DANIEL KLIONSKY

Summary

Affiliation: University of Michigan
Country: USA

Publications

  1. ncbi Autophagy revisited: a conversation with Christian de Duve
    Daniel J Klionsky
    University of Michigan, Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:740-3. 2008
  2. pmc The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy
    Wei Lien Yen
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 188:101-14. 2010
  3. pmc Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage
    Chao Wen Wang
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 2216, USA
    J Cell Biol 163:973-85. 2003
  4. pmc In vivo reconstitution of autophagy in Saccharomyces cerevisiae
    Yang Cao
    Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 182:703-13. 2008
  5. pmc Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast
    Congcong He
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 175:925-35. 2006
  6. pmc Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy
    Jiefei Geng
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 182:129-40. 2008
  7. pmc The Cytoplasm-to-Vacuole Targeting Pathway: A Historical Perspective
    Midori Umekawa
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 2216, USA
    Int J Cell Biol 2012:142634. 2012
  8. pmc Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae
    Kai Mao
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 193:755-67. 2011
  9. pmc In the beginning there was babble…
    Daniel J Klionsky
    Life Sciences Institute University of Michigan Ann Arbor, Michigan, USA
    Autophagy 8:1165-7. 2012
  10. pmc A comprehensive glossary of autophagy-related molecules and processes
    Daniel J Klionsky
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
    Autophagy 6:438-48. 2010

Research Grants

  1. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2000
  2. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2009
  3. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2008
  4. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2007
  5. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2007
  6. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2006
  7. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2005
  8. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2004
  9. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2003
  10. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2002

Detail Information

Publications92

  1. ncbi Autophagy revisited: a conversation with Christian de Duve
    Daniel J Klionsky
    University of Michigan, Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:740-3. 2008
    ....
  2. pmc The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy
    Wei Lien Yen
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 188:101-14. 2010
    ..In addition, mutations in the COG genes resulted in the mislocalization of Atg8 and Atg9, which are critical components involved in autophagosome formation...
  3. pmc Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage
    Chao Wen Wang
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109 2216, USA
    J Cell Biol 163:973-85. 2003
    ..Accordingly, we propose that the Ccz1-Mon1 complex is critical for the Ypt7-dependent tethering/docking stage leading to the formation of a trans-SNARE complex and subsequent vacuole fusion...
  4. pmc In vivo reconstitution of autophagy in Saccharomyces cerevisiae
    Yang Cao
    Department of Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 182:703-13. 2008
    ..In vivo reconstitution enables the study of autophagy within the context of the complex regulatory networks that control this process, an analysis that is not possible with an in vitro system...
  5. pmc Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast
    Congcong He
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 175:925-35. 2006
    ..We propose that a pool of Atg11 mediates the anterograde transport of Atg9 to the PAS that is dependent on the actin cytoskeleton during yeast vegetative growth...
  6. pmc Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy
    Jiefei Geng
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 182:129-40. 2008
    ..During autophagy, the amount of Atg8 at the PAS showed a periodic change, indicating the formation of autophagosomes. Application of this method and further analysis will provide more insight into the functions of Atg proteins...
  7. pmc The Cytoplasm-to-Vacuole Targeting Pathway: A Historical Perspective
    Midori Umekawa
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 2216, USA
    Int J Cell Biol 2012:142634. 2012
    ..Here, we relate some of the initial history, including some never-before-revealed facts, of the analysis of the Cvt pathway and the convergence of those studies with autophagy...
  8. pmc Two MAPK-signaling pathways are required for mitophagy in Saccharomyces cerevisiae
    Kai Mao
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Biol 193:755-67. 2011
    ..Slt2 also affects the recruitment of mitochondria to the phagophore assembly site (PAS), a critical step in the packaging of cargo for selective degradation...
  9. pmc In the beginning there was babble…
    Daniel J Klionsky
    Life Sciences Institute University of Michigan Ann Arbor, Michigan, USA
    Autophagy 8:1165-7. 2012
    ..Therefore is the name of it called Babel; because the Lord did there confound the language of all the earth…": : Genesis 11:7,9...
  10. pmc A comprehensive glossary of autophagy-related molecules and processes
    Daniel J Klionsky
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
    Autophagy 6:438-48. 2010
    ....
  11. doi A human autophagy interaction network
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
    Autophagy 8:439-41. 2012
    ..Here, I explain the approach used to invite authors to participate in the revised guidelines, and briefly demonstrate one aspect of their utility...
  12. pmc Guidelines for the use and interpretation of assays for monitoring autophagy
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
    Autophagy 8:445-544. 2012
    ..Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field...
  13. pmc Autophagy works out
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    Cell Metab 15:273-4. 2012
    ..He et al. now show in Nature that exercise-induced autophagy is needed for some of the beneficial effects of exercise on metabolism (He et al., 2012)...
  14. pmc Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 153:381-96. 2001
    ..These biochemical and morphological results demonstrate that Cvt9 and the P. pastoris homologue Gsa9 may function at the step of selective cargo sequestration...
  15. pmc Membrane recruitment of Aut7p in the autophagy and cytoplasm to vacuole targeting pathways requires Aut1p, Aut2p, and the autophagy conjugation complex
    J Kim
    Department of Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Cell Biol 152:51-64. 2001
    ..These findings define a series of steps that results in the modification of Aut7p and its subsequent binding to the sequestering transport vesicles of the autophagy and cytoplasm to vacuole targeting pathways...
  16. ncbi Autophagy
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, 48109, USA
    Curr Biol 15:R282-3. 2005
  17. ncbi A report from the EMBO conference on autophagy
    Daniel J Klionsky
    University of Michigan, Life Sciences Institute, Ann Arbor, MI, USA
    Autophagy 5:1235-9. 2009
    ..Accordingly, I am highlighting a small subset of the presented talks, focusing on researchers either new to the field, or those we do not hear from routinely...
  18. pmc Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:151-75. 2008
    ..In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response...
  19. ncbi Methods for monitoring autophagy from yeast to human
    Daniel J Klionsky
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Bioloy, University of Michigan, Ann Arbor, Michigan 48109, USA
    Autophagy 3:181-206. 2007
    ..This information is meant to provide a resource for newcomers as well as a stimulus for experienced researchers who may be prompted to develop additional assays to examine autophagy-related pathways...
  20. ncbi Autophagy: from phenomenology to molecular understanding in less than a decade
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, 210 Washtenaw Avenue, Ann Arbor, Michigan 48109 2216, USA
    Nat Rev Mol Cell Biol 8:931-7. 2007
    ..Amazingly, the molecular breakthroughs in autophagy have taken place during only the past decade...
  21. ncbi Autophagy and p70S6 kinase
    Daniel J Klionsky
    University of Michigan, Life Sciences Institute, Ann Arbor, Michigan, USA
    Autophagy 1:59-60; discussion 60-1. 2005
  22. ncbi How shall I eat thee?
    Daniel J Klionsky
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:413-6. 2007
  23. pmc The molecular machinery of autophagy: unanswered questions
    Daniel J Klionsky
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    J Cell Sci 118:7-18. 2005
    ....
  24. pmc There is more to autophagy than induction: regulating the roller coaster
    Daniel J Klionsky
    Life Sciences Institute, University of Michigan, Ann Arbor, MI USA
    Autophagy 7:801-2. 2011
    ..That is, once you turn it on, you do not want to let it continue unchecked. But how is autophagy downregulated when the inducing conditions still exist?..
  25. pmc A comprehensive glossary of autophagy-related molecules and processes (2nd edition)
    Daniel J Klionsky
    Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
    Autophagy 7:1273-94. 2011
    ....
  26. pmc Autophagy as a regulated pathway of cellular degradation
    D J Klionsky
    Department of Biology, University of Michigan, 830 North University, Ann Arbor, MI 48109 1048, USA
    Science 290:1717-21. 2000
    ..Macroautophagy plays an important role in developmental processes, human disease, and cellular response to nutrient deprivation...
  27. pmc Atg21 is a phosphoinositide binding protein required for efficient lipidation and localization of Atg8 during uptake of aminopeptidase I by selective autophagy
    Per E Strømhaug
    Life Sciences Institute and Departments of Molecular, Cellular, and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    Mol Biol Cell 15:3553-66. 2004
    ..A similar defect in localization of a second ubiquitin-like conjugate, Atg12-Atg5, suggests that Atg21 may be involved in the recruitment of membrane to the PAS...
  28. ncbi The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure
    Fulvio Reggiori
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Dev Cell 6:79-90. 2004
    ..We postulate that Atg9 employs a recycling system mechanistically similar to that used at yeast early and late endosomes...
  29. pmc Atg23 is essential for the cytoplasm to vacuole targeting pathway and efficient autophagy but not pexophagy
    Katherine A Tucker
    Life Sciences Institute, and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, 48109, USA
    J Biol Chem 278:48445-52. 2003
    ..Atg9 transiently interacts with Atg23 suggesting that it participates in the recruitment of this protein...
  30. pmc Atg8 controls phagophore expansion during autophagosome formation
    Zhiping Xie
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 19:3290-8. 2008
    ..This model provides a foundation for future analyses of the functions and dynamics of known autophagy-related proteins and for screening new genes...
  31. pmc Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway
    Takahiro Shintani
    Life Sciences Institute and Departments of Molecular, Cellular, and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 279:29889-94. 2004
    ....
  32. pmc Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway
    Takahiro Shintani
    University of Michigan, Department of Molecular, Cellular, and Developmental Biology, Ann Arbor 48109, USA
    Dev Cell 3:825-37. 2002
    ....
  33. pmc Roles of the lipid-binding motifs of Atg18 and Atg21 in the cytoplasm to vacuole targeting pathway and autophagy
    Usha Nair
    Department of Molecular, Cellular, and Developmental Biology and the Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 285:11476-88. 2010
    ....
  34. pmc The molecular mechanism of autophagy
    Chao Wen Wang
    Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Med 9:65-76. 2003
    ..In this review, we focus on the yeast system, which has provided most of the insight into the molecular mechanism of autophagy and the Cvt pathway, and highlight the most recent additions to our current knowledge of both pathways...
  35. pmc Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway
    Tomohiro Yorimitsu
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 16:1593-605. 2005
    ..These findings suggest that Atg11 plays an integral role in connecting cargo molecules with components of the vesicle-forming machinery...
  36. ncbi A cycling protein complex required for selective autophagy
    Julie E Legakis
    University of Michigan, Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:422-32. 2007
    ....
  37. pmc Double duty of Atg9 self-association in autophagosome biogenesis
    Congcong He
    Life Sciences Institute, and Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI, USA
    Autophagy 5:385-7. 2009
    ....
  38. ncbi Dual role of Atg1 in regulation of autophagy-specific PAS assembly in Saccharomyces cerevisiae
    Hessun Cheong
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:724-6. 2008
    ..In contrast, Atg1 kinase activity is needed for dissociation of Atg proteins from the PAS during autophagy inducing conditions, a function which is also critical for autophagy activity...
  39. doi Analysis of autophagosome membrane cycling by fluorescence microscopy
    Julie E Legakis
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 445:135-45. 2008
    ..We describe here a method that allows visualization of Atg membrane proteins in order to observe their potential source membranes and also to determine the temporal order of action of other Atg proteins with regard to their movement...
  40. ncbi Quantitative regulation of vesicle formation in yeast nonspecific autophagy
    Jiefei Geng
    University of Michigan, Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:955-7. 2008
    ..Combined with results from previous studies in starvation conditions, in this addendum we discuss the possible role of Atg8 and Atg9 in quantitatively regulating the vesicle formation process...
  41. ncbi Atg9 trafficking in autophagy-related pathways
    Congcong He
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:271-4. 2007
    ..Here, we discuss the implications of the model and present additional evidence that extends it with regard to membrane trafficking modes during pexophagy...
  42. pmc Convergence of multiple autophagy and cytoplasm to vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation
    John Kim
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 277:763-73. 2002
    ....
  43. pmc Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts
    Fulvio Reggiori
    University of Michigan, Life Sciences Institute, Departments of Molecular, Cellular and Developmental Biology and of Biological Chemistry, Ann Arbor, Michigan, USA
    Autophagy 1:101-9. 2005
    ..These data support a new model where mitochondria may provide at least part of the autophagosomal lipids and suggest a novel cellular function for this well-studied organelle...
  44. pmc Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy
    Hagai Abeliovich
    University of Michigan, Department of Molecular, Cellular and Developmental Biology, Ann Arbor 48109, USA
    Mol Biol Cell 14:477-90. 2003
    ..In addition, the data support a novel role for Apg1 in nucleation of autophagosomes that is distinct from its catalytic kinase activity and imply a qualitative difference in the mechanism of autophagosome and Cvt vesicle formation...
  45. ncbi Molecular machinery required for autophagy and the cytoplasm to vacuole targeting (Cvt) pathway in S. cerevisiae
    Waheeda A Khalfan
    University of Michigan, Department of Molecular, Cellular and Developmental Biology, Ann Arbor, MI 48109 1048, USA
    Curr Opin Cell Biol 14:468-75. 2002
    ..Additional analysis of this location will help in further dissecting the early events of vesicle formation and identifying the source of the sequestering membrane...
  46. pmc Atg27 is required for autophagy-dependent cycling of Atg9
    Wei Lien Yen
    Life Sciences Institute, and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 18:581-93. 2007
    ..These data support a hypothesis that multiple membrane sources supply the lipids needed for autophagosome formation...
  47. pmc The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery pathways
    Chao Wen Wang
    Department of Molecular, Cellular, and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    J Biol Chem 277:47917-27. 2002
    ....
  48. pmc Mitophagy in yeast occurs through a selective mechanism
    Tomotake Kanki
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    J Biol Chem 283:32386-93. 2008
    ..These findings suggest that the degradation of mitochondria is a tightly regulated process and that these organelles are largely protected from nonspecific autophagic degradation...
  49. pmc Assaying autophagic activity in transgenic GFP-Lc3 and GFP-Gabarap zebrafish embryos
    Congcong He
    Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology, and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Autophagy 5:520-6. 2009
    ..In addition, zebrafish Gabarap accumulates within lysosomes upon autophagy induction. Thus, we established a convenient zebrafish tool to assay autophagic activity during embryogenesis in vivo...
  50. ncbi Dissecting autophagosome formation: the missing pieces
    Zhiping Xie
    Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 4:920-2. 2008
    ..Key questions remain open, however, on how the actions of other proteins at the PAS are coordinated with that of Atg8 and on the precise role of Atg8...
  51. pmc Atg32 is a mitochondrial protein that confers selectivity during mitophagy
    Tomotake Kanki
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    Dev Cell 17:98-109. 2009
    ..Therefore, Atg32 confers selectivity for mitochondrial sequestration as a cargo and is necessary for recruitment of this organelle by the autophagy machinery for mitophagy...
  52. pmc Determining Atg protein stoichiometry at the phagophore assembly site by fluorescence microscopy
    Jiefei Geng
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
    Autophagy 6:144-7. 2010
    ..This article describes a practical guide on this method. Its application and further analysis will improve our understanding of the quantitative properties of autophagy...
  53. pmc Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy
    Molly A Lynch-Day
    Departments of Molecular, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 2216, USA
    Proc Natl Acad Sci U S A 107:7811-6. 2010
    ..Consistent with the observation that a Ypt1 GEF is directed to the PAS, we find that Ypt1 is essential for autophagy. This is an example of a Rab GEF that is specifically targeted for canonical autophagosome formation...
  54. pmc Indirect estimation of the area density of Atg8 on the phagophore
    Zhiping Xie
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 5:217-20. 2009
    ..Using this method, we found that the estimated area density of Atg8 is comparable with that of proteins that form the COPII coat...
  55. pmc Post-Golgi Sec proteins are required for autophagy in Saccharomyces cerevisiae
    Jiefei Geng
    Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology, and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 21:2257-69. 2010
    ..We propose that following autophagy induction the function of Sec2 and Sec4 are diverted to direct membrane flow to autophagosome formation...
  56. ncbi Atg11 directs autophagosome cargoes to the PAS along actin cables
    Iryna Monastyrska
    Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, Michigan, USA
    Autophagy 2:119-21. 2006
    ..3) In this addendum, we discuss the possible central role of Atg11 as a molecule connecting cargoes, actin and pre-utophagosomal structure (PAS) elements...
  57. ncbi Atg27 is a second transmembrane cycling protein
    Wei Lien Yen
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:254-6. 2007
    ..In this addendum, we discuss the trafficking of Atg27 in yeast and compare it with that of Atg9, and consider the possible meaning of Atg27 Golgi localization...
  58. pmc The transmembrane domain of acid trehalase mediates ubiquitin-independent multivesicular body pathway sorting
    Ju Huang
    Life Sciences Institute, Department of Molecular, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 18:2511-24. 2007
    ..Mutagenesis analyses aimed at identifying the unknown targeting signal revealed that the transmembrane domain of Ath1 contains the information sufficient for its selective sequestration into MVB internal vesicles...
  59. doi Biochemical methods to monitor autophagy-related processes in yeast
    Heesun Cheong
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, USA
    Methods Enzymol 451:1-26. 2008
    ..Processing of the precursor form of the resident vacuolar hydrolase aminopeptidase I (Ape1) is applicable to fungi, whereas cleavage of the GFP-Atg8 and Pex14-GFP chimeras can be used in a wide array of systems...
  60. ncbi Autophagosome formation: core machinery and adaptations
    Zhiping Xie
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology and Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Nat Cell Biol 9:1102-9. 2007
    ..Additional components allow autophagy to adapt to the changing needs of the cell...
  61. pmc The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae
    Heesun Cheong
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 19:668-81. 2008
    ....
  62. pmc Endoplasmic reticulum stress triggers autophagy
    Tomohiro Yorimitsu
    Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 281:30299-304. 2006
    ..We found that Atg1 had high kinase activity during ER stress-induced autophagy. Together, these results indicate that ER stress can induce an autophagic response...
  63. pmc Early stages of the secretory pathway, but not endosomes, are required for Cvt vesicle and autophagosome assembly in Saccharomyces cerevisiae
    Fulvio Reggiori
    Life Sciences Institute and Departments of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 15:2189-204. 2004
    ..Finally, we also show that none of the yeast t-SNAREs are located at the preautophagosomal structure, the presumed site of double-membrane vesicle formation. Based on our results, we propose two models for Cvt vesicle biogenesis...
  64. ncbi Autophagy in yeast: a review of the molecular machinery
    Wei Pang Huang
    Departments of Molecular, Cellular and Developmental Biology and Biological Chemistry, Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 1048, USA
    Cell Struct Funct 27:409-20. 2002
    ..In this review, we discuss the most recent developments in yeast autophagy and point out the challenges we face in the future...
  65. pmc Regulation mechanisms and signaling pathways of autophagy
    Congcong He
    Life Sciences Institute and Departments of Molecular, Cellular and Developmental Biology, and Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA
    Annu Rev Genet 43:67-93. 2009
    ..We also review the recent advances on the molecular mechanisms that regulate the autophagy machinery at various levels, from transcriptional activation to post-translational protein modification...
  66. pmc Tap42-associated protein phosphatase type 2A negatively regulates induction of autophagy
    Tomohiro Yorimitsu
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 5:616-24. 2009
    ..Furthermore, inactivation of PP2A stimulated autophagy and overexpression of a catalytic subunit of PP2A blocked rapamycin-induced autophagy. Our data support a model in which autophagy is negatively regulated by the Tap42-PP2A pathway...
  67. pmc Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy
    Daniel C Nice
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 277:30198-207. 2002
    ..The data suggest a role for PtdIns(3)P in the Cvt pathway and demonstrate that this lipid is required at the pre-autophagosomal structure...
  68. pmc Atg22 recycles amino acids to link the degradative and recycling functions of autophagy
    Zhifen Yang
    Life Sciences Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 17:5094-104. 2006
    ..We propose a "recycling" model that includes the efflux of macromolecules from the lysosome/vacuole as the final step of autophagy...
  69. pmc Vps51 is part of the yeast Vps fifty-three tethering complex essential for retrograde traffic from the early endosome and Cvt vesicle completion
    Fulvio Reggiori
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    J Biol Chem 278:5009-20. 2003
    ..In particular, those factors are essential to correctly target the prApe1-Cvt19-Cvt9 complex to the preautophagosomal structure, the site of Cvt vesicle formation...
  70. pmc The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae
    Fulvio Reggiori
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 16:5843-56. 2005
    ..These phenomena correlate with a defect in Atg9 trafficking from the mitochondria to the PAS...
  71. pmc Self-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy
    Congcong He
    Life Sciences Institute and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 19:5506-16. 2008
    ..Our results support a model in which Atg9 multimerization facilitates membrane flow to the PAS for phagophore formation...
  72. pmc Arp2 links autophagic machinery with the actin cytoskeleton
    Iryna Monastyrska
    Life Sciences Institute and Departments of Molecular, Cellular, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 19:1962-75. 2008
    ..We propose that proteins of the Arp2/3 complex regulate Atg9 transport for specific types of autophagy...
  73. ncbi Permeases recycle amino acids resulting from autophagy
    Zhifen Yang
    Life Sciences Institute, and Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 2216, USA
    Autophagy 3:149-50. 2007
    ..Instead, we found that Atg22, Avt3 and Avt4 are partially redundant vacuolar effluxers, which mediate the efflux of leucine and other amino acids resulting from autophagy...
  74. pmc Regulation of macroautophagy in Saccharomyces cerevisiae
    Yuko Inoue
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 2216, USA
    Semin Cell Dev Biol 21:664-70. 2010
    ....
  75. ncbi Atg26 is not involved in autophagy-related pathways in Saccharomyces cerevisiae
    Yang Cao
    Life Sciences Institute, Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Autophagy 3:17-20. 2007
    ..These studies highlight the importance of examining mutants in multiple organisms...
  76. ncbi Development by self-digestion: molecular mechanisms and biological functions of autophagy
    Beth Levine
    Department of Medicine, Columbia University, New York, NY 10032, USA
    Dev Cell 6:463-77. 2004
    ..In this review, we summarize our current knowledge about the molecular machinery of autophagy and the role of the autophagic machinery in eukaryotic development...
  77. ncbi Autophagy and vacuole homeostasis: a case for self-degradation?
    Dalibor Mijaljica
    Department of Biochemistry and Molecular Biology, and the ARC Centre of Excellence in Structural and Functional Microbial Genomics, Monash University, Clayton Campus, Victoria, Australia
    Autophagy 3:417-21. 2007
    ....
  78. pmc Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae
    Taras Y Nazarko
    Institute of Cell Biology, National Academy of Sciences of Ukraine, Lviv, Ukraine
    Autophagy 1:37-45. 2005
    ..A parallel genetic screen in S. cerevisiae also identified the trs85 mutant. Here, we report that Trs85 is required for nonspecific autophagy, pexophagy and the cytoplasm to vacuole targeting pathway in both yeasts...
  79. ncbi The correct way to monitor autophagy in higher eukaryotes
    Daniel J Klionsky
    Autophagy 1:65. 2005
  80. pmc Atg9 sorting from mitochondria is impaired in early secretion and VFT-complex mutants in Saccharomyces cerevisiae
    Fulvio Reggiori
    Department of Cell Biology, Cell Microscopy Center and Institute of Biomembranes, University Medical Centre Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
    J Cell Sci 119:2903-11. 2006
    ..All mutants have been previously shown to be required for the normal progression of both the Cvt pathway and autophagy, but their precise role in these transport routes was unknown...
  81. ncbi Harpooning the Cvt complex to the phagophore assembly site
    Iryna Monastyrska
    Department of Cell Biology and Institute of Biomembranes, University Medical Centre Utrecht, Utrecht, The Netherlands
    Autophagy 4:914-6. 2008
    ..The contribution at a molecular level of these factors, however, remains unknown. In this addendum, we present mechanistic models that take into account possible roles of actin and the Arp2/3 complex in the Cvt pathway...
  82. ncbi Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival
    Ruth Tal
    Department of Biochemistry and Food Science, Faculty of Agricultural, Food, and Environmental Quality Sciences, Hebrew University of Jerusalem, Rehovot 76100, Israel
    J Biol Chem 282:5617-24. 2007
    ..Our data suggest that Aup1p may be part of a signal transduction mechanism that marks mitochondria for sequestration into autophagosomes...
  83. pmc Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae
    Tomohiro Yorimitsu
    Life Sciences Institute, Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 18:4180-9. 2007
    ..The present results suggest that autophagy is controlled by the signals from at least three partly separate nutrient-sensing pathways that include PKA, Sch9, and TORC1...
  84. ncbi Monitoring autophagy in yeast: the Pho8Delta60 assay
    Daniel J Klionsky
    Department of Molecular, Cellular, and Developmental Biology, Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
    Methods Mol Biol 390:363-71. 2007
    ..Cells expressing the cytosolic form of Pho8, Pho8Delta60, are assayed for alkaline phosphatase activity before and after shifting to conditions that induce autophagy...
  85. ncbi Protein turnover via autophagy: implications for metabolism
    Noboru Mizushima
    Department of Physiology and Cell Biology, Tokyo Medical and Dental University, Tokyo 113 8519, Japan
    Annu Rev Nutr 27:19-40. 2007
    ..We review the current information on the mechanism of autophagy, with a focus on its role in protein metabolism and intracellular homeostasis...
  86. ncbi How cells clean house
    Vojo Deretic
    Molecular genetics and Microbiology Department, University of New Mexico Health Sciences Center, USA
    Sci Am 298:74-81. 2008
    ..A fuller understanding of autophagy is opening up new options for treating cancer, infectious disease, immune disorders and dementia, and it may one day even help to slow down aging...
  87. ncbi Cell biology: regulated self-cannibalism
    Daniel J Klionsky
    Nature 431:31-2. 2004
  88. pmc Atg17 regulates the magnitude of the autophagic response
    Heesun Cheong
    Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109, USA
    Mol Biol Cell 16:3438-53. 2005
    ..As a result, it is defective in peroxisome degradation and is partially defective for autophagy. Atg17 interacts with both Atg1 and Atg13, via two coiled-coil domains, and these interactions facilitate its inclusion in the Atg1 complex...
  89. ncbi Molecular mechanisms and regulation of specific and nonspecific autophagy pathways in yeast
    Usha Nair
    Life Sciences Institute and Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109, USA
    J Biol Chem 280:41785-8. 2005
  90. ncbi Does bafilomycin A1 block the fusion of autophagosomes with lysosomes?
    Daniel J Klionsky
    Autophagy 4:849-950. 2008
    ..However, data from one of our labs noted an apparently different result in a relatively recent manuscript. Therefore, we decided to look into this more carefully...
  91. pmc Autophagy in the eukaryotic cell
    Fulvio Reggiori
    Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109 1048, USA
    Eukaryot Cell 1:11-21. 2002

Research Grants12

  1. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2000
    ..An identification of the sorting determinant in ALP coupled with a characterization of the genes involved in its recognition and delivery should further our understanding of the transport process. ..
  2. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2009
    ..A full understanding of autophagy may also allow therapeutic modulation of a process that is implicated in a range of disease conditions. ..
  3. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2008
    ..A full understanding of autophagy may also allow therapeutic modulation of a process that is implicated in a range of disease conditions. ..
  4. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2007
    ..In addition, we will reconstitute the steps of cargo packaging, vesicle formation and membrane fusion in vitro in order to understand the molecular mechanism that regulates autophagy. ..
  5. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2007
    ..A full understanding of autophagy may also allow therapeutic modulation of a process that is implicated in a range of disease conditions. ..
  6. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2006
    ..In addition, we will reconstitute the steps of cargo packaging, vesicle formation and membrane fusion in vitro in order to understand the molecular mechanism that regulates autophagy. ..
  7. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2005
    ..In addition, we will reconstitute the steps of cargo packaging, vesicle formation and membrane fusion in vitro in order to understand the molecular mechanism that regulates autophagy. ..
  8. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2004
    ..In addition, we will reconstitute the steps of cargo packaging, vesicle formation and membrane fusion in vitro in order to understand the molecular mechanism that regulates autophagy. ..
  9. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2003
    ..In addition, we will reconstitute the steps of cargo packaging, vesicle formation and membrane fusion in vitro in order to understand the molecular mechanism that regulates autophagy. ..
  10. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2002
    ..An identification of the sorting determinant in ALP coupled with a characterization of the genes involved in its recognition and delivery should further our understanding of the transport process. ..
  11. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    DANIEL KLIONSKY; Fiscal Year: 2001
    ..An identification of the sorting determinant in ALP coupled with a characterization of the genes involved in its recognition and delivery should further our understanding of the transport process. ..
  12. ALTERNATIVE VACUOLAR TARGETING MECHANISMS IN YEAST
    Daniel J Klionsky; Fiscal Year: 2010
    ..A full understanding of autophagy may also allow therapeutic modulation of a process that is implicated in a range of disease conditions. ..