LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury

Nakamura, Shuhei; Shigeyama, Saki; Minami, Satoshi; Shima, Takayuki; Akayama, Shiori; Matsuda, Takehisa; Esposito, Alessandra; Napolitano, Gennaro; Kuma, Akiko; Namba‐Hamano, Tomoko; Nakamura, Jun; Yamamoto, Kenichi; Sasai, Miwa; Tokumura, Ayaka; Miyamoto, Mika; Oe, Yukako; Fujita, Tomoya; Terawaki, Seigo; Takahashi, Atsushi; Hamasaki, Maho; Yamamoto, Masahiro; Okada, Yukinori; Komatsu, Masaaki; Nagai, Takeharu; Takabatake, Yoshitsugu; Xu, Haoxing; Isaka, Yoshitaka; Ballabio, Andrea; Yoshimori, Tamotsu

doi:10.1038/s41556-020-00583-9

Cited by 159 publications

(174 citation statements)

References 48 publications

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“…SMAC can be pharmacologically induced by chemical probes that exhibit lysosomotropic and broad ionophore/protonophore-like properties but unfortunately these agents lack a molecular target 7 . Recently, it was reported that ATG8 proteins are directly conjugated to the lysosomal membrane upon disruption of lysosomal homeostasis by agents such as LLoMe, oxalate crystals, and membrane-permeabilizing pathogen virulence factors 27, 28 . This autophagy-independent ATG8 conjugation was required for the coordinated activation of TFEB, specifically uncoupling TFEB, but not other substrates, from regulation by mTOR.…”

Section: Introductionmentioning

confidence: 99%

GABARAP membrane conjugation sequesters the FLCN-FNIP tumor suppressor complex to activate TFEB and lysosomal biogenesis

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Hooper

et al. 2021

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Increased autophagic flux and endolysosomal stress coordinates lysosomal capacity through the TFEB/TFE3 transcription factors, yet the molecular details of their activation are unclear. LC3 and GABARAP members of the ATG8 protein family are required for selective autophagy and sensing perturbation within the endolysosomal system. Here we show that during single membrane ATG8 conjugation (SMAC), Parkin-dependent mitophagy, and Salmonella -induced xenophagy, the membrane conjugation of GABARAP, but not LC3, is required for activation of TFEB/TFE3 to control lysosomal homeostasis and capacity. GABARAP directly binds to a novel LC3-interacting motif (LIR) in the FLCN/FNIP tumor suppressor complex and sequesters it to membrane compartments. This disrupts the regulation of RagC/D by the FLCN/FNIP GAP complex, resulting in impaired mTOR-dependent phosphorylation of TFEB without changing mTOR activity towards other substrates. Thus, the GABARAP-FLCN/FNIP-TFEB axis serves as a universal molecular sensor that coordinates lysosomal homeostasis with perturbations and cargo flux within the autophagy-lysosomal network.

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Section: Introductionmentioning

confidence: 99%

GABARAP membrane conjugation sequesters the FLCN-FNIP tumor suppressor complex to activate TFEB and lysosomal biogenesis

Goodwin

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Hooper

et al. 2021

Preprint

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“…A recent study suggests that lysosomal damage induced by LLOMe stimulates lysosomal biogenesis via activation of TFEB, contributing to lysophagic clearance of damaged lysosomes (Nakamura et al, 2020). However, whether the lysosomal biogenesis mediated by MiT/TFE family members exerts a protective role against LLOMeinduced toxicity is not well studied.…”

Section: Discussionmentioning

confidence: 99%

“…The same mechanisms that regulate TFEB activity also appear to control the activity of other MiT/TFE members (Martina and Puertollano, 2013;Martina et al, 2014;Napolitano and Ballabio, 2016). Although the activation of TFEB after lysosomal-membrane damage has been reported (Chauhan et al, 2016;Jia et al, 2018;Arhzaouy et al, 2019;Rusmini et al, 2019;Nakamura et al, 2020), it is not clear whether this response contributes to suppressing the cell death associated with lysosomal-membrane damage. Therefore, we investigated in HeLa cells the contribution of MiT/TFE family members to reducing the cell death associated with lysosomal-membrane damage induced by LLOMe.…”

Section: Introductionmentioning

confidence: 99%

MiT/TFE family members suppress L-leucyl–L-leucine methyl ester-induced cell death

et al. 2021

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Lysosomes are degradative organelles essential for cell homeostasis. However, various internal and external stimuli, including L-leucyl-L-leucine methyl ester (LLOMe), which is one of the common lysosomotropic agents, permeabilize the lysosomal membrane, leading to lysosome-dependent cell death because of leakage of lysosomal contents to the cytosol. The microphthalmia/transcription factor E (MiT/TFE) family members, which include transcription factor EB (TFEB), transcription factor E3 (TFE3), and microphthalmia-associated transcription factor (MITF), are master regulators of lysosomal biogenesis and are known to be involved in the lysosomal stress response. However, their protective effects against cell death associated with lysosomal-membrane damage are still poorly understood. In this study, we confirmed that LLOMe-induced lysosomal damage triggered nuclear translocation of TFEB/ TFE3/MITF and increased the mRNA levels of their target genes encoding lysosomal hydrolases and lysosomal membrane proteins in HeLa cells. Furthermore, we revealed that TFEB/TFE3/MITF knockdown exacerbated LLOMe-induced cell death. However, TFEB overexpression only slightly attenuated LLOMe-induced cell death, despite enhanced LLOMe-induced increase in CTSD mRNA levels, implying that the endogenous levels of MiT/TFE family members might be sufficient to promote lysosomal biogenesis in response to lysosomal-membrane damage. Our results suggest that MiT/TFE family members suppress the cell death associated with lysosomal-membrane damage.

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“…HeLa cells (ATCC), HEK293T cells (ATCC), A549 cells (ATCC), and ATG7 -/- HeLa cells ( 27 ) (a generous gift from Prof. Yoshimori) were cultured in DMEM containing 10% fetal bovine serum (FBS) and antibiotics. Transfection experiments were performed using PEI (polyethylenimine) or lipofectamine RNAiMAX (Thermo Fisher).…”

Section: Methodsmentioning

confidence: 99%

Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy

et al. 2021

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Nuclear dot protein 52 kDa (NDP52, also known as CALCOCO2) functions as a selective autophagy receptor. The linear ubiquitin chain assembly complex (LUBAC) specifically generates the N-terminal Met1-linked linear ubiquitin chain, and regulates innate immune responses, such as nuclear factor-κB (NF-κB), interferon (IFN) antiviral, and apoptotic pathways. Although NDP52 and LUBAC cooperatively regulate bacterial invasion-induced xenophagy, their functional crosstalk remains enigmatic. Here we show that NDP52 suppresses canonical NF-κB signaling through the broad specificity of ubiquitin-binding at the C-terminal UBZ domain. Upon TNF-α-stimulation, NDP52 associates with LUBAC through the HOIP subunit, but does not disturb its ubiquitin ligase activity, and has a modest suppressive effect on NF-κB activation by functioning as a component of TNF-α receptor signaling complex I. NDP52 also regulates the TNF-α-induced apoptotic pathway, but not doxorubicin-induced intrinsic apoptosis. A chemical inhibitor of LUBAC (HOIPIN-8) cancelled the increased activation of the NF-κB and IFN antiviral pathways, and enhanced apoptosis in NDP52-knockout and -knockdown HeLa cells. Upon Salmonella-infection, colocalization of Salmonella, LC3, and linear ubiquitin was detected in parental HeLa cells to induce xenophagy. Treatment with HOIPIN-8 disturbed the colocalization and facilitated Salmonella expansion. In contrast, HOIPIN-8 showed little effect on the colocalization of LC3 and Salmonella in NDP52-knockout cells, suggesting that NDP52 is a weak regulator in LUBAC-mediated xenophagy. These results indicate that the crosstalk between NDP52 and LUBAC regulates innate immune responses, apoptosis, and xenophagy.

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LC3 lipidation is essential for TFEB activation during the lysosomal damage response to kidney injury

Cited by 159 publications

References 48 publications

GABARAP membrane conjugation sequesters the FLCN-FNIP tumor suppressor complex to activate TFEB and lysosomal biogenesis

GABARAP membrane conjugation sequesters the FLCN-FNIP tumor suppressor complex to activate TFEB and lysosomal biogenesis

MiT/TFE family members suppress L-leucyl–L-leucine methyl ester-induced cell death

Crosstalk Between NDP52 and LUBAC in Innate Immune Responses, Cell Death, and Xenophagy

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