bims-apauto 2022-07-03 papers

bims-apauto

Biomed News

on Apoptosis and autophagy

Issue of 2022–07–03
eight papers selected by
Su Hyun Lee, Seoul National University

A "short-cut" response of autophagy to oxidative stress: oxygen-dependent activity of a lysine demethylase guides the activity of ULK1 during hypoxia.
ER-phagy: selective autophagy of the endoplasmic reticulum.
Inhibition of lipid kinase PIKfyve reveals a role for phosphatase Inpp4b in the regulation of PI(3)P-mediated lysosome dynamics through VPS34 activity.
Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases.
A degradative to secretory autophagy switch mediates mitochondria clearance in the absence of the mATG8-conjugation machinery.
Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1.
Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains.
RhoA signaling increases mitophagy and protects cardiomyocytes against ischemia by stabilizing PINK1 protein and recruiting Parkin to mitochondria.

Autophagy. 2022 Jun 26. 1-3

A "short-cut" response of autophagy to oxidative stress: oxygen-dependent activity of a lysine demethylase guides the activity of ULK1 during hypoxia.

Ge Yu, Daniel J Klionsky.

  Hypoxia is a type of stress caused by an insufficient supply of oxygen. Macroautophagy/autophagy, a well-conserved pathway, is induced during hypoxia; however, the exact mechanism by which autophagy is regulated in a hypoxic environment remains to be elucidated. A recent study by Li et al. shed light on how hypoxia can regulate early steps of autophagy induction. In this study, the authors discovered a novel symmetrical dimethylation of ULK1 at arginine 170 (R170me2s) that accumulates during hypoxia and increases ULK1 kinase activity by promoting autophosphorylation of ULK1 at T180. The authors identified PRMT5 and KDM5C as the primary methyltransferase and demethylase regulating ULK1 R170me2s and show that the lack of oxygen directly leads to reduced activity of KDM5C, which is likely the cause of accumulation of ULK1 R170me2s during hypoxia. Furthermore, the authors showed that ULK1 R170me2s promotes mitochondrial turnover and maintains cell viability in response to hypoxia stress. Together these data provide a new perspective on how the oxygen level regulates autophagy induction and show the physiological role of ULK1 R170me2s.

Keywords:  Autophagy; KDM5C; PRMT5; ULK1; hypoxia; mitophagy; oxidative stress; oxygen-sensitive methylation; tumor

DOI:  https://doi.org/10.1080/15548627.2022.2089957
EMBO Rep. 2022 Jun 27. e55192

ER-phagy: selective autophagy of the endoplasmic reticulum.

Keisuke Mochida, Hitoshi Nakatogawa.

  Eukaryotic cells adequately control the mass and functions of organelles in various situations. Autophagy, an intracellular degradation system, largely contributes to this organelle control by degrading the excess or defective portions of organelles. The endoplasmic reticulum (ER) is an organelle with distinct structural domains associated with specific functions. The ER dynamically changes its mass, components, and shape in response to metabolic, developmental, or proteotoxic cues to maintain or regulate its functions. Therefore, elaborate mechanisms are required for proper degradation of the ER. Here, we review our current knowledge on diverse mechanisms underlying selective autophagy of the ER, which enable efficient degradation of specific ER subdomains according to different demands of cells.

Keywords:  ER-phagy; autophagy; endoplasmic reticulum; intracellular degradation

DOI:  https://doi.org/10.15252/embr.202255192
J Biol Chem. 2022 Jun 24. pii: S0021-9258(22)00629-9. [Epub ahead of print] 102187

Inhibition of lipid kinase PIKfyve reveals a role for phosphatase Inpp4b in the regulation of PI(3)P-mediated lysosome dynamics through VPS34 activity.

Golam T Saffi, Cheng An Wang, Emily M Mangialardi, Jean Vacher, Roberto J Botelho, Leonardo Salmena.

  Lysosome membranes contain diverse phosphoinositide (PtdIns) lipids that coordinate lysosome function and dynamics. The PtdIns repertoire on lysosomes is tightly regulated by the actions of diverse PtdIns kinases and phosphatases; however, specific roles for PtdIns in lysosomal functions and dynamics are currently unclear and require further investigation. It was previously shown that PIKfyve, a lipid kinase that synthesizes PtdIns(3,5)P2 from PtdIns(3)P, controls lysosome "fusion-fission" cycle dynamics, autophagosome turnover, and endocytic cargo delivery. Furthermore, INPP4B, a PtdIns 4-phosphatase that hydrolyzes PtdIns(3,4)P2 to form PtdIns(3)P, is emerging as a cancer-associated protein with roles in lysosomal biogenesis and other lysosomal functions. Here, we investigated the consequences of disrupting PIKfyve function in Inpp4b-deficient mouse embryonic fibroblasts. Through confocal fluorescence imaging, we observed the formation of massively enlarged lysosomes, accompanied by exacerbated reduction of endocytic trafficking, disrupted lysosome fusion-fission dynamics, and inhibition of autophagy. Finally, HPLC scintillation quantification of 3H-myo-inositol labelled phosphoinositides and phosphoinositide immunofluorescence staining, we observed that lysosomal PtdIns(3)P levels were significantly elevated in Inpp4b-deficient cells due to the hyperactivation of phosphatidylinositol 3-kinase catalytic subunit VPS34 enzymatic activity. In conclusion, our study identifies a novel signaling axis that maintains normal lysosomal homeostasis and dynamics, which includes the catalytic functions of Inpp4b, PIKfyve, and VPS34.

Keywords:  Apilimod; Inpp4b; Lysosomes; PIKfyve; PtdIns(3)P; Vps34

DOI:  https://doi.org/10.1016/j.jbc.2022.102187
J Biol Chem. 2022 Jun 25. pii: S0021-9258(22)00640-8. [Epub ahead of print] 102198

Mechanisms orchestrating the enzymatic activity and cellular functions of deubiquitinases.

Benjamin Estavoyer, Clémence Messmer, Mohamed Echbicheb, Christopher E Rudd, Eric Milot, El Bachir Affar.

  Deubiquitinases (DUBs) are required for the reverse reaction of ubiquitination and act as major regulators of ubiquitin signaling processes. Emerging evidence suggests that these enzymes are regulated at multiple levels in order to ensure proper and timely substrate targeting, and to prevent the adverse consequences of promiscuous deubiquitination. The importance of DUB regulation is highlighted by disease-associated mutations that inhibit or activate DUBs, deregulating their ability to coordinate cellular processes. Here, we describe the diverse mechanisms governing protein stability, enzymatic activity and function of DUBs. In particular, we outline how DUBs are regulated by their protein domains and interacting partners. Intramolecular interactions can promote protein stability of DUBs, influence their subcellular localization and/or modulate their enzymatic activity. Remarkably, these intramolecular interactions can induce self-deubiquitination to counteract DUB ubiquitination by cognate E3 ubiquitin ligases. In addition to intramolecular interactions, DUBs can also oligomerize and interact with a wide variety of cellular proteins, thereby forming obligate or facultative complexes that regulate their enzymatic activity and function. The importance of signaling and post-translational modifications in the integrated control of DUB function will also be discussed. While several DUBs are described with respect to the multiple layers of their regulation, the tumor suppressor BAP1 will be outlined as a model enzyme whose localization, stability, enzymatic activity and substrate recognition are highly orchestrated by interacting partners and post-translational modifications.

Keywords:  BAP1; DUB activity; Quality control; deubiquitinase; folding; multi-protein complex; post-translational modifications; ubiquitin

DOI:  https://doi.org/10.1016/j.jbc.2022.102198
Nat Commun. 2022 Jun 28. 13(1): 3720

A degradative to secretory autophagy switch mediates mitochondria clearance in the absence of the mATG8-conjugation machinery.

Hayden Weng Siong Tan, Guang Lu, Han Dong, Yik-Lam Cho, Auginia Natalia, Liming Wang, Charlene Chan, Dennis Kappei, Reshma Taneja, Shuo-Chien Ling, Huilin Shao, Shih-Yin Tsai, Wen-Xing Ding, Han-Ming Shen.

PINK1-Parkin mediated mitophagy, a selective form of autophagy, represents one of the most important mechanisms in mitochondrial quality control (MQC) via the clearance of damaged mitochondria. Although it is well known that the conjugation of mammalian ATG8s (mATG8s) to phosphatidylethanolamine (PE) is a key step in autophagy, its role in mitophagy remains controversial. In this study, we clarify the role of the mATG8-conjugation system in mitophagy by generating knockouts of the mATG8-conjugation machinery. Unexpectedly, we show that mitochondria could still be cleared in the absence of the mATG8-conjugation system, in a process independent of lysosomal degradation. Instead, mitochondria are cleared via extracellular release through a secretory autophagy pathway, in a process we define as Autophagic Secretion of Mitochondria (ASM). Functionally, increased ASM promotes the activation of the innate immune cGAS-STING pathway in recipient cells. Overall, this study reveals ASM as a mechanism in MQC when the cellular mATG8-conjugation machinery is dysfunctional and highlights the critical role of mATG8 lipidation in suppressing inflammatory responses.

DOI: https://doi.org/10.1038/s41467-022-31213-7
Nat Commun. 2022 Jun 25. 13(1): 3650

Structural mechanism of protein recognition by the FW domain of autophagy receptor Nbr1.

Jianxiu Zhang, Ying-Ying Wang, Zhao-Qian Pan, Yulu Li, Jianhua Sui, Li-Lin Du, Keqiong Ye.

Neighbor of BRCA1 (Nbr1) is a conserved autophagy receptor that provides cargo selectivity to autophagy. The four-tryptophan (FW) domain is a signature domain of Nbr1, but its exact function remains unclear. Here, we show that Nbr1 from the filamentous fungus Chaetomium thermophilum uses its FW domain to bind the α-mannosidase Ams1, a cargo of selective autophagy in both budding yeast and fission yeast, and delivers Ams1 to the vacuole by conventional autophagy in heterologous fission yeast. The structure of the Ams1-FW complex was determined at 2.2 Å resolution by cryo-electron microscopy. The FW domain adopts an immunoglobulin-like β-sandwich structure and recognizes the quaternary structure of the Ams1 tetramer. Notably, the N-terminal di-glycine of Ams1 is specifically recognized by a conserved pocket of the FW domain. The FW domain becomes degenerated in fission yeast Nbr1, which binds Ams1 with a ZZ domain instead. Our findings illustrate the protein binding mode of the FW domain and reveal the versatility of Nbr1-mediated cargo recognition.

DOI: https://doi.org/10.1038/s41467-022-31439-5
EMBO Rep. 2022 Jun 28. e55056

Mechanistic insights into enhancement or inhibition of phase separation by different polyubiquitin chains.

Thuy P Dao, Yiran Yang, Maria F Presti, Michael S Cosgrove, Jesse B Hopkins, Weikang Ma, Stewart N Loh, Carlos A Castañeda.

  Ubiquitin-binding shuttle UBQLN2 mediates crosstalk between proteasomal degradation and autophagy, likely via interactions with K48- and K63-linked polyubiquitin chains, respectively. UBQLN2 comprises self-associating regions that drive its homotypic liquid-liquid phase separation (LLPS). Specific interactions between one of these regions and ubiquitin inhibit UBQLN2 LLPS. Here, we show that, unlike ubiquitin, the effects of multivalent polyubiquitin chains on UBQLN2 LLPS are highly dependent on chain types. Specifically, K11-Ub4 and K48-Ub4 chains generally inhibit UBQLN2 LLPS, whereas K63-Ub4, M1-Ub4 chains, and a designed tetrameric ubiquitin construct significantly enhance LLPS. We demonstrate that these opposing effects stem from differences in chain conformations but not in affinities between chains and UBQLN2. Chains with extended conformations and increased accessibility to the ubiquitin-binding surface promote UBQLN2 LLPS by enabling a switch between homotypic to partially heterotypic LLPS that is driven by both UBQLN2 self-interactions and interactions between multiple UBQLN2 units with each polyubiquitin chain. Our study provides mechanistic insights into how the structural and conformational properties of polyubiquitin chains contribute to heterotypic LLPS with ubiquitin-binding shuttles and adaptors.

Keywords:  UBQLN2; liquid-liquid phase separation; polyphasic linkage; polyubiquitin; protein quality control

DOI:  https://doi.org/10.15252/embr.202255056
Cell Death Differ. 2022 Jun 27.

RhoA signaling increases mitophagy and protects cardiomyocytes against ischemia by stabilizing PINK1 protein and recruiting Parkin to mitochondria.

Michelle Tu, Valerie P Tan, Justin D Yu, Raghav Tripathi, Zahna Bigham, Melissa Barlow, Jeffrey M Smith, Joan Heller Brown, Shigeki Miyamoto.

Mitophagy, a mitochondria-specific form of autophagy, removes dysfunctional mitochondria and is hence an essential process contributing to mitochondrial quality control. PTEN-induced kinase 1 (PINK1) and the E3 ubiquitin ligase Parkin are critical molecules involved in stress-induced mitophagy, but the intracellular signaling mechanisms by which this pathway is regulated are unclear. We tested the hypothesis that signaling through RhoA, a small GTPase, induces mitophagy via modulation of the PINK1/Parkin pathway as a protective mechanism against ischemic stress. We demonstrate that expression of constitutively active RhoA as well as sphingosine-1-phosphate induced activation of endogenous RhoA in cardiomyocytes result in an accumulation of PINK1 at mitochondria. This is accompanied by translocation of Parkin to mitochondria and ubiquitination of mitochondrial proteins leading to recognition of mitochondria by autophagosomes and their lysosomal degradation. Expression of RhoA in cardiomyocytes confers protection against ischemia, and this cardioprotection is attenuated by siRNA-mediated PINK1 knockdown. In vivo myocardial infarction elicits increases in mitochondrial PINK1, Parkin, and ubiquitinated mitochondrial proteins. AAV9-mediated RhoA expression potentiates these responses and a concurrent decrease in infarct size is observed. Interestingly, induction of mitochondrial PINK1 accumulation in response to RhoA signaling is neither mediated through its transcriptional upregulation nor dependent on depolarization of the mitochondrial membrane, the canonical mechanism for PINK1 accumulation. Instead, our results reveal that RhoA signaling inhibits PINK1 cleavage, thereby stabilizing PINK1 protein at mitochondria. We further show that active RhoA localizes at mitochondria and interacts with PINK1, and that the mitochondrial localization of RhoA is regulated by its downstream effector protein kinase D. These findings demonstrate that RhoA activation engages a unique mechanism to regulate PINK1 accumulation, induce mitophagy and protect against ischemic stress, and implicates regulation of RhoA signaling as a potential strategy to enhance mitophagy and confer protection under stress conditions.

DOI: https://doi.org/10.1038/s41418-022-01032-w