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Tonoplast intrinsic proteins (TIPs) and plasma membrane intrinsic proteins (PIPs) form subgroups of plant major intrinsic proteins (MIPs) that channel water as well as various small neutral molecules across the tonoplast and plasma membrane. Most MIPs are believed to form homotetramers, while some plant PIPs have been shown to form heterotetramers composed of different isoforms. This study investigated in vivo molecular interactions between different Arabidopsis TIP isoforms and between TIPs and a PIP member. The interactions were assayed by bimolecular fluorescence complementation optimized for use in Saccharomyces cerevisiae as a heterologous expression system. Fluorescence of re-assembled Venus yellow fluorescent protein was monitored by fluorescence microscopy and flow cytometry. The results showed strong interactions between TIP1;2, TIP2;1 and TIP3;1. Surprisingly, the three TIP isoforms also interacted with PIP2;1. The potassium channel AKT1 was used as a negative control and exhibited no interaction with any of the MIPs. The observed interactions may play a role in targeting and regulation of MIPs in plants.