Table of Contents
International Journal of Plant Genomics
Volume 2009, Article ID 451357, 14 pages
http://dx.doi.org/10.1155/2009/451357
Review Article

Techniques to Study Autophagy in Plants

Biological Science and Bioengineering Program, Faculty of Engineering and Natural Sciences, Sabanci University, Orhanli, Tuzla 34956, Istanbul, Turkey

Received 7 December 2008; Revised 15 May 2009; Accepted 18 June 2009

Academic Editor: Boulos Chalhoub

Copyright © 2009 Géraldine Mitou et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. W. A. Dunn Jr., J. M. Cregg, J. A. Kiel et al., “Pexophagy: the selective autophagy of peroxisomes,” Autophagy, vol. 1, no. 2, pp. 75–83, 2005. View at Google Scholar
  2. G. E. Mortimore, B. R. Lardeux, and C. E. Adams, “Regulation of microautophagy and basal protein turnover in rat liver. Effects of short-term starvation,” The Journal of Biological Chemistry, vol. 263, no. 5, pp. 2506–2512, 1988. View at Google Scholar
  3. D. J. Klionsky, “The molecular machinery of autophagy: unanswered questions,” Journal of Cell Science, vol. 118, no. 1, pp. 7–18, 2005. View at Publisher · View at Google Scholar · View at PubMed
  4. A. C. Massey, C. Zhang, and A. M. Cuervo, “Chaperone-mediated autophagy in aging and disease,” Current Topics in Developmental Biology, vol. 73, pp. 205–235, 2006. View at Publisher · View at Google Scholar · View at PubMed
  5. D. C. Bassham, M. Laporte, F. Marty et al., “Autophagy in development and stress responses of plants,” Autophagy, vol. 2, no. 1, pp. 2–11, 2006. View at Google Scholar
  6. S. Aubert, E. Gout, R. Bligny et al., “Ultrastructural and biochemical characterization of autophagy in higher plant cells subjected to carbon deprivation: control by the supply of mitochondria with respiratory substrates,” The Journal of Cell Biology, vol. 133, no. 6, pp. 1251–1263, 1996. View at Publisher · View at Google Scholar
  7. T. L. Rose, L. Bonneau, C. Der, D. Marty-Mazars, and F. Marty, “Starvation-induced expression of autophagy-related genes in Arabidopsis,” Biology of the Cell, vol. 98, no. 1, pp. 53–67, 2006. View at Publisher · View at Google Scholar · View at PubMed
  8. Y. Xiong, A. L. Contento, P. Q. Nguyen, and D. C. Bassham, “Degradation of oxidized proteins by autophagy during oxidative stress in Arabidopsis,” Plant Physiology, vol. 143, no. 1, pp. 291–299, 2007. View at Publisher · View at Google Scholar · View at PubMed
  9. A. R. Thompson and R. D. Vierstra, “Autophagic recycling: lessons from yeast help define the process in plants,” Current Opinion in Plant Biology, vol. 8, no. 2, pp. 165–173, 2005. View at Publisher · View at Google Scholar · View at PubMed
  10. M. Seay, S. Patel, and S. P. Dinesh-Kumar, “Autophagy and plant innate immunity,” Cellular Microbiology, vol. 8, no. 6, pp. 899–906, 2006. View at Publisher · View at Google Scholar · View at PubMed
  11. M. G. Gutierrez, S. S. Master, S. B. Singh, G. A. Taylor, M. I. Colombo, and V. Deretic, “Autophagy is a defense mechanism inhibiting BCG and Mycobacterium tuberculosis survival in infected macrophages,” Cell, vol. 119, no. 6, pp. 753–766, 2004. View at Publisher · View at Google Scholar · View at PubMed
  12. D. Gozuacik and A. Kimchi, “Autophagy and cell death,” Current Topics in Developmental Biology, vol. 78, pp. 217–245, 2007. View at Publisher · View at Google Scholar · View at PubMed
  13. D. C. Bassham, “Plant autophagy—more than a starvation response,” Current Opinion in Plant Biology, vol. 10, no. 6, pp. 587–593, 2007. View at Publisher · View at Google Scholar · View at PubMed
  14. W. G. van Doorn and E. J. Woltering, “Many ways to exit? Cell death categories in plants,” Trends in Plant Science, vol. 10, no. 3, pp. 117–122, 2005. View at Publisher · View at Google Scholar
  15. H. T. Horner, R. A. Healy, T. Cervantes-Martinez, and R. C. Palmer, “Floral nectary fine structure and development in Glycine max L. (Fabaceae),” International Journal of Plant Sciences, vol. 164, no. 5, pp. 675–690, 2003. View at Publisher · View at Google Scholar
  16. Z. Xie and D. J. Klionsky, “Autophagosome formation: core machinery and adaptations,” Nature Cell Biology, vol. 9, no. 10, pp. 1102–1109, 2007. View at Publisher · View at Google Scholar · View at PubMed
  17. D. J. Klionsky, J. M. Cregg, W. A. Dunn Jr. et al., “A unified nomenclature for yeast autophagy-related genes,” Developmental Cell, vol. 5, no. 4, pp. 539–545, 2003. View at Publisher · View at Google Scholar
  18. D. Gozuacik and A. Kimchi, “Autophagy as a cell death and tumor suppressor mechanism,” Oncogene, vol. 23, no. 16, pp. 2891–2906, 2004. View at Publisher · View at Google Scholar · View at PubMed
  19. G. Thomas and M. N. Hall, “TOR signalling and control of cell growth,” Current Opinion in Cell Biology, vol. 9, no. 6, pp. 782–787, 1997. View at Publisher · View at Google Scholar
  20. S. G. Dann and G. Thomas, “The amino acid sensitive TOR pathway from yeast to mammals,” FEBS Letters, vol. 580, no. 12, pp. 2821–2829, 2006. View at Publisher · View at Google Scholar · View at PubMed
  21. S. Díaz-Troya, M. E. Pérez-Pérez, F. J. Florencio, and J. L. Crespo, “The role of TOR in autophagy regulation from yeast to plants and mammals,” Autophagy, vol. 4, no. 7, pp. 851–865, 2008. View at Google Scholar
  22. T. Noda and Y. Ohsumi, “Tor, a phosphatidylinositol kinase homologue, controls autophagy in yeast,” The Journal of Biological Chemistry, vol. 273, no. 7, pp. 3963–3966, 1998. View at Publisher · View at Google Scholar
  23. J. Kunz, R. Henriquez, U. Schneider, M. Deuter-Reinhard, N. R. Movva, and M. N. Hall, “Target of rapamycin in yeast, TOR2, is an essential phosphatidylinositol kinase homolog required for G1 progression,” Cell, vol. 73, no. 3, pp. 585–596, 1993. View at Publisher · View at Google Scholar
  24. R. Sormani, Y. Lei, B. Menand et al., “Saccharomyces cerevisiae FKBP12 binds Arabidopsis thaliana TOR and its expression in plants leads to rapamycin susceptibility,” BMC Plant Biology, vol. 7, article 26, pp. 1–8, 2007. View at Publisher · View at Google Scholar · View at PubMed
  25. T. Beck and M. N. Hall, “The TOR signalling pathway controls nuclear localization of nutrient-regulated transcription factors,” Nature, vol. 402, no. 6762, pp. 689–692, 1999. View at Publisher · View at Google Scholar · View at PubMed
  26. K. Natarajan, M. R. Meyer, B. M. Jackson et al., “Transcriptional profiling shows that Gcn4p is a master regulator of gene expression during amino acid starvation in yeast,” Molecular and Cellular Biology, vol. 21, no. 13, pp. 4347–4368, 2001. View at Publisher · View at Google Scholar · View at PubMed
  27. Y. Kamada, T. Funakoshi, T. Shintani, K. Nagano, M. Ohsumi, and Y. Ohsumi, “Tor-mediated induction of autophagy via an Apg1 protein kinase complex,” The Journal of Cell Biology, vol. 150, no. 6, pp. 1507–1513, 2000. View at Publisher · View at Google Scholar
  28. A. Matsuura, M. Tsukada, Y. Wada, and Y. Ohsumi, “Apg1p, a novel protein kinase required for the autophagic process in Saccharomyces cerevisiae,” Gene, vol. 192, no. 2, pp. 245–250, 1997. View at Publisher · View at Google Scholar
  29. H. Abeliovich, C. Zhang, W. A. Dunn Jr., K. M. Shokat, and D. J. Klionsky, “Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy,” Molecular Biology of the Cell, vol. 14, no. 2, pp. 477–490, 2003. View at Publisher · View at Google Scholar · View at PubMed
  30. P. Codogno, “[ATG genes and macroautophagy],” Médecine Sciences, vol. 20, no. 8-9, pp. 734–736, 2004. View at Google Scholar
  31. F. Reggiori, K. A. Tucker, P. E. Stromhaug, and D. J. Klionsky, “The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure,” Developmental Cell, vol. 6, no. 1, pp. 79–90, 2004. View at Publisher · View at Google Scholar
  32. A. Kihara, T. Noda, N. Ishihara, and Y. Ohsumi, “Two distinct Vps34 phosphatidylinositol 3-kinase complexes function in autophagy and carboxypeptidase Y sorting in Saccharomyces cerevisiae,” The Journal of Cell Biology, vol. 152, no. 3, pp. 519–530, 2001. View at Publisher · View at Google Scholar
  33. A. Petiot, E. Ogier-Denis, E. F. C. Blommaart, A. J. Meijer, and P. Codogno, “Distinct classes of phosphatidylinositol 3-kinases are involved in signaling pathways that control macroautophagy in HT-29 cells,” The Journal of Biological Chemistry, vol. 275, no. 2, pp. 992–998, 2000. View at Publisher · View at Google Scholar
  34. N. Mizushima, T. Noda, T. Yoshimori et al., “A protein conjugation system essential for autophagy,” Nature, vol. 395, no. 6700, pp. 395–398, 1998. View at Publisher · View at Google Scholar · View at PubMed
  35. T. Shintani, N. Mizushima, Y. Ogawa, A. Matsuura, T. Noda, and Y. Ohsumi, “Apg10p, a novel protein-conjugating enzyme essential for autophagy in yeast,” The EMBO Journal, vol. 18, no. 19, pp. 5234–5241, 1999. View at Publisher · View at Google Scholar · View at PubMed
  36. I. Tanida, N. Mizushima, M. Kiyooka et al., “Apg7p/Cvt2p: a novel protein-activating enzyme essential for autophagy,” Molecular Biology of the Cell, vol. 10, no. 5, pp. 1367–1379, 1999. View at Google Scholar
  37. N. Mizushima, T. Noda, and Y. Ohsumi, “Apg16p is required for the function of the Apg12p-Apg5p conjugate in the yeast autophagy pathway,” The EMBO Journal, vol. 18, no. 14, pp. 3888–3896, 1999. View at Publisher · View at Google Scholar · View at PubMed
  38. N. Mizushima, A. Yamamoto, M. Hatano et al., “Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells,” The Journal of Cell Biology, vol. 152, no. 4, pp. 657–668, 2001. View at Publisher · View at Google Scholar
  39. Y. Ichimura, T. Kirisako, T. Takao et al., “A ubiquitin-like system mediates protein lipidation,” Nature, vol. 408, no. 6811, pp. 488–492, 2000. View at Publisher · View at Google Scholar · View at PubMed
  40. Y. Fujioka, N. N. Noda, K. Fujii, K. Yoshimoto, Y. Ohsumi, and F. Inagaki, “In vitro reconstitution of plant Atg8 and Atg12 conjugation systems essential for autophagy,” The Journal of Biological Chemistry, vol. 283, no. 4, pp. 1921–1928, 2008. View at Publisher · View at Google Scholar · View at PubMed
  41. Y. Kabeya, N. Mizushima, T. Ueno et al., “LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing,” The EMBO Journal, vol. 19, no. 21, pp. 5720–5728, 2000. View at Publisher · View at Google Scholar · View at PubMed
  42. Y. Sagiv, A. Legesse-Miller, A. Porat, and Z. Elazar, “GATE-16, a membrane transport modulator, interacts with NSF and the Golgi v-SNARE GOS-28,” The EMBO Journal, vol. 19, no. 7, pp. 1494–1504, 2000. View at Publisher · View at Google Scholar · View at PubMed
  43. T. Ketelaar, C. Voss, S. A. Dimmock, M. Thumm, and P. J. Hussey, “Arabidopsis homologues of the autophagy protein Atg8 are a novel family of microtubule binding proteins,” FEBS Letters, vol. 567, no. 2-3, pp. 302–306, 2004. View at Publisher · View at Google Scholar · View at PubMed
  44. J. H. Doelling, J. M. Walker, E. M. Friedman, A. R. Thompson, and R. D. Vierstra, “The APG8/12-activating enzyme APG7 is required for proper nutrient recycling and senescence in Arabidopsis thaliana,” The Journal of Biological Chemistry, vol. 277, no. 36, pp. 33105–33114, 2002. View at Publisher · View at Google Scholar · View at PubMed
  45. T. Darsow, S. E. Rieder, and S. D. Emr, “A multispecificity syntaxin homologue, Vam3p, essential for autophagic and biosynthetic protein transport to the vacuole,” The Journal of Cell Biology, vol. 138, no. 3, pp. 517–529, 1997. View at Publisher · View at Google Scholar
  46. C. Ungermann and D. Langosch, “Functions of SNAREs in intracellular membrane fusion and lipid bilayer mixing,” Journal of Cell Science, vol. 118, no. 17, pp. 3819–3828, 2005. View at Publisher · View at Google Scholar · View at PubMed
  47. H. Abeliovich and D. J. Klionsky, “Autophagy in yeast: mechanistic insights and physiological function,” Microbiology and Molecular Biology Reviews, vol. 65, no. 3, pp. 463–479, 2001. View at Publisher · View at Google Scholar · View at PubMed
  48. I. Kim, S. Rodriguez-Enriquez, and J. J. Lemasters, “Selective degradation of mitochondria by mitophagy,” Archives of Biochemistry and Biophysics, vol. 462, no. 2, pp. 245–253, 2007. View at Publisher · View at Google Scholar · View at PubMed
  49. W. Van der Wilden, E. M. Herman, and M. J. Chrispeels, “Protein bodies of mung bean cotyledons as autophagic organelles,” Proceedings of the National Academy of Sciences of the United States of America, vol. 77, no. 1, pp. 428–432, 1980. View at Publisher · View at Google Scholar
  50. M. Poxleitner, S. W. Rogers, A. L. Samuels, J. Browse, and J. C. Rogers, “A role for caleosin in degradation of oil-body storage lipid during seed germination,” The Plant Journal, vol. 47, no. 6, pp. 917–933, 2006. View at Publisher · View at Google Scholar · View at PubMed
  51. K. Toyooka, Y. Moriyasu, Y. Goto, M. Takeuchi, H. Fukuda, and K. Matsuoka, “Protein aggregates are transported to vacuoles by a macroautophagic mechanism in nutrient-starved plant cells,” Autophagy, vol. 2, no. 2, pp. 96–106, 2006. View at Google Scholar
  52. Y. Inoue, T. Suzuki, M. Hattori, K. Yoshimoto, Y. Ohsumi, and Y. Moriyasu, “AtATG genes, homologs of yeast autophagy genes, are involved in constitutive autophagy in Arabidopsis root tip cells,” Plant & Cell Physiology, vol. 47, no. 12, pp. 1641–1652, 2006. View at Publisher · View at Google Scholar · View at PubMed
  53. H. Hanaoka, T. Noda, Y. Shirano et al., “Leaf senescence and starvation-induced chlorosis are accelerated by the disruption of an Arabidopsis autophagy gene,” Plant Physiology, vol. 129, no. 3, pp. 1181–1193, 2002. View at Publisher · View at Google Scholar · View at PubMed
  54. K. Yoshimoto, H. Hanaoka, S. Sato et al., “Processing of ATG8s, ubiquitin-like proteins, and their deconjugation by ATG4s are essential for plant autophagy,” The Plant Cell, vol. 16, no. 11, pp. 2967–2983, 2004. View at Publisher · View at Google Scholar · View at PubMed
  55. A. R. Thompson, J. H. Doelling, A. Suttangkakul, and R. D. Vierstra, “Autophagic nutrient recycling in Arabidopsis directed by the ATG8 and ATG12 conjugation pathways,” Plant Physiology, vol. 138, no. 4, pp. 2097–2110, 2005. View at Publisher · View at Google Scholar · View at PubMed
  56. A. L. Contento, S.-J. Kim, and D. C. Bassham, “Transcriptome profiling of the response of Arabidopsis suspension culture cells to Suc starvation,” Plant Physiology, vol. 135, no. 4, pp. 2330–2347, 2004. View at Publisher · View at Google Scholar · View at PubMed
  57. S. Sláviková, G. Shy, Y. Yao et al., “The autophagy-associated Atg8 gene family operates both under favourable growth conditions and under starvation stresses in Arabidopsis plants,” Journal of Experimental Botany, vol. 56, no. 421, pp. 2839–2849, 2005. View at Publisher · View at Google Scholar · View at PubMed
  58. E. Van Der Graaff, R. Schwacke, A. Schneider, M. Desimone, U. I. Flügge, and R. Kunze, “Transcription analysis of Arabidopsis membrane transporters and hormone pathways during developmental and induced leaf senescence,” Plant Physiology, vol. 141, no. 2, pp. 776–792, 2006. View at Publisher · View at Google Scholar · View at PubMed
  59. D. Osuna, B. Usadel, R. Morcuende et al., “Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings,” The Plant Journal, vol. 49, no. 3, pp. 463–491, 2007. View at Publisher · View at Google Scholar · View at PubMed
  60. C. Wagstaff, T. J. W. Yang, A. D. Stead, V. Buchanan-Wollaston, and J. A. Roberts, “A molecular and structural characterization of senescing Arabidopsis siliques and comparison of transcriptional profiles with senescing petals and leaves,” The Plant Journal, vol. 57, no. 4, pp. 690–705, 2009. View at Publisher · View at Google Scholar · View at PubMed
  61. H. O. Ghiglione, F. G. Gonzalez, R. Serrago et al., “Autophagy regulated by day length determines the number of fertile florets in wheat,” The Plant Journal, vol. 55, no. 6, pp. 1010–1024, 2008. View at Publisher · View at Google Scholar · View at PubMed
  62. C. Takatsuka, Y. Inoue, K. Matsuoka, and Y. Moriyasu, “3-methyladenine inhibits autophagy in tobacco culture cells under sucrose starvation conditions,” Plant & Cell Physiology, vol. 45, no. 3, pp. 265–274, 2004. View at Publisher · View at Google Scholar
  63. Y. Xiong, A. L. Contento, and D. C. Bassham, “Disruption ol autophagy results in constitutive oxidative stress in Arabidopsis,” Autophagy, vol. 3, no. 3, pp. 257–258, 2007. View at Google Scholar
  64. Y. Niwa, T. Kato, S. Tabata et al., “Disposal of chloroplasts with abnormal function into the vacuole in Arabidopsis thaliana cotyledon cells,” Protoplasma, vol. 223, no. 2–4, pp. 229–232, 2004. View at Google Scholar
  65. K. Yano, M. Hattori, and Y. Moriyasu, “A novel type of autophagy occurs together with vacuole genesis in miniprotoplasts prepared from tobacco culture cells,” Autophagy, vol. 3, no. 3, pp. 215–221, 2007. View at Google Scholar
  66. S. Slavikova, S. Ufaz, T. Avin-Wittenberg, H. Levanony, and G. Galili, “An autophagy-associated Atg8 protein is involved in the responses of Arabidopsis seedlings to hormonal controls and abiotic stresses,” Journal of Experimental Botany, vol. 59, no. 14, pp. 4029–4043, 2008. View at Publisher · View at Google Scholar · View at PubMed
  67. A. L. Contento, Y. Xiong, and D. C. Bassham, “Visualization of autophagy in Arabidopsis using the fluorescent dye monodansylcadaverine and a GFP-AtATG8e fusion protein,” The Plant Journal, vol. 42, no. 4, pp. 598–608, 2005. View at Publisher · View at Google Scholar · View at PubMed
  68. M. H. Chen, L. F. Liu, Y. R. Chen, Wu Hsin Kan, and S. M. Yu, “Expression of α-amylase, carbohydrate metabolism, and autophagy in cultured rice cells is coordinately regulated by sugar nutrient,” The Plant Journal, vol. 6, no. 5, pp. 625–636, 1994. View at Publisher · View at Google Scholar
  69. Y. Moriyasu and Y. Ohsumi, “Autophagy in tobacco suspension-cultured cells in response to sucrose starvation,” Plant Physiology, vol. 111, no. 4, pp. 1233–1241, 1996. View at Google Scholar
  70. R. Brouquisse, J. P. Gaudillère, and P. Raymond, “Induction of a carbon-starvation-related proteolysis in whole maize plants submitted to light/dark cycles and to extended darkness,” Plant Physiology, vol. 117, no. 4, pp. 1281–1291, 1998. View at Publisher · View at Google Scholar
  71. D. G. Robinson, G. Hinz, and S. E. H. Holstein, “The molecular characterization of transport vesicles,” Plant Molecular Biology, vol. 38, no. 1-2, pp. 49–76, 1998. View at Publisher · View at Google Scholar
  72. G. Galili and E. M. Herman, “Protein bodies: storage vacuoles in seeds,” Advances in Botanical Research, vol. 25, pp. 113–140, 1997. View at Publisher · View at Google Scholar
  73. H. Levanony, R. Rubin, Y. Altschuler, and G. Galili, “Evidence for a novel route of wheat storage proteins to vacuoles,” The Journal of Cell Biology, vol. 119, no. 5, pp. 1117–1128, 1992. View at Publisher · View at Google Scholar
  74. F. Marty, “Cytochemical studies on GERL, provacuoles, and vacuoles in root meristematic cells of Euphorbia,” Proceedings of the National Academy of Sciences of the United States of America, vol. 75, no. 2, pp. 852–856, 1978. View at Publisher · View at Google Scholar
  75. F. Marty, “Plant vacuoles,” The Plant Cell, vol. 11, no. 4, pp. 587–600, 1999. View at Publisher · View at Google Scholar
  76. K. Toyooka, T. Okamoto, and T. Minamikawa, “Cotyledon cells of Vigna mungo seedlings use at least two distinct autophagic machineries for degradation of starch granules and cellular components,” The Journal of Cell Biology, vol. 154, no. 5, pp. 973–982, 2001. View at Publisher · View at Google Scholar · View at PubMed
  77. K. P. Gaffal, G. J. Friedrichs, and S. El-Gammal, “Ultrastructural evidence for a dual function of the phloem and programmed cell death in the floral nectary of Digitalis purpurea,” Annals of Botany, vol. 99, no. 4, pp. 593–607, 2007. View at Publisher · View at Google Scholar · View at PubMed
  78. E. Lam, “Controlled cell death, plant survival and development,” Nature Reviews Molecular Cell Biology, vol. 5, no. 4, pp. 305–315, 2004. View at Publisher · View at Google Scholar · View at PubMed
  79. Y. Liu, M. Schiff, K. Czymmek, Z. Tallóczy, B. Levine, and S. P. Dinesh-Kumar, “Autophagy regulates programmed cell death during the plant innate immune response,” Cell, vol. 121, no. 4, pp. 567–577, 2005. View at Publisher · View at Google Scholar · View at PubMed
  80. S. Patel and S. P. Dinesh-Kumar, “Arabidopsis ATG6 is required to limit the pathogen-associated cell death response,” Autophagy, vol. 4, no. 1, pp. 20–27, 2008. View at Google Scholar
  81. W. Su, H. Ma, C. Liu, J. Wu, and J. Yang, “Identification and characterization of two rice autophagy associated genes, OsAtg8 and OsAtg4,” Molecular Biology Reports, vol. 33, no. 4, pp. 273–278, 2006. View at Publisher · View at Google Scholar · View at PubMed
  82. T. P. Ashford and K. R. Porter, “Cytoplasmic components in hepatic cell lysosomes,” The Journal of Cell Biology, vol. 12, no. 1, pp. 198–202, 1962. View at Publisher · View at Google Scholar
  83. M. Fengsrud, E. S. Erichsen, T. O. Berg, C. Raiborg, and P. O. Seglen, “Ultrastructural characterization of the delimiting membranes of isolated autophagosomes and amphisomes by freeze-fracture electron microscopy,” European Journal of Cell Biology, vol. 79, no. 12, pp. 871–882, 2000. View at Publisher · View at Google Scholar
  84. D. J. Klionsky, H. Abeliovich, P. Agostinis et al., “Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes,” Autophagy, vol. 4, no. 2, pp. 151–175, 2008. View at Google Scholar
  85. E. L. Eskelinen, “To be or not to be? Examples of incorrect identification of autophagic compartments in conventional transmission electron microscopy of mammalian cells,” Autophagy, vol. 4, no. 2, pp. 257–260, 2008. View at Google Scholar
  86. C. L. Birmingham, V. Canadien, E. Gouin et al., “Listeria monocytogenes evades killing by autophagy during colonization of host cells,” Autophagy, vol. 3, no. 5, pp. 442–451, 2007. View at Google Scholar
  87. T. M. Mayhew, “Quantitative immunoelectron microscopy: alternative ways of assessing subcellular patterns of gold labeling,” Methods in Molecular Biology, vol. 369, pp. 309–329, 2007. View at Publisher · View at Google Scholar
  88. P. He, Z. Peng, Y. Luo et al., “High-throughput functional screening for autophagy-related genes and identification of TM9SF1 as an autophagosome-inducing gene,” Autophagy, vol. 5, no. 1, pp. 52–60, 2009. View at Google Scholar
  89. A. R. Phillips, A. Suttangkakul, and R. D. Vierstra, “The ATG12-conjugating enzyme ATG10 is essential for autophagic vesicle formation in Arabidopsis thaliana,” Genetics, vol. 178, no. 3, pp. 1339–1353, 2008. View at Publisher · View at Google Scholar · View at PubMed
  90. H. Ishida, K. Yoshimoto, M. Izumi et al., “Mobilization of Rubisco and stroma-localized fluorescent proteins of chloroplasts to the vacuole by an ATG gene-dependent autophagic process,” Plant Physiology, vol. 148, no. 1, pp. 142–155, 2008. View at Publisher · View at Google Scholar · View at PubMed
  91. E. Shvets, E. Fass, and Z. Elazar, “Utilizing flow cytometry to monitor autophagy in living mammalian cells,” Autophagy, vol. 4, no. 5, pp. 621–628, 2008. View at Google Scholar
  92. I. Cummins, P. G. Steel, and R. Edwards, “Identification of a carboxylesterase expressed in protoplasts using fluorescence-activated cell sorting,” Plant Biotechnology Journal, vol. 5, no. 2, pp. 354–359, 2007. View at Publisher · View at Google Scholar · View at PubMed
  93. M. Mäe, H. Myrberg, Y. Jiang, H. Paves, A. Valkna, and U. Langel, “Internalisation of cell-penetrating peptides into tobacco protoplasts,” Biochimica et Biophysica Acta, vol. 1669, no. 2, pp. 101–107, 2005. View at Publisher · View at Google Scholar · View at PubMed
  94. N. Yao, B. J. Eisfelder, J. Marvin, and J. T. Greenberg, “The mitochondrion—an organelle commonly involved in programmed cell death in Arabidopsis thaliana,” The Plant Journal, vol. 40, no. 4, pp. 596–610, 2004. View at Publisher · View at Google Scholar · View at PubMed
  95. N. Mizushima and T. Yoshimori, “How to interpret LC3 immunoblotting,” Autophagy, vol. 3, no. 6, pp. 542–545, 2007. View at Google Scholar
  96. A. Kuma, M. Matsui, and N. Mizushima, “LC3, an autophagosome marker, can be incorporated into protein aggregates independent of autophagy: caution in the interpretation of LC3 localization,” Autophagy, vol. 3, no. 4, pp. 323–328, 2007. View at Google Scholar
  97. K. Suzuki, T. Kirisako, Y. Kamada, N. Mizushima, T. Noda, and Y. Ohsumi, “The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation,” The EMBO Journal, vol. 20, no. 21, pp. 5971–5981, 2001. View at Publisher · View at Google Scholar · View at PubMed
  98. E. Shvets and Z. Elazar, “Autophagy-independent incorporation of GFP-LC3 into protein aggregates is dependent on its interaction with p62/SQSTM1,” Autophagy, vol. 4, no. 8, pp. 1054–1056, 2008. View at Google Scholar
  99. T. Ueno, W. Sato, Y. Horie et al., “Loss of Pten, a tumor suppressor, causes the strong inhibition of autophagy without affecting LC3 lipidation,” Autophagy, vol. 4, no. 5, pp. 692–700, 2008. View at Google Scholar
  100. P. Giménez-Xavier, R. Francisco, F. Platini, R. Pérez, and S. Ambrosio, “LC3-I conversion to LC3-II does not necessarily result in complete autophagy,” International Journal of Molecular Medicine, vol. 22, no. 6, pp. 781–785, 2008. View at Publisher · View at Google Scholar
  101. Z. Yue, S. Jin, C. Yang, A. J. Levine, and N. Heintz, “Beclin 1, an autophagy gene essential for early embryonic development, is a haploinsufficient tumor suppressor,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 25, pp. 15077–15082, 2003. View at Publisher · View at Google Scholar · View at PubMed
  102. S. Pattingre, A. Tassa, X. Qu et al., “Bcl-2 antiapoptotic proteins inhibit Beclin 1-dependent autophagy,” Cell, vol. 122, no. 6, pp. 927–939, 2005. View at Publisher · View at Google Scholar · View at PubMed
  103. O. V. Vieira, R. J. Botelho, L. Rameh et al., “Distinct roles of class I and class III phosphatidylinositol 3-kinases in phagosome formation and maturation,” The Journal of Cell Biology, vol. 155, no. 1, pp. 19–25, 2001. View at Publisher · View at Google Scholar · View at PubMed
  104. D. H. Kim, Y. J. Eu, C. M. Yoo et al., “Trafficking of phosphatidylinositol 3-phosphate from the trans-Golgi network to the lumen of the central vacuole in plant cells,” The Plant Cell, vol. 13, no. 2, pp. 287–301, 2001. View at Publisher · View at Google Scholar
  105. K. Matsunaga, T. Saitoh, K. Tabata et al., “Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages,” Nature Cell Biology, vol. 11, no. 4, pp. 385–396, 2009. View at Publisher · View at Google Scholar · View at PubMed
  106. N. Mizushima, A. Kuma, Y. Kobayashi et al., “Mouse Apg16L, a novel WD-repeat protein, targets to the autophagic isolation membrane with the Apg12-Apg5 conjugate,” Journal of Cell Science, vol. 116, no. 9, pp. 1679–1688, 2003. View at Publisher · View at Google Scholar
  107. T. Proikas-Cezanne, S. Ruckerbauer, Y. D. Stierhof, C. Berg, and A. Nordheim, “Human WIPI-1 puncta-formation: a novel assay to assess mammalian autophagy,” FEBS Letters, vol. 581, no. 18, pp. 3396–3404, 2007. View at Publisher · View at Google Scholar · View at PubMed
  108. S. Waddell, J. R. Jenkins, and T. Proikas-Cezanne, “A “no-hybrids” screen for functional antagonizers of human p53 transactivator function: dominant negativity in fission yeast,” Oncogene, vol. 20, no. 42, pp. 6001–6008, 2001. View at Publisher · View at Google Scholar · View at PubMed
  109. T. Proikas-Cezanne, S. Waddell, A. Gaugel, T. Frickey, A. Lupas, and A. Nordheim, “WIPI-1α (WIPI49), a member of the novel 7-bladed WIPI protein family, is aberrantly expressed in human cancer and is linked to starvation-induced autophagy,” Oncogene, vol. 23, no. 58, pp. 9314–9325, 2004. View at Publisher · View at Google Scholar · View at PubMed
  110. R. Ketteier and B. Seed, “Quantitation of autophagy by luciferase release assay,” Autophagy, vol. 4, no. 6, pp. 801–806, 2008. View at Google Scholar
  111. T. Tekinay, M. Y. Wu, G. P. Otto, O. R. Anderson, and R. H. Kessin, “Function of the Dictyostelium discoideum Atg1 kinase during autophagy and development,” Eukaryotic Cell, vol. 5, no. 10, pp. 1797–1806, 2006. View at Publisher · View at Google Scholar · View at PubMed
  112. S. B. Lee, S. Kim, J. Lee et al., “ATG1, an autophagy regulator, inhibits cell growth by negatively regulating S6 kinase,” EMBO Reports, vol. 8, no. 4, pp. 360–365, 2007. View at Publisher · View at Google Scholar · View at PubMed
  113. T. Hara, A. Takamura, C. Kishi et al., “FIP200, a ULK-interacting protein, is required for autophagosome formation in mammalian cells,” The Journal of Cell Biology, vol. 181, no. 3, pp. 497–510, 2008. View at Publisher · View at Google Scholar · View at PubMed
  114. E. Y. W. Chan, A. Longatti, N. C. McKnight, and S. A. Tooze, “Kinase-inactivated ULK proteins inhibit autophagy via their conserved C-terminal domains using an Atg13-independent mechanism,” Molecular and Cellular Biology, vol. 29, no. 1, pp. 157–171, 2009. View at Publisher · View at Google Scholar · View at PubMed
  115. T. Chung, A. Suttangkakul, and R. D. Vierstra, “The ATG autophagic conjugation system in maize: ATG transcripts and abundance of the ATG8-lipid adduct are regulated by development and nutrient availability,” Plant Physiology, vol. 149, no. 1, pp. 220–234, 2009. View at Publisher · View at Google Scholar · View at PubMed
  116. K. Zatloukal, C. Stumptner, A. Fuchsbichler et al., “p62 is a common component of cytoplasmic inclusions in protein aggregation diseases,” American Journal of Pathology, vol. 160, no. 1, pp. 255–263, 2002. View at Google Scholar
  117. E. Shvets, E. Fass, R. Scherz-Shouval, and Z. Elazar, “The N-terminus and Phe52 residue of LC3 recruit p62/SQSTM1 into autophagosomes,” Journal of Cell Science, vol. 121, no. 16, pp. 2685–2695, 2008. View at Publisher · View at Google Scholar · View at PubMed
  118. S. Pankiv, T. H. Clausen, T. Lamark et al., “p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy,” The Journal of Biological Chemistry, vol. 282, no. 33, pp. 24131–24145, 2007. View at Publisher · View at Google Scholar · View at PubMed
  119. J. P. Pursiheimo, K. Rantanen, P. T. Heikkinen, T. Johansen, and P. M. Jaakkola, “Hypoxia-activated autophagy accelerates degradation of SQSTM1/p62,” Oncogene, vol. 28, no. 3, pp. 334–344, 2009. View at Publisher · View at Google Scholar · View at PubMed
  120. G. Bjørkøy, T. Lamark, A. Brech et al., “p62/SQSTM1 forms protein aggregates degraded by autophagy and has a protective effect on huntingtin-induced cell death,” The Journal of Cell Biology, vol. 171, no. 4, pp. 603–614, 2005. View at Publisher · View at Google Scholar · View at PubMed
  121. M. Harada, S. Hanada, D. M. Toivola, N. Ghori, and M. B. Omary, “Autophagy activation by rapamycin eliminates mouse Mallory-Denk bodies and blocks their proteasome inhibitor-mediated formation,” Hepatology, vol. 47, no. 6, pp. 2026–2035, 2008. View at Publisher · View at Google Scholar · View at PubMed
  122. Y. Moriyasu, M. Hattori, G.-Y. Jauh, and J. C. Rogers, “Alpha tonoplast intrinsic protein is specifically associated with vacuole membrane involved in an autophagic process,” Plant and Cell Physiology, vol. 44, no. 8, pp. 795–802, 2003. View at Publisher · View at Google Scholar
  123. S. Paglin, T. Hollister, T. Delohery et al., “A novel response of cancer cells to radiation involves autophagy and formation of acidic vesicles,” Cancer Research, vol. 61, no. 2, pp. 439–444, 2001. View at Google Scholar
  124. T. Kanazawa, I. Taneike, R. Akaishi et al., “Amino acids and insulin control autophagic proteolysis through different signaling pathways in relation to mTOR in isolated rat hepatocytes,” The Journal of Biological Chemistry, vol. 279, no. 9, pp. 8452–8459, 2004. View at Publisher · View at Google Scholar · View at PubMed
  125. D. B. Munafó and M. I. Colombo, “A novel assay to study autophagy: regulation of autophagosome vacuole size by amino acid deprivation,” Journal of Cell Science, vol. 114, no. 20, pp. 3619–3629, 2001. View at Google Scholar
  126. H. Takeuchi, T. Kanzawa, Y. Kondo, and S. Kondo, “Inhibition of platelet-derived growth factor signalling induces autophagy in malignant glioma cells,” British Journal of Cancer, vol. 90, no. 5, pp. 1069–1075, 2004. View at Publisher · View at Google Scholar · View at PubMed
  127. L. Yu, F. Wan, S. Dutta et al., “Autophagic programmed cell death by selective catalase degradation,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 13, pp. 4952–4957, 2006. View at Publisher · View at Google Scholar · View at PubMed
  128. A. Biederbick, H. F. Kern, and H. P. Elsasser, “Monodansylcadaverine (MDC) is a specific in vivo marker for autophagic vacuoles,” European Journal of Cell Biology, vol. 66, no. 1, pp. 3–14, 1995. View at Google Scholar
  129. E. T. Bampton, C. G. Goemans, D. Niranjan, N. Mizushima, and A. M. Tolkovsky, “The dynamics of autophagy visualized in live cells: from autophagosome formation to fusion with endo/lysosomes,” Autophagy, vol. 1, no. 1, pp. 23–36, 2005. View at Google Scholar
  130. N. Mizushima, “Methods for monitoring autophagy,” The International Journal of Biochemistry & Cell Biology, vol. 36, no. 12, pp. 2491–2502, 2004. View at Publisher · View at Google Scholar · View at PubMed
  131. P. O. Seglen, P. B. Gordon, and A. Poli, “Amino acid inhibition of the autophagic/lysosomal pathway of protein degradation in isolated rat hepatocytes,” Biochimica et Biophysica Acta, vol. 630, no. 1, pp. 103–118, 1980. View at Google Scholar
  132. P. O. Seglen and P. B. Gordon, “3-methyladenine: specific inhibitor of autophagic/lysosomal protein degradation in isolated rat hepatocytes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 79, no. 6, pp. 1889–1892, 1982. View at Publisher · View at Google Scholar
  133. R. Venerando, G. Miotto, M. Kadowaki, N. Siliprandi, and G. E. Mortimore, “Multiphasic control of proteolysis by leucine and alanine in the isolated rat hepatocyte,” American Journal of Physiology, vol. 266, no. 2, part 1, pp. C455–C461, 1994. View at Google Scholar
  134. W. Weckwerth, K. Wenzel, and O. Fiehn, “Process for the integrated extraction, identification and quantification of metabolites, proteins and RNA to reveal their co-regulation in biochemical networks,” Proteomics, vol. 4, no. 1, pp. 78–83, 2004. View at Publisher · View at Google Scholar · View at PubMed
  135. C. J. Nelson, E. L. Huttlin, A. D. Hegeman, A. C. Harms, and M. R. Sussman, “Implications of N15-metabolic labeling for automated peptide identification in Arabidopsis thaliana,” Proteomics, vol. 7, no. 8, pp. 1279–1292, 2007. View at Publisher · View at Google Scholar · View at PubMed
  136. W. R. Engelsberger, A. Erban, J. Kopka, and W. X. Schulze, “Metabolic labeling of plant cell cultures with K15NO3 as a tool for quantitative analysis of proteins and metabolites,” Plant Methods, vol. 2, article 14, pp. 1–11, 2006. View at Publisher · View at Google Scholar · View at PubMed
  137. A. Gruhler, W. X. Schulze, R. Matthiesen, M. Mann, and O. N. Jensen, “Stable isotope labeling of Arabidopsis thaliana cells and quantitative proteomics by mass spectrometry,” Molecular & Cellular Proteomics, vol. 4, no. 11, pp. 1697–1709, 2005. View at Publisher · View at Google Scholar · View at PubMed
  138. P. B. Gordon, H. Tolleshaug, and P. O. Seglen, “Use of digitonin extraction to distinguish between autophagic-lysosomal sequestration and mitochondrial uptake of [C14]sucrose in hepatocytes,” Biochemical Journal, vol. 232, no. 3, pp. 773–780, 1985. View at Google Scholar
  139. P. B. Gordon, H. Høyvik, and P. O. Seglen, “Sequestration and hydrolysis of electroinjected [C14]lactose as a means of investigating autophagosome-lysosome fusion in isolated rat hepatocytes,” Progress in Clinical and Biological Research, vol. 180, pp. 475–477, 1985. View at Google Scholar
  140. J. A. Barnett, R. W. Payne, and D. Yarrow, Yeasts: Characteristics and Identification, Cambridge University Press, Cambridge, UK, 3rd edition, 1983. View at Publisher · View at Google Scholar
  141. D. J. Klionsky, “Monitoring autophagy in yeast: the Pho8Delta60 assay,” in Protein Targeting Protocols, vol. 390 of Methods in Molecular Biology, pp. 363–371, Humana Press, New York, NY, USA, 2nd edition, 2007. View at Publisher · View at Google Scholar
  142. H. Ishida and K. Yoshimoto, “Chloroplasts are partially mobilized to the vacuole by autophagy,” Autophagy, vol. 4, no. 7, pp. 961–962, 2008. View at Google Scholar
  143. N. Furuya, T. Kanazawa, S. Fujimura, T. Ueno, E. Kominami, and M. Kadowaki, “Leupeptin-induced appearance of partial fragment of betaine homocysteine methyltransferase during autophagic maturation in rat hepatocytes,” The Journal of Biochemistry, vol. 129, no. 2, pp. 313–320, 2001. View at Google Scholar
  144. F. Nimmerjahn, S. Milosevic, U. Behrends et al., “Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy,” European Journal of Immunology, vol. 33, no. 5, pp. 1250–1259, 2003. View at Publisher · View at Google Scholar · View at PubMed
  145. G. S. Taylor, H. M. Long, T. A. Haigh, M. Larsen, J. Brooks, and A. B. Rickinson, “A role for intercellular antigen transfer in the recognition of EBV-transformed B cell Lines by EBV nuclear antigen-specific CD4+ T cells,” The Journal of Immunology, vol. 177, no. 6, pp. 3746–3756, 2006. View at Google Scholar
  146. S. Rodriguez-Enriquez, L. He, and J. J. Lemasters, “Role of mitochondrial permeability transition pores in mitochondrial autophagy,” The International Journal of Biochemistry & Cell Biology, vol. 36, no. 12, pp. 2463–2472, 2004. View at Publisher · View at Google Scholar · View at PubMed
  147. T. Kanki and D. J. Klionsky, “Mitophagy in yeast occurs through a selective mechanism,” The Journal of Biological Chemistry, vol. 283, no. 47, pp. 32386–32393, 2008. View at Publisher · View at Google Scholar · View at PubMed
  148. L. Xue, G. C. Fletcher, and A. M. Tolkovsky, “Mitochondria are selectively eliminated from eukaryotic cells after blockade of caspases during apoptosis,” Current Biology, vol. 11, no. 5, pp. 361–365, 2001. View at Publisher · View at Google Scholar
  149. E. P. Journet, R. Bligny, and R. Douce, “Biochemical changes during sucrose deprivation in higher plant cells,” The Journal of Biological Chemistry, vol. 261, no. 7, pp. 3193–3199, 1986. View at Google Scholar
  150. D. J. Klionsky, “Autophagy: from phenomenology to molecular understanding in less than a decade,” Nature Reviews Molecular Cell Biology, vol. 8, no. 11, pp. 931–937, 2007. View at Publisher · View at Google Scholar · View at PubMed
  151. N. N. Suzuki, K. Yoshimoto, Y. Fujioka, Y. Ohsumi, and F. Inagaki, “The crystal structure of plant ATG12 and its biological implication in autophagy,” Autophagy, vol. 1, no. 2, pp. 119–126, 2005. View at Google Scholar
  152. Y. Fujiki, K. Yoshimoto, and Y. Ohsumi, “An Arabidopsis homolog of yeast ATG6/VPS30 is essential for pollen germination,” Plant Physiology, vol. 143, no. 3, pp. 1132–1139, 2007. View at Publisher · View at Google Scholar · View at PubMed
  153. N. J. Harrison-Lowe and L. J. Olsen, “Autophagy protein 6 (ATG6) is required for pollen germination in Arabidopsis thaliana,” Autophagy, vol. 4, no. 3, pp. 339–348, 2008. View at Google Scholar
  154. Y. Xiong, A. L. Contento, and D. C. Bassham, “AtATG18a is required for the formation of autophagosomes during nutrient stress and senescence in Arabidopsis thaliana,” The Plant Journal, vol. 42, no. 4, pp. 535–546, 2005. View at Publisher · View at Google Scholar · View at PubMed