bims-auttor 2019-07-21 papers

Issue of 2019–07–21
five papers selected by
Viktor Korolchuk, Newcastle University

J Mol Biol. 2019 Jul 13. pii: S0022-2836(19)30445-0. [Epub ahead of print]

Selective Autophagy: ATG8 Family Proteins, LIR Motifs and Cargo Receptors.

Selective autophagy relies on soluble or membrane-bound cargo receptors that recognize cargo and bring about autophagosome formation at the cargo. The cargo-bound receptors interact with lipidated ATG8 family proteins anchored in the membrane at the concave side of the forming autophagosome. The interaction is mediated by 15-20 amino acid long sequence motifs called LC3-interacting region (LIR) motifs that bind to the LIR docking site (LDS) of ATG8 proteins. In this review we focus on LIR-ATG8 interactions and the soluble mammalian selective autophagy receptors (SARs). We discuss the roles of ATG8 family proteins as membrane scaffolds in autophagy and the LIR-LDS interaction and how specificity for binding to GABARAP or LC3 subfamily proteins is achieved. We also discuss atypical LIR-LDS interactions and a novel LIR-independent interaction. Recently, it has become clear that several of the soluble cargo receptors are able to recruit components of the core autophagy apparatus to aid in assembling autophagosome formation at the site of cargo sequestration. A model on phagophore recruitment and expansion on a SAR-coated cargo incorporating the latest findings is presented.

Keywords: ATG8; GABARAP; LC3; LIR; SAR; SLR; selective autophagy

DOI: https://doi.org/10.1016/j.jmb.2019.07.016

Autophagy. 2019 Jul 18. 1-2

Suppressing the dark side of autophagy.

Ben Zhou, Alexander A Soukas.

A wide variety of genetic, pharmacological and nutrient manipulations that extend lifespan in model organisms do so in a manner dependent upon increased autophagic flux. However, our recent findings suggest that when mitochondrial membrane integrity is compromised, macroautophagy/autophagy can be detrimental. In C. elegans lacking the serine/threonine kinase mechanistic target of rapamycin kinase complex 2 and its downstream effector SGK-1 (Serum- and Glucocorticoid-inducible Kinase homolog), lifespan is shortened in spite of increased levels of autophagy, whereas reducing autophagy restores normal lifespan. This is due to a concomitant defect in mitochondrial permeability in mutants defective in either SGK-1 or mechanistic target of rapamycin kinase complex 2, attributable to increased VDAC-1 (VDAC Voltage Dependent Anion Channel homolog) protein level. More generally, we find that induction of mitochondrial permeability reverses each and every tested paradigm of autophagy-dependent lifespan extension and, further, exacerbates ischemia-reperfusion injury. In this punctum, we discuss our finding that autophagy with increased mitochondrial permeability is a detrimental combination conserved from nematode to mammals.

Keywords: Aging; MTOR (mechanistic target of rapamycin kinase); MTOR complex 2 (MTORC2); SGK-1 (serum and glucocorticoid-regulated kinase); VDAC1 (voltage dependent anion channel 1); autophagy; ischemia/reperfusion injury; lifespan; mitochondrial permeability transition pore (mPTP)

DOI: https://doi.org/10.1080/15548627.2019.1644077

Elife. 2019 Jul 16. pii: e44219. [Epub ahead of print]8

Expression of WIPI2B counteracts age-related decline in autophagosome biogenesis in neurons.

Andrea Kh Stavoe, Pallavi P Gopal, Andrea Gubas, Sharon A Tooze, Erika Lf Holzbaur.

Autophagy defects are implicated in multiple late-onset neurodegenerative diseases including Amyotrophic Lateral Sclerosis (ALS) and Alzheimer's, Huntington's, and Parkinson's diseases. Since aging is the most common shared risk factor in neurodegeneration, we assessed rates of autophagy in mammalian neurons during aging. We identified a significant decrease in the rate of constitutive autophagosome biogenesis during aging and observed pronounced morphological defects in autophagosomes in neurons from aged mice. While early stages of autophagosome formation were unaffected, we detected the frequent production of stalled LC3B-negative isolation membranes in neurons from aged mice. These stalled structures recruited the majority of the autophagy machinery, but failed to develop into LC3B-positive autophagosomes. Importantly, ectopically expressing WIPI2B effectively restored autophagosome biogenesis in aged neurons. This rescue is dependent on the phosphorylation state of WIPI2B at the isolation membrane, suggesting a novel therapeutic target in age-associated neurodegeneration.

Keywords: WIPI2B; aging; autophagosome biogenesis; autophagy; cell biology; mouse; neurons; neuroscience

DOI: https://doi.org/10.7554/eLife.44219

EMBO J. 2019 Jul 15. 38(14): e100978

RNF34 functions in immunity and selective mitophagy by targeting MAVS for autophagic degradation.

Xiang He, Yongjie Zhu, Yanhong Zhang, Yunqi Geng, Jing Gong, Jin Geng, Pingping Zhang, Xiaotong Zhang, Ning Liu, Yumeng Peng, Chenbin Wang, Yujie Wang, Xin Liu, Luming Wan, Feng Gong, Congwen Wei, Hui Zhong.

Viral infection triggers the formation of mitochondrial antiviral signaling protein (MAVS) aggregates, which potently promote immune signaling. Autophagy plays an important role in controlling MAVS-mediated antiviral signaling; however, the exact molecular mechanism underlying the targeted autophagic degradation of MAVS remains unclear. Here, we investigated the mechanism by which RNF34 regulates immunity and mitophagy by targeting MAVS. RNF34 binds to MAVS in the mitochondrial compartment after viral infection and negatively regulates RIG-I-like receptor (RLR)-mediated antiviral immunity. Moreover, RNF34 catalyzes the K27-/K29-linked ubiquitination of MAVS at Lys 297, 311, 348, and 362 Arg, which serves as a recognition signal for NDP52-dependent autophagic degradation. Specifically, RNF34 initiates the K63- to K27-linked ubiquitination transition on MAVS primarily at Lys 311, which facilitates the autophagic degradation of MAVS upon RIG-I stimulation. Notably, RNF34 is required for the clearance of damaged mitochondria upon viral infection. Thus, we elucidated the mechanism by which RNF34-mediated autophagic degradation of MAVS regulates the innate immune response, mitochondrial homeostasis, and infection.

Keywords: MAVS ; RNF34; innate immune response; selective mitophagy; ubiquitination

DOI: https://doi.org/10.15252/embj.2018100978

J Biol Chem. 2019 Jul 17. pii: jbc.AC119.009977. [Epub ahead of print]

Human ATG4 autophagy proteases counteract attachment of ubiquitin-like LC3/GABARAP proteins to other cellular proteins.

Alexander Agrotis, Lucas von Chamier, Harriet Oliver, Koshiro Kiso, Tanya Singh, Robin Ketteler.

Microtubule-associated protein 1 light chain 3 alpha (LC3)/GABA type A receptor-associated protein (GABARAP) comprises a family of ubiquitin-like proteins involved in (macro)autophagy, an important intracellular degradation pathway that delivers cytoplasmic material to lysosomes via double-membrane vesicles called autophagosomes. The only currently known cellular molecules covalently modified by LC3/GABARAP are membrane phospholipids such as phosphatidylethanolamine in the autophagosome membrane. Autophagy-related 4A cysteine peptidase (ATG4) proteases process inactive pro-LC3/GABARAP before lipidation, and the same proteases can also deconjugate LC3/GABARAP from lipids. To determine whether LC3/GABARAP has other molecular targets, here we generated a preprocessed LC3B mutant (Q116P) that is resistant to ATG4-mediated deconjugation. Upon expression in human cells and when assessed by immunoblotting under reducing and denaturing conditions, deconjugation-resistant LC3B accumulated in multiple forms and at much higher molecular weights than free LC3B. We observed a similar accumulation when preprocessed versions of all mammalian LC3/GABARAP isoforms were expressed in ATG4-deficient cell lines, suggesting that LC3/GABARAP can attach also to other larger molecules. We identified ATG3, the E2-like enzyme involved in LC3/GABARAP lipidation, as one target of conjugation with multiple copies of LC3/GABARAP. We show that LC3B-ATG3 conjugates are distinct from the LC3B-ATG3 thioester intermediate formed before lipidation, and we biochemically demonstrate that ATG4B can cleave LC3B-ATG3 conjugates. Finally, we determined ATG3 residue K243 as an LC3B modification site. Overall, we provide the first cellular evidence that mammalian LC3/GABARAP post-translationally modifies proteins akin to ubiquitination ('LC3ylation'), with ATG4 proteases acting like deubiquitinating enzymes to counteract this modification ('deLC3ylation').

Keywords: ATG4B; Atg8; GABARAPL2; LC3ylation; autophagy; cysteine protease; deconjugation; deubiquitylation (deubiquitination); post-translational modification (PTM); ubiquitin-conjugating enzyme (E2 enzyme)

DOI: https://doi.org/10.1074/jbc.AC119.009977