Editorial Material
Cell Biology
Tatsuro Maruyama, Nobuo N. Noda
Summary: Atg8, a central factor in autophagosome biogenesis, exhibits physicochemical activity towards membranes and cargo recognition, essential for efficient autophagosome formation, but its mechanistic roles remain open for further exploration.
Review
Biochemistry & Molecular Biology
Steven Edward Reid, Srinivasa Prasad Kolapalli, Thorbjorn M. Nielsen, Lisa B. B. Frankel
Summary: This review discusses the canonical and non-canonical roles of ATG8 proteins in autophagy, focusing on their post-translational modifications and their alternative functions through binding to different membranes. In addition to degradation, they may also play roles in plasma membrane repair and secretion of selected substrates.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Review
Biochemistry & Molecular Biology
Sharon A. Tooze, Wenxin Zhang, Gianmarco Lazzeri, Deepanshi Gahlot, Lipi Thukral, Roberto Covino, Taki Nishimura
Summary: Autophagy is a crucial intracellular pathway for the survival of all eukaryotes. It removes damaged components from cells, ranging from unfolded proteins to entire mitochondria. ATG proteins are essential for the formation and capture of autophagosomes, and recent studies have highlighted the importance of small membrane-associated domains in these proteins. Specifically, the role of α-helical structures in the ATG8 conjugation machinery and ATG8s has been unexpectedly revealed. These findings demonstrate how unique membrane association modules can regulate autophagosome formation.
Article
Biochemistry & Molecular Biology
Viktor A. Anashkin, Alexander A. Baykov
Summary: The study revealed that membrane-integral inorganic pyrophosphatases exhibit structural symmetry, but asymmetry increased upon substrate binding, opening water channel exit. This asymmetrical change may have a regulatory function in the vacuole.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Plant Sciences
Claudia Pereira, Vanessa Vieira, Jose Pissarra, Susana Pereira
Summary: Cardosin A is an aspartic proteinase found in the native plant cardoon, accumulating in protein storage and lytic vacuoles and protein bodies. It is involved in reproduction, reserve mobilization, and membrane remodeling. Studies have shown that cardosin A can be targeted to different vacuolar routes via two sorting determinants, and its accumulation during seed germination events has been investigated.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Microbiology
Federica Piro, Riccardo Focaia, Zhicheng Dou, Silvia Masci, David Smith, Manlio Di Cristina
Summary: Obligate intracellular parasites have developed strategies such as forming a parasitophorous vacuole and secreting proteins to scavenge nutrients from host cells. They overcome barriers in nutrient transport by modifying host cell membrane transporters, remodeling the PV membrane, and selectively taking up substrates at the parasite plasma membrane.
Article
Plant Sciences
Natalia V. Ozolina, Irina S. Kapustina, Veronika V. Gurina, Ekaterina V. Spiridonova, Vadim N. Nurminsky
Summary: The study compares the changes in lipid content of plant cell boundary membranes under hyperosmotic stress and highlights the significant role of the vacuolar membrane in the stress response.
Article
Cell Biology
Vanessa Maria Knab, Dagmar Gotthardt, Klara Klein, Reinhard Grausenburger, Gerwin Heller, Ingeborg Menzl, Daniela Prinz, Jana Trifinopoulos, Julia List, Daniela Fux, Agnieszka Witalisz-Siepracka, Veronika Sexl
Summary: CDK8 plays a crucial role in TNBC tumors, leading to tumor regrowth and metastasis, and affecting immune-mediated clearance. CDK8 drives EMT in TNBC cells and influences the expression of PD-L1.
CELL DEATH & DISEASE
(2021)
Article
Cell Biology
Enrique J. Garcia, Pin-Chao Liao, Gary Tan, Jason D. Vevea, Cierra N. Sing, Catherine A. Tsang, J. Michael McCaffery, Istvan R. Boldogh, Liza A. Pon
Summary: Previous studies have shown that ER stress induces mu LP, a process where vacuolar fragmentation precedes LD uptake, and ESCRT proteins play a direct role in this process, highlighting the importance of lipid droplets in ER proteostasis during stress.
Article
Plant Sciences
Taotao Wang, Xinjing Li, Ningjing Liu, Yi Yang, Qingqiu Gong
Summary: This study used an enzyme-catalyzed proximity labelling method to describe the interactome of Arabidopsis VPS34. The results revealed that VPS34 is associated with carbohydrate metabolism and membrane potential, two key processes involved in maintaining cellular homeostasis.
JOURNAL OF PLANT PHYSIOLOGY
(2023)
Article
Chemistry, Multidisciplinary
Simli Dey, Dayana Surendran, Oskar Engberg, Ankur Gupta, Sashaina E. Fanibunda, Anirban Das, Barun Kumar Maity, Arpan Dey, Vicky Visvakarma, Mamata Kallianpur, Holger A. Scheidt, Gilbert Walker, Vidita A. Vaidya, Daniel Huster, Sudipta Maiti
Summary: Serotonin can modulate membrane properties and cellular function by directly binding to the membrane, independent of receptor activity. This interaction potentiates key cellular processes, such as transferrin receptor endocytosis, in a receptor-independent fashion.
CHEMISTRY-A EUROPEAN JOURNAL
(2021)
Article
Biochemistry & Molecular Biology
Marina N. N. Iriondo, Asier Etxaniz, Yaiza R. R. Varela, Uxue Ballesteros, Melisa Lazaro, Mikel Valle, Dorotea Fracchiolla, Sascha Martens, L. Ruth Montes, Felix M. Goni, Alicia Alonso
Summary: In macroautophagy, the ATG12-ATG5-ATG16L1 or E3-like complex plays a crucial role in AP formation by promoting LC3/GABARAP proteins anchoring to the AP membrane. However, E3 inhibits LC3/GABARAP capacity to induce inter-vesicular lipid mixing or subsequent fusion. Our results suggest a model of AP expansion in which the LC3/GABARAP proteins involved should be susceptible to lipidation in the absence of E3, or else a regulatory mechanism would allow vesicle incorporation and phagophore growth when E3 is present.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Lisa Marquardt, Michael Thumm
Summary: Atg18, Atg21, and Hsv2 are beta-propeller proteins that bind to PI3P and PI(3,5)P2. Atg18 is involved in organizing lipid transferring protein complexes at contact sites of the growing autophagosome with the ER and the vacuole. Atg21 is restricted to the vacuole-phagophore contact and plays a role in organizing part of the Atg8-lipidation machinery. The function of Hsv2 is not well understood, but it is involved in micronucleophagy to some extent.
BIOLOGICAL CHEMISTRY
(2023)
Review
Cell Biology
Liming Wang, Daniel J. Klionsky, Han-Ming Shen
Summary: Microautophagy is a type of autophagy that involves the direct engulfment of cytoplasmic components by lysosomes and late endosomes. Although it has only recently emerged as an important cellular process, microautophagy plays a critical role in diseases and provides potential targets for intervention strategies.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Mitsutoshi Nakamura, Justin Hui, Viktor Stjepic, Susan M. Parkhurst
Summary: Rho family GTPases play a role in regulating actin dynamics, and WAS family proteins are downstream effectors of Rho family GTPases. In this study, it is shown that the WAS protein Scar/WAVE and Rac GTPase are recruited to cell wounds in the Drosophila repair model and are necessary for the formation and maintenance of the actomyosin ring at the wound periphery. SCAR is recruited earlier than Rac and its recruitment is not affected by a Rac inhibitor. While Rac is important for actin recruitment, SCAR organizes and anchors the actomyosin ring to the plasma membrane.
SCIENTIFIC REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Yui Jin, Natsuko Jin, Yu Oikawa, Ron Benyair, Michiko Koizumi, Thomas E. Wilson, Yoshinori Ohsumi, Lois S. Weisman
Summary: The vacuole/lysosome plays a crucial role in cell growth and cell cycle progression via the TORC1 pathway. Bur1, an essential cyclin-dependent kinase, cooperates with TORC1 to regulate cell cycle progression, with mutations in BUR1 showing synthetic growth defects and high sensitivity to rapamycin. Together, Bur1 and TORC1 are required for the activation of Sch9 to promote cell cycle progression.
Article
Cell Biology
Keisuke Mochida, Toshifumi Otani, Yuto Katsumata, Hiromi Kirisako, Chika Kakuta, Tetsuya Kotani, Hitoshi Nakatogawa
Summary: In this study, the researchers uncovered the mechanism of action of the nucleophagy receptor Atg39 in the formation of NDVs. Atg39 is anchored to the outer nuclear membrane via its transmembrane domain and is also associated with the inner nuclear membrane through membrane-binding amphipathic helices, linking these membranes together. Additionally, the aggregation of Atg39 causes the nuclear envelope to protrude and pinch off to generate NDVs.
JOURNAL OF CELL BIOLOGY
(2022)
Editorial Material
Cell Biology
Zhao-Qian Pan, Keqiong Ye, Li-Lin Du
Summary: In selective macroautophagy, autophagy receptors play a crucial role in determining cargo specificity. Most autophagy receptors are found only in certain eukaryotic lineages, except for Nbr1 proteins, which are conserved across eukaryotes. Our study discovered that the FW domain in the Nbr1 protein of Chaetomium thermophilum can bind to the autophagy cargo alpha-mannosidase Ams1, and this binding promotes the autophagic delivery of Ams1 into vacuoles. We also revealed the structural mechanism of Ams1 recognition by the FW domain through solving the structure of the FW-Ams1 complex.
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.
Review
Oncology
Yutaro Hama, Yuta Ogasawara, Nobuo N. Noda
Summary: Autophagy is a cellular process that degrades biomolecules and organelles, contributing to cellular homeostasis. Its roles in cancer are complex, acting as either a promoter or suppressor depending on the cancer stage and type. This review summarizes the basic mechanisms of autophagy and discusses its complicated roles in cancer. Additionally, it provides an overview of clinical trials on autophagy inhibitors for cancer and the development of more specific inhibitors for future clinical application.
Article
Biochemistry & Molecular Biology
Ryo Ikeda, Daisuke Noshiro, Hideaki Morishita, Shuhei Takada, Shun Kageyama, Yuko Fujioka, Tomoko Funakoshi, Satoko Komatsu-Hirota, Ritsuko Arai, Elena Ryzhii, Manabu Abe, Tomoaki Koga, Hozumi Motohashi, Mitsuyoshi Nakao, Kenji Sakimura, Arata Horii, Satoshi Waguri, Yoshinobu Ichimura, Nobuo N. Noda, Masaaki Komatsu
Summary: ULK1 is a kinase responsible for the phosphorylation of p62, which activates NRF2. p62(S351E/+) mice, with phosphorylation-mimicking mutation, exhibit NRF2 hyperactivation and growth retardation.
Article
Genetics & Heredity
Guo-Song Jia, Wen-Cai Zhang, Yue Liang, Xi-Han Liu, Nicholas Rhind, Alison Pidoux, Michael Brysch-Herzberg, Li-Lin Du
Summary: This study sequenced the genomes of the recently identified fission yeast species S. osmophilus and found it to be most closely related to S. octosporus. Comparative analyses using the S. osmophilus reference genome revealed conservation of repeat arrangements and sequence motifs in centromere cores, identified telomeric sequences composed of 2 types of repeats, and characterized the evolution and transfer of transposons and mitochondrial selfish elements.
G3-GENES GENOMES GENETICS
(2023)
Editorial Material
Cell Biology
Tomoyuki Fukuda, Kentaro Furukawa, Tatsuro Maruyama, Nobuo N. Noda, Tomotake Kanki
Summary: Mitophagy is a selective form of autophagy that targets dysfunctional or superfluous mitochondria for degradation. Our recent study has identified Atg44 as a mitochondrial fission factor that generates mitochondrial fragments suitable for phagophore engulfment. We propose the term mitofissin to refer to Atg44 and its homologous proteins that might participate in diverse cellular processes.
Review
Biochemistry & Molecular Biology
Nobuo N. Noda
Summary: Autophagy is a conserved intracellular degradation system that involves the sequestration of degradation targets into autophagosomes. Autophagosome formation and cargo selectivity rely on core Atg proteins and cargo receptors, respectively. This review covers the 30-year history of structural studies on core Atg proteins and cargo receptors and discusses the molecular mechanisms of autophagosome formation and selective autophagy.
Article
Cell Biology
Kanae Hitomi, Tetsuya Kotani, Nobuo N. Noda, Yayoi Kimura, Hitoshi Nakatogawa
Summary: Hitomi et al. reveal that the phosphatidylinositol 3-kinase complex I is recruited to the autophagosome precursor via interactions with Vac8, Atg1 complex, and Atg9. These interactions cooperate to target the phosphatidylinositol 3-kinase complex I to the pre-autophagosomal structure and provide a molecular basis for its localization during autophagosome biogenesis.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Cell Biology
Yoko Kagohashi, Michiko Sasaki, Alexander I. May, Tomoko Kawamata, Yoshinori Ohsumi
Summary: This study provides insights into the function and mechanism of Atg15 phospholipase, further understanding the disruption of autophagosome inner membrane structure.
JOURNAL OF CELL BIOLOGY
(2023)
Article
Genetics & Heredity
Manuel Lera-Ramirez, Jurg Bahler, Juan Mata, Kim Rutherford, Charles S. Hoffman, Sarah Lambert, Snezhana Oliferenko, Sophie G. Martin, Kathleen L. Gould, Li-Lin Du, Sarah A. Sabatinos, Susan L. Forsburg, Olaf Nielsen, Paul Nurse, Valerie Wood
Summary: Standardized nomenclature for genes, gene products, and isoforms is crucial for clear communication and efficient sharing of scientific data. This publication extends the fission yeast clade gene nomenclature guidelines to support curation efforts at PomBase, introducing guidelines for noncoding RNA genes and updating allele and genotype nomenclature. Adoption of these rules will improve consistency in gene and genotype nomenclature and enhance machine-readability in publications or datasets.
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
Biochemistry & Molecular Biology
Chen-Xi Zou, Zhu-Hui Ma, Zhao-Di Jiang, Zhao-Qian Pan, Dan-Dan Xu, Fang Suo, Guang-Can Shao, Meng-Qiu Dong, Li-Lin Du, Sharon A. Tooze, Richard Hodge, Richard Hodge, Richard Hodge, Richard Hodge
Summary: This study reveals the requirement of a conserved ER-shaping protein for ER-phagy and nucleophagy processes in yeast. Lack of this protein leads to the accumulation of cargo structures (not enclosed within autophagosomes) in the cytoplasm.