Methods for analysis of autophagy in plants

Methods

Volumn 75, Issue , 2015, Pages 181-188

  Bassham, Diane C ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

Arabidopsis; ATG8; Autophagosome; Autophagy; Vacuole

Indexed keywords

ARTICLE; AUTOPHAGOSOME; AUTOPHAGY; CHEMICAL ANALYSIS; CONFOCAL MICROSCOPY; CONTROLLED STUDY; ELECTRON MICROSCOPY; FLUORESCENCE MICROSCOPY; IMMUNOBLOTTING; MICROSCOPY; NONHUMAN; PLANT CELL; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; SELECTIVE AUTOPHAGY; STEADY STATE; AMINO ACID SEQUENCE; ARABIDOPSIS; BIOASSAY; BIOSYNTHESIS; GENE EXPRESSION REGULATION; GENETICS; PROCEDURES;

ARABIDOPSIS; ARABIDOPSIS THALIANA;

ARABIDOPSIS PROTEIN; ATG8 PROTEIN, ARABIDOPSIS; MICROTUBULE ASSOCIATED PROTEIN;

AMINO ACID SEQUENCE; ARABIDOPSIS; ARABIDOPSIS PROTEINS; AUTOPHAGY; BIOLOGICAL ASSAY; GENE EXPRESSION REGULATION, PLANT; MICROTUBULE-ASSOCIATED PROTEINS;

EID: 84924425922     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2014.09.003     Document Type: Article

References (86)

1. Marty F. Plant Cell 1999, 11:587-599.
2. Liu Y., Bassham D.C. Annu. Rev. Plant Biol. 2012, 63:215-237.
3. Moriyasu Y., Ohsumi Y. Plant Physiol. 1996, 111:1233-1241.
4. Takatsuka C., Inoue Y., Matsuoka K., Moriyasu Y. Plant Cell Physiol. 2004, 45:265-274.
5. Le Bars R., Marion J., Le Borgne R., Satiat-Jeunemaitre B., Bianchi M.W. Nat. Commun. 2014, 5:4121.
6. Honig A., Avin-Wittenberg T., Ufaz S., Galili G. Plant Cell 2012, 24:288-303.
7. Zhuang X., Wang H., Lam S.K., Gao C., Wang X., Cai Y., Jiang L. Plant Cell 2013, 25:4596-4615.
8. Bassham D.C., Laporte M., Marty F., Moriyasu Y., Ohsumi Y., Olsen L.J., Yoshimoto K. Autophagy 2006, 2:2-11.
9. van Doorn W.G., Papini A. Autophagy 2013, 9:1922-1936.
10. Van der Wilden W., Herman E.M., Chrispeels M.J. Proc. Natl. Acad. Sci. U.S.A. 1980, 77:428-432.
11. Toyooka K., Okamoto T., Minamikawa T. J. Cell Biol. 2001, 154:973-982.
12. Niki T., Saito S., Gladish D.K. Protoplasma 2014, 251:1141-1149.
13. Doelling J.H., Walker J.M., Friedman E.M., Thompson A.R., Vierstra R.D. J. Biol. Chem. 2002, 277:33105-33114.
14. Hanaoka H., Noda T., Shirano Y., Kato T., Hayashi H., Shibata D., Tabata S., Ohsumi Y. Plant Physiol. 2002, 129:1181-1193.
15. Thompson A.R., Doelling J.H., Suttangkakul A., Vierstra R.D. Plant Physiol. 2005, 138:2097-2110.
16. Phillips A., Suttangkakul A., Vierstra R. Genetics 2008, 178:1339-1353.
17. Yoshimoto K., Hanaoka H., Sato S., Kato T., Tabata S., Noda T., Ohsumi Y. Plant Cell 2004, 16:2967-2983.
18. Inoue Y., Suzuki T., Hattori M., Yoshimoto K., Ohsumi Y., Moriyasu Y. Plant Cell Physiol. 2006, 47:1641-1652.
19. Ishida H., Yoshimoto K., Izumi M., Reisen D., Yano Y., Makino A., Ohsumi Y., Hanson M.R., Mae T. Plant Physiol. 2008, 148:142-155.
20. Xiong Y., Contento A.L., Bassham D.C. Plant J. 2005, 42:535-546.
21. Xiong Y., Contento A.L., Phan N.Q., Bassham D.C. Plant Physiol. 2007, 143:291-299.
22. Liu Y., Xiong Y., Bassham D.C. Autophagy 2009, 5:954-963.
23. Wang Y., Nishimura M.T., Zhao T., Tang D. Plant J. 2011, 68:74-87.
24. Liu Y., Burgos J.S., Deng Y., Srivastava R., Howell S.H., Bassham D.C. Plant Cell 2012, 24:4635-4651.
25. Liu Y., Schiff M., Czymmek K., Talloczy Z., Levine B., Dinesh-Kumar S.P. Cell 2005, 121:567-577.
26. Patel S., Dinesh-Kumar S. Autophagy 2008, 4:20-27.
27. Hofius D., Schultz-Larsen T., Joensen J., Tsitsigiannis D.I., Petersen N.H.T., Mattsson O., Jorgensen L.B., Jones J.D.G., Mundy J., Petersen M. Cell 2009, 137:773-783.
28. Lenz H.D., Haller E., Melzer E., Kober K., Wurster K., Stahl M., Bassham D.C., Vierstra R.D., Parker J.E., Bautor J., Molina A., Escudero V., Shindo T., van der Hoorn R.A., Gust A.A., Nurnberger T. Plant J. 2011, 66:818-830.
29. Kwon S.I., Cho H.J., Kim S.R., Park O.K. Plant Physiol. 2013, 161:1722-1736.
30. Wada S., Ishida H., Izumi M., Yoshimoto K., Ohsumi Y., Mae T., Makino A. Plant Physiol. 2009, 149:885-893.
31. Guiboileau A., Yoshimoto K., Soulay F., Bataille M.P., Avice J.C., Masclaux-Daubresse C. New Phytol. 2012, 194:732-740.
32. Guiboileau A., Avila-Ospina L., Yoshimoto K., Soulay F., Azzopardi M., Marmagne A., Lothier J., Masclaux-Daubresse C. New Phytol. 2013, 199:683-694.
33. Chung T., Suttangkakul A., Vierstra R. Plant Physiol. 2009, 149:220-234.
34. Rana R.M., Dong S., Ali Z., Huang J., Zhang H.S. Genet. Mol. Res. 2012, 11:3676-3687.
35. Shin J., Yoshimoto K., Ohsumi Y., Jeon J., An G. Mol. Cells 2009, 27:67-74.
36. Ghiglione H., Gonzalez F., Serrago R., Maldonado S., Chilcott C., Curá J., Miralles D., Zhu T., Casal J. Plant J. 2008, 55:1010-1024.
37. Kuzuoglu-Ozturk D., Cebeci Yalcinkaya O., Akpinar B.A., Mitou G., Korkmaz G., Gozuacik D., Budak H. Planta 2012, 236:1081-1092.
38. Floyd B.E., Morriss S.C., Macintosh G.C., Bassham D.C. J. Integr. Plant Biol. 2012, 54:907-920.
39. Svenning S., Lamark T., Krause K., Johansen T. Autophagy 2011, 7:993-1010.
40. Zientara-Rytter K., Lukomska J., Moniuszko G., Gwozdecki R., Surowiecki P., Lewandowska M., Liszewska F., Wawrzynska A., Sirko A. Autophagy 2011, 7:1145-1158.
41. Johansen T., Lamark T. Autophagy 2011, 7:279-296.
42. Zhou J., Wang J., Cheng Y., Chi Y.J., Fan B., Yu J.Q., Chen Z. PLoS Genet. 2013, 9:e1003196.
43. Zhou J., Zhang Y., Qi J., Chi Y., Fan B., Yu J.Q., Chen Z. PLoS Genet. 2014, 10:e1004116.
44. Geng J., Klionsky D.J. EMBO Rep. 2008, 9:859-864.
45. Slobodkin M.R., Elazar Z. Essays Biochem. 2013, 55:51-64.
46. Li F., Vierstra R.D. Trends Plant Sci. 2012, 17:526-537.
47. Slavikova S., Shy G., Yao Y.L., Giozman R., Levanony H., Pietrokovski S., Elazar Z., Galili G. J. Exp. Bot. 2005, 56:2839-2849.
48. Woo J., Park E., Dinesh-Kumar S.P. Proc. Natl. Acad. Sci. U.S.A. 2014, 111:863-868.
49. Contento A.L., Xiong Y., Bassham D.C. Plant J. 2005, 42:598-608.
50. Chung T., Phillips A.R., Vierstra R.D. Plant J. 2010, 62:483-493.
51. Li F., Chung T., Vierstra R.D. Plant Cell 2014, 26:788-807.
52. Suttangkakul A., Li F., Chung T., Vierstra R.D. Plant Cell 2011, 23:3761-3779.
53. Fujiki Y., Yoshimoto K., Ohsumi Y. Plant Physiol. 2007, 143:1132-1139.
54. Harrison-Lowe N., Olsen L. Autophagy 2008, 4:339-348.
55. Qin G., Ma Z., Zhang L., Xing S., Hou X., Deng J., Liu J., Chen Z., Qu L.J., Gu H. Cell Res. 2007, 17:249-263.
56. Takatsuka C., Inoue Y., Higuchi T., Hillmer S., Robinson D.G., Moriyasu Y. Plant Cell Physiol. 2011, 52:2074-2087.
57. Eskelinen E.L. Int. Rev. Cell Mol. Biol. 2008, 266:207-247.
58. Yano K., Matsui S., Tsuchiya T., Maeshima M., Kutsuna N., Hasezawa S., Moriyasu Y. Plant Cell Physiol. 2004, 45:951-957.
59. Moriyasu Y., Hattori M., Jauh G.Y., Rogers J.C. Plant Cell Physiol. 2003, 44:795-802.
60. Biederbick A., Kern H., Elsässer H. Eur. J. Cell Biol. 1995, 66:3-14.
61. Munafo D.B., Colombo M.I. J. Cell Sci. 2001, 114:3619-3629.
62. Merkulova E.A., Guiboileau A., Naya L., Masclaux-Daubresse C., Yoshimoto K. Plant Cell Physiol. 2014, 55:715-726.
63. Aubert S., Gout E., Bligny R., MartyMazars D., Barrieu F., Alabouvette J., Marty F., Douce R. J. Cell Biol. 1996, 133:1251-1263.
64. Rose T.L., Bonneau L., Der C., Marty-Mazars D., Marty F. Biol. Cell 2006, 98:53-67.
65. Marty F. Proc. Natl. Acad. Sci. U.S.A. 1978, 75:852-856.
66. Yano K., Hattori M., Moriyasu Y. Autophagy 2007, 3:215-221.
67. Wang Y., Yu B., Zhao J., Guo J., Li Y., Han S., Huang L., Du Y., Hong Y., Tang D., Liu Y. Plant Cell 2013, 25:1383-1399.
68. Dettmer J., Hong-Hermesdorf A., Stierhof Y.D., Schumacher K. Plant Cell 2006, 18:715-730.
69. Matsuoka K., Higuchi T., Maeshima M., Nakamura K. Plant Cell 1997, 9:533-546.
70. Reyes F.C., Buono R., Otegui M.S. Curr. Opin. Plant Biol. 2011, 14:666-673.
71. Oh-ye Y., Inoue Y., Moriyasu Y. Plant Signal. Behav. 2011, 6:1946-1949.
72. Bassham D.C. Curr. Opin. Plant Biol. 2007, 10:587-593.
73. Lee H.N., Kim J., Chung T. Front. Plant Sci. 2014, 5:139.
74. Hillwig M.S., Contento A.L., Meyer A., Ebany D., Bassham D.C., Macintosh G.C. Proc. Natl. Acad. Sci. U.S.A. 2011, 108:1093-1098.
75. Toyooka K., Moriyasu Y., Goto Y., Takeuchi M., Fukuda H., Matsuoka K. Autophagy 2006, 2:96-106.
76. Tsutsui H., Karasawa S., Shimizu H., Nukina N., Miyawaki A. EMBO Rep. 2005, 6:233-238.
77. Tasaki M., Asatsuma S., Matsuoka K. Front Plant Sci. 2014, 5:172.
78. Kim J., Lee H., Lee H.N., Kim S.H., Shin K.D., Chung T. Plant Cell 2013, 25:4956-4966.
79. Izumi M., Wada S., Makino A., Ishida H. Plant Physiol. 2010, 154:1196-1209.
80. Yoshimoto K., Shibata M., Kondo M., Oikawa K., Sato M., Toyooka K., Shirasu K., Nishimura M., Ohsumi Y. J. Cell Sci. 2014, 127:1161-1168.
81. Ichimura Y., Kirisako T., Takao T., Satomi Y., Shimonishi Y., Ishihara N., Mizushima N., Tanida I., Kominami E., Ohsumi M., Noda T., Ohsumi Y. Nature 2000, 408:488-492.
82. Kabeya Y., Mizushima N., Ueno T., Yamamoto A., Kirisako T., Noda T., Kominami E., Ohsumi Y., Yoshimori T. EMBO J. 2000, 19:5720-5728.
83. D.J. Klionsky, F.C. Abdalla, H. Abeliovich, R.T. Abraham, A. Acevedo-Arozena, K. Adeli, L. Agholme, M. Agnello, P. Agostinis, J.A. Aguirre-Ghiso, H.J. Ahn, O. Ait-Mohamed, S. Ait-Si-Ali, T. Akematsu, S. Akira, H.M. Al-Younes, M.A. Al-Zeer, M.L. Albert, R.L. Albin, J. Alegre-Abarrategui, M.F. Aleo, M. Alirezaei, A. Almasan, M. Almonte-Becerril, A. Amano, R. Amaravadi, S. Amarnath, A.O. Amer, N. Andrieu-Abadie, V. Anantharam, D.K. Ann, S. Anoopkumar-Dukie, H. Aoki, N. Apostolova, G. Arancia, J.P. Aris, K. Asanuma, N.Y. Asare, H. Ashida, V. Askanas, D.S. Askew, P. Auberger, M. Baba, S.K. Backues, E.H. Baehrecke, B.A. Bahr, X.Y. Bai, Y. Bailly, R. Baiocchi, G. Baldini, W. Balduini, A. Ballabio, B.A. Bamber, E.T. Bampton, G. Banhegyi, C.R. Bartholomew, D.C. Bassham, R.C. Bast, Jr., H. Batoko, B.H. Bay, I. Beau, D.M. Bechet, T.J. Begley, C. Behl, C. Behrends, S. Bekri, B. Bellaire, L.J. Bendall, L. Benetti, L. Berliocchi, H. Bernardi, F. Bernassola, S. Besteiro, I. Bhatia-Kissova, X. Bi, M. Biard-Piechaczyk, J.S. Blum, L.H. Boise, P. Bonaldo, D.L. Boone, B.C. Bornhauser, K.R. Bortoluci, I. Bossis, F. Bost, J.P. Bourquin, P. Boya, M. Boyer-Guittaut, P.V. Bozhkov, N.R. Brady, C. Brancolini, A. Brech, J.E. Brenman, A. Brennand, E.H. Bresnick, P. Brest, D. Bridges, M.L. Bristol, P.S. Brookes, et al. Autophagy 8 (2012) 445-544.
84. Perez-Perez M.E., Florencio F.J., Crespo J.L. Plant Physiol. 2010, 152:1874-1888.
85. Alvarez C., Garcia I., Moreno I., Perez-Perez M.E., Crespo J.L., Romero L.C., Gotor C. Plant Cell 2012, 24:4621-4634.
86. Shin K.D., Lee H.N., Chung T. Mol. Cells 2014, 37:399-405.