Engineering unnatural cells with a 21st amino acid as a living epigenetic sensor

Yu Hu, Yixian Wang, Linqi Cheng, Chenhang Wang, Yijie Liu, Yufei Wang, Yuda Chen, Shudan Yang, Yiming Guo, Shiyu Jiang, Kaiqiang Yang and Han Xiao ()
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Yu Hu: Rice University
Yixian Wang: Rice University
Linqi Cheng: Rice University
Chenhang Wang: Rice University
Yijie Liu: Rice University
Yufei Wang: Rice University
Yuda Chen: Rice University
Shudan Yang: Rice University
Yiming Guo: Rice University
Shiyu Jiang: Rice University
Kaiqiang Yang: Rice University
Han Xiao: Rice University

Nature Communications, 2025, vol. 16, issue 1, 1-17

Abstract: Abstract Living animals rely extensively on post-translational modifications (PTMs) to regulate protein activity, stability, subcellular localization, and protein-protein interactions. These modifications are tightly controlled by the balance of “writer” and “eraser” enzymes, which add or remove PTMs on proteins. Current strategies to measure writer and eraser activities in living animals largely depend on invasive methods, such as single-cell sequencing, quantitative mass spectrometry, or activity-based probes, which often lack cell or tissue specificity. In this study, we report the development of autonomous cells—both prokaryotic and eukaryotic—with the ability to biosynthesize and genetically encode acetyllysine using the genetic code expansion technology. These engineered living sensors with a site-specific acetyllysine modification can be transplanted into living animals, enabling real-time monitoring of PTM dynamics in living cells and animals. We further demonstrate the utility of these cells in tracking deacetylase activity and assessing the effects of deacetylase inhibitors on PTM dynamics in living animals in real time.

Date: 2025
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DOI: 10.1038/s41467-025-64448-1

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