bims-auttor Biomed News
on Autophagy and mTOR
Issue of 2019–04–28
ten papers selected by
Viktor Korolchuk, Newcastle University
  1. Intrinsically Disordered Protein TEX264 Mediates ER-phagy.
  2. TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress.
  3. The MTORC1-mediated autophagy is regulated by the FBXW7-SHOC2-RPTOR axis.
  4. The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway.
  5. An SH3PX1-Dependent Endocytosis-Autophagy Network Restrains Intestinal Stem Cell Proliferation by Counteracting EGFR-ERK Signaling.
  6. Autophagy, Apoptosis, and Mitochondria: Molecular Integration and Physiological Relevance in Skeletal Muscle.
  7. Notch Signaling Mediates Secondary Senescence.
  8. Selective Autophagy: RNA Comes from the Vault to Regulate p62/SQSTM1.
  9. Vault RNA emerges as a regulator of selective autophagy.
  10. Genome wide CRISPR screen reveals autophagy disruption as the convergence mechanism that regulates the NRF2 transcription factor.
  1. Mol Cell. 2019 Apr 11. pii: S1097-2765(19)30257-6. [Epub ahead of print]
    Intrinsically Disordered Protein TEX264 Mediates ER-phagy.
    Haruka Chino, Tomohisa Hatta, Tohru Natsume, Noboru Mizushima.
      Certain proteins and organelles can be selectively degraded by autophagy. Typical substrates and receptors of selective autophagy have LC3-interacting regions (LIRs) that bind to autophagosomal LC3 and GABARAP family proteins. Here, we performed a differential interactome screen using wild-type LC3B and a LIR recognition-deficient mutant and identified TEX264 as a receptor for autophagic degradation of the endoplasmic reticulum (ER-phagy). TEX264 is an ER protein with a single transmembrane domain and a LIR motif. TEX264 interacts with LC3 and GABARAP family proteins more efficiently and is expressed more ubiquitously than previously known ER-phagy receptors. ER-phagy is profoundly blocked by deletion of TEX264 alone and almost completely by additional deletion of FAM134B and CCPG1. A long intrinsically disordered region of TEX264 is required for its ER-phagy receptor function to bridge the gap between the ER and autophagosomal membranes independently of its amino acid sequence. These results suggest that TEX264 is a major ER-phagy receptor.
    Keywords:  ER-phagy; intrinsically disordered region; organellar contact site; selective autophagy
    DOI:  https://doi.org/10.1016/j.molcel.2019.03.033
  2. Mol Cell. 2019 Apr 11. pii: S1097-2765(19)30258-8. [Epub ahead of print]
    TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress.
    Heeseon An, Alban Ordureau, Joao A Paulo, Christopher J Shoemaker, Vladimir Denic, J Wade Harper.
      Cells respond to nutrient stress by trafficking cytosolic contents to lysosomes for degradation via macroautophagy. The endoplasmic reticulum (ER) serves as an initiation site for autophagosomes and is also remodeled in response to nutrient stress through ER-phagy, a form of selective autophagy. Quantitative proteome analysis during nutrient stress identified an unstudied single-pass transmembrane ER protein, TEX264, as an ER-phagy receptor. TEX264 uses an LC3-interacting region (LIR) to traffic into ATG8-positive puncta that often initiate from three-way ER tubule junctions and subsequently fuse with lysosomes. Interaction and proximity biotinylation proteomics identified a cohort of autophagy regulatory proteins and cargo adaptors located near TEX264 in an LIR-dependent manner. Global proteomics and ER-phagy flux analysis revealed the stabilization of a cohort of ER proteins in TEX264-/- cells during nutrient stress. This work reveals TEX264 as an unrecognized ER-phagy receptor that acts independently of other candidate ER-phagy receptors to remodel the ER during nutrient stress.
    Keywords:  ER-phagy; TEX264; selective autophagy
    DOI:  https://doi.org/10.1016/j.molcel.2019.03.034
  3. Autophagy. 2019 Apr 22.
    The MTORC1-mediated autophagy is regulated by the FBXW7-SHOC2-RPTOR axis.
    Chuan-Ming Xie, Yi Sun.
      MTORC1 is a well-known key regulator of macroautophagy/autophagy. However, the underlying regulatory mechanisms of MTORC1 activity remains elusive. We showed recently that SHOC2, a RAS activator, competes with MTOR for RPTOR (but not RICTOR) binding, leading to MTORC1 inactivation, autophagy induction and cell survival, whereas RPTOR competes with RAS for SHOC2 binding to inactivate RAS-MAPK and suppresses growth. Interestingly, SHOC2 is subjected to FBXW7 regulation. Upon growth stimulation, MAP2K1 phosphorylates SHOC2 on T507 to facilitate its binding with FBXW7B/FBXW7β for ubiquitination and degradation to terminate growth signaling, thus establishing a negative feedback loop. Human cancers with FBXW7 inactivation and SHOC2 overexpression would squeeze RPTOR from MTORC1, leading to MTORC1 inactivation and autophagy induction. Collectively, we propose a new mode of the FBXW7-SHOC2-RPTOR axis in control of MTORC1 activity that affects autophagy and cancer cell survival.
    Keywords:  Autophagy; FBXW7; MTOR; Proliferation and survival; Raptor; SHOC2
    DOI:  https://doi.org/10.1080/15548627.2019.1609864
  4. Autophagy. 2019 Apr 21. 1-13
    The autophagic degradation of cytosolic pools of peroxisomal proteins by a new selective pathway.
    Xiaofeng Wang, Pingping Wang, Zhuangzhuang Zhang, Jean-Claude Farré, Xuezhi Li, Ruonan Wang, Zhijie Xia, Suresh Subramani, Changle Ma.
      Damaged or redundant peroxisomes and their luminal cargoes are removed by pexophagy, a selective autophagy pathway. In yeasts, pexophagy depends mostly on the pexophagy receptors, such as Atg30 for Pichia pastoris and Atg36 for Saccharomyces cerevisiae, the autophagy scaffold proteins, Atg11 and Atg17, and the core autophagy machinery. In P. pastoris, the receptors for peroxisomal matrix proteins containing peroxisomal targeting signals (PTSs) include the PTS1 receptor, Pex5, and the PTS2 receptor and co-receptor, Pex7 and Pex20, respectively. These shuttling receptors are predominantly cytosolic and only partially peroxisomal. It remains unresolved as to whether, when and how the cytosolic pools of peroxisomal receptors, as well as the peroxisomal matrix proteins, are degraded under pexophagy conditions. These cytosolic pools exist both in normal and mutant cells impaired in peroxisome biogenesis. We report here that Pex5 and Pex7, but not Pex20, are degraded by an Atg30-independent, selective autophagy pathway. To enter this selective autophagy pathway, Pex7 required its major PTS2 cargo, Pot1. Similarly, the degradation of Pex5 was inhibited in cells missing abundant PTS1 cargoes, such as alcohol oxidases and Fox2 (hydratase-dehydrogenase-epimerase). Furthermore, in cells deficient in PTS receptors, the cytosolic pools of peroxisomal matrix proteins, such as Pot1 and Fox2, were also removed by Atg30-independent, selective autophagy, under pexophagy conditions. In summary, the cytosolic pools of PTS receptors and their cargoes are degraded via a pexophagy-independent, selective autophagy pathway under pexophagy conditions. These autophagy pathways likely protect cells from futile enzymatic reactions that could potentially cause the accumulation of toxic cytosolic products. Abbreviations: ATG: autophagy related; Cvt: cytoplasm to vacuole targeting; Fox2: hydratase-dehydrogenase-epimerase; PAGE: polyacrylamide gel electrophoresis; Pot1: thiolase; PMP: peroxisomal membrane protein; Pgk1: 3-phosphoglycerate kinase; PTS: peroxisomal targeting signal; RADAR: receptor accumulation and degradation in the absence of recycling; RING: really interesting new gene; SDS: sodium dodecyl sulphate; TCA, trichloroacetic acid; Ub: ubiquitin; UPS: ubiquitin-proteasome system Vid: vacuole import and degradation.
    Keywords:  Autophagy; PTS receptors; peroxisomal matrix proteins; peroxisome; pexophagy receptor
    DOI:  https://doi.org/10.1080/15548627.2019.1603546
  5. Dev Cell. 2019 Apr 12. pii: S1534-5807(19)30240-0. [Epub ahead of print]
    An SH3PX1-Dependent Endocytosis-Autophagy Network Restrains Intestinal Stem Cell Proliferation by Counteracting EGFR-ERK Signaling.
    Peng Zhang, Andreana N Holowatyj, Taylor Roy, Stephen M Pronovost, Marco Marchetti, Hanbin Liu, Cornelia M Ulrich, Bruce A Edgar.
      The effect of intracellular vesicle trafficking on stem-cell behavior is largely unexplored. We screened the Drosophila sorting nexins (SNXs) and discovered that one, SH3PX1, profoundly affects gut homeostasis and lifespan. SH3PX1 restrains intestinal stem cell (ISC) division through an endocytosis-autophagy network that includes Dynamin, Rab5, Rab7, Atg1, 5, 6, 7, 8a, 9, 12, 16, and Syx17. Blockages in this network stabilize ligand-activated EGFRs, recycling them via Rab11-dependent endosomes to the plasma membrane. This hyperactivated ERK, calcium signaling, and ER stress, autonomously stimulating ISC proliferation. The excess divisions induced epithelial stress, Yki activity, and Upd3 and Rhomboid production in enterocytes, catalyzing feedforward ISC hyperplasia. Similarly, blocking autophagy increased ERK activity in human cells. Many endocytosis-autophagy genes are mutated in cancers, most notably those enriched in microsatellite instable-high and KRAS-wild-type colorectal cancers. Disruptions in endocytosis and autophagy may provide an alternative route to RAS-ERK activation, resulting in EGFR-dependent cancers.
    Keywords:  Drosophila sorting nexins; EGFR-Ras-MAPK; Keren; Rab GTPases; SH3PX1; autophagy-related proteins; calcium signaling; colorectal cancer; endocytosis-autophagy network; intestinal stem-cell proliferation
    DOI:  https://doi.org/10.1016/j.devcel.2019.03.029
  6. Am J Physiol Cell Physiol. 2019 Apr 24.
    Autophagy, Apoptosis, and Mitochondria: Molecular Integration and Physiological Relevance in Skeletal Muscle.
    Darin Bloemberg, Joe Quadrilatero.
      Apoptosis and autophagy are processes resulting from the integration of cellular stress and death signals. Their individual importance is highlighted by the lethality of various mouse models missing apoptosis or autophagy related genes. In addition to their independent roles, significant overlap exists with respect to the signals which stimulate these processes as well as their effector consequences. While these cellular systems exemplify the programming redundancies which underlie many fundamental biological mechanisms, their intertwined relationship means that dysfunction can promote pathology. Although both autophagy and apoptotic signaling are active in skeletal muscle during various diseases and atrophy, their specific roles here are somewhat unique. Given our growing understanding of how specific changes at the cellular level impact whole-organism physiology, there is an equally growing interest in pharmacological manipulation of apoptosis and/or autophagy for altering human physiology and health.
    Keywords:  apoptosis; autophagy; mitochondria; mitophagy; skeletal muscle
    DOI:  https://doi.org/10.1152/ajpcell.00261.2018
  7. Cell Rep. 2019 Apr 23. pii: S2211-1247(19)30451-6. [Epub ahead of print]27(4): 997-1007.e5
    Notch Signaling Mediates Secondary Senescence.
    Yee Voan Teo, Nattaphong Rattanavirotkul, Nelly Olova, Angela Salzano, Andrea Quintanilla, Nuria Tarrats, Christos Kiourtis, Miryam Müller, Anthony R Green, Peter D Adams, Juan-Carlos Acosta, Thomas G Bird, Kristina Kirschner, Nicola Neretti, Tamir Chandra.
      Oncogene-induced senescence (OIS) is a tumor suppressive response to oncogene activation that can be transmitted to neighboring cells through secreted factors of the senescence-associated secretory phenotype (SASP). Currently, primary and secondary senescent cells are not considered functionally distinct endpoints. Using single-cell analysis, we observed two distinct transcriptional endpoints, a primary endpoint marked by Ras and a secondary endpoint marked by Notch activation. We find that secondary oncogene-induced senescence in vitro and in vivo requires Notch, rather than SASP alone, as previously thought. Moreover, Notch signaling weakens, but does not abolish, SASP in secondary senescence. Global transcriptomic differences, a blunted SASP response, and the induction of fibrillar collagens in secondary senescence point toward a functional diversification between secondary and primary senescence.
    Keywords:  CEBPB; Notch; TGFB; bystander senescence; oncogene induced senescence; paracrine senescence; secondary senescence; senescence; senescence associated secretory phenotype; single-cell RNA sequencing
    DOI:  https://doi.org/10.1016/j.celrep.2019.03.104
  8. Curr Biol. 2019 Apr 22. pii: S0960-9822(19)30273-8. [Epub ahead of print]29(8): R297-R299
    Selective Autophagy: RNA Comes from the Vault to Regulate p62/SQSTM1.
    Terje Johansen.
      A new study shows that the oligomerization of p62/Sequestosome-1 (SQSTM1) - a selective autophagy receptor and signaling adapter - is regulated directly by vault RNA. This riboregulation negatively affects the aggregation state of p62 and thereby its autophagic degradation and its role as a selective autophagy receptor.
    DOI:  https://doi.org/10.1016/j.cub.2019.03.008
  9. Autophagy. 2019 Apr 21.
    Vault RNA emerges as a regulator of selective autophagy.
    Rastislav Horos, Magdalena Büscher, Carsten Sachse, Matthias W Hentze.
      The selective autophagic receptor SQSTM1/p62 ushers cargo to phagophores, the precursors of autophagosomes, and serves as a platform for autophagy initiation. We discovered that SQSTM1 is an RNA-binding protein that interacts with vault RNAs. Vault RNAs are small non-coding RNAs found in many eukaryotes and transcribed by POLR3 (RNA polymerase III). The levels of VTRNA1-1 (vault RNA 1-1) regulate SQSTM1-mediated autophagy and ubiquitin aggregate clearance. Vault RNA interferes with oligomerization of SQSTM1, which is in turn critical for its autophagic function. Our study uncovered a novel mode of regulation of a protein's activity by RNA, termed riboregulation.
    Keywords:  ; SQSTM1; aggrephagy; non-coding RNA; p62; selective autophagy; vault RNA
    DOI:  https://doi.org/10.1080/15548627.2019.1609861
  10. Mol Cell Biol. 2019 Apr 22. pii: MCB.00037-19. [Epub ahead of print]
    Genome wide CRISPR screen reveals autophagy disruption as the convergence mechanism that regulates the NRF2 transcription factor.
    Michael J Kerins, Pengfei Liu, Wang Tian, William Mannheim, Donna Zhang, Aikseng Ooi.
      The nuclear factor (erythroid 2)-like 2 (NRF2, NFE2L2) transcription factor regulates the expression of many genes critical in maintaining cellular homeostasis. Its deregulation has been implicated in many diseases including cancer, metabolic, and neurodegenerative diseases. While several mechanisms by which NRF2 can be activated have gradually been identified over time, a more complete regulatory network of NRF2 is still lacking. Here we show through a genome wide CRISPR screen that a total of 273 genes, when knocked out, will lead to sustained NRF2 activation. Pathway analysis revealed a significant overrepresentation of genes (18 of the 273 genes) involved in autophagy. Molecular validation of a subset of the enriched genes identified 8 high confidence genes that negatively regulate NRF2 activity irrespective of cell type: ATG12, ATG7, GOSR1, IFT172, NRXN2, RAB6A, VPS37A, and the well-known negative regulator of NRF2, KEAP1 Of these, ATG12, ATG7, KEAP1, and VPS37A are known to be involved in autophagic processes. Our results present a comprehensive list of NRF2 negative regulators, and reveal an intimate link between autophagy and NRF2 regulation.
    DOI:  https://doi.org/10.1128/MCB.00037-19
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