Cell surface liposome binding (CLiB) allows lipid-binding probe engineering via high-throughput screening.

Authors

Taki Nishimura, Kotaro Tsuboyama, Yuki Nakagaki, Shiou-Ling Lu, Yuki Ishino, Nozomu Kono, Takeshi Noda, Eiji Yamamoto, Noboru Mizushima

Published in

Nature cell biology. Jul 02, 2026. Epub Jul 02, 2026.

Abstract

Lipid-binding domains, traditionally isolated from natural proteins, are essential tools for probing membrane lipid dynamics and specialized cellular compartments. Despite diverse applications, a general strategy for their engineering remains elusive. Here we present a robust and high-throughput method for monitoring protein-lipid interactions, named the cell surface liposome binding (CLiB) assay. Using the assay, we conducted directed evolution of the PX domain from SnxA, isolating high-affinity variants specific for phosphatidylinositol 3,5-bisphosphate (PI(3,5)P₂). Combining the CLiB assay with next-generation sequencing enabled parallel analysis of >6,000 clones, comprehensively identifying key residues critical for lipid binding. An engineered variant, PX-SnxA^GV, functioned as a lipid biosensor in yeast and mammalian cells, visualizing PI(3,5)P₂-enriched membrane subdomains upon hyperosmotic shock and during microautophagy, thereby suggesting localized PI(3,5)P₂ synthesis within spatially restricted regions. This study provides a framework for on-demand generation of lipid-binding probes, facilitating the discovery of membrane compartments characterized by unique lipid compositions.

PMID:
42393358
Bibliographic data and abstract were imported from PubMed on 03 Jul 2026.

Read full publication at:
Please sign in to see all details.

Stats

1-terrible, 9-excellent. How would you rate this publication? Sign in in to submit your rating.

Post a comment

You need to be signed in to post comments. You can sign in here.

Comments

There are no comments yet.