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/.

Figure 1.

Human rabome. (A) Seventy-nine human tissues were profiled in duplicate as described in Materials and Methods. Displayed in numerical order are the expression profiles of individual Rabs. (B) Hierarchical clustering was used to group Rabs (left column) based on the similarity of their expression profiles across the entire tissue array (top panel). A dendrogram is provided where lengths of the branches leading up to each node directly reflect the degree of correlation between the expression profiles as assessed by the pairwise similarity function described in Materials and Methods (also see Supplementary Methods for further discussion and a list of the actual correlation values used for the construction of this dendrogram). The online full text/PDF versions of this manuscript provide links to enhanced figure files that are keyword searchable using the search menu of the Adobe Acrobat Reader, and the blue highlighted components (gene names) are also hyperlinked to their corresponding entries at the SymAtlas web application (see Materials and Methods for further directions for accessing the interactive features of this manuscript's figures). (C) Highlighted are the expression profiles of Rab1, Rab5, Rab3, and Rab27 isoforms.

Figure 2.

Human rabome including Rab regulators, effectors, and related kinases/phosphatases. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable, and hyperlinked version of this figure).

Figure 3.

Human SNAREome. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable, and hyperlinked version of this figure).

Figure 4.

Human SNAREome including SNARE regulators and effectors. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable, and hyperlinked version of this figure).

Figure 5.

Human coat components, adaptors, regulators, and related kinases/phosphatases. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable, and hyperlinked version of this figure).

Figure 6.

Human Rabome and SNAREome. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable and hyperlinked version of this figure).

Figure 7.

Human membrome including currently known components involved in exocytic and endocytic membrane traffic. Key sections of the dendrogram that are mentioned in the manuscript text are shown in blue and they are also magnified on the left hand side. Expression profiling was performed as that described in Figure 1 (see the online full text/PDF versions of the manuscript to access high-resolution, keyword searchable, and hyperlinked version of this figure).