The Regulation of Rab GTPases by Phosphorylation

Abstract

Rab proteins are small GTPases that act as molecular switches for intracellular vesicle trafficking. Although their function is mainly regulated by regulatory proteins such as GTPase-activating proteins and guanine nucleotide exchange factors, recent studies have shown that some Rab proteins are physiologically phosphorylated in the switch II region by Rab kinases. As the switch II region of Rab proteins undergoes a conformational change depending on the bound nucleotide, it plays an essential role in their function as a 'switch'. Initially, the phosphorylation of Rab proteins in the switch II region was shown to inhibit the association with regulatory proteins. However, recent studies suggest that it also regulates the binding of Rab proteins to effector proteins, determining which pathways to regulate. These findings suggest that the regulation of the Rab function may be more dynamically regulated by phosphorylation than just through the association with regulatory proteins. In this review, we summarize the recent findings and discuss the physiological and pathological roles of Rab phosphorylation.

Keywords: LRRK1; LRRK2; Rab; TBK1; membrane trafficking; phosphorylation.

Figure 1

Schematic illustrations of the lifecycle of Rab proteins and proposed effects of phosphorylation. (A) The general life cycle of Rab proteins. (B) A potentially inhibitory effect of Rab phosphorylation on the extraction by GDP-dissociation inhibitors (GDIs). (C) An alternative route activated by Rab phosphorylation. REP: Rab escort protein; RabGGTase: Rab geranylgeranyl transferase; GEF: guanine nucleotide exchange factor; GAP: GTPase-activating protein; Pi: inorganic phosphate; GXP: GTP or GDP. ‘P’ in a yellow circle and blank yellow circles mean phosphorylation.

Figure 2

Domain architectures of the Rab kinases and their substrate Rab proteins. Domain architectures of (A) leucine-rich repeat kinase 1 (LRRK1), (B) leucine-rich repeat kinase 2 (LRRK2) and (C) TANK-binding kinase 1 (TBK1), and their substrate Rab proteins as well as the phosphorylation sites. Ank: ankyrin repeats; Arm: armadillo repeats; LRR: leucine-rich repeats; ROC: Ras of complex proteins; COR: carboxyl-terminal of ROC; WD40: WD40 repeats; CC: coiled-coil.

Figure 3

Proposed biological roles of Rab phosphorylation by LRRK2. (A) Proposed effectors of phosphorylated Rab proteins. They form complexes with motor proteins, thereby, in most cases except Folliculin (FLCN)-FLCN-interacting protein 1 (FNIP1), accelerating cargo transport. ‘P’ in a yellow circle and blank yellow circles mean phosphorylation. (B) Phosphorylation of Rab8/10 by LRRK2 plays important roles in macrophages under conditions such as lysosomal stress and bacterial infection. Ly: lysosomes; Ph: phagosomes. (C) Phosphorylation of Rab10 by LRRK2 functions as a molecular switch upon macropinocytosis; the macropinosomes are recycled back to the plasma membrane in a LRRK2-independent manner, whereas LRRK2-mediated phosphorylation of Rab10 activates a pathway in which the macropinosomes become maturated to signaling endosomes that somehow activate chemotactic pathways. (D) Aberrant phosphorylation of Rab10 by LRRK2 abnormally accelerates the transport of the Rab-interacting lysosomal protein-like protein 1/2 (RILPL1/2) cargo, the accumulation of which, in the pericentriolar region, might prevent centrosomal protein 164 (CEP164) and tau-tubulin kinase 2 (TTBK2) from localizing to the mother centriole, maintain centrosomal protein of 110 kDa (CP110) on the mother centriole and inhibit membrane transport necessary for ciliogenesis.

Figure 4

Proposed biological roles of Rab7A phosphorylation. (A) Phosphorylation of Rab7A by LRRK1 increases its affinity to RILP or other effectors, thereby facilitating the transport of EGFR-containing vesicles. Phosphorylation of Rab7A by LRRK1 is activated by PKC. (B) On the outer membrane of depolarized mitochondria, ubiquitylation of outer membrane proteins by Parkin recruits ubiquitin receptors such as optineurin. TBK1, which forms a complex with the Ub receptors, is recruited to the outer membrane and phosphorylates Rab7A as well as the receptors. Phosphorylated Rab7A recruits FLCN-FNIP1, thereby further promoting the mitophagy process.