Small GTPase Rab is generally thought to control intracellular membrane trafficking through interaction with specific effector molecules. Because of the large number of Rab
isoforms in mammals, however, the effectors of most of the mammalian Rabs have never been identified, and the Rab binding specificity of the Rab effectors previously reported has never been thoroughly investigated. In this study we systematically screened for novel Rab effectors by a yeast two-hybrid assay with 28 different mouse or human Rabs (Rab1-30) as bait and identified 27 Rab-
binding proteins, including 19 novel ones. We further investigated their Rab binding specificity by a yeast two-hybrid assay with a panel of 60 different
GTP-locked mouse or human Rabs. Unexpectedly most (17 of 27) of the Rab-
binding proteins we identified exhibited broad Rab binding specificity and bound multiple Rab
isoforms. As an example,
inositol-polyphosphate 5-phosphatase OCRL (
oculocerebrorenal syndrome of Lowe) bound the greatest number of Rabs (i.e. 16 distinct Rabs). Others, however, specifically recognized only a single Rab
isoform or only two closely related Rab
isoforms. The interaction of eight of the novel Rab-
binding proteins identified (e.g. INPP5E and Cog4) with a specific Rab
isoform was confirmed by co-immunoprecipitation assay and/or colocalization analysis in mammalian cell cultures, and the novel Rab2B-binding domain of Golgi-associated Rab2B interactor (GARI) and GARI-like
proteins was identified by deletion and homology search analyses. The findings suggest that most Rab effectors (or Rab-
binding proteins) regulate intracellular membrane trafficking through interaction with several Rab
isoforms rather than through a single Rab
isoform.