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Targeting Rab GTPases to distinct membrane compartments

Key Points

  • Rab GTPases are important for transport-vesicle budding, motility, docking and fusion, and human cells have more than 60 Rabs that are localized to distinct membrane compartments. Their C-terminal hypervariable domain contains important and distinct targeting information.

  • Rab GTPases are stably prenylated at their C termini, and this modification leads to their stable association with cellular membranes. However, Rabs can be removed from membranes by a protein that is known as GDP-dissociation inhibitor (GDI), which keeps a fraction of each Rab in a cytosolic pool at steady state.

  • Complexes of prenylated Rabs and GDI contain all the information that is needed for their accurate membrane targeting. The recent crystallization of Rab–GDI complexes highlights interesting information regarding the mechanism by which Rabs are retrieved from their membrane target and returned to their membrane of origin.

  • The structure of yeast (Saccharomyces cerevisiae) GDI that is bound to monoprenylated Rab1 (Ypt1) highlighted a pocket at the bottom of GDI that can accommodate the prenyl group. In addition, a second, distinct prenyl-binding site has been identified that might also be important for GDI function.

  • A family of proteins — known as Ypt-interacting proteins (Yips) — has been implicated in interacting with Rab–GDI complexes to accomplish the delivery of Rab GTPases to membranes. Yip3 dissociates endosomal Rabs from GDI, but it does not function on complexes of endoplasmic reticulum/Golgi Rabs that are bound to GDI.

  • The human genome encodes 16 Yip-related proteins that can be grouped into 7 subfamilies, 6 of which are conserved in yeast. Yips seem to have different localizations and might occur as heterodimers.

  • Yip proteins might be present in distinct membrane-trafficking pathways to provide an initial membrane-access site for prenylated Rab GTPases. Once in a pathway, Rabs might be stabilized by interactions with Rab-specific, downstream effector proteins.

Abstract

Rab GTPases are key to membrane-trafficking events in eukaryotic cells, and human cells contain more than 60 Rab proteins that are localized to distinct compartments. The recent determination of the structure of a monoprenylated Rab GTPase bound to GDP-dissociation inhibitor provides new molecular details that are relevant to models of Rab delivery. The further discovery of an integral membrane protein that can dissociate prenylated Rab proteins from GDP-dissociation inhibitor gives new insights into the mechanisms of Rab localization.

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Figure 1: The structures of the bovine and yeast GDP-dissociation inhibitors (GDIs).
Figure 2: The topology of human Yip3/PRA1.
Figure 3: A phylogenetic-tree analysis of the Yip1 and Yip2 membrane-protein families.
Figure 4: A model for the membrane recruitment of Rab proteins.

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Acknowledgements

Research in the Pfeffer laboratory is supported by a grant from the National Institutes of Health.

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Correspondence to Suzanne Pfeffer.

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DATABASES

Saccharomyces genome database

Bos1

Sec22

Yif1

Yip1

Yip2

Yip3

Yip4

Yip5

Ypt1

Ypt31

Swiss-Prot

GDIα

GDIβ

Rab1

Rab1B

Rab2

Rab3A

Rab5

Rab7

Rab9

REP

FURTHER INFORMATION

Entrez Gene

Entrez Protein

Genomics Institute of the Novartis Research Foundation

Glossary

RAB GTPases

Rab proteins are Ras-like GTPases that regulate membrane-trafficking events in eukaryotic cells. Rab proteins are active when they are bound to GTP and inactive when bound to GDP. Different Rab proteins are specific for different transport pathways and different subcellular compartments.

RAS-GTPase FAMILY

A group of small, monomeric GTPases that are involved, for example, in growth, differentiation and cellular signalling. They require the binding of GTP to become active.

RAB-EFFECTOR PROTEINS

Proteins that bind preferentially to the active, GTP-bound state of a particular Rab protein and that function in events such as vesicle budding, transport, tethering and fusion. Their functions and, in some cases, localizations are regulated by Rab GTPases.

GDP-DISSOCIATION INHIBITOR

(GDI). A cytosolic protein that binds to prenylated Rab proteins in their inactive, GDP-bound state. It is involved in Rab GTPase delivery to, and removal from, membranes.

PRENYL

An isoprenoid lipid. Rab proteins are modified with prenyl groups, usually two, at their C termini. Prenylation anchors Rab GTPases in membranes, and the prenyl groups that are attached to Rab proteins are called geranylgeranyl groups.

HYPERVARIABLE DOMAIN

The C-terminal, mostly unstructured, region of a Rab GTPase, which shows the highest level of variability between Rab proteins. It is important for determining Rab subcellular localization.

GERANYLGERANYL

A prenyl modification that is added to the C terminus of Rab proteins by geranylgeranyl transferase.

RAB-ESCORT PROTEIN

(REP). A protein that binds to newly synthesized Rab proteins in the cytosol and escorts them to geranylgeranyl transferase, which prenylates them. REP is structurally similar to GDP-dissociation inhibitor (GDI).

RAB GERANYLGERANYL TRANSFERASE

(GGTase). The enzyme that attaches the prenyl-lipid group to the C terminus of Rab proteins that are bound to the Rab-escort protein.

GDI-DISPLACEMENT FACTOR

(GDF). A proteinaceous factor that catalyses both the dissociation of prenylated, GDP-bound Rab proteins from GDP-dissociation inhibitor (GDI) and the subsequent transfer of Rab proteins onto the membrane.

YIP

(Ypt-interacting protein). Yips are a family of transmembrane proteins that bind to Rab proteins. Although most of their functions are unknown, Yip3 has been shown to have GDP-dissociation inhibitor (GDI)-displacement-factor activity for endosomal Rab proteins, and the Yip1–Yip1-interacting factor-1 (Yif1) complex is essential for ER-to-Golgi transport in yeast.

RAB GTPase-ACTIVATING PROTEIN

A protein that increases the GTP hydrolysis activity of a specific Rab GTPase and therefore inactivates it.

SECRETORY PATHWAY

The path by which proteins and lipids are transported from the endoplasmic reticulum, through the Golgi complex, to the cell surface.

ENDOCYTIC PATHWAY

The pathway by which cell-surface and extracellular components are internalized. It includes several intracellular compartments, such as the early and late endosomal compartments, and it terminates at the lysosome.

RHO-GTPase FAMILY

Ras-like small GTPases that are involved in controlling the polymerization of actin.

GUANINE NUCLEOTIDE-EXCHANGE FACTOR

A protein that activates a specific small GTPase by catalysing the exchange of bound GDP for GTP.

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Pfeffer, S., Aivazian, D. Targeting Rab GTPases to distinct membrane compartments. Nat Rev Mol Cell Biol 5, 886–896 (2004). https://doi.org/10.1038/nrm1500

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