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

Abstract

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/. INTRODUCTIONUnderstanding the molecular basis for the organization of the exocytic and endocytic membrane trafficking pathways in the eukaryotic cell remains a formidable challenge. The foundation of these pathways is the lipid bilayer that separates different subcellular compartments, their distinguishing features encoded by phospholipid composition, and unique sets of integral and peripheral membrane proteins. By harnessing and regulating the fundamental processes of membrane fission and fusion through the action of protein complexes, the lipid bilayer can be exploited to produce a variety of distinct subcellular compartments with unique chemical environments that play essential roles in cell and organ function. Moreover, it is now evident that these subcellular compartments are dynamic structures in continuous and specific communication through carrier vesicles and tubules that mobilize cargo to specific destinations. They can be disassembled and reassembled in a remarkably facile manner in response to cell signaling pathways, mitosis, or by simple chemical perturbants.Implicit in these dynamic pathways is the need to systematically and reversibly regulate protein interactions. Although traditional phylogenetic analyses provided significant insights into the diversity of components that direct membrane traffic (Pereira-Leal and Seabra, 2000;Chen and Scheller, 2001;Pereira-Leal and Seabra, 2001), our understanding of the basic cellular building blocks that organize this diversity into contiguous pathways is still fragmentary. Reductionist approaches using biochemical and molecular tools also provide important insights into specific steps of a pathway. However, understanding the global interconnectivities of complex biological pathways, such as cargo trafficking, will require new approaches utilizing modern ...

Thirty-One Flavors of Drosophila Rab Proteins

“…Rab2, Rab3, Rab26, and RabX4 transcripts are enriched mainly in neural cells (Figure 2). The expression patterns of Rab3 and Rab26 are consistent with a previous study that shows high expression of mammalian Rab3A and Rab26 in brain tissues (Gurkan et al 2005).…”

“…RabX4 is a member of the A branch of proteins ( Figure 1 Some fly Rab gene expression patterns do not correlate well with their mammalian counterparts. For example, Drosophila Rab32 is specifically transcribed in the Malpighian tubules, which serve a function similar to that of a kidney, while mammalian Rab32 is highly expressed in lymph, trachea, uterus, ovary, and liver, but not in the kidney (Gurkan et al 2005). The discrepancy between fly and mammalian expression patterns of Rab32 suggests that the two genes have functionally diverged.…”

RAB26 coordinates lysosome traffic and mitochondrial localization

“…By cycling between GTP-and GDP-bound forms, they work like simple machines to define specific membrane-associated compartments within cells. Many Rabs -like RAB4, RAB5, RAB7 and RAB11 -are ubiquitously expressed (Gurkan et al, 2005;Jin et al, 2012;Zhang et al, 2007), performing essentially the same function in diverse cells. RAB7, for example, aids the maturation of early endosomes into late endosomes and ultimately coordinates transport to lysosomes (Bucci et al, 2000;Feng et al, 1995).…”

Rab8 Regulates Basolateral Secretory, But Not Recycling, Traffic at the Recycling Endosome

“…More than 60 known Rabs collectively regulate the flow of nearly all membrane traffic within the cell (Pfeffer, 1994;Gurkan et al, 2005;Jordens et al, 2005). Of these, mammalian Rab8 has been associated with the flow of newly synthesized proteins to the basolateral surface in polarized epithelial cells (Huber et al, 1993b;Moritz et al, 2001).…”