Review
Plant Sciences
Wanqing Liu, Zinan Liu, Zulong Mo, Shaoying Guo, Yunfeng Liu, Qingjun Xie
Summary: Autophagy, an evolutionarily conserved vacuolar process in plants, is activated upon stress and regulated by multiple AuTophaGy-related genes, with the dual role of ATG8 in autophagosome biogenesis and recruitment of SARs. Dozens of AIM or UIM containing SARs have been identified, but knowledge of these motifs remains obscure.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biochemistry & Molecular Biology
Masaaki Komatsu
Summary: In this review, the author discusses the history of p62 research in relation to autophagy and provides an overview of the formation, degradation, and physiological functions of the p62 body, including efficient degradation of ubiquitinated proteins and involvement in antioxidant stress response.
Article
Plant Sciences
Injeong Song, Suji Hong, Sung Un Huh
Summary: The study revealed diverse functions of the StATG8 family in tuber maturation and multiple stress responses in potatoes, with its expression being influenced by various factors. Additionally, StATG8 may have an unrelated autophagy function in the nucleus with the WRKY transcription factor.
Article
Plant Sciences
Na Luo, Dandan Shang, Zhiwei Tang, Jinyan Mai, Xiao Huang, Li-Zhen Tao, Linchuan Liu, Caiji Gao, Yangwen Qian, Qingjun Xie, Faqiang Li
Summary: Protein-targeting technologies play crucial roles in biological research, but there is currently no direct method to degrade endogenous proteins in plants. In this study, a novel approach was developed to engineer autophagy receptors for targeted protein clearance, using a binder for target specificity and an ATG8-binding motif (AIM) to link targets to autophagosomes. The method was demonstrated to be specific and versatile in degrading different tagged proteins and peroxisomes in tobacco, and its feasibility was further confirmed in Arabidopsis. This concept of engineered AIM-based selective autophagy could serve as a convenient and robust research tool for manipulating endogenous proteins in plants.
Review
Cell Biology
Marine Jacquet, Michael Guittaut, Annick Fraichard, Gilles Despouy
Summary: Atg8-family proteins, including GABARAP and LC3, play crucial roles in autophagy and cancer. While downregulation of GABARAPs is associated with cancer progression, the expression of LC3s does not correlate with specific tumor types or stages. The exact role of Atg8-family proteins in cancer remains unclear, but it seems to be related to their involvement in selective protein degradation through autophagy.
Editorial Material
Cell Biology
Jun-Ichi Sakamaki, Noboru Mizushima
Summary: Conjugation of Atg8-family proteins to phosphatidylethanolamine (PE) is important for auto-phagosome formation. PE conjugation was previously thought to be specific to Atg8 among the ubiquitin-family proteins, but our recent study found that ubiquitin is also conjugated to PE on endosomes and the vacuole. Other ubiquitin-like proteins, like NEDD8 and ISG15, can also bind to phospholipids covalently. We propose that conjugation to phospholipids could be a common feature of the ubiquitin family.
Article
Multidisciplinary Sciences
Andrew Z. Lin, Kiersten M. Ruff, Furqan Dar, Ameya Jalihal, Matthew R. King, Jared M. Lalmansingh, Ammon E. Posey, Nadia A. Erkamp, Ian Seim, Amy S. Gladfelter, Rohit V. Pappu
Summary: The authors report that protein-RNA condensates with shared proteins and distinct RNAs can form and persist in vitro and in cells as distinct entities if the nonshared RNA molecules are dynamically arrested, but the shared protein components are dynamically exchangeable.
NATURE COMMUNICATIONS
(2023)
Editorial Material
Cell Biology
Reo Kurusu, Hideaki Morishita, Masaaki Komatsu
Summary: SQSTM1/p62 bodies are phase-separated condensates that play a crucial role in intracellular quality control and stress responses. A recent study discovered a novel substrate for selective autophagy called vault, which directly binds to NBR1 and is degraded by selective autophagy dependent on the phase separation of SQSTM1/p62. This process, named vault-phagy, is related to nonalcoholic steatohepatitis (NASH)-derived hepatocellular carcinoma.
Article
Cell Biology
Fei Yi, Chunmiao Cai, Banzhan Ruan, Mingang Hao, Syn Kok Yeo, Michael Haas, Fuchun Yang, Xiaoting Zhang, Jun-Lin Guan
Summary: RB1CC1/FIP200 is an important autophagy protein that plays a crucial role in various biological processes and diseases. This study reveals a new post-translational mechanism of RB1CC1 regulation through acetylation. Additionally, RB1CC1 contains an intrinsically disordered region capable of liquid-liquid phase separation, leading to the formation of puncta independent of other autophagy receptors.
Review
Biochemistry & Molecular Biology
Manuel J. Mallen-Ponce, Samuel Gamez-Arcas, Maria Esther Perez-Perez
Summary: Autophagy is a catabolic pathway that maintains cellular homeostasis by degrading and recycling cellular materials. It involves the formation of autophagosomes, double-membrane vesicles that engulf the material to be degraded and recycled. However, the mechanisms and regulation of autophagy in photosynthetic organisms like microalgae are not fully understood.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Article
Chemistry, Physical
Khandekar Jishan Bari, Dube Dheeraj Prakashchand
Summary: The article evaluates different methods for structural characterization of liquid-liquid phase separation in intrinsically disordered proteins, and discusses the role of computational simulations in enhancing our understanding of the driving forces behind phase separation.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Review
Biochemistry & Molecular Biology
Saskia Barz, Franziska Kriegenburg, Pablo Sanchez-Martin, Claudine Kraft
Summary: Autophagy is a degradative pathway involving controlled lipid and membrane rearrangements to form autophagosomes for turnover within the lytic compartment. Atg8 proteins play a key role in autophagosome biogenesis and interact with various Rab GTPase regulators, potentially linking autophagy progression with Rab GTPase activity. This review focuses on membrane dynamics during autophagosome biogenesis, highlighting the role of Atg8 proteins and selected Rab GTPases.
BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH
(2021)
Article
Cell Biology
Shuangli Sun, Lanlan Feng, Kin Pan Chung, Ka-Ming Lee, Hayley Hei-Yin Cheung, Mengqian Luo, Kaike Ren, Kai Ching Law, Liwen Jiang, Kam-Bo Wong, Xiaohong Zhuang
Summary: The study uncovered an atypical interaction mode of Arabidopsis ATG8f with the plant unique adaptor protein SH3P2, showing unique conformational changes in ATG8f upon binding to the AIM sequence of the autophagic receptor NBR1. Additionally, the gel filtration assay revealed that the ubiquitin-associated domain of NBR1 outcompetes the SH3 domain of SH3P2 for ATG8f interaction. Biochemical and cellular analysis demonstrated distinct interfaces used by ATG8f to interact with NBR1 and SH3P2.
Article
Chemistry, Physical
Xuanfu Zhu, Gengwu Zhang, Lukman O. Alimi, Basem M. Moosa, Abdul-Hamid Emwas, Fang Fang, Niveen M. Khashab
Summary: This study presents an energy-efficient method for the adsorptive separation of para-halotoluene (PHT) using a TI macrocycle. The selectivity is determined by the specific interactions between the macrocycle and the guest molecules. The results demonstrate the viability of using molecular sieves for sustainable chemical separation processes.
CHEMISTRY OF MATERIALS
(2023)
Article
Immunology
Parimal Samir, David E. Place, R. K. Subbarao Malireddi, Thirumala-Devi Kanneganti
Summary: The study shows that innate immune signaling through the TLR-IKK complex axis can inhibit the assembly and promote disassembly of stress granules, revealing a regulatory mechanism for the dynamics of stress granule assembly-disassembly.
JOURNAL OF IMMUNOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Junya Sango, Taichi Kakihana, Masahiko Takahashi, Yoshinori Katsuragi, Sergei Anisimov, Masaaki Komatsu, Masahiro Fujii
Summary: Nrf2 is an antioxidant transcriptional activator that plays a role in various human disorders. This study shows that the protein USP10 reduces dopamine-induced ROS production and apoptosis in neuronal cells by stimulating the antioxidant activity of Nrf2. USP10 is a key regulator of Nrf2 antioxidant activity in neuronal cells.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Masahiko Takahashi, Hiroki Kitaura, Akiyoshi Kakita, Taichi Kakihana, Yoshinori Katsuragi, Osamu Onodera, Yuriko Iwakura, Hiroyuki Nawa, Masaaki Komatsu, Masahiro Fujii
Summary: TDP-43 is a causative factor of ALS, and cytoplasmic TDP-43 aggregates are a characteristic pathology of the disease. USP10 promotes the clearance of TDP-43-positive stress granules (SGs), leading to the formation of TDP-43-positive aggregates. The interaction between TDP-35 and USP10 is RNA-binding-dependent, and impaired RNA binding of TDP-35 results in the formation of USP10-negative aggregates.
MOLECULAR AND CELLULAR BIOLOGY
(2022)
Article
Neurosciences
Mai Sakai, Zhiqian Yu, Ryo Hirayama, Masa Nakasato, Yoshie Kikuchi, Chiaki Ono, Hiroshi Komatsu, Miharu Nakanishi, Hatsumi Yoshii, David Stellwagen, Tomoyuki Furuyashiki, Masaaki Komatsu, Hiroaki Tomita
Summary: This study explores the changes in autophagy signaling in the prefrontal cortex (PFC) under repeated social defeat (RSD) and their potential involvement in behavioral changes induced by stress. The results suggest that enhanced autophagy may alleviate stress-induced depression, and microglial autophagy plays a role in stress-induced behavioral changes.
Article
Biochemistry & Molecular Biology
Akiko Suzuki, Chihiro Iwaya, Kenichi Ogata, Hiroki Yoshioka, Junbo Shim, Isei Tanida, Masaaki Komatsu, Norihiro Tada, Junichi Iwata
Summary: Sjogren's syndrome is a chronic autoimmune disease characterized by immune cell infiltration of the exocrine glands. Deficiency in enzymes involved in the ubiquitin modification pathway leads to a Sjogren's syndrome-like phenotype, and activation of GATE16 is crucial for exocytosis.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2022)
Letter
Gastroenterology & Hepatology
Wen-Xing Ding, Hong-Min Ni, Satoshi Waguri, Masaaki Komatsu
JOURNAL OF HEPATOLOGY
(2022)
Article
Cell Biology
Maiko Ono, Masaaki Komatsu, Bin Ji, Yuhei Takado, Masafumi Shimojo, Takeharu Minamihisamatsu, Eiji Warabi, Toru Yanagawa, Gen Matsumoto, Ichio Aoki, Nicholas M. Kanaan, Tetsuya Suhara, Naruhiko Sahara, Makoto Higuchi
Summary: In this study, evidence is provided that p62 exerts a protective role against neuronal death and neuroinflammation induced by abnormal tau accumulation. By eliminating neurotoxic tau species, p62 may act as a potential therapeutic target for the treatment of tauopathies.
Article
Cell Biology
Sang-Won Park, Pureum Jeon, Akinori Yamasaki, Hye Eun Lee, Haneul Choi, Ji Young Mun, Yong-Woo Jun, Ju-Hui Park, Seung-Hwan Lee, Soo-Kyeong Lee, You-Kyung Lee, Hyun Kyu Song, Michael Lazarou, Dong-Hyong Cho, Masaaki Komatsu, Nobuo N. Noda, Deok-Jin Jang, Jin-A Lee
Summary: This study identified the selective interactions of various membrane-anchored mATG8 proteins in mammals and developed tools to regulate the autophagy of disease-related protein aggregates. This has significant implications for understanding the functional roles of mATG8 proteins on autophagic membranes in autophagy research.
Correction
Cell Biology
Shuhei Nakamura, Saki Shigeyama, Satoshi Minami, Takayuki Shima, Shiori Akayama, Tomoki Matsuda, Alessandra Esposito, Gennaro Napolitano, Akiko Kuma, Tomoko Namba-Hamano, Jun Nakamura, Kenichi Yamamoto, Miwa Sasai, Ayaka Tokumura, Mika Miyamoto, Yukako Oe, Toshiharu Fujita, Seigo Terawaki, Atsushi Takahashi, Maho Hamasaki, Masahiro Yamamoto, Yukinori Okada, Masaaki Komatsu, Takeharu Nagai, Yoshitsugu Takabatake, Haoxing Xu, Yoshitaka Isaka, Andrea Ballabio, Tamotsu Yoshimori
NATURE CELL BIOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Masaaki Komatsu
Summary: In this review, the author discusses the history of p62 research in relation to autophagy and provides an overview of the formation, degradation, and physiological functions of the p62 body, including efficient degradation of ubiquitinated proteins and involvement in antioxidant stress response.
Editorial Material
Cell Biology
Reo Kurusu, Hideaki Morishita, Masaaki Komatsu
Summary: SQSTM1/p62 bodies are phase-separated condensates that play a crucial role in intracellular quality control and stress responses. A recent study discovered a novel substrate for selective autophagy called vault, which directly binds to NBR1 and is degraded by selective autophagy dependent on the phase separation of SQSTM1/p62. This process, named vault-phagy, is related to nonalcoholic steatohepatitis (NASH)-derived hepatocellular carcinoma.
Article
Multidisciplinary Sciences
Ryosuke Ishimura, Sota Ito, Gaoxin Mao, Satoko Komatsu-Hirota, Toshifumi Inada, Nobuo N. Noda, Masaaki Komatsu
Summary: Research has shown that UFM1 plays a role in processes such as endoplasmic reticulum-associated protein degradation, ribosome-associated protein quality control, and ER-phagy, and the UFM1 E3 complex is involved in both ufmylation and ER-RQC.
Article
Microbiology
Michitaka Suzuki, Tomoko Funakoshi, Keigo Kumagai, Masaaki Komatsu, Satoshi Waguri
Summary: Chlamydia trachomatis infection can be regulated by autophagy-related (ATG) genes. Depletion of ATG9A suppressed C. trachomatis growth in HeLa cells, and this growth was restored by re-expressing ATG9A or an ATG9A mutant. The depletion of lipid transfer proteins ATG2A/B did not significantly alter the growth, highlighting the non-autophagic function of ATG9A in supporting C. trachomatis infection. Re-expression of a mutant lacking an N-terminal adapter protein-binding domain did not rescue C. trachomatis growth, emphasizing the importance of this domain. These findings suggest that the proper trafficking of ATG9A assists C. trachomatis growth in the inclusion.
MICROBIOLOGY SPECTRUM
(2023)
Review
Biochemistry & Molecular Biology
Reo Kurusu, Hideaki Morishita, Masaaki Komatsu
Summary: Cellular zoning and the formation of membraneless organelles play crucial roles in regulating biochemical reactions inside cells, with p62 bodies maintaining cellular homeostasis through selective autophagy and activating the anti-oxidative stress response.
JOURNAL OF BIOCHEMISTRY
(2023)
Article
Medicine, Research & Experimental
Ge Peng, Saya Tsukamoto, Risa Ikutama, Hai Le Thanh Nguyen, Yoshie Umehara, Juan V. Trujillo-Paez, Hainan Yue, Miho Takahashi, Takasuke Ogawa, Ryoma Kishi, Mitsutoshi Tominaga, Kenji Takamori, Jiro Kitaura, Shun Kageyama, Masaaki Komatsu, Ko Okumura, Hideoki Ogawa, Shigaku Ikeda, Francois Niyonsaba
Summary: A study found that autophagy in keratinocytes is restrained in patients with atopic dermatitis (AD) and mouse models of AD. Human β-defensin-3 (hBD-3) alleviates the impairment of the tight junction barrier through activation of keratinocyte autophagy, and reduces skin inflammation. This suggests that autophagy contributes to the pathogenesis of AD, and hBD-3 could be used therapeutically.
JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Biochemistry & Molecular Biology
Shun-Suke Sakai, Atsushi Hasegawa, Ryosuke Ishimura, Naoki Tamura, Shun Kageyama, Satoko Komatsu-Hirota, Manabu Abe, Yiwei Ling, Shujiro Okuda, Manabu Funayama, Mika Kikkawa, Yoshiki Miura, Kenji Sakimura, Ichiei Narita, Satoshi Waguri, Ritsuko Shimizu, Masaaki Komatsu
Summary: A study found that the copy number duplication of ATG2B and GSKIP genes is associated with myeloproliferative neoplasm (MPN). Mice lacking both Atg2b and Gskip genes showed decreased hematopoiesis, leading to fetal death and anemia. The number of hematopoietic stem cells (HSCs), especially long-term HSCs, was significantly decreased due to increased cell death. The results demonstrate the synergistic effect of Atg2b and Gskip in maintaining the pool size of HSCs.
MOLECULAR AND CELLULAR BIOLOGY
(2022)