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1. Autophagy in Yeast: ATOR-Mediated Response to Nutrient Starvation

Author

Kamada, Y., Sekito, T., Ohsumi, Y., Compans, R. W., editor, Cooper, M. D., editor, Koprowski, H., editor, Melchers, F., editor, Oldstone, M. B. A., editor, Olsnes, S., editor, Potter, M., editor, Vogt, P. K., editor, Wagner, H., editor, Thomas, George, editor, Sabatini, David M., editor, and Hall, Michael N., editor

Published
2004
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6. Membrane Morphology Is Actively Transformed by Covalent Binding of the Protein Atg8 to PE-Lipids

Author

Knorr, R., Nakatogawa, H., Ohsumi, Y., Lipowsky, R., https://orcid.org/0000-0001-8417-8567, Baumgart, T., Dimova, R., and https://orcid.org/0000-0002-3872-8502

Subjects
Cell Physiology, Saccharomyces cerevisiae Proteins, Adhesion Molecules, Cell Membranes, lcsh:Medicine, Biochemistry, Membrane Structures, Molecular Cell Biology, Membrane Technology, lcsh:Science, Phosphatidylethanolamines, lcsh:R, Biology and Life Sciences, Membrane Proteins, Cell Biology, Autophagy-Related Protein 8 Family, Molecular Development, Lipids, Membrane Trafficking, Liposomes, Cytochemistry, Engineering and Technology, lcsh:Q, Cellular Structures and Organelles, Microtubule-Associated Proteins, Research Article, Membrane Composition, Developmental Biology, Protein Binding
Abstract

Autophagy is a cellular degradation pathway involving the shape transformation of lipid bilayers. During the onset of autophagy, the water-soluble protein Atg8 binds covalently to phosphatdylethanolamines (PEs) in the membrane in an ubiquitin-like reaction coupled to ATP hydrolysis. We reconstituted the Atg8 conjugation system in giant and nm-sized vesicles with a minimal set of enzymes and observed that formation of Atg8-PE on giant vesicles can cause substantial tubulation of membranes even in the absence of Atg12-Atg5-Atg16. Our findings show that ubiquitin-like processes can actively change properties of lipid membranes and that membrane crowding by proteins can be dynamically regulated in cells. Furthermore we provide evidence for curvature sorting of Atg8-PE. Curvature generation and sorting are directly linked to organelle shapes and, thus, to biological function. Our results suggest that a positive feedback exists between the ubiquitin-like reaction and the membrane curvature, which is important for dynamic shape changes of cell membranes, such as those involved in the formation of autophagosomes.

Published
2014

7. A Unified Nomenclature for Yeast Autophagy-Related Genes

Author

Klionsky, DJ, Cregg, JM, Dunn, WA, Emr, SD, Sakai, Y, Sandoval, [No Value], Sibirny, A, Subramani, S, Thumm, M, Veenhuis, M, Ohsumi, Y, Klionsky, Daniel J., Cregg, James M., Dunn, Jr., Emr, Scott D., Sandoval, Ignacio V., Groningen Biomolecular Sciences and Biotechnology, and Molecular Cell Biology

Subjects
MEMBRANE-TRANSPORT PATHWAYS, Macropexophagy, Saccharomyces cerevisiae, Biology, Peroxisome degradation, General Biochemistry, Genetics and Molecular Biology, SACCHAROMYCES-CEREVISIAE, PEROXISOME DEGRADATION, 03 medical and health sciences, 0302 clinical medicine, VACUOLE TARGETING PATHWAY, SELECTIVE DEGRADATION, Terminology as Topic, Autophagy, ACTIVATING ENZYME, Aminopeptidase I, PROTEIN CONJUGATION SYSTEM, GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries), Molecular Biology, Nomenclature, 030304 developmental biology, 0303 health sciences, PICHIA-PASTORIS REQUIRES, Autophagy database, AMINOPEPTIDASE-I, Cell Biology, Biochemistry, Selective degradation, 030220 oncology & carcinogenesis, ComputingMethodologies_DOCUMENTANDTEXTPROCESSING, Micropexophagy, HANSENULA-POLYMORPHA, Hansenula polymorpha, Classics, Developmental Biology
Abstract

The authors would like to thank Drs. Jan A.K.W. Kiel, Ida J. van der Klei, Beth Levine, Fulvio Reggiori, and Takahiro Shintani for helpful comments on the manuscript, and the many researchers in the yeast field who have agreed to changes in the standard names of various genes.

Published
2003
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9. Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting

Author

Scott, SV, Nice, DC, Nau, JJ, Weisman, LS, Kamada, Y, Keizer-Gunnink, [No Value], Funakoshi, T, Veenhuis, M, Ohsumi, Y, Klionsky, DJ, Scott, Sidney V., Nice III, Daniel C., Weisman, Lois S., Keizer-Gunnink, Ineke, Klionsky, Daniel J., Groningen Biomolecular Sciences and Biotechnology, Cell Biochemistry, Analytical Biochemistry, and Molecular Cell Biology

Subjects
Cytoplasm, Time Factors, Vesicular Transport Proteins, Autophagy-Related Proteins, DEFICIENT MUTANTS, PROTEIN, Vacuole, CVT pathway, Aminopeptidases, Biochemistry, SACCHAROMYCES-CEREVISIAE, PATHWAY, 0302 clinical medicine, YEAST VACUOLE, Cytoplasm-to-vacuole targeting, 0303 health sciences, Autophagy-related protein 13, Cell biology, Phosphorylation, AUTOPHAGY, Cell fractionation, Plasmids, Protein Binding, Subcellular Fractions, Saccharomyces cerevisiae Proteins, Lipoproteins, Saccharomyces cerevisiae, Protein Serine-Threonine Kinases, Biology, Models, Biological, 03 medical and health sciences, Two-Hybrid System Techniques, Molecular Biology, Adaptor Proteins, Signal Transducing, Gene Library, 030304 developmental biology, Autophagy, Membrane Proteins, AMINOPEPTIDASE-I, Biological Transport, Cell Biology, Phosphoproteins, Precipitin Tests, GENE, TRANSPORT, Protein Structure, Tertiary, Kinetics, Microscopy, Electron, Vacuoles, MEMBRANE, 030217 neurology & neurosurgery
Abstract

We have been studying protein components that function in the cytoplasm to vacuole targeting (Cvt) pathway and the overlapping process of macroautophagy. The Vac8 and Apg13 proteins are required for the import of aminopeptidase I (API) through the Cvt pathway. We have identified a protein-protein interaction between Vac8p and Apg13p by both two-hybrid and co-immunoprecipitation analysis. Subcellular fractionation of API indicates that Vac8p and Apg13p are involved in the vesicle formation step of the Cvt pathway. Kinetic analysis of the Cvt pathway and autophagy indicates that, although Vac8p is essential for Cvt transport, it is less important for autophagy, In vivo phosphorylation experiments demonstrate that both Vac8p and Apg13p are phosphorylated proteins, and Apg13p phosphorylation is regulated by changing nutrient conditions. Although Apg13p interacts with the serine/threonine kinase Apg1p, this protein is not required for phosphorylation of either Vac8p or Apg13p, Subcellular fractionation experiments indicate that Apg13p and a fraction of Apg1p are membrane-associated, Vac8p and Apg13p may be part of a larger protein complex that includes Apg1p and additional interacting proteins. Together, these components may form a protein complex that regulates the conversion between Cvt transport and autophagy in response to changing nutrient conditions.

Published
2000

11. Crystal structure of Kluyveromyces marxianus Atg7NTD

Author

Yamaguchi, M., primary, Matoba, K., additional, Sawada, R., additional, Fujioka, Y., additional, Nakatogawa, H., additional, Yamamoto, H., additional, Kobashigawa, Y., additional, Hoshida, H., additional, Akada, R., additional, Ohsumi, Y., additional, Noda, N.N., additional, and Inagaki, F., additional

Published
2012
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12. Crystal structure of Kluyveromyces marxianus Atg7NTD-Atg10 complex

Author

Yamaguchi, M., primary, Matoba, K., additional, Sawada, R., additional, Fujioka, Y., additional, Nakatogawa, H., additional, Yamamoto, H., additional, Kobashigawa, Y., additional, Hoshida, H., additional, Akada, R., additional, Ohsumi, Y., additional, Noda, N.N., additional, and Inagaki, F., additional

Published
2012
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13. Solution structures of KmAtg10

Author

Yamaguchi, M., primary, Noda, N.N., additional, Yamamoto, H., additional, Shima, T., additional, Kumeta, H., additional, Kobashigawa, Y., additional, Akada, R., additional, Ohsumi, Y., additional, and Inagaki, F., additional

Published
2012
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15. NMR structure of Atg8-Atg7C30 complex

Author

Kumeta, H., primary, Satoo, K., additional, Noda, N.N., additional, Fujioka, Y., additional, Ogura, K., additional, Nakatogawa, H., additional, Ohsumi, Y., additional, and Inagaki, F., additional

Published
2011
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17. The NMR structure of the autophagy-related protein Atg8

Author

Kumeta, H., primary, Watanabe, M., additional, Nakatogawa, H., additional, Yamaguchi, M., additional, Ogura, K., additional, Adachi, W., additional, Fujioka, Y., additional, Noda, N.N., additional, Ohsumi, Y., additional, and Inagaki, F., additional

Published
2010
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18. LC3 p62 complex structure

Author

Noda, N., primary, Kumeta, H., additional, Nakatogawa, H., additional, Satoo, K., additional, Adachi, W., additional, Ishii, J., additional, Fujioka, Y., additional, Ohsumi, Y., additional, and Inagaki, F., additional

Published
2008
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48. A protein conjugation system in yeast with homology to biosynthetic enzyme reaction of prokaryotes.

Author

Furukawa, K, Mizushima, N, Noda, T, and Ohsumi, Y

Abstract

Protein conjugation, such as ubiquitination, is the process by which the C-terminal glycine of a small modifier protein is covalently attached to target protein(s) through sequential reactions with an activating enzyme and conjugating enzymes. Here we report on a novel protein conjugation system in yeast. A newly identified ubiquitin related modifier, Urm1 is a 99-amino acid protein terminated with glycine-glycine. Urm1 is conjugated to target proteins, which requires the C-terminal glycine of Urm1. At the first step of this reaction, Urm1 forms a thioester with a novel E1-like protein, Uba4. Deltaurm1 and Deltauba4 cells showed a temperature-sensitive growth phenotype. Urm1 and Uba4 show similarity to prokaryotic proteins essential for molybdopterin and thiamin biosynthesis, although the Urm1 system is not involved in these pathways. This is the fifth conjugation system in yeast, following ubiquitin, Smt3, Rub1, and Apg12, but it is unique in respect to relation to prokaryotic enzyme systems. This fact may provide an important clue regarding evolution of protein conjugation systems in eukaryotic cells.

Published
2000

49. A new protein conjugation system in human. The counterpart of the yeast Apg12p conjugation system essential for autophagy.

Author

Mizushima, N, Sugita, H, Yoshimori, T, and Ohsumi, Y

Abstract

Autophagy is an intracellular process for bulk degradation of cytoplasmic components. We recently found a protein conjugation system essential for autophagy in the yeast, Saccharomyces cerevisiae. The C-terminal glycine of a novel modifier protein, Apg12p, is conjugated to a lysine residue of Apg5p via an isopeptide bond. This conjugation reaction is mediated by Apg7p, a ubiquitin activating enzyme (E1)-like enzyme, and Apg10p, suggesting that it is a ubiquitination-like system (Mizushima, N., Noda, T., Yoshimori, T., Tanaka, Y., Ishii, T., George, M. D., Klionsky, D. J., Ohsumi, M. , and Ohsumi, Y. (1998) Nature 395, 395-398). Although autophagy is a ubiquitous process in eukaryotic cells, no molecule involved in autophagy has yet been identified in higher eukaryotes. We reasoned that this conjugation system could be conserved. Here we report cloning and characterization of the human homologue of Apg12 (hApg12). It is a 140-amino acid protein and possesses 27% identity and 48% similarity with the yeast Apg12p, but no apparent homology to ubiquitin. Northern blot analysis showed that its expression was ubiquitous in human tissues. We found that it was covalently attached to another protein. This target protein was identified to be the human Apg5 homologue (hApg5). Mutagenic analyses suggested that this conjugation was formed via an isopeptide bond between the C-terminal glycine of hApg12 and Lys-130 of hApg5. These findings indicate that the Apg12 system is well conserved and may function in autophagy also in human cells.

Published
1998

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