Characterization of macroautophagic flux in vivo using a leupeptin-based assay

References

• Klionsky DJ, Emr SD. Autophagy as a regulated pathway of cellular degradation. Science 2000; 290:1717 - 1721
   PubMed Web of Science ®Google Scholar
• Ericsson JL. Studies on induced cellular autophagy. I. Electron microscopy of cells with in vivo labelled lysosomes. Exp Cell Res 1969; 55:95 - 106
   PubMed Web of Science ®Google Scholar
• Yang Z, Klionsky DJ. Permeases recycle amino acids resulting from autophagy. Autophagy 2007; 3:149 - 150
   PubMed Web of Science ®Google Scholar
• Yu L, McPhee CK, Zheng L, Mardones GA, Rong Y, Peng J, et al. Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature 2010; 465:942 - 946
   PubMed Web of Science ®Google Scholar
• David H, Ellermann J, Uerlings I. Primary phase of hepatocytic autophagocytosis under ischaemic conditions. Exp Toxicol Pathol 1992; 44:74 - 80
   PubMedGoogle Scholar
• Schworer CM, Cox JR, Mortimore GE. Alteration of lysosomal density by sequestered glycogen during deprivation-induced autophagy in rat liver. Biochem Biophys Res Commun 1979; 87:163 - 170
   PubMed Web of Science ®Google Scholar
• Suzuki K, Kubota Y, Sekito T, Ohsumi Y. Hierarchy of Atg proteins in pre-autophagosomal structure organization. Genes Cells 2007; 12:209 - 218
   PubMed Web of Science ®Google Scholar
• Levine B, Kroemer G. Autophagy in the pathogenesis of disease. Cell 2008; 132:27 - 42
   PubMed Web of Science ®Google Scholar
• Jung CH, Jun CB, Ro SH, Kim YM, Otto NM, Cao J, et al. ULK-Atg13-FIP200 complexes mediate mTOR signaling to the autophagy machinery. Mol Biol Cell 2009; 20:1992 - 2003
   PubMed Web of Science ®Google Scholar
• Cao Y, Klionsky DJ. Physiological functions of Atg6/Beclin 1: a unique autophagy-related protein. Cell Res 2007; 17:839 - 849
   PubMed Web of Science ®Google Scholar
• Itakura E, Mizushima N. Atg14 and UVRAG: mutually exclusive subunits of mammalian Beclin 1-PI3K complexes. Autophagy 2009; 5:534 - 536
   PubMed Web of Science ®Google Scholar
• Obara K, Sekito T, Niimi K, Ohsumi Y. The Atg18-Atg2 complex is recruited to autophagic membranes via phosphatidylinositol-3-phosphate and exerts an essential function. J Biol Chem 2008; 283:23972 - 23980
   PubMed Web of Science ®Google Scholar
• Kabeya Y, Mizushima N, Yamamoto A, Oshitani-Okamoto S, Ohsumi Y, Yoshimori T. LC3, GABARAP and GATE16 localize to autophagosomal membrane depending on form-II formation. J Cell Sci 2004; 117:2805 - 2812
   PubMed Web of Science ®Google Scholar
• Kabeya Y, Mizushima N, Ueno T, Yamamoto A, Kirisako T, Noda T, et al. LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J 2000; 19:5720 - 5728
   PubMed Web of Science ®Google Scholar
• Fujita N, Hayashi-Nishino M, Fukumoto H, Omori H, Yamamoto A, Noda T, et al. An Atg4B mutant hampers the lipidation of LC3 paralogues and causes defects in autophagosome closure. Mol Biol Cell 2008; 19:4651 - 4659
   PubMed Web of Science ®Google Scholar
• Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, et al. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4:151 - 175
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yamamoto A, Matsui M, Yoshimori T, Ohsumi Y. In vivo analysis of autophagy in response to nutrient starvation using transgenic mice expressing a fluorescent autophagosome marker. Mol Biol Cell 2004; 15:1101 - 1111
   PubMed Web of Science ®Google Scholar
• Ueno T, Takahashi K. A cathepsin L-specific inhibitor preferentially inhibits degradation of autophagosomal LC3 and GABARAP in HeLa and Huh-7 cells. Autophagy 2009; 5:878 - 879
   PubMed Web of Science ®Google Scholar
• Tanida I, Ueno T, Kominami E. LC3 conjugation system in mammalian autophagy. Int J Biochem Cell Biol 2004; 36:2503 - 2518
   PubMed Web of Science ®Google Scholar
• Swanlund JM, Kregel KC, Oberley TD. Investigating autophagy: quantitative morphometric analysis using electron microscopy. Autophagy 2010; 6:270 - 277
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yoshimori T. How to interpret LC3 immunoblotting. Autophagy 2007; 3:542 - 545
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yoshimori T, Levine B. Methods in mammalian autophagy research. Cell 2010; 140:313 - 326
   PubMed Web of Science ®Google Scholar
• Rubinsztein DC, Cuervo AM, Ravikumar B, Sarkar S, Korolchuk V, Kaushik S, et al. In search of an “autophagomometer”. Autophagy 2009; 5:585 - 589
   PubMed Web of Science ®Google Scholar
• Tanida I, Minematsu-Ikeguchi N, Ueno T, Kominami E. Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy. Autophagy 2005; 1:84 - 91
   PubMed Web of Science ®Google Scholar
• Shvets E, Elazar Z. Flow cytometric analysis of autophagy in living mammalian cells. Methods Enzymol 2009; 452:131 - 141
   Google Scholar
• Farkas T, Hoyer-Hansen M, Jaattela M. Identification of novel autophagy regulators by a luciferase-based assay for the kinetics of autophagic flux. Autophagy 2009; 5:1018 - 1025
   PubMed Web of Science ®Google Scholar
• Larsen KB, Lamark T, Overvatn A, Harneshaug I, Johansen T, Bjorkoy G. A reporter cell system to monitor autophagy based on p62/SQSTM1. Autophagy 2010; 6:784 - 793
   PubMed Web of Science ®Google Scholar
• Kimura S, Noda T, Yoshimori T. Dissection of the autophagosome maturation process by a novel reporter protein, tandem fluorescent-tagged LC3. Autophagy 2007; 3:452 - 460
   PubMed Web of Science ®Google Scholar
• Eng KE, Panas MD, Karlsson Hedestam GB, McInerney GM. A novel quantitative flow cytometry-based assay for autophagy. Autophagy 2010; 6:634 - 641
   PubMed Web of Science ®Google Scholar
• Bjorkoy G, Lamark T, Pankiv S, Overvatn A, Brech A, Johansen T. Monitoring autophagic degradation of p62/SQSTM1. Methods Enzymol 2009; 452:181 - 197
   PubMed Web of Science ®Google Scholar
• Dennis PB, Mercer CA. The GST-BHMT assay and related assays for autophagy. Methods Enzymol 2009; 452:97 - 118
   PubMed Web of Science ®Google Scholar
• Ju JS, Miller SE, Jackson E, Cadwell K, Piwnica-Worms D, Weihl CC. Quantitation of selective autophagic protein aggregate degradation in vitro and in vivo using luciferase reporters. Autophagy 2009; 5:511 - 519
   PubMed Web of Science ®Google Scholar
• Iwai-Kanai E, Yuan H, Huang C, Sayen MR, Perry-Garza CN, Kim L, et al. A method to measure cardiac autophagic flux in vivo. Autophagy 2008; 4:322 - 329
   PubMed Web of Science ®Google Scholar
• Ju JS, Varadhachary AS, Miller SE, Weihl CC. Quantitation of “autophagic flux” in mature skeletal muscle. Autophagy 2010; 6:929 - 935
   PubMed Web of Science ®Google Scholar
• Marino G, Fernandez AF, Cabrera S, Lundberg YW, Cabanillas R, Rodriguez F, et al. Autophagy is essential for mouse sense of balance. J Clin Invest 2010; 120:2331 - 2344
   PubMed Web of Science ®Google Scholar
• Furuno K, Ishikawa T, Kato K. Appearance of autolysosomes in rat liver after leupeptin treatment. J Biochem 1982; 91:1485 - 1494
   PubMed Web of Science ®Google Scholar
• Glaumann H, Ahlberg J. Comparison of different autophagic vacuoles with regard to ultrastructure, enzymatic composition and degradation capacity—formation of crinosomes. Exp Mol Pathol 1987; 47:346 - 362
   PubMed Web of Science ®Google Scholar
• Berg TO, Fengsrud M, Stromhaug PE, Berg T, Seglen PO. Isolation and characterization of rat liver amphisomes. Evidence for fusion of autophagosomes with both early and late endosomes. J Biol Chem 1998; 273:21883 - 21892
   PubMed Web of Science ®Google Scholar
• Karim MR, Kanazawa T, Daigaku Y, Fujimura S, Miotto G, Kadowaki M. Cytosolic LC3 ratio as a sensitive index of macroautophagy in isolated rat hepatocytes and H4-II-E cells. Autophagy 2007; 3:553 - 560
   PubMed Web of Science ®Google Scholar
• Singh R, Kaushik S, Wang Y, Xiang Y, Novak I, Komatsu M, et al. Autophagy regulates lipid metabolism. Nature 2009; 458:1131 - 1135
   PubMed Web of Science ®Google Scholar
• Graham JM. Isolation of lysosomes from tissues and cells by differential and density gradient centrifugation. Curr Protoc Cell Biol 2001; 3:3 - 6
   PubMedGoogle Scholar
• Sewell RB, Dillon C, Grinpukel S, Yeomans ND, Smallwood RA. Pericanalicular location of hepatocyte lysosomes and effects of fasting: a morphometric analysis. Hepatology 1986; 6:305 - 311
   PubMed Web of Science ®Google Scholar
• Ichimura Y, Kumanomidou T, Sou YS, Mizushima T, Ezaki J, Ueno T, et al. Structural basis for sorting mechanism of p62 in selective autophagy. J Biol Chem 2008; 283:22847 - 22857
   PubMed Web of Science ®Google Scholar
• Komatsu M, Waguri S, Koike M, Sou YS, Ueno T, Hara T, et al. Homeostatic levels of p62 control cytoplasmic inclusion body formation in autophagy-deficient mice. Cell 2007; 131:1149 - 1163
   PubMed Web of Science ®Google Scholar
• Pankiv S, Clausen TH, Lamark T, Brech A, Bruun JA, Outzen H, et al. p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J Biol Chem 2007; 282:24131 - 24145
   PubMed Web of Science ®Google Scholar
• Sugawara K, Suzuki NN, Fujioka Y, Mizushima N, Ohsumi Y, Inagaki F. The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8. Genes Cells 2004; 9:611 - 618
   PubMed Web of Science ®Google Scholar
• Trakatellis AC, Montjar M, Axelrod AE. Effect of Cycloheximide on Polysomes and Protein Synthesis in the Mouse Liver. Biochemistry 1965; 4:2065 - 2071
   Google Scholar
• Zhou P. Determining protein half-lives. Methods Mol Biol 2004; 284:67 - 77
   PubMedGoogle Scholar
• Kopitz J, Kisen GO, Gordon PB, Bohley P, Seglen PO. Nonselective autophagy of cytosolic enzymes by isolated rat hepatocytes. J Cell Biol 1990; 111:941 - 953
   PubMed Web of Science ®Google Scholar
• Schworer CM, Shiffer KA, Mortimore GE. Quantitative relationship between autophagy and proteolysis during graded amino acid deprivation in perfused rat liver. J Biol Chem 1981; 256:7652 - 7658
   PubMed Web of Science ®Google Scholar
• Hofert JF, Boutwell RK. Puromycin-Induced Glycogenolysis as an Even Independent from Inhibited Protein Synthesis in Mouse Liver; Effects of Puromycin Analogs. Arch Biochem Biophys 1963; 103:338 - 344
   PubMed Web of Science ®Google Scholar
• Anand P, Gruppuso PA. Rapamycin inhibits liver growth during refeeding in rats via control of ribosomal protein translation but not cap-dependent translation initiation. J Nutr 2006; 136:27 - 33
   PubMed Web of Science ®Google Scholar
• Qu X, Yu J, Bhagat G, Furuya N, Hibshoosh H, Troxel A, et al. Promotion of tumorigenesis by heterozygous disruption of the beclin 1 autophagy gene. J Clin Invest 2003; 112:1809 - 1820
   PubMed Web of Science ®Google Scholar
• Zhu H, Tannous P, Johnstone JL, Kong Y, Shelton JM, Richardson JA, et al. Cardiac autophagy is a maladaptive response to hemodynamic stress. J Clin Invest 2007; 117:1782 - 1793
   PubMed Web of Science ®Google Scholar
• Kim PK, Hailey DW, Mullen RT, Lippincott-Schwartz J. Ubiquitin signals autophagic degradation of cytosolic proteins and peroxisomes. Proc Natl Acad Sci USA 2008; 105:20567 - 20574
   PubMed Web of Science ®Google Scholar
• Katunuma N, Kominami E. Lysosomal sequestration of cytosolic enzymes and lysosomal thiol cathepsins. Adv Enzyme Regul 1985; 23:159 - 168
   PubMedGoogle Scholar
• Kominami E, Hashida S, Khairallah EA, Katunuma N. Sequestration of cytoplasmic enzymes in an autophagic vacuole-lysosomal system induced by injection of leupeptin. J Biol Chem 1983; 258:6093 - 6100
   PubMed Web of Science ®Google Scholar
• Jang CH, Choi JH, Byun MS, Jue DM. Chloroquine inhibits production of TNFalpha, IL-1beta and IL-6 from lipopolysaccharide-stimulated human monocytes/macrophages by different modes. Rheumatology (Oxford) 2006; 45:703 - 710
   PubMed Web of Science ®Google Scholar
• Weber SM, Levitz SM. Chloroquine interferes with lipopolysaccharide-induced TNFalpha gene expression by a nonlysosomotropic mechanism. J Immunol 2000; 165:1534 - 1540
   PubMed Web of Science ®Google Scholar
• Ding AH, Porteu F, Sanchez E, Nathan CF. Downregulation of tumor necrosis factor receptors on macrophages and endothelial cells by microtubule depolymerizing agents. J Exp Med 1990; 171:715 - 727
   PubMed Web of Science ®Google Scholar
• Salminen A, Kihlstrom M, Vihko V. Acid proteolytic activities in mouse liver and muscle tissues after treatment with protease inhibitor leupeptin. Comp Biochem Physiol C 1984; 79:93 - 95
   PubMed Web of Science ®Google Scholar
• Sutherland JH, Greenbaum LM. Paradoxical effect of leupeptin in vivo on cathepsin B activity. Biochem Biophys Res Commun 1983; 110:332 - 338
   PubMed Web of Science ®Google Scholar
• Fass E, Shvets E, Degani I, Hirschberg K, Elazar Z. Microtubules support production of starvation-induced autophagosomes but not their targeting and fusion with lysosomes. J Biol Chem 2006; 281:36303 - 36316
   PubMed Web of Science ®Google Scholar
• Behrends C, Sowa ME, Gygi SP, Harper JW. Network organization of the human autophagy system. Nature 2010; 466:68 - 76
   PubMed Web of Science ®Google Scholar
• Weidberg H, Shvets E, Shpilka T, Shimron F, Shinder V, Elazar Z. LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis. EMBO J 2010; 29:1792 - 1802
   PubMed Web of Science ®Google Scholar
• Ebato C, Uchida T, Arakawa M, Komatsu M, Ueno T, Komiya K, et al. Autophagy is important in islet homeostasis and compensatory increase of beta cell mass in response to high-fat diet. Cell Metab 2008; 8:325 - 332
   PubMed Web of Science ®Google Scholar
• Koga H, Kaushik S, Cuervo AM. Altered lipid content inhibits autophagic vesicular fusion. FASEB J 2010; 24:3052 - 3065
   PubMed Web of Science ®Google Scholar
• Du L, Hickey RW, Bayir H, Watkins SC, Tyurin VA, Guo F, et al. Starving neurons show sex difference in autophagy. J Biol Chem 2009; 284:2383 - 2396
   PubMed Web of Science ®Google Scholar
• Del Roso A, Vittorini S, Cavallini G, Donati A, Gori Z, Masini M, et al. Ageing-related changes in the in vivo function of rat liver macroautophagy and proteolysis. Exp Gerontol 2003; 38:519 - 527
   PubMed Web of Science ®Google Scholar
• Sachdeva UM, Thompson CB. Diurnal rhythms of autophagy: implications for cell biology and human disease. Autophagy 2008; 4:581 - 589
   PubMed Web of Science ®Google Scholar
• Kirkin V, Lamark T, Sou YS, Bjorkoy G, Nunn JL, Bruun JA, et al. A role for NBR1 in autophagosomal degradation of ubiquitinated substrates. Mol Cell 2009; 33:505 - 516
   PubMed Web of Science ®Google Scholar
• Ichimura Y, Kominami E, Tanaka K, Komatsu M. Selective turnover of p62/A170/SQSTM1 by autophagy. Autophagy 2008; 4:1063 - 1066
   PubMed Web of Science ®Google Scholar
• Nakatogawa H, Ichimura Y, Ohsumi Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 2007; 130:165 - 178
   PubMed Web of Science ®Google Scholar
• Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, et al. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 2009; 461:654 - 658
   PubMed Web of Science ®Google Scholar
• Murayama K, Fujimura T, Morita M, Shindo N. One-step subcellular fractionation of rat liver tissue using a Nycodenz density gradient prepared by freezing-thawing and two-dimensional sodium dodecyl sulfate electrophoresis profiles of the main fraction of organelles. Electrophoresis 2001; 22:2872 - 2880
   PubMed Web of Science ®Google Scholar