in the human genome

Tim Wang, Kıvanç Birsoy, Nicholas W. Hughes et al.

Science 10.1126/science.aac7041

[23]

10.1007/s00335-023-09984-1

[24]

10.1038/s41598-020-60456-x

[25]

PROTAC targeted protein degraders: the past is prologue

Miklós Békés, David R. Langley, Craig M. Crews

Nature Reviews Drug Discovery 10.1038/s41573-021-00371-6

[26]

10.1038/s42003-018-0105-8

[27]

10.1074/mcp.t300009-mcp200

[28]

Protacs: Chimeric molecules that target proteins to the Skp1–Cullin–F box complex for ubiquitination and degradation

Kathleen M. Sakamoto, Kyung B. Kim, Akiko Kumagai et al.

Proceedings of the National Academy of Sciences 10.1073/pnas.141230798

[29]

10.1016/j.ddtec.2018.12.002

[30]

10.1038/nn.3637

[31]

Phthalimide conjugation as a strategy for in vivo target protein degradation

Georg E. Winter, Dennis L. Buckley, Joshiawa Paulk et al.

Science 10.1126/science.aab1433

[32]

Lysosome-targeting chimaeras for degradation of extracellular proteins

Steven M. Banik, Kayvon Pedram, Simon Wisnovsky et al.

Nature 10.1038/s41586-020-2545-9

[33]

10.1016/j.molcel.2019.09.009

[34]

10.1038/nmeth.1401

[35]

A Rapid, Reversible, and Tunable Method to Regulate Protein Function in Living Cells Using Synthetic Small Molecules

Laura A. Banaszynski, Ling-chun Chen, Lystranne A. Maynard-Smith et al.

Cell 10.1016/j.cell.2006.07.025

[36]

10.1016/j.cell.2017.10.033

[37]

10.1038/s41467-020-19532-z

[38]

10.1038/ncomms11742

[39]

10.1038/s41592-019-0512-x

[40]

10.1146/annurev-genet-120116-024656

[41]

Generation of conditional auxin-inducible degron (AID) cells and tight control of degron-fused proteins using the degradation inhibitor auxinole

Aisha Yesbolatova, Toyoaki Natsume, Ken-ichiro Hayashi et al.

Methods 10.1016/j.ymeth.2019.04.010

[42]

Rapid Protein Depletion in Human Cells by Auxin-Inducible Degron Tagging with Short Homology Donors

Toyoaki Natsume, Tomomi Kiyomitsu, Yumiko Saga et al.

Cell Reports 10.1016/j.celrep.2016.03.001

[43]

10.1016/j.devcel.2018.09.003

[44]

10.1007/s10577-017-9559-7

[45]

10.1101/gad.328237.119

[46]

10.1002/cpmb.124

[47]

Yunusova A. "Auxin Triggers AHR Pathway Activation in the Auxin‐Inducible Degron System in Mammalian Cells" Biochemistry (2024)

[48]

10.1038/s41467-025-61848-1

[49]

10.1038/s41467-024-54308-9

[50]

10.1080/19336934.2016.1168552

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Details

Published: Oct 05, 2025
Vol/Issue: 47(12)
License: View

Authors

S

Sailasree Rajalekshmi

Department of Medical Microbiology Immunology, and Cell Biology Southern Illinois University School of Medicine Springfield Illinois USA

K

Kizhakke Mattada Sathyan

Department of Medical Microbiology Immunology, and Cell Biology Southern Illinois University School of Medicine Springfield Illinois USA; Simmons Cancer Institute Southern Illinois University School of Medicine Springfield Illinois USA

Funding

School of Medicine, Southern Illinois University

Cite This Article

Sailasree Rajalekshmi, Kizhakke Mattada Sathyan (2025). Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems. BioEssays, 47(12). https://doi.org/10.1002/bies.70075

Direct Protein Degradation: Emerging Tools to Probe Biological Complexity in Mammalian Systems

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