K ⁺ channel interactions detected by a genetic system optimized for systematic studies of membrane protein interactions

TLDR

Protein complex formation is essential for cellular functions, yet current proteomic methods poorly detect membrane‑associated interactions. The study introduces a mating‑based split ubiquitin system to systematically identify interactions between membrane proteins and between membrane and soluble proteins. mbSUS enables in‑vivo cloning of PCR products into vectors, regulated bait expression, interaction detection by mating, and streamlined selection, facilitated by lambda attachment sites for Gateway cloning. The system uncovered homo‑ and heteromeric interactions among Arabidopsis K⁺ channels, showed that the C‑termini of KAT1 and AKT1 are required for complex assembly, revealed differential oligomerization patterns and novel partners, and demonstrated mbSUS’s suitability for systematic membrane protein interaction analysis.

Abstract

Organization of proteins into complexes is crucial for many cellular functions. However, most proteomic approaches primarily detect protein interactions for soluble proteins but are less suitable for membrane-associated complexes. Here we describe a mating-based split ubiquitin system (mbSUS) for systematic identification of interactions between membrane proteins as well as between membrane and soluble proteins. mbSUS allows in vivo cloning of PCR products into a vector set, detection of interactions via mating, regulated expression of baits, and improved selection of interacting proteins. Cloning is simplified by introduction of lambda attachment sites for GATEWAY. Homo- and heteromeric interactions between Arabidopsis K(+) channels KAT1, AKT1, and AKT2 were identified. Tests with deletion mutants demonstrate that the C terminus of KAT1 and AKT1 is necessary for physical assembly of complexes. Screening of a sorted collection of 84 plant proteins with K(+) channels as bait revealed differences in oligomerization between KAT1, AKT1, and AtKC1, and allowed detection of putative interacting partners of KAT1 and AtKC1. These results show that mbSUS is suited for systematic analysis of membrane protein interactions.