bims-nocaut 2025-12-28 papers

Issue of 2025–12–28
four papers selected by
Quentin Frenger, University of Strasbourg

Autophagy. 2025 Dec 26.

The dual role of core autophagy E1 enzyme ATG7: revealing a new negative feedback mechanism as a substrate for protein ATG8ylation.

Huazhong Xie, Jiahui Long, Min Li.

The conjugation of mammalian Atg8 (ATG8)-family proteins to membrane components is a fundamental process in membrane ATG8ylation (lipidation). While membrane ATG8ylation is well-characterized, protein ATG8ylation, the direct conjugation of ATG8 to cellular proteins, remains enigmatic. In this study, we demonstrate that protein ATG8ylation depends exclusively on ATG4, ATG3, and ATG7. We discovered that the core macroautophagy/autophagy E1 enzyme ATG7 serves a dual role: it is not only the essential E1 enzyme for protein ATG8ylation but also a key substrate. We determined that ATG7 K140 is the modification site and show that protein ATG8ylation of ATG7 forms a mono-LC3B conjugate. We demonstrated that this self-modification creates a negative-feedback loop by hindering the ATG7-ATG3 interaction, thereby attenuating autophagic flux. Our findings redefine ATG7 as a central player and regulator in the protein ATG8ylation cascade, revealing a new mechanism of autophagy regulation.

Keywords: ATG7; LC3; post-translational modification; protein ATG8ylation; self-regulation

DOI: https://doi.org/10.1080/15548627.2025.2609929

Autophagy. 2025 Dec;21(12): 2535-2536

MAPK/p38-ULK1-PI4KB signaling defines a non-canonical autophagy mechanism in KRAS-Mutant tumors.

Xin Wen, Daniel J Klionsky.

Although KRAS-driven tumors exhibit elevated macroautophagy/autophagy, the extent to which this process diverges from canonical regulatory pathways has not been well characterized. In a recent study published in Cell Research, Wang et al. unveil a novel form of non-canonical autophagy driven by oncogenic RAS mutations, which they termed RAS-induced non-canonical autophagy via ATG8ylation (RINCAA). This pathway operates through a unique MAPK/p38-ULK1-PI4KB axis, diverging significantly from canonical starvation-induced autophagy. The research not only elucidates a new regulatory mechanism but also identifies a potential, highly specific therapeutic target for RAS-mutant cancers.Abbreviations: PI4KB, phosphatidylinositol 4-kinase beta; PtdIns4P, phosphatidylinositol-4-phosphate; RINCAA, RAS-induced non-canonical autophagy via Atg8ylation; ULK1, unc-51 like autophagy activating kinase 1; WIPI2, WD repeat domain phosphoinositide-interacting protein 2.

Keywords: Autophagy; RAS; RINCAA; oncogene; p38-ULK1-PI4KB axis

DOI: https://doi.org/10.1080/15548627.2025.2555048

Autophagy. 2025 Dec 26.

Proteotoxic stress triggers TFEB- and TFE3-mediated autophagy and lysosomal biogenesis via non-canonical MTORC1 inactivation.

Zhou Zhu, Jing Yang, Sandro Montefusco, Siyu Xia, Jinhuan Ou, Haibo Tong, Qingzhong Zeng, Fengmei Xu, Lingyun Dai, Jichao Sun, Chengchao Xu, Diego Luis Medina, Jigang Wang, Wei Zhang, Chuanbin Yang.

Proteotoxic stress, arising from conditions that cause misfolded protein accumulation, is closely linked to the pathogenesis of multiple diseases. Macroautophagy/autophagy activation is considered a compensatory mechanism to maintain protein homeostasis, but the underlying regulatory mechanisms remain incompletely understood. Here, we show that proteotoxic stress induced by proteasome inhibition, puromycin treatment, or polyglutamine-expanded HTT (huntingtin) expression promotes nuclear accumulation of TFEB and TFE3, key regulators of lysosomal biogenesis and autophagy. Mechanistically, TFEB activation under proteotoxic stress occurs independently of canonical MTORC1 inactivation mediated by TSC2 or ATF4. Instead, it involves non-canonical inhibition of MTORC1 via RRAG GTPases. Proteotoxic stress disrupts the RRAGC-TFEB interaction, preventing TFEB recruitment to lysosomes and subsequent MTORC1 phosphorylation. An activated RRAGC mutant rescues impaired lysosomal localization and nuclear accumulation of TFEB, while co-overexpression of FLCN and FNIP2, a GAP for RRAGC, partially restores stress-induced TFEB dephosphorylation. In addition, proteasome inhibition activates non-canonical autophagy. Deletion of ATG16L1 or ATG5, which blocks Atg8-familyh protein lipidation and sequesters the FLCN-FNIP2 complex, partially abolishes proteotoxic stress-induced TFEB dephosphorylation and nuclear accumulation. Together, these findings demonstrate that proteotoxic stress triggers both non-canonical autophagy and TFEB-mediated canonical autophagy, with Atg8-family protein lipidation contributing to TFEB activation. Our results provide novel insights into how proteotoxic stress engages non-canonical MTORC1 inhibition and TFEB activation, thereby enhancing understanding of cellular adaptation to proteotoxic stress.

Keywords: Autophagy; MTORC1; RRAG GTPase; TFEB; lysosomal biogenesis; proteosome

DOI: https://doi.org/10.1080/15548627.2025.2608973

Mol Biol Cell. 2025 Dec 24. mbcE25040190

TNIP1 and Autophagy Receptors regulate STING Signaling.

Eric N Bunker, Tara D Fischer, Peng-Peng Zhu, François Le Guerroué, Kory R Johnson, Richard J Youle.

Activation of the cGAS-STING pathway stimulates innate immune signaling as well as LC3B lipidation and ubiquitylation at Golgi-related vesicles upon STING trafficking. Although ubiquitylation at these subcellular sites has been associated with regulating NF-κB-related innate immune signaling, the mechanisms of Golgi-localized polyubiquitin chain regulation of immune signaling is not well understood. We report here that the ubiquitin- and LC3B-binding proteins, TNIP1 and autophagy receptors p62, NBR1, NDP52, TAX1BP1, and OPTN associate with STING-induced ubiquitin and LC3B-labeled vesicles, and that p62 and NBR1 act redundantly in spatial clustering of the LC3B-labeled vesicles in the perinuclear region. We also find that while TBK1 kinase activity is not required for the recruitment of TNIP1 and the autophagy receptors, it plays a role in sequestration of the LC3B-labeled vesicles. The ubiquitin binding domains, rather than the LC3-interacting regions, of TNIP1 and OPTN are specifically important for their recruitment to Ub/LC3B-associated perinuclear vesicles, and OPTN is also recruited through a TBK1-dependent mechanism. Functionally, we find that TNIP1 plays a role in STING-mediated innate immune signaling, acting as a negative regulator of IRF3-mediated gene expression. Together, these results highlight autophagy-independent mechanisms of autophagy receptors and TNIP1 with unanticipated roles in regulating STING-mediated innate immunity.

DOI: https://doi.org/10.1091/mbc.E25-04-0190