Highly multiplexed design of an allosteric transcription factor to sense new ligands

Kyle K. Nishikawa, Jackie Chen, Justin F. Acheson, Svetlana V. Harbaugh, Phil Huss, Max Frenkel, Nathan Novy, Hailey R. Sieren, Ella C. Lodewyk, Daniel H. Lee, Jorge L. Chávez, Brian G. Fox and Srivatsan Raman ()
Additional contact information
Kyle K. Nishikawa: University of Wisconsin-Madison
Jackie Chen: University of Wisconsin-Madison
Justin F. Acheson: University of Wisconsin-Madison
Svetlana V. Harbaugh: Air Force Research Laboratory
Phil Huss: University of Wisconsin-Madison
Max Frenkel: University of Wisconsin-Madison
Nathan Novy: University of Wisconsin-Madison
Hailey R. Sieren: University of Wisconsin-Madison
Ella C. Lodewyk: University of Wisconsin-Madison
Daniel H. Lee: University of Wisconsin-Madison
Jorge L. Chávez: Air Force Research Laboratory
Brian G. Fox: University of Wisconsin-Madison
Srivatsan Raman: University of Wisconsin-Madison

Nature Communications, 2024, vol. 15, issue 1, 1-18

Abstract: Abstract Allosteric transcription factors (aTF) regulate gene expression through conformational changes induced by small molecule binding. Although widely used as biosensors, aTFs have proven challenging to design for detecting new molecules because mutation of ligand-binding residues often disrupts allostery. Here, we develop Sensor-seq, a high-throughput platform to design and identify aTF biosensors that bind to non-native ligands. We screen a library of 17,737 variants of the aTF TtgR, a regulator of a multidrug exporter, against six non-native ligands of diverse chemical structures – four derivatives of the cancer therapeutic tamoxifen, the antimalarial drug quinine, and the opiate analog naltrexone – as well as two native flavonoid ligands, naringenin and phloretin. Sensor-seq identifies biosensors for each of these ligands with high dynamic range and diverse specificity profiles. The structure of a naltrexone-bound design shows shape-complementary methionine-aromatic interactions driving ligand specificity. To demonstrate practical utility, we develop cell-free detection systems for naltrexone and quinine. Sensor-seq enables rapid and scalable design of new biosensors, overcoming constraints of natural biosensors.

Date: 2024
References: View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-54260-8 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-54260-8

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-54260-8

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().