Guidelines for the Use and Interpretation of Assays for Monitoring Autophagy 2

574. Kirisako T, Baba M, Ishihara N, Miyazawa K, Ohsumi M, Yoshimori T, Noda T, Ohsumi Y. Formation process of autophagosome is traced with Apg8/Aut7p in yeast. The Journal of cell biology 1999; 147:435-46.

575. Jin M, He D, Backues SK, Freeberg MA, Liu X, Kim JK, Klionsky DJ. Transcriptional regulation by Pho23 modulates the frequency of autophagosome formation. Current biology : CB 2014; 24:1314-22.

576. Kouroku Y, Fujita E, Tanida I, Ueno T, Isoai A, Kumagai H, Ogawa S, Kaufman RJ, Kominami E, Momoi T. ER stress (PERK/eIF2[alpha] phosphorylation) mediates the polyglutamine-induced LC3 conversion, an essential step for autophagy formation. Cell death and differentiation 2007; 14:230-9.

577. Xiong X, Tao R, DePinho RA, Dong XC. The autophagy-related gene 14 (Atg14) is regulated by forkhead box O transcription factors and circadian rhythms and plays a critical role in hepatic autophagy and lipid metabolism. The Journal of biological chemistry 2012; 287:39107-14.

578. Moussay E, Kaoma T, Baginska J, Muller A, Van Moer K, Nicot N, Nazarov PV, Vallar L, Chouaib S, Berchem G, et al. The acquisition of resistance to TNFalpha in breast cancer cells is associated with constitutive activation of autophagy as revealed by a transcriptome analysis using a custom microarray. Autophagy 2011; 7:760-70.

579. Mitroulis I, Kourtzelis I, Kambas K, Rafail S, Chrysanthopoulou A, Speletas M, Ritis K. Regulation of the autophagic machinery in human neutrophils. Eur J Immunol 2010; 40:1461-72.

580. Rodriguez-Muela N, Germain F, Marino G, Fitze PS, Boya P. Autophagy promotes survival of retinal ganglion cells after optic nerve axotomy in mice. Cell death and differentiation 2012; 19:162-9.

581. Vázquez P, Arroba AI, Cecconi F, de la Rosa EJ, Boya P, De Pablo F. Atg5 and Ambra1 differentially modulate neurogenesis in neural stem cells. 2012; 8:in press.

582. Rouschop KM, van den Beucken T, Dubois L, Niessen H, Bussink J, Savelkouls K, Keulers T, Mujcic H, Landuyt W, Voncken JW, et al. The unfolded protein response protects human tumor cells during hypoxia through regulation of the autophagy genes MAP1LC3B and ATG5. The Journal of clinical investigation 2010; 120:127-41.

583. Las G, Serada SB, Wikstrom JD, Twig G, Shirihai OS. Fatty acids suppress autophagic turnover in beta-cells. The Journal of biological chemistry 2011; 286:42534-44.

584. Woldt E, Sebti Y, Solt LA, Duhem C, Lancel S, Eeckhoute J, Hesselink MK, Paquet C, Delhaye S, Shin Y, et al. Rev-erb-alpha modulates skeletal muscle oxidative capacity by regulating mitochondrial biogenesis and autophagy. Nature medicine 2013; 19:1039-46.

585. Lee JM, Wagner M, Xiao R, Kim KH, Feng D, Lazar MA, Moore DD. Nutrient-sensing nuclear receptors coordinate autophagy. Nature 2014; 516:112-5.

586. Seok S, Fu T, Choi SE, Li Y, Zhu R, Kumar S, Sun X, Yoon G, Kang Y, Zhong W, et al. Transcriptional regulation of autophagy by an FXR-CREB axis. Nature 2014; 516:108-11.

587. Gorski SM, Chittaranjan S, Pleasance ED, Freeman JD, Anderson CL, Varhol RJ, Coughlin SM, Zuyderduyn SD, Jones SJ, Marra MA. A SAGE approach to discovery of genes involved in autophagic cell death. Current biology : CB 2003; 13:358-63.

588. Lee C-Y, Clough EA, Yellon P, Teslovich TM, Stephan DA, Baehrecke EH. Genome-wide analyses of steroid- and radiation-triggered programmed cell death in Drosophila. Current biology : CB 2003; 13:350-7.

589. Denton D, Shravage B, Simin R, Baehrecke EH, Kumar S. Larval midgut destruction in Drosophila: not dependent on caspases but suppressed by the loss of autophagy. Autophagy 2010; 6:163-5.

590. Franzetti E, Huang ZJ, Shi YX, Xie K, Deng XJ, Li JP, Li QR, Yang WY, Zeng WN, Casartelli M, et al. Autophagy precedes apoptosis during the remodeling of silkworm larval midgut. Apoptosis 2012; in press.

591. Tian L, Ma L, Guo E, Deng X, Ma S, Xia Q, Cao Y, Li S. 20-Hydroxyecdysone upregulates Atg genes to induce autophagy in the Bombyx fat body. Autophagy 2013; 9:1172-87.

592. Juhasz G, Puskas LG, Komonyi O, Erdi B, Maroy P, Neufeld TP, Sass M. Gene expression profiling identifies FKBP39 as an inhibitor of autophagy in larval Drosophila fat body. Cell death and differentiation 2007; 14:1181-90.

593. Erdi B, Nagy P, Zvara A, Varga A, Pircs K, Menesi D, Puskas LG, Juhasz G. Loss of the starvation-induced gene Rack1 leads to glycogen deficiency and impaired autophagic responses in Drosophila. Autophagy 2012; 8:1124-35.

594. Barth JM, Szabad J, Hafen E, Kohler K. Autophagy in Drosophila ovaries is induced by starvation and is required for oogenesis. Cell death and differentiation 2011; 18:915-24.

595. Lecker SH, Jagoe RT, Gilbert A, Gomes M, Baracos V, Bailey J, Price SR, Mitch WE, Goldberg AL. Multiple types of skeletal muscle atrophy involve a common program of changes in gene expression. The FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2004; 18:39-51.

596. Phillips AR, Suttangkakul A, Vierstra RD. The ATG12-conjugating enzyme ATG10 Is essential for autophagic vesicle formation in Arabidopsis thaliana. Genetics 2008; 178:1339-53.

597. Seiliez I, Gutierrez J, Salmeron C, Skiba-Cassy S, Chauvin C, Dias K, Kaushik S, Tesseraud S, Panserat S. An in vivo and in vitro assessment of autophagy-related gene expression in muscle of rainbow trout (Oncorhynchus mykiss). Comparative biochemistry and physiology Part B, Biochemistry & molecular biology 2010; 157:258-66.

598. Lapierre LR, Gelino S, Melendez A, Hansen M. Autophagy and lipid metabolism coordinately modulate life span in germline-less C. elegans. Current biology : CB 2011; 21:1507-14.

599. Lapierre LR, De Magalhaes Filho CD, McQuary PR, Chu CC, Visvikis O, Chang JT, Gelino S, Ong B, Davis AE, Irazoqui JE, et al. The TFEB orthologue HLH-30 regulates autophagy and modulates longevity in Caenorhabditis elegans. Nature communications 2013; 4:2267.

600. Sandri M. Autophagy in health and disease. 3. Involvement of autophagy in muscle atrophy. American journal of physiology Cell physiology 2010; 298:C1291-7.

601. Eisenberg T, Knauer H, Schauer A, Buttner S, Ruckenstuhl C, Carmona-Gutierrez D, Ring J, Schroeder S, Magnes C, Antonacci L, et al. Induction of autophagy by spermidine promotes longevity. Nature cell biology 2009; 11:1305-14.

602. Ropolo A, Grasso D, Pardo R, Sacchetti ML, Archange C, Lo Re A, Seux M, Nowak J, Gonzalez CD, Iovanna JL, et al. The pancreatitis-induced vacuole membrane protein 1 triggers autophagy in mammalian cells. The Journal of biological chemistry 2007; 282:37124-33.

603. Tian Y, Li Z, Hu W, Ren H, Tian E, Zhao Y, Lu Q, Huang X, Yang P, Li X, et al. C. elegans screen identifies autophagy genes specific to multicellular organisms. Cell 2010; 141:1042-55.

604. Lo Re AE, Fernandez-Barrena MG, Almada LL, Mills LD, Elsawa SF, Lund G, Ropolo A, Molejon MI, Vaccaro MI, Fernandez-Zapico ME. Novel AKT1-GLI3-VMP1 pathway mediates KRAS oncogene-induced autophagy in cancer cells. The Journal of biological chemistry 2012; 287:25325-34.

605. Settembre C, Di Malta C, Polito VA, Garcia Arencibia M, Vetrini F, Erdin S, Erdin SU, Huynh T, Medina D, Colella P, et al. TFEB links autophagy to lysosomal biogenesis. Science 2011; 332:1429-33.

606. Sardiello M, Palmieri M, di Ronza A, Medina DL, Valenza M, Gennarino VA, Di Malta C, Donaudy F, Embrione V, Polishchuk RS, et al. A gene network regulating lysosomal biogenesis and function. Science 2009; 325:473-7.

607. Palmieri M, Impey S, Kang H, di Ronza A, Pelz C, Sardiello M, Ballabio A. Characterization of the CLEAR network reveals an integrated control of cellular clearance pathways. Human molecular genetics 2011; 20:3852-66.

608. Martina JA, Chen Y, Gucek M, Puertollano R. MTORC1 functions as a transcriptional regulator of autophagy by preventing nuclear transport of TFEB. Autophagy 2012; 8:903-14.

609. Settembre C, Zoncu R, Medina DL, Vetrini F, Erdin S, Erdin S, Huynh T, Ferron M, Karsenty G, Vellard MC, et al. A lysosome-to-nucleus signalling mechanism senses and regulates the lysosome via mTOR and TFEB. The EMBO journal 2012; 31:1095-108.

610. Nezich CL, Wang C, Fogel AI, Youle RJ. MiT/TFE transcription factors are activated during mitophagy downstream of Parkin and Atg5. The Journal of cell biology 2015; 210:435-50.

611. Perera RM, Stoykova S, Nicolay BN, Ross KN, Fitamant J, Boukhali M, Lengrand J, Deshpande V, Selig MK, Ferrone CR, et al. Transcriptional control of autophagy-lysosome function drives pancreatic cancer metabolism. Nature 2015; 524:361-5.

612. Kang YA, Sanalkumar R, O'Geen H, Linnemann AK, Chang CJ, Bouhassira EE, Farnham PJ, Keles S, Bresnick EH. Autophagy driven by a master regulator of hematopoiesis. Molecular and cellular biology 2012; 32:226-39.

613. Zhao J, Brault JJ, Schild A, Cao P, Sandri M, Schiaffino S, Lecker SH, Goldberg AL. FoxO3 coordinately activates protein degradation by the autophagic/lysosomal and proteasomal pathways in atrophying muscle cells. Cell metabolism 2007; 6:472-83.

614. Ma D, Panda S, Lin JD. Temporal orchestration of circadian autophagy rhythm by C/EBP{beta}. The EMBO journal 2011.

615. Brest P, Lapaquette P, Souidi M, Lebrigand K, Cesaro A, Vouret-Craviari V, Mari B, Barbry P, Mosnier JF, Hebuterne X, et al. A synonymous variant in IRGM alters a binding site for miR-196 and causes deregulation of IRGM-dependent xenophagy in Crohn's disease. Nature genetics 2011; 43:242-5.

616. Meenhuis A, van Veelen PA, de Looper H, van Boxtel N, van den Berge IJ, Sun SM, Taskesen E, Stern P, de Ru AH, van Adrichem AJ, et al. MiR-17/20/93/106 promote hematopoietic cell expansion by targeting sequestosome 1-regulated pathways in mice. Blood 2011; 118:916-25.

617. Roccaro AM, Sacco A, Jia X, Azab AK, Maiso P, Ngo HT, Azab F, Runnels J, Quang P, Ghobrial IM. microRNA-dependent modulation of histone acetylation in Waldenstrom macroglobulinemia. Blood 2010; 116:1506-14.

618. Martinet W, De Meyer GR, Andries L, Herman AG, Kockx MM. In situ detection of starvation-induced autophagy. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 2006; 54:85-96.

619. Banreti A, Sass M, Graba Y. The emerging role of acetylation in the regulation of autophagy. Autophagy 2013; 9:819-29.

620. Jin M, Klionsky DJ. Regulation of autophagy: Modulation of the size and number of autophagosomes. FEBS letters 2014; 588:2457-63.

621. Feng Y, Yao Z, Klionsky DJ. How to control self-digestion: transcriptional, post-transcriptional, and post-translational regulation of autophagy. Trends in cell biology 2015; 25:354-63.

622. Xie Y, Kang R, Sun X, Zhong M, Huang J, Klionsky DJ, Tang D. Posttranslational modification of autophagy-related proteins in macroautophagy. Autophagy 2015; 11:28-45.

623. Pietrocola F, Marino G, Lissa D, Vacchelli E, Malik SA, Niso-Santano M, Zamzami N, Galluzzi L, Maiuri MC, Kroemer G. Pro-autophagic polyphenols reduce the acetylation of cytoplasmic proteins. Cell cycle 2012; 11:3851-60.

624. Marino G, Pietrocola F, Madeo F, Kroemer G. Caloric restriction mimetics: natural/physiological pharmacological autophagy inducers. Autophagy 2014; 10:1879-82.

625. Madeo F, Pietrocola F, Eisenberg T, Kroemer G. Caloric restriction mimetics: towards a molecular definition. Nature reviews Drug discovery 2014; 13:727-40.

626. Lee IH, Finkel T. Regulation of autophagy by the p300 acetyltransferase. The Journal of biological chemistry 2009; 284:6322-8.

627. Huang R, Xu Y, Wan W, Shou X, Qian J, You Z, Liu B, Chang C, Zhou T, Lippincott-Schwartz J, et al. Deacetylation of Nuclear LC3 Drives Autophagy Initiation under Starvation. Molecular cell 2015.

628. Pattingre S, Petiot A, Codogno P. Analyses of G[a]-interacting protein and activator of G-protein-signaling-3 functions in macroautophagy. Methods in enzymology 2004; 390:17-31.

629. Bauvy C, Meijer AJ, Codogno P. Assaying of autophagic protein degradation. Methods in enzymology 2009; 452:47-61.

630. Zhang J, Wang J, Ng S, Lin Q, Shen HM. Development of a novel method for quantification of autophagic protein degradation by AHA labeling. Autophagy 2014; 10:901-12.

631. Ichimura Y, Kumanomidou T, Sou YS, Mizushima T, Ezaki J, Ueno T, Kominami E, Yamane T, Tanaka K, Komatsu M. Structural basis for sorting mechanism of p62 in selective autophagy. The Journal of biological chemistry 2008; 283:22847-57.

632. Kabuta T, Furuta A, Aoki S, Furuta K, Wada K. Aberrant interaction between Parkinson disease-associated mutant UCH-L1 and the lysosomal receptor for chaperone-mediated autophagy. The Journal of biological chemistry 2008; 283:23731-8.

633. Saitoh Y, Fujikake N, Okamoto Y, Popiel HA, Hatanaka Y, Ueyama M, Suzuki M, Gaumer S, Murata M, Wada K, et al. p62 plays a protective role in the autophagic degradation of polyglutamine protein oligomers in polyglutamine disease model flies. The Journal of biological chemistry 2015; 290:1442-53.

634. Ding WX, Ni HM, Gao W, Yoshimori T, Stolz DB, Ron D, Yin XM. Linking of autophagy to ubiquitin-proteasome system is important for the regulation of endoplasmic reticulum stress and cell viability. The American journal of pathology 2007; 171:513-24.

635. Iwata A, Riley BE, Johnston JA, Kopito RR. HDAC6 and microtubules are required for autophagic degradation of aggregated huntingtin. The Journal of biological chemistry 2005; 280:40282-92.

636. Pandey UB, Nie Z, Batlevi Y, McCray BA, Ritson GP, Nedelsky NB, Schwartz SL, DiProspero NA, Knight MA, Schuldiner O, et al. HDAC6 rescues neurodegeneration and provides an essential link between autophagy and the UPS. Nature 2007; 447:859-63.

637. Tomek K, Wagner R, Varga F, Singer CF, Karlic H, Grunt TW. Blockade of fatty acid synthase induces ubiquitination and degradation of phosphoinositide-3-kinase signaling proteins in ovarian cancer. Molecular cancer research : MCR 2011:1767-79.

638. Zimmermann AC, Zarei M, Eiselein S, Dengjel J. Quantitative proteomics for the analysis of spatio-temporal protein dynamics during autophagy. Autophagy 2010; 6:1009-16.

639. Kristensen AR, Schandorff S, Hoyer-Hansen M, Nielsen MO, Jaattela M, Dengjel J, Andersen JS. Ordered organelle degradation during starvation-induced autophagy. Molecular & cellular proteomics : MCP 2008; 7:2419-28.

640. Furuya N, Kanazawa T, Fujimura S, Ueno T, Kominami E, Kadowaki M. Leupeptin-induced appearance of partial fragment of betaine homocysteine methyltransferase during autophagic maturation in rat hepatocytes. J Biochem (Tokyo) 2001; 129:313-20.

641. Ueno T, Ishidoh K, Mineki R, Tanida I, Murayama K, Kadowaki M, Kominami E. Autolysosomal membrane-associated betaine homocysteine methyltransferase. Limited degradation fragment of a sequestered cytosolic enzyme monitoring autophagy. The Journal of biological chemistry 1999; 274:15222-9.

642. Overbye A, Saetre F, Hagen LK, Johansen HT, Seglen PO. Autophagic activity measured in whole rat hepatocytes as the accumulation of a novel BHMT fragment (p10), generated in amphisomes by the asparaginyl proteinase, legumain. Autophagy 2011; 7:1011-27.

643. Seglen PO, Overbye A, Saetre F. Sequestration assays for mammalian autophagy. Methods in enzymology 2009; 452:63-83.

644. Mercer CA, Kaliappan A, Dennis PB. Macroautophagy-dependent, intralysosomal cleavage of a betaine homocysteine methyltransferase fusion protein requires stable multimerization. Autophagy 2008; 4:185-94.

645. Nimmerjahn F, Milosevic S, Behrends U, Jaffee EM, Pardoll DM, Bornkamm GW, Mautner J. Major histocompatibility complex class II-restricted presentation of a cytosolic antigen by autophagy. Eur J Immunol 2003; 33:1250-9.

646. Taylor GS, Long HM, Haigh TA, Larsen M, Brooks J, Rickinson AB. A role for intercellular antigen transfer in the recognition of EBV-transformed B cell lines by EBV nuclear antigen-specific CD4+ T cells. Journal of immunology 2006; 177:3746-56.

647. Klionsky DJ, Emr SD. Membrane protein sorting: biosynthesis, transport and processing of yeast vacuolar alkaline phosphatase. The EMBO journal 1989; 8:2241-50.

648. Venerando R, Miotto G, Kadowaki M, Siliprandi N, Mortimore GE. Multiphasic control of proteolysis by leucine and alanine in the isolated rat hepatocyte. Am J Physiol 1994; 266:C455-61.

649. Häussinger D, Hallbrucker C, vom Dahl S, Lang F, Gerok W. Cell swelling inhibits proteolysis in perfused rat liver. The Biochemical journal 1990; 272:239-42.

650. vom Dahl S, Häussinger D. Cell hydration and proteolysis control in liver. The Biochemical journal 1995; 312:988-9.

651. Cuervo AM, Stefanis L, Fredenburg R, Lansbury PT, Sulzer D. Impaired degradation of mutant a-synuclein by chaperone-mediated autophagy. Science (New York, NY 2004; 305:1292-5.

652. Vincow ES, Merrihew G, Thomas RE, Shulman NJ, Beyer RP, MacCoss MJ, Pallanck LJ. The PINK1-Parkin pathway promotes both mitophagy and selective respiratory chain turnover in vivo. Proceedings of the National Academy of Sciences of the United States of America 2013; 110:6400-5.

653. Reggiori F, Monastyrska I, Shintani T, Klionsky DJ. The actin cytoskeleton is required for selective types of autophagy, but not nonspecific autophagy, in the yeast Saccharomyces cerevisiae. Molecular biology of the cell 2005; 16:5843-56.

654. Manjithaya R, Jain S, Farre JC, Subramani S. A yeast MAPK cascade regulates pexophagy but not other autophagy pathways. The Journal of cell biology 2010; 189:303-10.

655. Journo D, Mor A, Abeliovich H. Aup1-mediated regulation of Rtg3 during mitophagy. The Journal of biological chemistry 2009; 284:35885-95.

656. Kanki T, Klionsky DJ. Mitophagy in yeast occurs through a selective mechanism. The Journal of biological chemistry 2008; 283:32386-93.

657. Kanki T, Wang K, Baba M, Bartholomew CR, Lynch-Day MA, Du Z, Geng J, Mao K, Yang Z, Yen WL, et al. A genomic screen for yeast mutants defective in selective mitochondria autophagy. Molecular biology of the cell 2009; 20:4730-8.

658. Kanki T, Wang K, Cao Y, Baba M, Klionsky DJ. Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Developmental cell 2009; 17:98-109.

659. Okamoto K, Kondo-Okamoto N, Ohsumi Y. Mitochondria-anchored receptor Atg32 mediates degradation of mitochondria via selective autophagy. Developmental cell 2009; 17:87-97.

660. Sakai Y, Koller A, Rangell LK, Keller GA, Subramani S. Peroxisome degradation by microautophagy in Pichia pastoris: identification of specific steps and morphological intermediates. The Journal of cell biology 1998; 141:625-36.

661. Nazarko TY, Nicaud JM, Sibirny AA. Observation of the Yarrowia lipolytica peroxisome-vacuole dynamics by fluorescence microscopy with a single filter set. Cell Biol Int 2005; 29:65-70.

662. Roetzer A, Gratz N, Kovarik P, Schuller C. Autophagy supports Candida glabrata survival during phagocytosis. Cell Microbiol 2010; 12:199-216.

663. Bormann C, Sahm H. Degradation of microbodies in relation to activities of alcohol oxidase and catalase in Candida boidinii. Archives of microbiology 1978; 117:67-72.

664. Clare DA, Duong MN, Darr D, Archibald F, Fridovich I. Effects of molecular oxygen on detection of superoxide radical with nitroblue tetrazolium and on activity stains for catalase. Analytical biochemistry 1984; 140:532-7.

665. Vachova L, Kucerova H, Devaux F, Ulehlova M, Palkova Z. Metabolic diversification of cells during the development of yeast colonies. Environmental microbiology 2009; 11:494-504.

666. Stasyk OV, Nazarko TY, Sibirny AA. Methods of plate pexophagy monitoring and positive selection for ATG gene cloning in yeasts. Methods in enzymology 2008; 451:229-39.

667. Hutchins MU, Veenhuis M, Klionsky DJ. Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. Journal of cell science 1999; 112:4079-87.

668. Mukaiyama H, Oku M, Baba M, Samizo T, Hammond AT, Glick BS, Kato N, Sakai Y. Paz2 and 13 other PAZ gene products regulate vacuolar engulfment of peroxisomes during micropexophagy. Genes to cells : devoted to molecular & cellular mechanisms 2002; 7:75-90.

669. Tuttle DL, Dunn WA, Jr. Divergent modes of autophagy in the methylotrophic yeast Pichia pastoris. Journal of cell science 1995; 108 ( Pt 1):25-35.

670. Nazarko TY, Huang J, Nicaud JM, Klionsky DJ, Sibirny AA. Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae. Autophagy 2005; 1:37-45.

671. Veenhuis M, Douma A, Harder W, Osumi M. Degradation and turnover of peroxisomes in the yeast Hansenula polymorpha induced by selective inactivation of peroxisomal enzymes. Archives of microbiology 1983; 134:193-203.

672. Monosov EZ, Wenzel TJ, Luers GH, Heyman JA, Subramani S. Labeling of peroxisomes with green fluorescent protein in living P. pastoris cells. The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society 1996; 44:581-9.

673. Wiemer EA, Wenzel T, Deerinck TJ, Ellisman MH, Subramani S. Visualization of the peroxisomal compartment in living mammalian cells: dynamic behavior and association with microtubules. The Journal of cell biology 1997; 136:71-80.

674. Monastyrska I, van der Heide M, Krikken AM, Kiel JAKW, van der Klei IJ, Veenhuis M. Atg8 is essential for macropexophagy in Hansenula polymorpha. Traffic 2005; 6:66-74.

675. Devenish RJ, Prescott M, Turcic K, Mijaljica D. Monitoring organelle turnover in yeast using fluorescent protein tags. Methods in enzymology 2008; 451:109-31.

676. Mao K, Wang K, Liu X, Klionsky DJ. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Developmental cell 2013; 26:9-18.

677. Kerppola TK. Design and implementation of bimolecular fluorescence complementation (BiFC) assays for the visualization of protein interactions in living cells. Nature Protocols 2006; 1:1278-86.

678. Shyu YJ, Liu H, Deng X, Hu CD. Identification of new fluorescent protein fragments for bimolecular fluorescence complementation analysis under physiological conditions. BioTechniques 2006; 40:61-6.

679. Farre JC, Manjithaya R, Mathewson RD, Subramani S. PpAtg30 tags peroxisomes for turnover by selective autophagy. Developmental cell 2008; 14:365-76.

680. He Y, Deng YZ, Naqvi NI. Atg24-assisted mitophagy in the foot cells is necessary for proper asexual differentiation in Magnaporthe oryzae. Autophagy 2013; 9:1818-27.

681. Kanki T, Klionsky DJ. The molecular mechanism of mitochondria autophagy in yeast. Molecular microbiology 2010; 75:795-800.

682. Tal R, Winter G, Ecker N, Klionsky DJ, Abeliovich H. Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival. The Journal of biological chemistry 2007; 282:5617-24.

683. Abeliovich H. Stationary-phase mitophagy in respiring Saccharomyces cerevisiae. Antioxidants & redox signaling 2011; 14:2003-11.

684. East DA, Fagiani F, Crosby J, Georgakopoulos ND, Bertrand H, Schaap M, Fowkes A, Wells G, Campanella M. PMI: a DeltaPsim independent pharmacological regulator of mitophagy. Chem Biol 2014; 21:1585-96.

685. Aksam EB, Koek A, Kiel JAKW, Jourdan S, Veenhuis M, van der Klei IJ. A peroxisomal lon protease and peroxisome degradation by autophagy play key roles in vitality of Hansenula polymorpha cells. Autophagy 2007; 3:96-105.

686. Roberts P, Moshitch-Moshkovitz S, Kvam E, O'Toole E, Winey M, Goldfarb DS. Piecemeal microautophagy of nucleus in Saccharomyces cerevisiae. Molecular biology of the cell 2003; 14:129-41.

687. Krick R, Muehe Y, Prick T, Bremer S, Schlotterhose P, Eskelinen EL, Millen J, Goldfarb DS, Thumm M. Piecemeal microautophagy of the nucleus requires the core macroautophagy genes. Molecular biology of the cell 2008; 19:4492-505.