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Vol. 16, Issue 8, 3847-3864, August 2005

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Large-Scale Profiling of Rab GTPase Trafficking Networks: The Membrome

Cemal Gurkan ^*, Hilmar Lapp , Christelle Alory ^*, Andrew I. Su , John B. Hogenesch , and William E. Balch ^* 

^* Departments of Cell and Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037; The Institute for Childhood and Neglected Disease, The Scripps Research Institute, La Jolla, CA 92037; and The Genomics Institute of the Novartis Research Foundation, San Diego, CA 92121

Submitted January 24, 2005; Accepted May 10, 2005
Monitoring Editor: Suzanne Pfeffer

Rab GTPases and SNARE fusion proteins direct cargo trafficking through the exocytic and endocytic pathways of eukaryotic cells. We have used steady state mRNA expression profiling and computational hierarchical clustering methods to generate a global overview of the distribution of Rabs, SNAREs, and coat machinery components, as well as their respective adaptors, effectors, and regulators in 79 human and 61 mouse nonredundant tissues. We now show that this systems biology approach can be used to define building blocks for membrane trafficking based on Rab-centric protein activity hubs. These Rab-regulated hubs provide a framework for an integrated coding system, the membrome network, which regulates the dynamics of the specialized membrane architecture of differentiated cells. The distribution of Rab-regulated hubs illustrates a number of facets that guides the overall organization of subcellular compartments of cells and tissues through the activity of dynamic protein interaction networks. An interactive website for exploring datasets comprising components of the Rab-regulated hubs that define the membrome of different cell and organ systems in both human and mouse is available at http://www.membrome.org/.

Abbreviations used: AP, adaptor protein complex; COPI, coat protein complex I; COPII, coat protein complex II; ER, endoplasmic reticulum; GAPs, GTPase-activating proteins; GEFs, guanine nucleotide exchange factors; GGAs, Golgi-associated, -ear-containing, Arf-binding proteins; PI, phosphatidylinositol; SNARE, soluble N-ethyl-maleimide-sensitive factor attachment protein receptor

The online version of this article contains supplemental material at MBC Online (http://www.molbiolcell.org).

Address correspondence to: William E. Balch (webalch{at}scripps.edu).

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