Ragulator-Rag complex

The Ragulator-Rag complex is a regulator of lysosomal signalling and trafficking in eukaryotic cells, which plays an important role in regulating cell metabolism and growth in response to nutrient availability in the cell.[1] The Ragulator-Rag Complex is composed of five LAMTOR subunits, which work to regulate MAPK and mTOR complex 1.[2] The LAMTOR subunits form a complex with Rag GTPase and v-ATPase, which sits on the cell’s lysosomes and detects the availability of amino acids.[1] If the Ragulator complex receives signals for low amino acid count, it will start the process of catabolizing the cell. If there is an abundance of amino acids available to the cell, the Ragulator complex will signal that the cell can continue to grow.[1] Ragulator proteins come in two different forms: Rag A/Rag B and Rag C/Rag D. These interact to form heterodimers with one another.

Lamtor1
Identifiers
Symbol	26068
Alt. symbols	p18
Alt. names	p18
NCBI gene	55004
OMIM	613510
RefSeq	NM_017907.2
UniProt	Q6IAA8
Other data
Locus	Chr. 11 q13.4

Lamtor2
Identifiers
Symbol	29796
Alt. symbols	p14
NCBI gene	28956
OMIM	610389
RefSeq	NM_014017.3
UniProt	Q9Y2Q5
Other data
Locus	Chr. 1 q22

Lamtor3
Identifiers
Symbol	15606
Alt. symbols	MP1
NCBI gene	8649
OMIM	603296
RefSeq	NM_021970.3
UniProt	Q9UHA4
Other data
Locus	Chr. 4 q23

Lamtor4
Identifiers
Symbol	33772
Alt. symbols	c7orf59
NCBI gene	389541
RefSeq	NM_001008395.3
UniProt	Q0VGL1
Other data
Locus	Chr. 7 q22.1

Lamtor5
Identifiers
Symbol	17955
Alt. symbols	HBXIP
NCBI gene	10542
OMIM	608521
RefSeq	NM_006402.2
UniProt	O43504
Other data
Locus	Chr. 1 p13.3

Ragulator-Rag Complex, inactive.

Ragulator-Rag Complex, active

History

mTORC1 is a complex within the lysosome membrane that initiates growth when promoted by a stimulus, such as growth factors. A GTPase is a key component in cell signaling, and there were, in 2010, four RAG complexes discovered within the lysosomes of cells. In 2008, it was thought that these RAG complexes would slow down autophagy and activate cell growth by interacting with mTORC1.[3] However, in 2010, the Ragulator was discovered. Researchers determined that the function of this Ragulator was to interact with the RAG A, B, C, and D complexes to promote cell growth. This discovery also led to the first use of the term “Rag-Ragulator” complex, because of the interaction between these two.[4]

The amino acid level, cell growth, and other important factors are influenced by the mTOR Complex 1 pathway. On the lysosomal surface, the amino acids signal the activation of the four Rag proteins (RagA, RagB, RagC, and RagD) to translocate mTORC1 to the site of activation.[5]

A 2014 study noted that AMPK (AMP-activated protein kinase) and mTOR play important roles in managing different metabolic programs. It was also found that the protein complex v-ATPase-Ragulator was essential for activation of mTOR and AMPK. The v-ATPase-Ragulator complex is also used as an initiating sensor for energy stress, and serves as an endosomal docking site for LKB1-mediated AMPK activation by forming the v-ATPase-Ragulator-AXIN/LKB1-AMPK complex. This allows a switch between catabolism and anabolism.

In 2016, it was established that RagA and Lamtor4 were key to microglia functioning and biogenesis regulation within the lysosome. Further studies also indicate that the Ragulator-Rag complex interacts with proteins other than mTORC1, including an interaction with v-ATPase, which facilitates functions within microglia of the lysosome.[6]

In 2017, the Ragulator was thought to regulate the position of the lysosome, and interact with BORC, a multi subunit complex located on the surface of the lysosomal membrane.[7] Both BORC and mTORC1 work together in activating the GTPases to change the position of the lysosome. It was concluded that BORC and GTPases compete for a binding site in the LAMTOR 2 protein to reposition the lysosome.[8]

Function

While the intricate functions of the Ragulator-Rag Complex are not fully understood, it is known that the Ragulator-Rag Complex associates with the lysosome and plays a key role in mTOR (mammalian target of rapamycin) signaling regulation.[9] mTOR signaling is sensitive to amino acid concentrations in the cytoplasm of the cell, and the Ragulator complex works to detect amino acid concentration and transmit signals that activate, or inhibit, mTORC1.[10]

The Ragulator, along with the Rag GTPases and v-ATPases, are part of an amino acid identifying pathway, and are necessary for the localization of the mTORC1 to the lysosome surface. The Ragulator and v-ATPases reside on the lysosomal surface. The Rag GTPases cannot be directly bound to the lysosome because they lack the proteins necessary to bind to its lipid bilayer, so Rag GTPases must instead be anchored to the Ragulator.[11] The Ragulator is bound to the surface via the V-ATPase.[12] The Ragulator is a crystalized structure composed of five different subunits; LAMTOR 1, LAMTOR 2, LAMTOR 3, LAMTOR 4, LAMTOR 5. There are two sets of obligate heterodimers in the complex, LAMTOR 2/3, which sits right above LAMTOR 4/5.[11] The LAMTOR 1 dimer does not have the same structure as the other subunits. LAMTOR 1 surrounds most of the two heterodimers, providing structural support and keeping the heterodimers in place. When amino acids are present, the subunits are folded and positioned in such a way that allows for the Rag-GTPases to be anchored to its primary docking site of LAMTOR 2/3 on the Ragulator.[11] The Rag-GTPases consist of two sets of heterodimers; RAGs A/B and RAGs C/D. Before Rag-GTPases can bind to the Ragulator, Rag A/B must be GTP loaded via guanine nucleotide exchange factors (GEFs), and RAG C/D must be GDP loaded.[13] Once Rag-GTPases are bound to the regulator complex, the mTORC1 can be translocated to the surface of the lysosome. At the lysosomal surface, the mTORC1 will then bind to Rheb, but only if Rheb was first loaded to a GTP via GEFs.[12] If the amount of nutrients and the concentration of amino acids are sufficient, mTORC1 will be activated.

Activation of mTORC1

The lysosomal membrane is the main area in which mTORC1 is activated. However, some activation can occur in the Golgi apparatus and the peroxisome.[14] In mammalian cells, GTPase RagA and RagB are heterodimers with RagC and RagD, respectively. When enough amino acids are present, RagA/B GTPase becomes activated, which leads to the translocation of mTORC1 from the cytoplasm to the lysosome surface, via the Raptor. This process brings mTORC1 in close enough proximity to Rheb for Rheb to either (1) cause a conformational change to mTORC1, leading to and increase in substrate turnover, or (2) induce kinase activity of mTORC1. Rags do not contain membrane-targeting sequences, and as a result, depend on the entire Ragulator-Rag Complex to bind to the lysosome, activating mTORC1.[15]

While most amino acids indirectly activate mTORC1 in mammals, Leucine has the ability to directly activate mTORC1 in cells that are depleted of amino acids. Yeast contain LRS (leucyltRNA synthetase), which is a molecule that can interact with Rags, directly activating the molecule.[15]

Structure

Ragulator complex with Lamtor 1 in green, Lamtor 2 in blue, Lamtor 3 in red, Lamtor 4 in yellow, Lamtor 5 in purple. (PDB: 5Y39​)

The complex consists of five subunits,[2] named LAMTOR 1-5 (Late endosomal/lysosomal adaptor, mapk and mtor activator 1), however several have alternative names.

• LAMTOR1
• LAMTOR2
• LAMTOR3 (MAP2K1IP1)
• LAMTOR4
• LAMTOR5 (HBXIP)

References

1. Efeyan A, Zoncu R, Sabatini DM (September 2012). "Amino acids and mTORC1: from lysosomes to disease". Trends in Molecular Medicine. 18 (9): 524–33. doi:10.1016/j.molmed.2012.05.007. PMC 3432651. PMID 22749019.
2. Zhang, Tianlong; Wang, Rong; Wang, Zhijing; Wang, Xiangxiang; Wang, Fang; Ding, Jianping (2017-11-09). "Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1". Nature Communications. 8 (1): 1394. Bibcode:2017NatCo...8.1394Z. doi:10.1038/s41467-017-01567-4. ISSN 2041-1723. PMC 5680233. PMID 29123114.
3. Kim E, Goraksha-Hicks P, Li L, Neufeld TP, Guan KL (August 2008). "Regulation of TORC1 by Rag GTPases in nutrient response". Nature Cell Biology. 10 (8): 935–45. doi:10.1038/ncb1753. PMC 2711503. PMID 18604198.
4. Sancak Y, Bar-Peled L, Zoncu R, Markhard AL, Nada S, Sabatini DM (April 2010). "Ragulator-Rag complex targets mTORC1 to the lysosomal surface and is necessary for its activation by amino acids". Cell. 141 (2): 290–303. doi:10.1016/j.cell.2010.02.024. PMC 3024592. PMID 20381137.
5. Bar-Peled L, Schweitzer LD, Zoncu R, Sabatini DM (September 2012). "Ragulator is a GEF for the rag GTPases that signal amino acid levels to mTORC1". Cell. 150 (6): 1196–208. doi:10.1016/j.cell.2012.07.032. PMC 3517996. PMID 22980980.
6. Shen K, Sidik H, Talbot WS (January 2016). "The Rag-Ragulator Complex Regulates Lysosome Function and Phagocytic Flux in Microglia". Cell Reports. 14 (3): 547–559. doi:10.1016/j.celrep.2015.12.055. PMC 4731305. PMID 26774477.
7. Pu J, Schindler C, Jia R, Jarnik M, Backlund P, Bonifacino JS (April 2015). "BORC, a multisubunit complex that regulates lysosome positioning". Developmental Cell. 33 (2): 176–88. doi:10.1016/j.devcel.2015.02.011. PMC 4788105. PMID 25898167.
8. Colaço A, Jäättelä M (December 2017). "Ragulator-a multifaceted regulator of lysosomal signaling and trafficking". The Journal of Cell Biology. 216 (12): 3895–3898. doi:10.1083/jcb.201710039. PMC 5716293. PMID 29138253.
9. Bar-Peled L, Sabatini DM (July 2014). "Regulation of mTORC1 by amino acids". Trends in Cell Biology. 24 (7): 400–6. doi:10.1016/j.tcb.2014.03.003. PMC 4074565. PMID 24698685.
10. Laplante M, Sabatini DM (April 2012). "mTOR signaling in growth control and disease". Cell. 149 (2): 274–93. doi:10.1016/j.cell.2012.03.017. PMC 3331679. PMID 22500797.
11. Su MY, Morris KL, Kim DJ, Fu Y, Lawrence R, Stjepanovic G, Zoncu R, Hurley JH (December 2017). "Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex". Molecular Cell. 68 (5): 835–846.e3. doi:10.1016/j.molcel.2017.10.016. PMC 5722659. PMID 29107538.
12. Wolfson RL, Sabatini DM (August 2017). "The Dawn of the Age of Amino Acid Sensors for the mTORC1 Pathway". Cell Metabolism. 26 (2): 301–309. doi:10.1016/j.cmet.2017.07.001. PMC 5560103. PMID 28768171.
13. Cherfils J (December 2017). "Encoding Allostery in mTOR Signaling: The Structure of the Rag GTPase/Ragulator Complex". Molecular Cell. 68 (5): 823–824. doi:10.1016/j.molcel.2017.11.027. PMID 29220648.
14. Yao Y, Jones E, Inoki K (July 2017). "Lysosomal Regulation of mTORC1 by Amino Acids in Mammalian Cells". Biomolecules. 7 (3): 51. doi:10.3390/biom7030051. PMC 5618232. PMID 28686218.
15. Groenewoud MJ, Zwartkruis FJ (August 2013). "Rheb and Rags come together at the lysosome to activate mTORC1". Biochemical Society Transactions. 41 (4): 951–5. doi:10.1042/BST20130037. PMID 23863162.