title: A membrane protein/signaling protein interaction network for Arabidopsis version AMPv2.
abstract: Interactions between membrane proteins and the soluble fraction are essential for signal transduction and for regulating nutrient transport. To gain insights into the membrane-based interactome, 3,852 open reading frames (ORFs) out of a target list of 8,383 representing membrane and signaling proteins from Arabidopsis thaliana were cloned into a Gateway-compatible vector. The mating-based split ubiquitin system was used to screen for potential protein-protein interactions (pPPIs) among 490 Arabidopsis ORFs. A binary robotic screen between 142 receptor-like kinases (RLKs), 72 transporters, 57 soluble protein kinases and phosphatases, 40 glycosyltransferases, 95 proteins of various functions, and 89 proteins with unknown function detected 387 out of 90,370 possible PPIs. A secondary screen confirmed 343 (of 386) pPPIs between 179 proteins, yielding a scale-free network (r(2) = 0.863). Eighty of 142 transmembrane RLKs tested positive, identifying 3 homomers, 63 heteromers, and 80 pPPIs with other proteins. Thirty-one out of 142 RLK interactors (including RLKs) had previously been found to be phosphorylated; thus interactors may be substrates for respective RLKs. None of the pPPIs described here had been reported in the major interactome databases, including potential interactors of G-protein-coupled receptors, phospholipase C, and AMT ammonium transporters. Two RLKs found as putative interactors of AMT1;1 were independently confirmed using a split luciferase assay in Arabidopsis protoplasts. These RLKs may be involved in ammonium-dependent phosphorylation of the C-terminus and regulation of ammonium uptake activity. The robotic screening method established here will enable a systematic analysis of membrane protein interactions in fungi, plants and metazoa.
authors.affiliation: Department of Plant Biology, Carnegie Institution for Science Stanford, CA, USA. slalonde@stanford.edu
authors.forename: Sylvie
authors.initials: S
authors.lastname: Lalonde
authors.forename: Antoinette
authors.initials: A
authors.lastname: Sero
authors.forename: Réjane
authors.initials: R
authors.lastname: Pratelli
authors.forename: Guillaume
authors.initials: G
authors.lastname: Pilot
authors.forename: Jin
authors.initials: J
authors.lastname: Chen
authors.forename: Maria I
authors.initials: MI
authors.lastname: Sardi
authors.forename: Saman A
authors.initials: SA
authors.lastname: Parsa
authors.forename: Do-Young
authors.initials: DY
authors.lastname: Kim
authors.forename: Biswa R
authors.initials: BR
authors.lastname: Acharya
authors.forename: Erica V
authors.initials: EV
authors.lastname: Stein
authors.forename: Heng-Chen
authors.initials: HC
authors.lastname: Hu
authors.forename: Florent
authors.initials: F
authors.lastname: Villiers
authors.forename: Kouji
authors.initials: K
authors.lastname: Takeda
authors.forename: Yingzhen
authors.initials: Y
authors.lastname: Yang
authors.forename: Yong S
authors.initials: YS
authors.lastname: Han
authors.forename: Rainer
authors.initials: R
authors.lastname: Schwacke
authors.forename: William
authors.initials: W
authors.lastname: Chiang
authors.forename: Naohiro
authors.initials: N
authors.lastname: Kato
authors.forename: Dominique
authors.initials: D
authors.lastname: Loqué
authors.forename: Sarah M
authors.initials: SM
authors.lastname: Assmann
authors.forename: June M
authors.initials: JM
authors.lastname: Kwak
authors.forename: Julian I
authors.initials: JI
authors.lastname: Schroeder
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
authors.forename: Wolf B
authors.initials: WB
authors.lastname: Frommer