Signal integration in the (m)TORC1 growth pathway

Probably not a substantial claim: may not pass S4 (based). May combine two claims.

Integration of cellular signals occurs upstream of the (m)TOR kinase and remains incompletely understood.

“however the integration of cellular signals occurs upstream of the kinase and remains incompletely understood”

May combine two claims.

The crystal structure of the arginine-bound CASTOR1 homodimer revealed that each monomer contains four ACT domains, and arginine binds to each monomer in a deep cleft at the intramolecular ACT2/4 interface.

“The crystal structure of the arginine-bound CASTOR1 homodimer (Gai et al., 2016b; Saxton et al., 2016a; Xia et al., 2016) revealed that each monomer contains four ACT domains (Fig. 2D), and arginine binds to each monomer in a deep cleft at the intramolecular ACT2/4 interface”

• cites Gai et al., 2016bNot checked yet

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• cites Saxton et al., 2016aNot checked yet

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• cites Xia et al., 2016 sourceNot checked yet

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May combine two claims.

CASTOR1 and CASTOR2 homo- and heterodimerize, with the CASTOR1 homodimer interacting with GATOR2 most strongly.

“CASTOR1 and 2 homo- and heterodimerize with one another, with the CASTOR1 homodimer interacting with GATOR2 most strongly.”

May combine two claims.

Full mTORC1 activation requires its recruitment to the lysosome by heterodimeric Rag GTPases, whereupon GTP-bound Rheb GTPases allosterically activate the kinase.

“Full mTORC1 activation requires its recruitment to the lysosome by heterodimeric Rag GTPases (Sancak et al., 2008), whereupon GTP-bound Rheb GTPases allosterically activate the kinase (Long et al., 2005; Sato et al., 2009)”

• cites Sancak et al., 2008 sourceNot checked yet

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• cites Long et al., 2005 sourceNot checked yet

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• cites Sato et al., 2009 sourceNot checked yet

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May combine two claims.

The CASTOR1-GATOR2 interaction is arginine-dependent, with arginine suppressing the association of CASTOR1 with GATOR2 to sense arginine upstream of mTORC1.

“In this case the CASTOR1-GATOR2 interaction is arginine-dependent, with arginine supressing the association of CASTOR1 with GATOR2 to sense arginine upstream of mTORC1.”

May combine two claims.

CASTOR2 binding to GATOR2 is amino acid-insensitive; thus CASTOR2 may serve to retain responsivity of mTORC1 to nutrient signals through CASTOR1 by damping the initial activation of the kinase.

“CASTOR2 binding to GATOR2, on the other hand, was amino acid-insensitive; thus, CASTOR2 may serve to retain responsivity of mTORC1 to nutrient signals through CASTOR1 by damping the initial activation of the kinase, affecting the properties of signal feedback as opposed to direct amino acid detection.”

May combine two claims.

Homologs of only the SESNs have been detected by sequence analysis in other higher eukaryotes such as C. elegans and D. melanogaster, and the known sensor proteins in general are only present in few fungal species, potentially representing species-specific nutritional dependencies.

“Homologs of only the SESNs have been detected by sequence analysis in other higher eukaryotes such as C. elegans and D. melanogaster, and the known sensor proteins in general are only present in few fungal species, potentially representing species-specific nutritional dependencies (Wolfson and Sabatini, 2017).”

• cites Wolfson and Sabatini, 2017Not checked yet

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May combine two claims.

Ectopic SESN2 expression prevents mTORC1 localization to the lysosome in the presence of amino acids, while reducing GATOR1-GATOR2 and increasing GATOR1-RagB association, hence acting as a negative regulator of mTORC1 signaling.

“Ectopic SESN2 expression prevents mTORC1 localization to the lysosome in the presence of amino acids (Parmigiani et al., 2014; Peng et al., 2014), while reducing GATOR1-GATOR2, and increasing GATOR1-RagB, association (Kim J S et al., 2015), hence acting as a negative regulator of mTORC1 signaling.”

• cites Parmigiani et al., 2014 sourceNot checked yet

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• cites Peng et al., 2014 sourceNot checked yet

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• cites Kim J S et al., 2015Not checked yet

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May combine two claims. The quote only partly states this claim.

SESN2 has been suggested to act as a guanine nucleotide dissociation inhibitor for RagA, but subsequent structural studies have not supported this hypothesis, and RagA/B-GDI activity remains unproven.

“It has alternatively been suggested to act as a guanine nucleotide dissociation inhibitor (GDI) for RagA (Peng et al., 2014) however subsequent structural studies have not supported this hypothesis.”

• cites Peng et al., 2014 sourceNot checked yet

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May combine two claims.

SESN2 interacts with GATOR2, with the interaction conditionally strengthened by both amino acid deprivation and DNA damage-induced stress.

“SESN2 interacts with GATOR2 (Chantranupong et al., 2014; Parmigiani et al., 2014; Kim J S et al., 2015), with the interaction conditionally strengthened by both amino acid deprivation (Chantranupong et al., 2014) and DNA damage-induced stress (Parmigiani et al., 2014).”

• cites Chantranupong et al., 2014 sourceNot checked yet

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• cites Parmigiani et al., 2014 sourceNot checked yet

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• cites Kim J S et al., 2015Not checked yet

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May combine two claims.

Several human proteins are now recognized as key metabolite sensors for the mTORC1 pathway: SESN1 and SESN2, CASTOR1, and SAMTOR, and may also include SLC38A9 and the vacuolar (v)-ATPase.

“However, several human proteins are now recognized as key metabolite sensors for the mTORC1 pathway. These include SESN1 and SESN2 (Chantranupong et al., 2014; Parmigiani et al., 2014; Peng et al., 2014), CASTOR1 (Chantranupong et al., 2016), and SAMTOR (Gu et al., 2017), and may also include SLC38A9 (Jung et al., 2015; Rebsamen et al., 2015; Wang et al., 2015) and the vacuolar (v)-ATPase (Zoncu”

• cites Chantranupong et al., 2014 sourceNot checked yet

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• cites Parmigiani et al., 2014 sourceNot checked yet

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• cites Peng et al., 2014 sourceNot checked yet

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May combine two claims.

The interaction between SESN2 and GATOR2 is leucine-dependent and intrinsically coupled to its interaction with GATOR2 and consequently to mTORC1 regulation.

“Experimentation with individual amino acids led to the discovery that the interaction between SESN2 and GATOR2 is leucine-dependent (Wolfson et al., 2016), and intrinsically coupled to its interaction with GATOR2, and consequently to mTORC1 regulation”

• cites Wolfson et al., 2016Not checked yet

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May combine two claims.

(m)TORC1 activity is stimulated by growth factor signaling and nutrients such as glucose and amino acids, whereas under conditions of stress such as starvation, energy or oxygen deficiency, or DNA damage, (m)TORC1 activity is robustly suppressed.

“(m)TORC1 activity has been shown to be stimulated by growth factor signaling and nutrients such as glucose and amino acids, whereas under conditions of stress, such as starvation, energy or oxygen deficiency, or DNA damage, (m)TORC1 activity is robustly supressed”

• cites Laplante and Sabatini, 2012 sourceNot checked yet

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Probably not a substantial claim: may not pass S2 (checkable), S4 (based).

A molecular understanding of the signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth.

“A molecular understanding of this signal integration pathway is required to understand how (m)TORC1 activation is reconciled with the many diverse and contradictory stimuli affecting cell growth.”

May combine two claims.

Upstream regulation of the Rag GTPases features at least four large protein complexes: GATOR1, a GAP for RagA/RagB/Gtr1; FLCN-FNIP, a GAP for RagC/RagD/Gtr2; GATOR2, an inhibitor of GATOR1; and KICSTOR, which is thought to regulate the GATOR complexes.

“Upstream regulation of the Rag GTPases is more baroque, featuring at least four large protein complexes including: GATOR1, a GAP for RagA/RagB/Gtr1 (Neklesa and Davis, 2009; Bar-Peled et al., 2013; Panchaud et al., 2013a); FLCN-FNIP (Lst4-Lst7 in yeast), a GAP for RagC/RagD/Gtr2 (Péli-Gulli et al., 2015; Petit et al., 2013; Tsun et al., 2013); GATOR2, an inhibitor of GATOR1 (Bar-Peled et al., 2013”

• cites Neklesa and Davis, 2009 sourceNot checked yet

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• cites Bar-Peled et al., 2013 sourceNot checked yet

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• cites Panchaud et al., 2013aNot checked yet

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May combine two claims.

ULK1 is able to stimulate phosphorylation of SESN2 either directly or indirectly, suggesting SESNs may constitute a switch between biogenesis and autophagy.

“SESNs have also been suggested to constitute a switch between biogenesis and autophagy given the observation that ULK1, a kinase controlling the induction of autophagy, is able to stimulate phosphorylation of SESN2 either directly or indirectly (Kimball et al., 2016).”

• cites Kimball et al., 2016 sourceNot checked yet

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May combine two claims.

Mutation of CASTOR1 residues D304 and S111 resulted in complete loss of arginine binding, as well as constitutive GATOR2 binding and strong mTORC1 inhibition even in the presence of arginine.

“Mutation of critical residues D304, which coordinates the arginine guanidinium group, and S111, which binds the free amine, resulted in complete loss of arginine binding, as well as constitutive GATOR2 binding and strong mTORC1 inhibition even in the presence of arginine.”

May combine two claims.

The binding of the CASTOR1 homodimer to GATOR2 is not competitive with SESN2: both proteins can bind the GATOR2 complex simultaneously.

“Intriguingly, the binding of the CASTOR1 homodimer to GATOR2 is not competitive with SESN2: both proteins can bind the GATOR2 complex simultaneously.”

May combine two claims.

The integrity of KICSTOR depends on SZT2; SZT2 is responsible for the interaction of KICSTOR with GATOR1, as well as GATOR2, although the latter interaction is indirect.

“The integrity of KICSTOR depends on the largest subunit, SZT2; this component is also responsible for the interaction of KICSTOR with GATOR1, as well as GATOR2, although the latter interaction is indirect (Wolfson et al., 2017).”

• cites Wolfson et al., 2017Not checked yet

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May combine two claims.

Knockout studies targeting SZT2 impair the localization of GATOR1 to lysosomes, but not that of GATOR2 or the Rag GTPases.

“Knockout studies targeting SZT2 impair the localization of GATOR1 to lysosomes, but not that of GATOR2 or the Rag GTPases.”

May combine two claims.

The structure of the mammalian GATOR1 complex was recently resolved by cryo-EM, revealing the architecture of each GATOR1 component and the structure of a stable complex with the Rag GTPases.

“While GATOR2 remains structurally uncharacterised, the structure of the mammalian GATOR1 complex was recently resolved by cryo-EM (Shen et al., 2018), revealing the architecture of each GATOR1 component (Fig. 3A) and the structure of a stable complex with the Rag GTPases (Fig. 3B).”

• cites Shen et al., 2018 sourceNot checked yet

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May combine two claims.

Residues Y118, Q119 and D121 are necessary for the CASTOR1-GATOR2 interaction and form patches on the same side of the CASTOR1 homodimer, distinct from the arginine binding pocket.

“Residues Y118, Q119 and D121 were identified as necessary for the GATOR2 interaction (Saxton et al., 2016a; Gai et al., 2016b) and further noted to form patches on the same side of the CASTOR1 homodimer, which are distinct surfaces to the arginine binding pocket (Gai et al., 2016b).”

• cites Saxton et al., 2016aNot checked yet

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• cites Gai et al., 2016bNot checked yet

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May combine two claims.

GATOR1 is presumed to interact with the Rag heterodimer in two ways: an inhibitory conformation that binds GTP-bound RagA with higher relative affinity but insufficient to activate GTP hydrolysis, and a lower-affinity interaction dependent on the NPRL2-NPRL3 heterodimer that stimulates GTPase activity.

“GATOR1 is thus presumed to interact with the Rag heterodimer in two ways: the ‘inhibitory’ conformation, captured in the resolved cryo-EM structure, which binds to GTP-bound RagA with higher relative affinity but insufficient to activate GTP hydrolysis, and a lower-affinity interaction dependent on the NPRL2-NPRL3 heterodimer that stimulates GTPase activity.”

• cites Shen et al., 2018 sourceNot checked yet

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May combine two claims.

SAM binding appears to constitute a physiologic signal of methionine sufficiency, and overexpression of wild type SAMTOR is sufficient to inhibit mTORC1 signaling, implying the apo-form represents the negative regulator.

“SAM binding appears to constitute a physiologic signal of methionine sufficiency, and overexpression of even wild type SAMTOR is sufficient to inhibit mTORC1 signaling, implying that the apo-form represents the negative regulator, as for the SESN and CASTOR proteins.”

• cites Gu et al., 2017Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing).

The known interaction of FLCN-FNIP with AMPK implies a close connection to cellular energy state and therefore the direct integration of metabolic signals.

“The known interaction with AMPK might well also imply a close connection to cellular energy state, and therefore the integration of metabolic signals directly.”

May combine two claims.

The DEPDC5 SHEN domain interacts with GTP analog-bound RagA proximal to the nucleotide binding pocket, but the interaction captured in the structure does not appear to be responsible for stimulation of GTP hydrolysis.

“The DEPDC5 Steric Hindrance for Enhancement of Nucleotidase activity (SHEN) domain interacts with GTP analog-bound RagA proximal to the nucleotide binding pocket (Fig. 3C), however the interaction captured in the structure does not appear to be responsible for stimulation of GTP hydrolysis.”

May combine two claims.

Those nutrient sensors discovered to date are diverse in structure but follow an established paradigm by interacting with further proteins within the pathway in the case of insufficiency rather than sufficiency of the nutrient in question.

“Those discovered to date are diverse in structure, but follow an established paradigm by interacting with further proteins within the pathway in the case of insufficiency rather than sufficiency of the nutrient in question.”

May combine two claims.

A loop comprising residues 270-280 sits over the CASTOR1 arginine binding site and locks the bound amino acid in place, but is disordered in the apo-state.

“A loop comprising residues 270-280 sits over the arginine binding site and ‘locks’ the bound amino acid in place, however is disordered in the apo-state (Guo and Deng; PDB ID: 5GT8)”

• cites Guo and Deng; PDB ID: 5GT8Not checked yet

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May combine two claims.

WDR24 and SEH1L form a minimal complex sufficient for interaction with SESN2, and these GATOR2 components with the addition of MIOS are sufficient to bind CASTOR1.

“WDR24 and SEH1L are known to form a minimal complex sufficient for interaction with SESN2 (Parmigiani et al., 2014), and these GATOR2 components, with the addition of MIOS, were also identified as sufficient to bind CASTOR1 (Chantranupong et al., 2016; Gai et al., 2016b).”

• cites Parmigiani et al., 2014 sourceNot checked yet

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• cites Chantranupong et al., 2016 sourceNot checked yet

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• cites Gai et al., 2016bNot checked yet

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May combine two claims.

An obligate FLCN-FNIP complex is necessary for the Rag interaction, since RagA and RagC coimmunoprecipitate with FLCN only when FNIP2 is coexpressed, and this interaction is strengthened during nutrient starvation and resulted in inhibition of (m)TORC1 activity.

“An obligate FLCN-FNIP complex is necessary for the Rag interaction, since RagA and RagC coimmunoprecipitate with FLCN only when FNIP2 is coexpressed, and this interaction is strengthened during nutrient starvation and resulted in inhibition of (m)TORC1 activity (Tsun et al., 2013; Péli-Gulli et al., 2015).”

• cites Tsun et al., 2013 sourceNot checked yet

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• cites Péli-Gulli et al., 2015 sourceNot checked yet

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May combine two claims.

The KICSTOR complex is a key component of the RagA/B control pathway, responsible for the localization of the Rag-GAP GATOR1 to its GTPase substrates.

“The KICSTOR complex is also a key component of the RagA/B control pathway, responsible for the localization of the Rag-GAP GATOR1 to its GTPase substrates.”

May combine two claims.

FLCN and FNIP both contain conserved N-terminal longin and C-terminal DENN domains, which are highly represented in Rab GEFs.

“FLCN and FNIP both contain conserved N-terminal longin and C-terminal Differentially Expressed in Normal cells and Neoplasia (DENN) domains (Fig. S3A), which are highly represented in Rab GEFs (Zhang D et al., 2012).”

• cites Zhang D et al., 2012Not checked yet

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Probably not a substantial claim: may not pass S1 (asserted), S3 (load-bearing).

A similar feedback mechanism may occur in mammalian cells, where posttranslational modifications impinging on the intra-DENN regions of FNIP could cause dispersal from the lysosome under conditions of nutrient sufficiency.

“Given this insight, a similar feedback mechanism may occur in mammalian cells, where posttranslational modifications impinging on the intra-DENN regions of FNIP could cause dispersal from the lysosome under conditions of nutrient sufficiency.”

May combine two claims.

Sequence analysis of SAMTOR suggests a class I Rossman fold, corroborated by in vitro binding assays establishing micromolar affinity for SAM and SAH.

“Sequence analysis of SAMTOR suggests the presence of a class I Rossman fold, typically found in methyltransferases (Fig. 2A), which has been corroborated by in vitro binding assays establishing micromolar affinity binding coefficients for both S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH).”

May combine two claims.

Endogenous FLCN-FNIP1/2 and Lst4-Lst7 complexes exhibit lysosomal or vacuolar localization during nutrient deficiency, and once there FLCN-FNIP2 acts as the GAP for RagC/D.

“Endogenous FLCN-FNIP1/2 and Lst4-Lst7 complexes exhibit lysosomal or vacuolar localization during nutrient deficiency, respectively (Petit et al., 2013; Tsun et al., 2013; Péli-Gulli et al., 2015), and once there FLCN-FNIP2 acts as the GAP for RagC/D.”

• cites Petit et al., 2013 sourceNot checked yet

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• cites Tsun et al., 2013 sourceNot checked yet

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• cites Péli-Gulli et al., 2015 sourceNot checked yet

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May combine two claims.

Kinetic assays for GTP hydrolysis suggest that a weaker interaction mediates true GAP activity, and this is thought to be performed by NPRL2-NPRL3.

“Kinetic assays for GTP hydrolysis suggest that a weaker interaction mediates true GAP activity, and this is thought to be performed by NPRL2-NPRL3 (Shen et al., 2018, 2017).”

• cites Shen et al., 2018, 2017Not matched

  Couldn’t be matched to a paper in Crossref, so it can’t be checked.

May combine two claims.

SZT2 is necessary for GATOR1-dependent inactivation of mTORC1 on the lysosome, as its loss results in constitutive mTORC1 activity and lysosomal localization.

“The SZT2 component appears to be necessary for coordinated GATOR1 and GATOR2 binding, and is necessary for GATOR1-dependent inactivation ofmTORC1 on the lysosome, as its loss results in constitutive mTORC1 activity and lysosomal localization (Wolfson et al., 2017; Peng et al., 2017).”

• cites Wolfson et al., 2017Not checked yet

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• cites Peng et al., 2017 sourceNot checked yet

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May combine two claims.

GATOR1 is a negative regulator of (m)TORC1 signaling, whereas GATOR2 inhibits GATOR1 in turn, thereby acting as a positive regulator.

“GATOR1 is a negative regulator of (m) TORC1 signaling, whereas GATOR2 inhibits GATOR1 in turn, thereby acting as a positive regulator.”

May combine two claims.

SAMTOR is thought to interact with the GATOR1 and KICSTOR complexes simultaneously, possibly through a tripartite interface given that all three proteins are required for any interaction.

“SAMTOR is thought to interact with the GATOR1 and KICSTOR complexes simultaneously (Gu et al., 2017; Wolfson et al., 2017), possibly through a tripartite interface given that all three proteins are required for any interaction.”

• cites Gu et al., 2017Not checked yet

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• cites Wolfson et al., 2017Not checked yet

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May combine two claims.

When the Rag heterodimer binds Ragulator, the N-terminal portion of LAMTOR1 encompassing residues 47-64 is resolved, forming an α-helix which packs against the RagC roadblock domain, whereas in the Ragulator complex alone this region of LAMTOR1 was disordered.

“It is important to note that when the Rag heterodimer binds Ragulator, the N-terminal portion of LAMTOR1 encompassing residues 47-64 is resolved, forming an α-helix which packs against the RagC roadblock domain, whereas in the Ragulator complex alone this region of LAMTOR1 was disordered (de Araujo et al., 2017; Yonehara et al., 2017).”

• cites de Araujo et al., 2017 sourceNot checked yet

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• cites Yonehara et al., 2017 sourceNot checked yet

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May combine two claims.

Recruitment of (m)TORC1 to the lysosome is controlled predominantly in response to signals corresponding to the intracellular nutrient and energy state, whereas its activation once there is controlled by RhebGTP in response to a wide variety of external and survival signals feeding into a single point of control.

“Whereas recruitment of (m)TORC1 to the lysosome is controlled in response predominantly to signals corresponding to the intracellular nutrient and energy state, its activation once there is controlled by RhebGTP in response to a wide variety of external and survival signals feeding into a single point of control.”

• cites Durán and Hall, 2012 sourceNot checked yet

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• cites Groenewoud and Zwartkruis, 2013 sourceNot checked yet

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May combine two claims.

The heptameric Ragulator-Rag complex structure showed Rag C-terminal roadblock domains binding to the LAMTOR2-LAMTOR3 heterodimer, building a tower of three roadblock domain-mediated heterodimers tied together by the extended LAMTOR1 subunit, and presenting the GTPase domains for interaction with RAPTOR.

“The heptameric Ragulator-Rag complex structure showed Rag C-terminal roadblock domains binding to the LAMTOR2-LAMTOR3 heterodimer (de Araujo et al., 2017; Su et al., 2017; Yonehara et al., 2017) (Fig. 4B), thus building a tower of three roadblock domain-mediated heterodimers tied together by the extended LAMTOR1 subunit, and presenting the GTPase domains for interaction with RAPTOR.”

• cites de Araujo et al., 2017 sourceNot checked yet

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• cites Su et al., 2017Not checked yet

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• cites Yonehara et al., 2017 sourceNot checked yet

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May combine two claims.

Overall, the Ragulator-Rag structures reveal a long molecular surface comprising three pairs of roadblock domain heterodimers, over which other protein complexes like the GAPs GATOR1 and FLCN-FNIP, as well as mTORC1, can bind.

“Overall, the Ragulator-Rag structures reveal a long molecular surface comprising three pairs of roadblock domain heterodimers, over which other protein complexes like the GAPs GATOR1 and FLCN-FNIP, as well as mTORC1, can bind.”

May combine two claims.

The Rag and Rheb GTPases constitute a coincidence detector which cooperate synergistically to robustly induce mTORC1 activity and fail to do so when either is only singly activated under physiologic conditions.

“Together, these GTPases constitute a coincidence detector which cooperate synergistically to robustly induce mTORC1 activity and fail to do so when either is only singly activated under physiologic conditions (Durán and Hall, 2012; Groenewoud and Zwartkruis, 2013).”

• cites Durán and Hall, 2012 sourceNot checked yet

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• cites Groenewoud and Zwartkruis, 2013 sourceNot checked yet

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May combine two claims.

In comparison to a Gtr1GMPPNP-Gtr2GMPPNP structure, the Gtr2GDP switch I region extends into an α-helix away from the nucleotide binding pocket with a concomitant global rotation, establishing a small novel interface between the GTPase domains whereby Gtr1 residues directly contact the Gtr2 nucleotide binding pocket and bound nucleotide itself.

“In comparison to a Gtr1GMPPNP-Gtr2GMPPNP structure (Gong et al., 2011), the Gtr2GDP switch I region extends into an α-helix away from the nucleotide binding pocket with a concomitant global rotation (Fig. 4D) establishing a small novel interface between the GTPase domains whereby Gtr1 residues directly contact the Gtr2 nucleotide binding pocket and bound nucleotide itself (Fig. 4E).”

• cites Gong et al., 2011 sourceNot checked yet

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May combine two claims.

The structures of LAMTOR2, LAMTOR3 and LAMTOR5 revealed roadblock folds for the individual LAMTOR3 and LAMTOR5 monomers and the formation of MP1/p14 heterodimers by edge-to-edge juxtaposition of the roadblock domains.

“The structures of LAMTOR2, LAMTOR3 and LAMTOR5 were the first to be characterized prior to the discovery of the Ragulator complex (Kurzbauer et al., 2004; Cui et al., 2008; Lunin et al., 2004; Qian et al., 2005; Garcia-Saez et al., 2011), revealing roadblock folds for the individual LAMTOR3 and LAMTOR5 monomers, and the formation of MP1/p14 heterodimers by edge-to-edge juxtaposition of the roadb”

• cites Kurzbauer et al., 2004 sourceNot checked yet

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• cites Cui et al., 2008 sourceNot checked yet

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• cites Lunin et al., 2004Not checked yet

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May combine two claims.

BORC has been implicated in regulating lysosome positioning in concert with amino acid signaling through Ragulator-Rag and also lysosome-autophagosome fusion during autophagy.

“BORC has been implicated in regulating lysosome positioning in concert with amino acid signaling through Ragulator-Rag (Filipek et al., 2017; Pu et al., 2017) and also lysosome-autophagosome fusion during autophagy (Jia et al., 2017)”

• cites Filipek et al., 2017 sourceNot checked yet

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• cites Pu et al., 2017Not checked yet

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• cites Jia et al., 2017 sourceNot checked yet

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May combine two claims.

The yeast EGOC structure, containing an Ego2-Ego3 heterodimer and the LAMTOR1 homolog Ego1, demonstrated a remarkably similar architecture, with Ego1 overlapping considerably with LAMTOR1, and Ego2 and Ego3 overlapping with LAMTOR5 and LAMTOR2 respectively.

“The yeast EGOC structure, containing an Ego2-Ego3 heterodimer, and the LAMTOR1 homolog Ego1, demonstrated a remarkably similar architecture, with Ego1 overlapping considerably with LAMTOR1, and Ego2 and Ego3 overlapping with LAMTOR5 and LAMTOR2 respectively.”

• cites Powis et al., 2015 sourceNot checked yet

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May combine two claims.

The structure of S. cerevisiae Ego3 provided evidence that the EGOC and Ragulator components are structurally conserved despite substantial sequence divergence, exhibiting a dimeric architecture very similar to that of LAMTOR2-LAMTOR3.

“The structure of S. cerevisiae Ego3 provided evidence that the EGOC and Ragulator components are structurally conserved, despite substantial sequence divergence (Kogan et al., 2010; Zhang et al., 2012), exhibiting a dimeric architecture very similar to that of LAMTOR2-LAMTOR3.”

• cites Kogan et al., 2010 sourceNot checked yet

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• cites Zhang et al., 2012Not checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

The interaction between Ragulator and the Rag heterodimers has been suggested to be dependent on the v-ATPase, which is thought to transmit intra-lysosomal amino acid signals to the Rags by affecting Ragulator GEF activity.

“The interaction between Ragulator and the Rag heterodimers has been suggested to be dependent on the v-ATPase (Zoncu et al., 2011), which is thought to transmit intra-lysosomal amino acid signals to the Rags by affecting Ragulator GEF activity.”

• cites Zoncu et al., 2011 sourceNot checked yet

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May combine two claims.

Presence of amino acids decreases the amount of Ragulator coimmunoprecipitating with RagB; the interaction is strengthened when the Rags are in a nucleotide-free state, and addition of GTP to an in vitro binding assay weakens the interaction.

“Presence of amino acids decreases the amount of Ragulator coimmunoprecipitating with RagB; furthermore, this interaction is strengthened when the Rags are in a nucleotide-free state, as the addition of GTP to an in vitro binding assay weakened the interaction (Bar-Peled et al., 2012).”

• cites Bar-Peled et al., 2012 sourceNot checked yet

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May combine two claims.

RagA/B, when GTP-bound, and RagC/D, when GDP-bound, recruit RAPTOR, thereby recruiting the mTORC1 kinase complex to late endosomes and lysosomes.

“RagA and RagC regulate mTORC1 in an amino acid-sensitive manner; RagA/B, when GTP-bound, and RagC/D, when GDP-bound, recruit RAPTOR, a core (m)TORC1 component (Sancak et al., 2008), thereby recruiting the kinase complex to late endosomes and lysosomes.”

• cites Sancak et al., 2008 sourceNot checked yet

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May combine two claims.

The integration of the majority of external and survival signals feeding into the (m)TORC1 pathway occurs through the TSC complex (TSCC), composed of TSC1, TSC2, and TBC1D7, which is the key signal integrator and negative regulator upstream of Rheb.

“The integration of the majority of external and survival signals feeding into the (m)TORC1 pathway occurs through the TSC complex (TSCC), composed of tuberous sclerosis complex protein 1 (TSC1) and TSC2, also known as hamartin and tuberin, and TBC1D7, which is the key signal integrator and negative regulator upstream of Rheb.”

• cites Inoki et al., 2002 sourceNot checked yet

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• cites Tee et al., 2002 sourceNot checked yet

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May combine two claims.

Five proteins, MP1, p14, p18, HBXIP and C7orf59, form a lysosomally-localized complex, interact with the Rag GTPases, and are required to recruit the Rag GTPases to their cognate compartment.

“None of the Rag proteins contain any lipid modification motifs that would result in their lysosomal localization, and therefore five proteins, MP1, p14, p18, HBXIP and C7orf59, which form a lysosomally-localized complex and which interact with the Rag GTPases, were found to be required to recruit them to their cognate compartment (Bar-Peled et al., 2012;Sancak et al., 2010).”

• cites Bar-Peled et al., 2012 sourceNot checked yet

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• cites Sancak et al., 2010 sourceNot checked yet

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May combine two claims.

TSCC is phosphorylated by many kinases, each of which contributes either activating or inhibiting modifications under various environmental conditions, including S6K1, CDK1, AMPK and Akt, which is itself activated by mTORC2.

“TSCC is phosphorylated by many kinases, each of which contributes either activating or inhibiting modifications under various environmental conditions, including S6K1, cyclin-dependent kinase 1 (CDK1), AMPK and Akt, which is itself activated by mTORC2 (Huang and Manning, 2009).”

• cites Huang and Manning, 2009 sourceNot checked yet

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Rheb is known to function on endomembranes in the mTORC1 pathway as a potent activator of the kinase and is the physiologic target of TSC2.

“Despite a lack of clear experimental evidence pointing to a defined localization pattern, Rheb is known to function on endomembranes in the mTORC1 pathway as a potent activator of the kinase (Long et al., 2005; Sato et al., 2009) and is the physiologic target of TSC2 (Castro et al., 2003; Garami et al., 2003; Inoki et al., 2003; Saucedo et al., 2003; Stocker et al., 2003; Tee et al., 2003; Zhang e”

• cites Long et al., 2005 sourceNot checked yet

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• cites Sato et al., 2009 sourceNot checked yet

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• cites Castro et al., 2003 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

Chromatographic analyses suggest that TSCCs also contain multiple copies of TSC1 and TSC2, and it is postulated that including multiple copies of each constituent protein may increase the sensitivity of the complex to allosteric regulation.

“Chromatographic analyses suggest that TSCCs also contains multiple copies of TSC1 and TSC2, and it is postulated that including multiple copies of each constituent protein may increase the sensitivity of the complex to allosteric regulation (Hoogeveen-Westerveld et al., 2012).”

• cites Hoogeveen-Westerveld et al., 2012 sourceNot checked yet

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The molecular features that enable Rheb to maintain a high GTP state prepare for de-inhibition by TSC2 to lead to rapid activation of mTORC1, thereby consolidating the function of Rheb as a potent activator of mTORC1.

“The molecular features which enable this behavior thus prepare for de-inhibition by TSC2 to lead to rapid activation of mTORC1, thereby consolidating the function of Rheb as a potent activator of mTORC1.”

May combine two claims.

In the complex solved by Qin et al., two TBC1D7 and four TSC1 molecules per asymmetric unit, whereby each TBC1D7 complexed with two TSC1 molecules, forming a triple helical bundle; the last ~15 residues of each TSC1 molecule were not visible.

“In contrast, the complex solved by Qin et al. shows two TBC1D7 and four TSC1 molecules per asymmetric unit, whereby each TBC1D7 complexed with two TSC1 molecules, forming a triple helical bundle (Fig. 5F). In this structure, the last ~15 residues of each TSC1 molecule – which formed the kinked helix in the crystal structure by Gai et al. – were not visible.”

• cites Qin et al., 2016 sourceNot checked yet

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Unlike other TBC proteins, TBC1D7 does not appear to have GAP activity relevant to the Rheb signaling axis upstream of mTORC1, instead likely increasing the sensitivity and responsivity of the entire complex to environmental signals.

“Unlike other TBC proteins, which are generally known to act as GAPs for the Rab family of GTPases (Fukuda, 2011), TBC1D7 does not appear to have GAP activity relevant to the Rheb signaling axis upstream of mTORC1, instead likely increasing the sensitivity and responsivity of the entire complex to environmental signals.”

• cites Fukuda, 2011 sourceNot checked yet

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In both TBC1D7-TSC1 structures, one TBC1D7 molecule was able to interact simultaneously with two TSC1 coiled-coil fragments, and alignment of these domains highlights structural similarity.

“In both cases, one TBC1D7 molecule was able to interact simultaneously with two TSC1 coiled-coil fragments, and alignment of these domains highlights structural similarity (Fig. 5G).”

• cites Gai et al., 2016aNot checked yet

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• cites Qin et al., 2016 sourceNot checked yet

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TSC2 has been shown to interact with 14-3-3 proteins when phosphorylated, and this interaction disrupts the function of the TSC1-TSC2 complex.

“Notably, TSC2 has already been shown to interact with 143-3 proteins when phosphorylated, and that this interaction disrupts the function of the TSC1-TSC2 complex (Nellist et al., 2003;Shumway et al., 2003).”

• cites Nellist et al., 2003Not checked yet

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• cites Shumway et al., 2003 sourceNot checked yet

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The N-terminal core domain of S. pombe TSC1 is exclusively α-helical, as predicted by bioinformatic analyses, and forms a solenoid built of HEAT repeats.

“These authors found that the core domain is exclusively α-helical, as predicted by bioinformatic analyses, and forms a solenoid built of HEAT repeats.”

• cites Sun et al., 2013 sourceNot checked yet

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May combine two claims.

Whereas specific metabolites signal to mTORC1 through the Rag GTPase axis, stress conditions such as hypoxia, DNA damage stress, ER stress, and growth factor and survival signaling are filtered through to the Rheb GTPase through TSCC by post-translational modification.

“Whereas it appears that specific metabolites signal to mTORC1 through the Rag GTPase axis, stress conditions such as hypoxia, DNA damage stress, ER stress, and growth factor and survival signaling, are filtered through to the Rheb GTPase through TSCC by post-translational modification (Kwiatkowski, 2003; Huang and Manning, 2008; Tomasoni and Mondino, 2011; Demetriades et al., 2016).”

• cites Kwiatkowski, 2003 sourceNot checked yet

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• cites Huang and Manning, 2008 sourceNot checked yet

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• cites Demetriades et al., 2016 sourceNot checked yet

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May combine two claims.

TSC1-TSC2 were unequivocally identified as inhibitors of the mTORC1 signaling pathway, specifically by virtue of TSC2 GAP activity toward the small GTPase Rheb.

“This identification of this regulatory mechanism, shown using the human proteins, unequivocally identified TSC1-TSC2 as inhibitors of the mTORC1 signaling pathway (Inoki et al., 2002; Tee et al., 2002), specifically by virtue of TSC2 GAP activity toward the small GTPase Rheb (Castro et al., 2003; Garami et al., 2003; Inoki et al., 2003; Saucedo et al., 2003;”

• cites Inoki et al., 2002 sourceNot checked yet

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• cites Tee et al., 2002 sourceNot checked yet

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• cites Castro et al., 2003 sourceNot checked yet

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TSC2 contains a domain with homology to Rap1-GAP and forms a complex in vivo with TSC1, mediated by predicted coiled-coil domains at the TSC1 C terminus and the TSC2 N terminus.

“TSC2 contains a domain with homology to Rap 1-GAP (van Slegtenhorst et al., 1997), and forms a complex in vivo with TSC1, mediated by predicted coiled-coil domains at the TSC1 C terminus and the TSC2 N terminus (van Slegtenhorst et al., 1998; Nellist et al., 1999) (Fig. 5A).”

• cites van Slegtenhorst et al., 1997 sourceNot checked yet

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• cites van Slegtenhorst et al., 1998 sourceNot checked yet

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• cites Nellist et al., 1999Not checked yet

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As supported by analytical ultracentrifugation data from both studies, the exact stoichiometry of the TBC1D7-TSC1 coiled-coil interaction appears to be dependent on the ratio between the two molecules, and this may underlie physiologic activity of TBC1D7 in regulating TSCC oligomerisation.

“As supported by analytical ultracentrifugation data from both studies (Gai et al., 2016a; Qin et al., 2016), the exact stoichiometry of the TBC1D7-TSC1 coiled-coil interaction appears to be dependent on the ratio between the two molecules, and this may underlie physiologic activity of TBC1D7 in regulation TSCC oligomerisation.”

• cites Gai et al., 2016aNot checked yet

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• cites Qin et al., 2016 sourceNot checked yet

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The N-terminal TSC2 fragment is sufficient to pull down the full-length and C-terminal half of TSC1, and these interacting regions are conserved in the human proteins.

“This fragment of TSC2 was also shown to be sufficient to pull down the full-length, and C-terminal half of, TSC1, and these interacting regions are conserved in the human proteins (Zech et al., 2016).”

• cites Zech et al., 2016 sourceNot checked yet

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May combine two claims.

Y35 prevents GTP dissociation by closing over the nucleotide binding pocket, coordinating the phosphates more tightly than in Ras and Rap.

“Y35 also prevents GTP dissociation by closing over the nucleotide binding pocket (Fig. 6C), coordinating the phosphates more tightly than in Ras and Rap (Mazhab-Jafari et al., 2012).”

• cites Mazhab-Jafari et al., 2012 sourceNot checked yet

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The TBC1D7 apo structure reveals an architecture highly conserved with other TBC domain proteins, with little conformational difference in comparison to the TSC1-complexed structures.

“The apo structure (Fig. 5D) reveals an architecture highly conserved with other TBC domain proteins (Fischer et al., 2016; Fukuda, 2011; Park et al., 2011), with little conformational difference in comparison to the TSC1-complexed structures.”

• cites Fischer et al., 2016 sourceNot checked yet

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• cites Fukuda, 2011 sourceNot checked yet

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• cites Park et al., 2011 sourceNot checked yet

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Hypoxia-dependent regulation through REDD1 disrupts cytosolic 14-3-3-bound TSC2 and enables subsequent TSC2 localization to the lysosome where it can inhibit Rheb.

“Another example of this localization dependency includes hypoxia-dependent regulation through REDD1 (Brugarolas et al., 2004), which disrupts cytosolic 14-3-3-bound TSC2 and enables subsequent TSC2 localization to the lysosome where it can inhibit Rheb (DeYoung et al., 2008).”

• cites Brugarolas et al., 2004 sourceNot checked yet

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• cites DeYoung et al., 2008 sourceNot checked yet

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Q64 is displaced by >4 Å from the counterpart RasGTP structure due to an unusual conformation of switch II, and its sidechain is buried in a hydrophobic pocket.

“Q64, which is required for polarization/activation of the water molecule that initiates nucleophilic attack, is displaced by > 4 Å from the counterpart RasGTP structure, due to an unusual conformation of switch II, and furthermore its sidechain is buried in a hydrophobic pocket.”

• cites Yu et al., 2005Not checked yet

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The binding of Rheb to mTORC1 exhibits enforced cooperativity, since a singly-bound Rheb would result in a highly unfavorable dimerization interface; mTORC1 is therefore robustly activated by the binding of two Rheb GTPases per kinase complex.

“The binding of Rheb to mTORC1 exhibits enforced cooperativity, since a singly-bound Rheb would result in a highly unfavorable dimerization interface; mTORC1 is therefore robustly activated by the binding of two Rheb GTPases per kinase complex, which causes a global rearrangement culminating in the priming of the active site for catalysis.”

May combine two claims.

Density corresponding to Rheb was observed at the N-terminal portions of the N-HEAT, M-HEAT and FAT domains, resulting in a four-way interface where Rheb switch I residues bound the M-HEAT solenoid and FAT domain, and switch II formed contacts with all three mTORC1 domains.

“Density corresponding to Rheb was observed at the N-terminal portions of the N- HEAT, M-HEAT and FAT domains, thereby resulting in a four-way interface where Rheb switch I residues bound the M-HEAT solenoid and FAT domain, and switch II formed contacts with all three mTORC1 domains.”

• cites Yang et al., 2017 sourceNot checked yet

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The structure of the mTORC1 core, consisting of an mTOR mLST8 "FATKIN" unit, was solved in 2013 by Yang and colleagues, providing the first structural data on the kinase and enabling a molecular-level understanding of kinase inhibition by rapamycin.

“The structure of the mTORC1 core, consisting of an mTOR mLST8 “FATKIN” unit, was solved in 2013 by Yang and colleagues, providing the first structural data on the kinase and enabling a molecular-level understanding of kinase inhibition by rapamycin (Yang et al., 2013).”

• cites Yang et al., 2013 sourceNot checked yet

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The mTORC1 crystal structure revealed that the kinase domain exhibited a classical bilobed structure, just as in the PI3K family, and the PIKK-specific FAT domain encircles the kinase domain.

“The crystal structure revealed that the kinase domain exhibited a classical bilobed structure, just as in the PI3K family, and the PIKK-specific FAT domain encircles the kinase domain, raising the possibility that interaction of regulatory proteins with this region will allosterically impact the kinase domain structure as well.”

• cites Yang et al., 2013 sourceNot checked yet

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Probably not a substantial claim: may not pass S3 (load-bearing). May combine two claims.

mTOR contains a FRAP, ATM and TRAPP (FAT) domain, a catalytic kinase domain and a C-terminal FATC domain found only in PIKKs.

“Being one of the mammalian PI3K-related protein kinases (PIKKs), mTOR was known by sequence homology to contain a FRAP, ATM and TRAPP (FAT) domain, a catalytic kinase domain and a C-terminal ‘FATC ’ domain found only in PIKKs (Bosotti et al., 2000).”

• cites Bosotti et al., 2000 sourceNot checked yet

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