- Email: [email protected]
TOR Signaling Is Going through a Phase
Cell Metabolism
Previews activity, metabolic regulation and mTOR activity for cancer formation. But it also throws light on the possibility that the position of a hepatocyte within the liver lobule and its metabolic state matter more for destiny than predetermined identity does. ACKNOWLEDGMENTS W.G. is supported by NIH R24OD017870, R01DK090311, and R01DK105198; the Claudia Adams Barr Program in Cancer Research; and the Pew Charitable Trusts Biomedical Sciences Scholars Program. DECLARATION OF INTERESTS W.G. is a consultant and scientific advisory board member of Camp4 Therapeutics. REFERENCES Adebayo Michael, A.O., Ko, S., Tao, J., Moghe, A., Yang, H., Xu, M., Russell, J.O., PradhanSundd, T., Liu, S., Singh, S., et al. (2019).
Inhibiting glutamine-dependent mTORC1 activation ameliorates liver cancers driven by betaCatenin mutations. Cell Metab. 29, this issue, 1135–1150. Benhamouche, S., Decaens, T., Godard, C., Chambrey, R., Rickman, D.S., Moinard, C., Vasseur-Cognet, M., Kuo, C.J., Kahn, A., Perret, C., and Colnot, S. (2006). Apc tumor suppressor gene is the ‘‘zonation-keeper’’ of mouse liver. Dev. Cell 10, 759–770. Chaturantabut, S., Shwartz, A., Evason, K.J., Cox, A.G., Labella, K., Schepers, A.G., Yang, S., Aravena, M., Houvras, Y., Mancio-Silva, L., et al. (2019). Estrogen activation of G-protein-coupled estrogen receptor 1 regulates phosphoinositide 3-Kinase and mTOR signaling to promote liver growth in zebrafish and proliferation of human hepatocytes. Gastroenterology. https://doi.org/10. 1053/j.gastro.2019.01.010. Cox, A.G., Hwang, K.L., Brown, K.K., Evason, K., Beltz, S., Tsomides, A., O’Connor, K., Galli, G.G., Yimlamai, D., Chhangawala, S., et al. (2016). Yap reprograms glutamine metabolism to increase nucleotide biosynthesis and enable liver growth. Nat. Cell Biol. 18, 886–896. €lke, C., Geissler, E.K., Schnitzbauer, A.A., Zu Lamby, P.E., Proneth, A., Duvoux, C., Burra, P.,
Jauch, K.W., Rentsch, M., Ganten, T.M., et al. (2016). Sirolimus use in liver transplant recipients with hepatocellular carcinoma: a randomized, multicenter, open-label phase 3 trial. Transplantation 100, 116–125. Russell, J.O., and Monga, S.P. (2018). Wnt/ b-catenin signaling in liver development, homeostasis, and pathobiology. Annu. Rev. Pathol. 13, 351–378. Sekine, S., Lan, B.Y., Bedolli, M., Feng, S., and Hebrok, M. (2006). Liver-specific loss of beta-catenin blocks glutamine synthesis pathway activity and cytochrome p450 expression in mice. Hepatology 43, 817–825. Villanueva, A. (2019). Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462. Villanueva, A., Chiang, D.Y., Newell, P., Peix, J., Thung, S., Alsinet, C., Tovar, V., Roayaie, S., Minguez, B., Sole, M., et al. (2008). Pivotal role of mTOR signaling in hepatocellular carcinoma. Gastroenterology 135, 1972–1983, 1983.e1–11. Zhu, A.X., Kudo, M., Assenat, E., Cattan, S., Kang, Y.K., Lim, H.Y., Poon, R.T., Blanc, J.F., Vogel, A., Chen, C.L., et al. (2014). Effect of everolimus on survival in advanced hepatocellular carcinoma after failure of sorafenib: the EVOLVE-1 randomized clinical trial. JAMA 312, 57–67.
TOR Signaling Is Going through a Phase Manoel Prouteau1,2 and Robbie Loewith1,2,3,* 1Department
of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland
2Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva Medical School (CMU) 1, rue Michel-Servet, CH – 1211 Geneva 4,
Switzerland 3Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland *Correspondence: [email protected] https://doi.org/10.1016/j.cmet.2019.04.010
Recently in Cell, Kato et al. (2019) and Yang et al. (2019) report that reversible oxidation of multiple methionines in a region of Pbp1, the yeast paralog of ataxin-2 protein, couples metabolic redox status to phase separation of Pbp1 into liquid-like condensates. In turn, Pbp1 condensates inhibit target of rapamycin complex 1 (TORC1) signaling and thereby induce autophagy and restore metabolic homeostasis. Cells, particularly unicellular organisms, experience a wide range of environmental conditions that impact their growth. To successfully negotiate these differing environments, dedicated signaling pathways have evolved that sense metabolite flux and accordingly adapt enzyme activity and cell behavior to achieve metabolic homeostasis. Metabolic homeostasis set points enable cells to optimally utilize available nutrients while providing an energy and nutrient buffering capacity to
enable potentially costly, biochemical reprogramming upon acute changes in metabolic requirements. A central factor in the signaling pathways dedicated to metabolic homeostasis in eukaryote cells is the target of rapamycin (TOR) protein kinase. TOR assembles into two multiprotein complexes, TORC1 and TORC2, which contribute to different aspects of cellular homeostasis (Eltschinger and Loewith, 2016). TORC1, the better studied of the two complexes, is particularly
appreciated for its roles in simultaneously promoting anabolism such as ribosome biogenesis and inhibiting catabolism including turnover of macromolecules through various autophagic processes. However, identification of the pertinent chemical and biophysical growth sentinels sensed upstream of these complexes and how this information is signaled to regulate TOR kinase activities remain active areas of research. An exciting major advance in this endeavor
Cell Metabolism 29, May 7, 2019 ª 2019 Elsevier Inc. 1019
Cell Metabolism
Previews
Figure 1. Redox-Regulated Phase Separation of Pbp1 Protein Couples Mitochondrial Function to TORC1 Activity The Pab1-binding protein 1 (Pbp1) possesses a C-terminal low-complexity (LC) domain that enables the protein to self-associate into cross-b polymers that form a gel-like phase visualized in vivo as a nonuniform distribution of the GFP-tagged protein. Pbp1 in this gel-like condensate physically interacts with TORC1, leading to reduced kinase activity through unknown mechanisms. Loss of TORC1 activity leads to autophagy induction and cessation of growth programs such as ribosome biogenesis. Unlike other aggregate-prone LC domains, which are enriched in aromatic amino acids, the LC domain of Pbp1 is enriched in methionine (denoted with S’s in the boxes). Oxidative stress, for example from dysfunctional mitochondria, leads to oxidation of these methionine residues, decondensation of Pbp1 gels, and enhanced TORC1 signaling. Pbp1 can be reduced through the concerted actions of the methionine sulfoxide reductases (Mrs1/2), thioredoxin (Trx1), thioredoxin reductase (Trr1), and NADP+/NADPH.
has now been detailed in back-to-back papers in Cell (Kato et al., 2019; Yang et al., 2019). The story begins some years ago with a study by the Tu lab investigating autophagy induction in yeast grown under respiratory conditions (Wu and Tu, 2011). Specifically, they found that switching respiring yeast cells from relatively nutrient-rich medium containing yeast extract (YPL) to chemically defined, nutrient-poor medium (SL) strongly induces autophagy. This observation in and of itself was not particularly surprising—autophagy induction under these conditions serves to dismantle existing metabolic infrastructures and to relin1020 Cell Metabolism 29, May 7, 2019
quish metabolites to be employed in the subsequent rewiring of metabolism— however, what was curious was that this autophagy induction paradigm utilized novel signaling pathways not apparently employed in the more classically studied autophagy induced by nitrogen withdrawal in the presence of glucose, i.e., in fermentative growth conditions. In retrospect, such differences may also not be so surprising given the very different initial metabolic setups of respiring versus fermenting cells, particularly regarding mitochondrial output, which, in respiratory conditions, must include ATP in addition to nitrogenous metabolites (Chen et al., 2017)
Subsequent genetic and molecular characterization of YPL / SL-induced autophagy identified several factors essential to this process including the proteins Iml1, Npr2, and Npr3 (Wu and Tu, 2011) and the metabolite S-adenosylmethionine (SAM) (Sutter et al., 2013). Iml1, Npr2, and Npr3 act together in a complex, known as SEACIT in yeast or GATOR1 in mammals, that inhibits TORC1 signaling (Eltschinger and Loewith, 2016). Consistently, shift to SL (but not nitrogen starvation per se) leads to TORC1 inactivation and consequently autophagy induction in wild-type (WT) cells, but not seacit mutants. In contrast, SAM appears to inhibit YPL / SLinduced autophagy at multiple levels: it is used by the methyltransferase Ppm1 to methylate the catalytic subunits of the PP2A phosphatase, altering the latter’s activity toward a potentially large number of substrates. Interestingly, one of these substrates is Npr2, which, when dephosphorylated, compromises the ability of SEACIT to inhibit TORC1. These results position SAM as a sentinel metabolite in maintaining metabolic homeostasis but do not exclude other metabolites from playing a similarly important role. In this vein, Yang et al. (2019) now identify the poly(A)-binding protein 1 (Pab1)binding protein 1 (Pbp1) as a new player in YPL / SL-induced autophagy. Like seacit mutants identified previously, pbp1 cells were found to similarly fail to induce autophagy upon shift to SL medium. The molecular functions of Pbp1 are not understood, but this protein is well known to phase separate into RNA-containing stress granules upon glucose deprivation or heat shock. Intriguingly, these condensates have been suggested to be mechanistically important for inactivation of TORC1 under these stress conditions (DeMille et al., 2015; Takahara and Maeda, 2012). Building on these prior observations, Yang et al. identified two domains in Pbp1 important for TORC1 inhibition: an approximately 100 amino acid sequence downstream of the putative RNA-binding domains that physically interacts with the Kog1 (Raptor) subunit of TORC1 and a C-terminal low-complexity (LC) domain necessary for Pbp1 phase separation in vitro and in vivo. Subsequent experiments clearly demonstrate that phase separation is essential for Pbp1-mediated TORC1 inactivation, but the molecular
Cell Metabolism
Previews mechanism through which TORC1 inactivation is achieved remains mysterious. One possible mechanism, suggested by the authors, is that interaction with Pbp1 condensates provokes the assembly of TORC1 particles into an allosterically inactivated, higher-order TORC1 condensate potentially analogous to the recently described TOROIDs observed upon glucose depletion (Prouteau et al., 2017). Although the mechanism leading to TORC1 inactivation by Pbp1 condensates remains to be defined, the metabolic changes leading to Pbp1 phase separation are much more developed. Yang et al. noted that the LC domain of Pbp1 is unusually rich in methionines in contrast to aromatic amino acids typically found in LC domains. Replacing these methionines with serines yielded Pbp1 variants that were no longer able to properly inhibit TORC1. These intriguing observations were followed up in Kato et al. (2019), who demonstrated that the LC methionines can be oxidized, in vitro and in vivo, and that oxidation leads to the decondensation of Pbp1 gels and subsequent TORC1 activation. Conversely, H2O2-mediated ‘‘melting’’ of Pbp1 gels is reversed through the re-reduction of oxidized methionines via the coupled reactions of two methionine sulfoxide reductases, thioredoxin, thioredoxin reductase, and NADPH. Collectively, these results position the LC domain of Pbp1 as a sensor of redox, potentially as a readout of metabolic status of mitochondria, in the signaling pathways that serve to maintain metabolic homeostasis (Figure 1).
Unsurprisingly, these studies provoke additional important questions, including the epistatic relationship between SEACIT and Pbp1 in the regulation of TORC1. It will also be interesting to see if pbp1 mutants, like seacit mutants, fail to establish robust metabolic cycles under sustained slow growth conditions. Pbp1 is conserved, and mutations in the ATXN2 gene that encodes its human paralog, ataxin-2, are associated with neurodegenerative diseases including spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis. Ataxin-2, like Pbp1, possesses a C-terminal LC domain with conserved methionines, suggesting that it too serves as a redox sensor to control metabolic homeostasis. A better understanding of ataxin-2 functions should shed light on these debilitating diseases and suggest novel therapeutic strategies, for example, mTORC1 inhibition. Along these lines, mutations in genes encoding Gator-1 components are also associated with neurological disease (Bar-Peled and Sabatini, 2014). Last, but not least: so far SAM and redox have been identified as important sentinels of respiratory metabolism, sensed by the signaling pathways that regulate metabolic homeostasis; what other sentinels are there, how are these sensed, and is dysregulation of these sensors also implicated in disease?
REFERENCES Bar-Peled, L., and Sabatini, D.M. (2014). Regulation of mTORC1 by amino acids. Trends Cell Biol. 24, 400–406. Chen, J., Sutter, B.M., Shi, L., and Tu, B.P. (2017). GATOR1 regulates nitrogenic cataplerotic reactions of the mitochondrial TCA cycle. Nat. Chem. Biol. 13, 1179–1186. DeMille, D., Badal, B.D., Evans, J.B., Mathis, A.D., Anderson, J.F., and Grose, J.H. (2015). PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1. Mol. Biol. Cell 26, 569–582. Eltschinger, S., and Loewith, R. (2016). TOR complexes and the maintenance of cellular homeostasis. Trends Cell Biol. 26, 148–159. Kato, M., Yang, Y.S., Sutter, B.M., Wang, Y., McKnight, S.L., and Tu, B.P. (2019). Redox state controls phase separation of the yeast ataxin-2 protein via reversible oxidation of its methioninerich low-complexity domain. Cell 177, 711–721. Prouteau, M., Desfosses, A., Sieben, C., Bourgoint, C., Lydia Mozaffari, N., Demurtas, D., Mitra, A.K., Guichard, P., Manley, S., and Loewith, R. (2017). TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 550, 265–269. Sutter, B.M., Wu, X., Laxman, S., and Tu, B.P. (2013). Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell 154, 403–415. Takahara, T., and Maeda, T. (2012). Transient sequestration of TORC1 into stress granules during heat stress. Mol. Cell 47, 242–252.
ACKNOWLEDGMENTS
Wu, X., and Tu, B.P. (2011). Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Mol. Biol. Cell 22, 4124–4133.
The Loewith lab acknowledges financial support from the Canton of Geneva, the Swiss National Science Foundation, the Swiss National Centre of Competence in Research Chemical Biology, and the European Research Council (CoG TORCH).
Yang, Y.S., Kato, M., Wu, X., Litsios, A., Sutter, B.M., Wang, Y., Hsu, C.H., Wood, N.E., Lemoff, A., Mirzaei, H., et al. (2019). Yeast ataxin-2 forms an Intracellular condensate required for the inhibition of TORC1 signaling during respiratory growth. Cell 177, 697–710.
Cell Metabolism 29, May 7, 2019 1021
Previews activity, metabolic regulation and mTOR activity for cancer formation. But it also throws light on the possibility that the position of a hepatocyte within the liver lobule and its metabolic state matter more for destiny than predetermined identity does. ACKNOWLEDGMENTS W.G. is supported by NIH R24OD017870, R01DK090311, and R01DK105198; the Claudia Adams Barr Program in Cancer Research; and the Pew Charitable Trusts Biomedical Sciences Scholars Program. DECLARATION OF INTERESTS W.G. is a consultant and scientific advisory board member of Camp4 Therapeutics. REFERENCES Adebayo Michael, A.O., Ko, S., Tao, J., Moghe, A., Yang, H., Xu, M., Russell, J.O., PradhanSundd, T., Liu, S., Singh, S., et al. (2019).
Inhibiting glutamine-dependent mTORC1 activation ameliorates liver cancers driven by betaCatenin mutations. Cell Metab. 29, this issue, 1135–1150. Benhamouche, S., Decaens, T., Godard, C., Chambrey, R., Rickman, D.S., Moinard, C., Vasseur-Cognet, M., Kuo, C.J., Kahn, A., Perret, C., and Colnot, S. (2006). Apc tumor suppressor gene is the ‘‘zonation-keeper’’ of mouse liver. Dev. Cell 10, 759–770. Chaturantabut, S., Shwartz, A., Evason, K.J., Cox, A.G., Labella, K., Schepers, A.G., Yang, S., Aravena, M., Houvras, Y., Mancio-Silva, L., et al. (2019). Estrogen activation of G-protein-coupled estrogen receptor 1 regulates phosphoinositide 3-Kinase and mTOR signaling to promote liver growth in zebrafish and proliferation of human hepatocytes. Gastroenterology. https://doi.org/10. 1053/j.gastro.2019.01.010. Cox, A.G., Hwang, K.L., Brown, K.K., Evason, K., Beltz, S., Tsomides, A., O’Connor, K., Galli, G.G., Yimlamai, D., Chhangawala, S., et al. (2016). Yap reprograms glutamine metabolism to increase nucleotide biosynthesis and enable liver growth. Nat. Cell Biol. 18, 886–896. €lke, C., Geissler, E.K., Schnitzbauer, A.A., Zu Lamby, P.E., Proneth, A., Duvoux, C., Burra, P.,
Jauch, K.W., Rentsch, M., Ganten, T.M., et al. (2016). Sirolimus use in liver transplant recipients with hepatocellular carcinoma: a randomized, multicenter, open-label phase 3 trial. Transplantation 100, 116–125. Russell, J.O., and Monga, S.P. (2018). Wnt/ b-catenin signaling in liver development, homeostasis, and pathobiology. Annu. Rev. Pathol. 13, 351–378. Sekine, S., Lan, B.Y., Bedolli, M., Feng, S., and Hebrok, M. (2006). Liver-specific loss of beta-catenin blocks glutamine synthesis pathway activity and cytochrome p450 expression in mice. Hepatology 43, 817–825. Villanueva, A. (2019). Hepatocellular carcinoma. N. Engl. J. Med. 380, 1450–1462. Villanueva, A., Chiang, D.Y., Newell, P., Peix, J., Thung, S., Alsinet, C., Tovar, V., Roayaie, S., Minguez, B., Sole, M., et al. (2008). Pivotal role of mTOR signaling in hepatocellular carcinoma. Gastroenterology 135, 1972–1983, 1983.e1–11. Zhu, A.X., Kudo, M., Assenat, E., Cattan, S., Kang, Y.K., Lim, H.Y., Poon, R.T., Blanc, J.F., Vogel, A., Chen, C.L., et al. (2014). Effect of everolimus on survival in advanced hepatocellular carcinoma after failure of sorafenib: the EVOLVE-1 randomized clinical trial. JAMA 312, 57–67.
TOR Signaling Is Going through a Phase Manoel Prouteau1,2 and Robbie Loewith1,2,3,* 1Department
of Molecular Biology, University of Geneva, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland
2Institute of Genetics and Genomics of Geneva (iGE3), University of Geneva Medical School (CMU) 1, rue Michel-Servet, CH – 1211 Geneva 4,
Switzerland 3Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Sciences II, Room 3-308, 30 Quai Ernest-Ansermet, CH1211 Geneva, Switzerland *Correspondence: [email protected] https://doi.org/10.1016/j.cmet.2019.04.010
Recently in Cell, Kato et al. (2019) and Yang et al. (2019) report that reversible oxidation of multiple methionines in a region of Pbp1, the yeast paralog of ataxin-2 protein, couples metabolic redox status to phase separation of Pbp1 into liquid-like condensates. In turn, Pbp1 condensates inhibit target of rapamycin complex 1 (TORC1) signaling and thereby induce autophagy and restore metabolic homeostasis. Cells, particularly unicellular organisms, experience a wide range of environmental conditions that impact their growth. To successfully negotiate these differing environments, dedicated signaling pathways have evolved that sense metabolite flux and accordingly adapt enzyme activity and cell behavior to achieve metabolic homeostasis. Metabolic homeostasis set points enable cells to optimally utilize available nutrients while providing an energy and nutrient buffering capacity to
enable potentially costly, biochemical reprogramming upon acute changes in metabolic requirements. A central factor in the signaling pathways dedicated to metabolic homeostasis in eukaryote cells is the target of rapamycin (TOR) protein kinase. TOR assembles into two multiprotein complexes, TORC1 and TORC2, which contribute to different aspects of cellular homeostasis (Eltschinger and Loewith, 2016). TORC1, the better studied of the two complexes, is particularly
appreciated for its roles in simultaneously promoting anabolism such as ribosome biogenesis and inhibiting catabolism including turnover of macromolecules through various autophagic processes. However, identification of the pertinent chemical and biophysical growth sentinels sensed upstream of these complexes and how this information is signaled to regulate TOR kinase activities remain active areas of research. An exciting major advance in this endeavor
Cell Metabolism 29, May 7, 2019 ª 2019 Elsevier Inc. 1019
Cell Metabolism
Previews
Figure 1. Redox-Regulated Phase Separation of Pbp1 Protein Couples Mitochondrial Function to TORC1 Activity The Pab1-binding protein 1 (Pbp1) possesses a C-terminal low-complexity (LC) domain that enables the protein to self-associate into cross-b polymers that form a gel-like phase visualized in vivo as a nonuniform distribution of the GFP-tagged protein. Pbp1 in this gel-like condensate physically interacts with TORC1, leading to reduced kinase activity through unknown mechanisms. Loss of TORC1 activity leads to autophagy induction and cessation of growth programs such as ribosome biogenesis. Unlike other aggregate-prone LC domains, which are enriched in aromatic amino acids, the LC domain of Pbp1 is enriched in methionine (denoted with S’s in the boxes). Oxidative stress, for example from dysfunctional mitochondria, leads to oxidation of these methionine residues, decondensation of Pbp1 gels, and enhanced TORC1 signaling. Pbp1 can be reduced through the concerted actions of the methionine sulfoxide reductases (Mrs1/2), thioredoxin (Trx1), thioredoxin reductase (Trr1), and NADP+/NADPH.
has now been detailed in back-to-back papers in Cell (Kato et al., 2019; Yang et al., 2019). The story begins some years ago with a study by the Tu lab investigating autophagy induction in yeast grown under respiratory conditions (Wu and Tu, 2011). Specifically, they found that switching respiring yeast cells from relatively nutrient-rich medium containing yeast extract (YPL) to chemically defined, nutrient-poor medium (SL) strongly induces autophagy. This observation in and of itself was not particularly surprising—autophagy induction under these conditions serves to dismantle existing metabolic infrastructures and to relin1020 Cell Metabolism 29, May 7, 2019
quish metabolites to be employed in the subsequent rewiring of metabolism— however, what was curious was that this autophagy induction paradigm utilized novel signaling pathways not apparently employed in the more classically studied autophagy induced by nitrogen withdrawal in the presence of glucose, i.e., in fermentative growth conditions. In retrospect, such differences may also not be so surprising given the very different initial metabolic setups of respiring versus fermenting cells, particularly regarding mitochondrial output, which, in respiratory conditions, must include ATP in addition to nitrogenous metabolites (Chen et al., 2017)
Subsequent genetic and molecular characterization of YPL / SL-induced autophagy identified several factors essential to this process including the proteins Iml1, Npr2, and Npr3 (Wu and Tu, 2011) and the metabolite S-adenosylmethionine (SAM) (Sutter et al., 2013). Iml1, Npr2, and Npr3 act together in a complex, known as SEACIT in yeast or GATOR1 in mammals, that inhibits TORC1 signaling (Eltschinger and Loewith, 2016). Consistently, shift to SL (but not nitrogen starvation per se) leads to TORC1 inactivation and consequently autophagy induction in wild-type (WT) cells, but not seacit mutants. In contrast, SAM appears to inhibit YPL / SLinduced autophagy at multiple levels: it is used by the methyltransferase Ppm1 to methylate the catalytic subunits of the PP2A phosphatase, altering the latter’s activity toward a potentially large number of substrates. Interestingly, one of these substrates is Npr2, which, when dephosphorylated, compromises the ability of SEACIT to inhibit TORC1. These results position SAM as a sentinel metabolite in maintaining metabolic homeostasis but do not exclude other metabolites from playing a similarly important role. In this vein, Yang et al. (2019) now identify the poly(A)-binding protein 1 (Pab1)binding protein 1 (Pbp1) as a new player in YPL / SL-induced autophagy. Like seacit mutants identified previously, pbp1 cells were found to similarly fail to induce autophagy upon shift to SL medium. The molecular functions of Pbp1 are not understood, but this protein is well known to phase separate into RNA-containing stress granules upon glucose deprivation or heat shock. Intriguingly, these condensates have been suggested to be mechanistically important for inactivation of TORC1 under these stress conditions (DeMille et al., 2015; Takahara and Maeda, 2012). Building on these prior observations, Yang et al. identified two domains in Pbp1 important for TORC1 inhibition: an approximately 100 amino acid sequence downstream of the putative RNA-binding domains that physically interacts with the Kog1 (Raptor) subunit of TORC1 and a C-terminal low-complexity (LC) domain necessary for Pbp1 phase separation in vitro and in vivo. Subsequent experiments clearly demonstrate that phase separation is essential for Pbp1-mediated TORC1 inactivation, but the molecular
Cell Metabolism
Previews mechanism through which TORC1 inactivation is achieved remains mysterious. One possible mechanism, suggested by the authors, is that interaction with Pbp1 condensates provokes the assembly of TORC1 particles into an allosterically inactivated, higher-order TORC1 condensate potentially analogous to the recently described TOROIDs observed upon glucose depletion (Prouteau et al., 2017). Although the mechanism leading to TORC1 inactivation by Pbp1 condensates remains to be defined, the metabolic changes leading to Pbp1 phase separation are much more developed. Yang et al. noted that the LC domain of Pbp1 is unusually rich in methionines in contrast to aromatic amino acids typically found in LC domains. Replacing these methionines with serines yielded Pbp1 variants that were no longer able to properly inhibit TORC1. These intriguing observations were followed up in Kato et al. (2019), who demonstrated that the LC methionines can be oxidized, in vitro and in vivo, and that oxidation leads to the decondensation of Pbp1 gels and subsequent TORC1 activation. Conversely, H2O2-mediated ‘‘melting’’ of Pbp1 gels is reversed through the re-reduction of oxidized methionines via the coupled reactions of two methionine sulfoxide reductases, thioredoxin, thioredoxin reductase, and NADPH. Collectively, these results position the LC domain of Pbp1 as a sensor of redox, potentially as a readout of metabolic status of mitochondria, in the signaling pathways that serve to maintain metabolic homeostasis (Figure 1).
Unsurprisingly, these studies provoke additional important questions, including the epistatic relationship between SEACIT and Pbp1 in the regulation of TORC1. It will also be interesting to see if pbp1 mutants, like seacit mutants, fail to establish robust metabolic cycles under sustained slow growth conditions. Pbp1 is conserved, and mutations in the ATXN2 gene that encodes its human paralog, ataxin-2, are associated with neurodegenerative diseases including spinocerebellar ataxia type 2 and amyotrophic lateral sclerosis. Ataxin-2, like Pbp1, possesses a C-terminal LC domain with conserved methionines, suggesting that it too serves as a redox sensor to control metabolic homeostasis. A better understanding of ataxin-2 functions should shed light on these debilitating diseases and suggest novel therapeutic strategies, for example, mTORC1 inhibition. Along these lines, mutations in genes encoding Gator-1 components are also associated with neurological disease (Bar-Peled and Sabatini, 2014). Last, but not least: so far SAM and redox have been identified as important sentinels of respiratory metabolism, sensed by the signaling pathways that regulate metabolic homeostasis; what other sentinels are there, how are these sensed, and is dysregulation of these sensors also implicated in disease?
REFERENCES Bar-Peled, L., and Sabatini, D.M. (2014). Regulation of mTORC1 by amino acids. Trends Cell Biol. 24, 400–406. Chen, J., Sutter, B.M., Shi, L., and Tu, B.P. (2017). GATOR1 regulates nitrogenic cataplerotic reactions of the mitochondrial TCA cycle. Nat. Chem. Biol. 13, 1179–1186. DeMille, D., Badal, B.D., Evans, J.B., Mathis, A.D., Anderson, J.F., and Grose, J.H. (2015). PAS kinase is activated by direct SNF1-dependent phosphorylation and mediates inhibition of TORC1 through the phosphorylation and activation of Pbp1. Mol. Biol. Cell 26, 569–582. Eltschinger, S., and Loewith, R. (2016). TOR complexes and the maintenance of cellular homeostasis. Trends Cell Biol. 26, 148–159. Kato, M., Yang, Y.S., Sutter, B.M., Wang, Y., McKnight, S.L., and Tu, B.P. (2019). Redox state controls phase separation of the yeast ataxin-2 protein via reversible oxidation of its methioninerich low-complexity domain. Cell 177, 711–721. Prouteau, M., Desfosses, A., Sieben, C., Bourgoint, C., Lydia Mozaffari, N., Demurtas, D., Mitra, A.K., Guichard, P., Manley, S., and Loewith, R. (2017). TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 550, 265–269. Sutter, B.M., Wu, X., Laxman, S., and Tu, B.P. (2013). Methionine inhibits autophagy and promotes growth by inducing the SAM-responsive methylation of PP2A. Cell 154, 403–415. Takahara, T., and Maeda, T. (2012). Transient sequestration of TORC1 into stress granules during heat stress. Mol. Cell 47, 242–252.
ACKNOWLEDGMENTS
Wu, X., and Tu, B.P. (2011). Selective regulation of autophagy by the Iml1-Npr2-Npr3 complex in the absence of nitrogen starvation. Mol. Biol. Cell 22, 4124–4133.
The Loewith lab acknowledges financial support from the Canton of Geneva, the Swiss National Science Foundation, the Swiss National Centre of Competence in Research Chemical Biology, and the European Research Council (CoG TORCH).
Yang, Y.S., Kato, M., Wu, X., Litsios, A., Sutter, B.M., Wang, Y., Hsu, C.H., Wood, N.E., Lemoff, A., Mirzaei, H., et al. (2019). Yeast ataxin-2 forms an Intracellular condensate required for the inhibition of TORC1 signaling during respiratory growth. Cell 177, 697–710.
Cell Metabolism 29, May 7, 2019 1021