The autophagic roles of Rab small GTPases and their upstream regulators

References

• Levine B, Kroemer G. Autophagy in the pathogenesis of disease. Cell 2008; 132:27 - 42; http://dx.doi.org/10.1016/j.cell.2007.12.018; PMID: 18191218
   PubMed Web of Science ®Google Scholar
• Mizushima N, Yoshimori T, Ohsumi Y. The role of Atg proteins in autophagosome formation. Annu Rev Cell Dev Biol 2011; 27:107 - 32; http://dx.doi.org/10.1146/annurev-cellbio-092910-154005; PMID: 21801009
   PubMed Web of Science ®Google Scholar
• Tong J, Yan X, Yu L. The late stage of autophagy: cellular events and molecular regulation. Protein Cell 2010; 1:907 - 15; http://dx.doi.org/10.1007/s13238-010-0121-z; PMID: 21204017
   PubMed Web of Science ®Google Scholar
• Stenmark H. Rab GTPases as coordinators of vesicle traffic. Nat Rev Mol Cell Biol 2009; 10:513 - 25; http://dx.doi.org/10.1038/nrm2728; PMID: 19603039
   PubMed Web of Science ®Google Scholar
• Zoppino FCM, Militello RD, Slavin I, Alvarez C, Colombo MI. Autophagosome formation depends on the small GTPase Rab1 and functional ER exit sites. Traffic 2010; 11:1246 - 61; http://dx.doi.org/10.1111/j.1600-0854.2010.01086.x; PMID: 20545908
   PubMed Web of Science ®Google Scholar
• Wang J, Menon S, Yamasaki A, Chou H-T, Walz T, Jiang Y, Ferro-Novick S. Ypt1 recruits the Atg1 kinase to the preautophagosomal structure. Proc Natl Acad Sci U S A 2013; 110:9800 - 5; http://dx.doi.org/10.1073/pnas.1302337110; PMID: 23716696
   PubMed Web of Science ®Google Scholar
• 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; http://dx.doi.org/10.4161/auto.1.1.1512; PMID: 16874038
   PubMed Web of Science ®Google Scholar
• Meiling-Wesse K, Epple UD, Krick R, Barth H, Appelles A, Voss C, Eskelinen E-L, Thumm M. Trs85 (Gsg1), a component of the TRAPP complexes, is required for the organization of the preautophagosomal structure during selective autophagy via the Cvt pathway. J Biol Chem 2005; 280:33669 - 78; http://dx.doi.org/10.1074/jbc.M501701200; PMID: 16079147
   PubMed Web of Science ®Google Scholar
• Lynch-Day MA, Bhandari D, Menon S, Huang J, Cai H, Bartholomew CR, Brumell JH, Ferro-Novick S, Klionsky DJ. Trs85 directs a Ypt1 GEF, TRAPPIII, to the phagophore to promote autophagy. Proc Natl Acad Sci U S A 2010; 107:7811 - 6; http://dx.doi.org/10.1073/pnas.1000063107; PMID: 20375281
   PubMed Web of Science ®Google Scholar
• Lipatova Z, Belogortseva N, Zhang XQ, Kim J, Taussig D, Segev N. Regulation of selective autophagy onset by a Ypt/Rab GTPase module. Proc Natl Acad Sci U S A 2012; 109:6981 - 6; http://dx.doi.org/10.1073/pnas.1121299109; PMID: 22509044
   PubMed Web of Science ®Google Scholar
• Yen W-L, Shintani T, Nair U, Cao Y, Richardson BC, Li Z, Hughson FM, Baba M, Klionsky DJ. The conserved oligomeric Golgi complex is involved in double-membrane vesicle formation during autophagy. J Cell Biol 2010; 188:101 - 14; http://dx.doi.org/10.1083/jcb.200904075; PMID: 20065092
   PubMed Web of Science ®Google Scholar
• Li L, Kim E, Yuan H, Inoki K, Goraksha-Hicks P, Schiesher RL, Neufeld TP, Guan K-L. Regulation of mTORC1 by the Rab and Arf GTPases. J Biol Chem 2010; 285:19705 - 9; http://dx.doi.org/10.1074/jbc.C110.102483; PMID: 20457610
   PubMed Web of Science ®Google Scholar
• Ravikumar B, Imarisio S, Sarkar S, O’Kane CJ, Rubinsztein DC. Rab5 modulates aggregation and toxicity of mutant huntingtin through macroautophagy in cell and fly models of Huntington disease. J Cell Sci 2008; 121:1649 - 60; http://dx.doi.org/10.1242/jcs.025726; PMID: 18430781
   PubMed Web of Science ®Google Scholar
• Su W-C, Chao T-C, Huang Y-L, Weng S-C, Jeng K-S, Lai MMC. Rab5 and class III phosphoinositide 3-kinase Vps34 are involved in hepatitis C virus NS4B-induced autophagy. J Virol 2011; 85:10561 - 71; http://dx.doi.org/10.1128/JVI.00173-11; PMID: 21835792
   PubMed Web of Science ®Google Scholar
• Dou Z, Chattopadhyay M, Pan J-A, Guerriero JL, Jiang Y-P, Ballou LM, Yue Z, Lin RZ, Zong W-X. The class IA phosphatidylinositol 3-kinase p110-beta subunit is a positive regulator of autophagy. J Cell Biol 2010; 191:827 - 43; http://dx.doi.org/10.1083/jcb.201006056; PMID: 21059846
   PubMed Web of Science ®Google Scholar
• Dou Z, Pan J-A, Dbouk HA, Ballou LM, DeLeon JL, Fan Y, Chen J-S, Liang Z, Li G, Backer JM, et al. Class IA PI3K p110β subunit promotes autophagy through Rab5 small GTPase in response to growth factor limitation. Mol Cell 2013; 50:29 - 42; http://dx.doi.org/10.1016/j.molcel.2013.01.022; PMID: 23434372
   PubMed Web of Science ®Google Scholar
• Bridges D, Fisher K, Zolov SN, Xiong T, Inoki K, Weisman LS, Saltiel AR. Rab5 proteins regulate activation and localization of target of rapamycin complex 1. J Biol Chem 2012; 287:20913 - 21; http://dx.doi.org/10.1074/jbc.M111.334060; PMID: 22547071
   PubMed Web of Science ®Google Scholar
• Talaber G, Miklossy G, Oaks Z, Liu Y, Tooze SA, Chudakov DM, Banki K, Perl A. HRES-1/Rab4 promotes the formation of LC3(+) autophagosomes and the accumulation of mitochondria during autophagy. PLoS One 2014; 9:e84392; http://dx.doi.org/10.1371/journal.pone.0084392; PMID: 24404161
   PubMed Web of Science ®Google Scholar
• Bains M, Zaegel V, Mize-Berge J, Heidenreich KA. IGF-I stimulates Rab7-RILP interaction during neuronal autophagy. Neurosci Lett 2011; 488:112 - 7; http://dx.doi.org/10.1016/j.neulet.2010.09.018; PMID: 20849920
   PubMed Web of Science ®Google Scholar
• Pankiv S, Alemu EA, Brech A, Bruun JA, Lamark T, Overvatn A, Bjørkøy G, Johansen T. FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport. J Cell Biol 2010; 188:253 - 69; http://dx.doi.org/10.1083/jcb.200907015; PMID: 20100911
   PubMed Web of Science ®Google Scholar
• Maday S, Wallace KE, Holzbaur ELF. Autophagosomes initiate distally and mature during transport toward the cell soma in primary neurons. J Cell Biol 2012; 196:407 - 17; http://dx.doi.org/10.1083/jcb.201106120; PMID: 22331844
   PubMed Web of Science ®Google Scholar
• Tabata K, Matsunaga K, Sakane A, Sasaki T, Noda T, Yoshimori T. Rubicon and PLEKHM1 negatively regulate the endocytic/autophagic pathway via a novel Rab7-binding domain. Mol Biol Cell 2010; 21:4162 - 72; http://dx.doi.org/10.1091/mbc.E10-06-0495; PMID: 20943950
   PubMed Web of Science ®Google Scholar
• Sun Q, Westphal W, Wong KN, Tan I, Zhong Q. Rubicon controls endosome maturation as a Rab7 effector. Proc Natl Acad Sci U S A 2010; 107:19338 - 43; http://dx.doi.org/10.1073/pnas.1010554107; PMID: 20974968
   PubMed Web of Science ®Google Scholar
• Hyttinen JMT, Niittykoski M, Salminen A, Kaarniranta K. Maturation of autophagosomes and endosomes: a key role for Rab7. Biochim Biophys Acta 2013; 1833:503 - 10; http://dx.doi.org/10.1016/j.bbamcr.2012.11.018; PMID: 23220125
   PubMed Web of Science ®Google Scholar
• 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. J Cell Biol 1999; 147:435 - 46; http://dx.doi.org/10.1083/jcb.147.2.435; PMID: 10525546
   PubMed Web of Science ®Google Scholar
• Gutierrez MG, Munafó DB, Berón W, Colombo MI. Rab7 is required for the normal progression of the autophagic pathway in mammalian cells. J Cell Sci 2004; 117:2687 - 97; http://dx.doi.org/10.1242/jcs.01114; PMID: 15138286
   PubMed Web of Science ®Google Scholar
• Jäger S, Bucci C, Tanida I, Ueno T, Kominami E, Saftig P, Eskelinen E-L. Role for Rab7 in maturation of late autophagic vacuoles. J Cell Sci 2004; 117:4837 - 48; http://dx.doi.org/10.1242/jcs.01370; PMID: 15340014
   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 - 60; PMID: 17534139
   PubMed Web of Science ®Google Scholar
• Su H, Li F, Ranek MJ, Wei N, Wang X. COP9 signalosome regulates autophagosome maturation. Circulation 2011; 124:2117 - 28; http://dx.doi.org/10.1161/CIRCULATIONAHA.111.048934; PMID: 21986281
   PubMed Web of Science ®Google Scholar
• Furuta N, Fujita N, Noda T, Yoshimori T, Amano A. Combinational soluble N-ethylmaleimide-sensitive factor attachment protein receptor proteins VAMP8 and Vti1b mediate fusion of antimicrobial and canonical autophagosomes with lysosomes. Mol Biol Cell 2010; 21:1001 - 10; http://dx.doi.org/10.1091/mbc.E09-08-0693; PMID: 20089838
   PubMed Web of Science ®Google Scholar
• Ganley IG, Wong P-M, Gammoh N, Jiang X. Distinct autophagosomal-lysosomal fusion mechanism revealed by thapsigargin-induced autophagy arrest. Mol Cell 2011; 42:731 - 43; http://dx.doi.org/10.1016/j.molcel.2011.04.024; PMID: 21700220
   PubMed Web of Science ®Google Scholar
• Yu L, McPhee CK, Zheng L, Mardones GA, Rong Y, Peng J, Mi N, Zhao Y, Liu Z, Wan F, et al. Termination of autophagy and reformation of lysosomes regulated by mTOR. Nature 2010; 465:942 - 6; http://dx.doi.org/10.1038/nature09076; PMID: 20526321
   PubMed Web of Science ®Google Scholar
• Lin W-J, Yang CY, Li LL, Yi YH, Chen KW, Lin Y-C, Liu CC, Lin CH. Lysosomal targeting of phafin1 mediated by Rab7 induces autophagosome formation. Biochem Biophys Res Commun 2012; 417:35 - 42; http://dx.doi.org/10.1016/j.bbrc.2011.11.043; PMID: 22115783
   PubMed Web of Science ®Google Scholar
• Sakurai A, Maruyama F, Funao J, Nozawa T, Aikawa C, Okahashi N, Shintani S, Hamada S, Ooshima T, Nakagawa I. Specific behavior of intracellular Streptococcus pyogenes that has undergone autophagic degradation is associated with bacterial streptolysin O and host small G proteins Rab5 and Rab7. J Biol Chem 2010; 285:22666 - 75; http://dx.doi.org/10.1074/jbc.M109.100131; PMID: 20472552
   PubMed Web of Science ®Google Scholar
• Yamaguchi H, Nakagawa I, Yamamoto A, Amano A, Noda T, Yoshimori T. An initial step of GAS-containing autophagosome-like vacuoles formation requires Rab7. PLoS Pathog 2009; 5:e1000670; http://dx.doi.org/10.1371/journal.ppat.1000670; PMID: 19956673
   PubMed Web of Science ®Google Scholar
• Flinn RJ, Yan Y, Goswami S, Parker PJ, Backer JM. The late endosome is essential for mTORC1 signaling. Mol Biol Cell 2010; 21:833 - 41; http://dx.doi.org/10.1091/mbc.E09-09-0756; PMID: 20053679
   PubMed Web of Science ®Google Scholar
• Dupont N, Jiang S, Pilli M, Ornatowski W, Bhattacharya D, Deretic V. Autophagy-based unconventional secretory pathway for extracellular delivery of IL-1β. EMBO J 2011; 30:4701 - 11; http://dx.doi.org/10.1038/emboj.2011.398; PMID: 22068051
   PubMed Web of Science ®Google Scholar
• Pilli M, Arko-Mensah J, Ponpuak M, Roberts E, Master S, Mandell MA, Dupont N, Ornatowski W, Jiang S, Bradfute SB, et al. TBK-1 promotes autophagy-mediated antimicrobial defense by controlling autophagosome maturation. Immunity 2012; 37:223 - 34; http://dx.doi.org/10.1016/j.immuni.2012.04.015; PMID: 22921120
   PubMed Web of Science ®Google Scholar
• Nozawa T, Aikawa C, Goda A, Maruyama F, Hamada S, Nakagawa I. The small GTPases Rab9A and Rab23 function at distinct steps in autophagy during Group A Streptococcus infection. Cell Microbiol 2012; 14:1149 - 65; http://dx.doi.org/10.1111/j.1462-5822.2012.01792.x; PMID: 22452336
   PubMed Web of Science ®Google Scholar
• Nishida Y, Arakawa S, Fujitani K, Yamaguchi H, Mizuta T, Kanaseki T, Komatsu M, Otsu K, Tsujimoto Y, Shimizu S. Discovery of Atg5/Atg7-independent alternative macroautophagy. Nature 2009; 461:654 - 8; http://dx.doi.org/10.1038/nature08455; PMID: 19794493
   PubMed Web of Science ®Google Scholar
• Longatti A, Lamb CA, Razi M, Yoshimura S, Barr FA, Tooze SA. TBC1D14 regulates autophagosome formation via Rab11- and ULK1-positive recycling endosomes. J Cell Biol 2012; 197:659 - 75; http://dx.doi.org/10.1083/jcb.201111079; PMID: 22613832
   PubMed Web of Science ®Google Scholar
• Knævelsrud H, Søreng K, Raiborg C, Håberg K, Rasmuson F, Brech A, Liestøl K, Rusten TE, Stenmark H, Neufeld TP, et al. Membrane remodeling by the PX-BAR protein SNX18 promotes autophagosome formation. J Cell Biol 2013; 202:331 - 49; http://dx.doi.org/10.1083/jcb.201205129; PMID: 23878278
   PubMed Web of Science ®Google Scholar
• Puri C, Renna M, Bento CF, Moreau K, Rubinsztein DC. Diverse autophagosome membrane sources coalesce in recycling endosomes. Cell 2013; 154:1285 - 99; http://dx.doi.org/10.1016/j.cell.2013.08.044; PMID: 24034251
   PubMed Web of Science ®Google Scholar
• Fader CM, Sánchez D, Furlán M, Colombo MI. Induction of autophagy promotes fusion of multivesicular bodies with autophagic vacuoles in k562 cells. Traffic 2008; 9:230 - 50; http://dx.doi.org/10.1111/j.1600-0854.2007.00677.x; PMID: 17999726
   PubMed Web of Science ®Google Scholar
• Fader CM, Sánchez DG, Mestre MB, Colombo MI. TI-VAMP/VAMP7 and VAMP3/cellubrevin: two v-SNARE proteins involved in specific steps of the autophagy/multivesicular body pathways. Biochim Biophys Acta 2009; 1793:1901 - 16; http://dx.doi.org/10.1016/j.bbamcr.2009.09.011; PMID: 19781582
   PubMed Web of Science ®Google Scholar
• Richards P, Didszun C, Campesan S, Simpson A, Horley B, Young KW, Glynn P, Cain K, Kyriacou CP, Giorgini F, et al. Dendritic spine loss and neurodegeneration is rescued by Rab11 in models of Huntington’s disease. Cell Death Differ 2011; 18:191 - 200; http://dx.doi.org/10.1038/cdd.2010.127; PMID: 21217767
   PubMed Web of Science ®Google Scholar
• Szatmári Z, Kis V, Lippai M, Hegedus K, Faragó T, Lorincz P, Tanaka T, Juhász G, Sass M. Rab11 facilitates cross-talk between autophagy and endosomal pathway through regulation of Hook localization. Mol Biol Cell 2014; 25:522 - 31; http://dx.doi.org/10.1091/mbc.E13-10-0574; PMID: 24356450
   PubMed Web of Science ®Google Scholar
• Munafó DB, Colombo MI. Induction of autophagy causes dramatic changes in the subcellular distribution of GFP-Rab24. Traffic 2002; 3:472 - 82; http://dx.doi.org/10.1034/j.1600-0854.2002.30704.x; PMID: 12047555
   PubMed Web of Science ®Google Scholar
• Hirota Y, Tanaka Y. A small GTPase, human Rab32, is required for the formation of autophagic vacuoles under basal conditions. Cell Mol Life Sci 2009; 66:2913 - 32; http://dx.doi.org/10.1007/s00018-009-0080-9; PMID: 19593531
   PubMed Web of Science ®Google Scholar
• Wang C, Liu Z, Huang X.. Rab32 Is Important for Autophagy and Lipid Storage in Drosophila. 2012; 7:1 - 9
   Google Scholar
• Itoh T, Fujita N, Kanno E, Yamamoto A, Yoshimori T, Fukuda M. Golgi-resident small GTPase Rab33B interacts with Atg16L and modulates autophagosome formation. Mol Biol Cell 2008; 19:2916 - 25; http://dx.doi.org/10.1091/mbc.E07-12-1231; PMID: 18448665
   PubMed Web of Science ®Google Scholar
• Itoh T, Kanno E, Uemura T, Waguri S, Fukuda M. OATL1, a novel autophagosome-resident Rab33B-GAP, regulates autophagosomal maturation. J Cell Biol 2011; 192:839 - 53; http://dx.doi.org/10.1083/jcb.201008107; PMID: 21383079
   PubMed Web of Science ®Google Scholar
• Numrich J, Ungermann C. Endocytic Rabs in membrane trafficking and signaling. Biol Chem 2014; 395:327 - 33; http://dx.doi.org/10.1515/hsz-2013-0258; PMID: 24158421
   PubMed Web of Science ®Google Scholar
• Murray JT, Panaretou C, Stenmark H, Miaczynska M, Backer JM. Role of Rab5 in the recruitment of hVps34/p150 to the early endosome. Traffic 2002; 3:416 - 27; http://dx.doi.org/10.1034/j.1600-0854.2002.30605.x; PMID: 12010460
   PubMed Web of Science ®Google Scholar
• van der Sluijs P, Hull M, Webster P, Mâle P, Goud B, Mellman I. The small GTP-binding protein rab4 controls an early sorting event on the endocytic pathway. Cell 1992; 70:729 - 40; http://dx.doi.org/10.1016/0092-8674(92)90307-X; PMID: 1516131
   PubMed Web of Science ®Google Scholar
• Sönnichsen B, De Renzis S, Nielsen E, Rietdorf J, Zerial M. Distinct membrane domains on endosomes in the recycling pathway visualized by multicolor imaging of Rab4, Rab5, and Rab11. J Cell Biol 2000; 149:901 - 14; http://dx.doi.org/10.1083/jcb.149.4.901; PMID: 10811830
   PubMed Web of Science ®Google Scholar
• Huotari J, Helenius A. Endosome maturation. EMBO J 2011; 30:3481 - 500; http://dx.doi.org/10.1038/emboj.2011.286; PMID: 21878991
   PubMed Web of Science ®Google Scholar
• Wang T, Ming Z, Xiaochun W, Hong W. Rab7: role of its protein interaction cascades in endo-lysosomal traffic. Cell Signal 2011; 23:516 - 21; http://dx.doi.org/10.1016/j.cellsig.2010.09.012; PMID: 20851765
   PubMed Web of Science ®Google Scholar
• Johansson M, Lehto M, Tanhuanpää K, Cover TL, Olkkonen VM. The oxysterol-binding protein homologue ORP1L interacts with Rab7 and alters functional properties of late endocytic compartments. Mol Biol Cell 2005; 16:5480 - 92; http://dx.doi.org/10.1091/mbc.E05-03-0189; PMID: 16176980
   PubMed Web of Science ®Google Scholar
• Johansson M, Rocha N, Zwart W, Jordens I, Janssen L, Kuijl C, Olkkonen VM, Neefjes J. Activation of endosomal dynein motors by stepwise assembly of Rab7-RILP-p150Glued, ORP1L, and the receptor betalll spectrin. J Cell Biol 2007; 176:459 - 71; http://dx.doi.org/10.1083/jcb.200606077; PMID: 17283181
   PubMed Web of Science ®Google Scholar
• Jordens I, Fernandez-Borja M, Marsman M, Dusseljee S, Janssen L, Calafat J, Janssen H, Wubbolts R, Neefjes J. The Rab7 effector protein RILP controls lysosomal transport by inducing the recruitment of dynein-dynactin motors. Curr Biol 2001; 11:1680 - 5; http://dx.doi.org/10.1016/S0960-9822(01)00531-0; PMID: 11696325
   PubMed Web of Science ®Google Scholar
• Kim BY, Krämer H, Yamamoto A, Kominami E, Kohsaka S, Akazawa C. Molecular characterization of mammalian homologues of class C Vps proteins that interact with syntaxin-7. J Biol Chem 2001; 276:29393 - 402; http://dx.doi.org/10.1074/jbc.M101778200; PMID: 11382755
   PubMed Web of Science ®Google Scholar
• Starai VJ, Hickey CM, Wickner W. HOPS proofreads the trans-SNARE complex for yeast vacuole fusion. Mol Biol Cell 2008; 19:2500 - 8; http://dx.doi.org/10.1091/mbc.E08-01-0077; PMID: 18385512
   PubMed Web of Science ®Google Scholar
• Mizuno K, Kitamura A, Sasaki T. Rabring7, a novel Rab7 target protein with a RING finger motif. Mol Biol Cell 2003; 14:3741 - 52; http://dx.doi.org/10.1091/mbc.E02-08-0495; PMID: 12972561
   PubMed Web of Science ®Google Scholar
• Liang C, Lee JS, Inn KS, Gack MU, Li Q, Roberts EA, Vergne I, Deretic V, Feng P, Akazawa C, et al. Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking. Nat Cell Biol 2008; 10:776 - 87; http://dx.doi.org/10.1038/ncb1740; PMID: 18552835
   PubMed Web of Science ®Google Scholar
• Matsunaga K, Saitoh T, Tabata K, Omori H, Satoh T, Kurotori N, Maejima I, Shirahama-Noda K, Ichimura T, Isobe T, et al. Two Beclin 1-binding proteins, Atg14L and Rubicon, reciprocally regulate autophagy at different stages. Nat Cell Biol 2009; 11:385 - 96; http://dx.doi.org/10.1038/ncb1846; PMID: 19270696
   PubMed Web of Science ®Google Scholar
• Zhong Y, Wang QJ, Li X, Yan Y, Backer JM, Chait BT, Heintz N, Yue Z. Distinct regulation of autophagic activity by Atg14L and Rubicon associated with Beclin 1-phosphatidylinositol-3-kinase complex. Nat Cell Biol 2009; 11:468 - 76; http://dx.doi.org/10.1038/ncb1854; PMID: 19270693
   PubMed Web of Science ®Google Scholar
• Lin MG, Zhong Q. Interaction between small GTPase Rab7 and PI3KC3 links autophagy and endocytosis: A new Rab7 effector protein sheds light on membrane trafficking pathways. Small GTPases 2011; 2:85 - 8; http://dx.doi.org/10.4161/sgtp.2.2.15256; PMID: 21776407
   PubMedGoogle Scholar
• Razi M, Chan EYW, Tooze SA. Early endosomes and endosomal coatomer are required for autophagy. J Cell Biol 2009; 185:305 - 21; http://dx.doi.org/10.1083/jcb.200810098; PMID: 19364919
   PubMed Web of Science ®Google Scholar
• Köchl R, Hu XW, Chan EYW, Tooze SA. Microtubules facilitate autophagosome formation and fusion of autophagosomes with endosomes. Traffic 2006; 7:129 - 45; http://dx.doi.org/10.1111/j.1600-0854.2005.00368.x; PMID: 16420522
   PubMed Web of Science ®Google Scholar
• Filimonenko M, Stuffers S, Raiborg C, Yamamoto A, Malerød L, Fisher EMC, Isaacs A, Brech A, Stenmark H, Simonsen A. Functional multivesicular bodies are required for autophagic clearance of protein aggregates associated with neurodegenerative disease. J Cell Biol 2007; 179:485 - 500; http://dx.doi.org/10.1083/jcb.200702115; PMID: 17984323
   PubMed Web of Science ®Google Scholar
• Gordon PB, Seglen PO. Prelysosomal convergence of autophagic and endocytic pathways. Biochem Biophys Res Commun 1988; 151:40 - 7; http://dx.doi.org/10.1016/0006-291X(88)90556-6; PMID: 3126737
   PubMed Web of Science ®Google Scholar
• Itakura E, Kishi-Itakura C, Mizushima N. The hairpin-type tail-anchored SNARE syntaxin 17 targets to autophagosomes for fusion with endosomes/lysosomes. Cell 2012; 151:1256 - 69; http://dx.doi.org/10.1016/j.cell.2012.11.001; PMID: 23217709
   PubMed Web of Science ®Google Scholar
• Takáts S, Nagy P, Varga Á, Pircs K, Kárpáti M, Varga K, Kovács AL, Hegedűs K, Juhász G. Autophagosomal Syntaxin17-dependent lysosomal degradation maintains neuronal function in Drosophila. J Cell Biol 2013; 201:531 - 9; http://dx.doi.org/10.1083/jcb.201211160; PMID: 23671310
   PubMed Web of Science ®Google Scholar
• Díaz-Troya S, Pérez-Pérez ME, Florencio FJ, Crespo JL. The role of TOR in autophagy regulation from yeast to plants and mammals. Autophagy 2008; 4:851 - 65; PMID: 18670193
   PubMed Web of Science ®Google Scholar
• Jewell JL, Russell RC, Guan K-L. Amino acid signalling upstream of mTOR. Nat Rev Mol Cell Biol 2013; 14:133 - 9; http://dx.doi.org/10.1038/nrm3522; PMID: 23361334
   PubMed Web of Science ®Google Scholar
• Dwivedi M, Sung H, Shen H, Park B-J, Lee S. Disruption of endocytic pathway regulatory genes activates autophagy in C. elegans. Mol Cells 2011; 31:477 - 81; http://dx.doi.org/10.1007/s10059-011-1035-1; PMID: 21618079
   PubMed Web of Science ®Google Scholar
• Otomo A, Kunita R, Suzuki-Utsunomiya K, Ikeda J-E, Hadano S. Defective relocalization of ALS2/alsin missense mutants to Rac1-induced macropinosomes accounts for loss of their cellular function and leads to disturbed amphisome formation. FEBS Lett 2011; 585:730 - 6; http://dx.doi.org/10.1016/j.febslet.2011.01.045; PMID: 21300063
   PubMed Web of Science ®Google Scholar
• Moyer BD, Allan BB, Balch WE. Rab1 interaction with a GM130 effector complex regulates COPII vesicle cis--Golgi tethering. Traffic 2001; 2:268 - 76; http://dx.doi.org/10.1034/j.1600-0854.2001.1o007.x; PMID: 11285137
   PubMed Web of Science ®Google Scholar
• Axe EL, Walker SA, Manifava M, Chandra P, Roderick HL, Habermann A, Griffiths G, Ktistakis NT. Autophagosome formation from membrane compartments enriched in phosphatidylinositol 3-phosphate and dynamically connected to the endoplasmic reticulum. J Cell Biol 2008; 182:685 - 701; http://dx.doi.org/10.1083/jcb.200803137; PMID: 18725538
   PubMed Web of Science ®Google Scholar
• Hayashi-Nishino M, Fujita N, Noda T, Yamaguchi A, Yoshimori T, Yamamoto A. A subdomain of the endoplasmic reticulum forms a cradle for autophagosome formation. Nat Cell Biol 2009; 11:1433 - 7; http://dx.doi.org/10.1038/ncb1991; PMID: 19898463
   PubMed Web of Science ®Google Scholar
• Ylä-Anttila P, Vihinen H, Jokitalo E, Eskelinen E-L. 3D tomography reveals connections between the phagophore and endoplasmic reticulum. Autophagy 2009; 5:1180 - 5; http://dx.doi.org/10.4161/auto.5.8.10274; PMID: 19855179
   PubMed Web of Science ®Google Scholar
• Itakura E, Mizushima N. Characterization of autophagosome formation site by a hierarchical analysis of mammalian Atg proteins. Autophagy 2010; 6:764 - 76; http://dx.doi.org/10.4161/auto.6.6.12709; PMID: 20639694
   PubMed Web of Science ®Google Scholar
• Ragusa MJ, Stanley RE, Hurley JH. Architecture of the Atg17 complex as a scaffold for autophagosome biogenesis. Cell 2012; 151:1501 - 12; http://dx.doi.org/10.1016/j.cell.2012.11.028; PMID: 23219485
   PubMed Web of Science ®Google Scholar
• Mari M, Griffith J, Rieter E, Krishnappa L, Klionsky DJ, Reggiori F. An Atg9-containing compartment that functions in the early steps of autophagosome biogenesis. J Cell Biol 2010; 190:1005 - 22; http://dx.doi.org/10.1083/jcb.200912089; PMID: 20855505
   PubMed Web of Science ®Google Scholar
• Yamamoto H, Kakuta S, Watanabe TM, Kitamura A, Sekito T, Kondo-Kakuta C, Ichikawa R, Kinjo M, Ohsumi Y. Atg9 vesicles are an important membrane source during early steps of autophagosome formation. J Cell Biol 2012; 198:219 - 33; http://dx.doi.org/10.1083/jcb.201202061; PMID: 22826123
   PubMed Web of Science ®Google Scholar
• Yorimitsu T, Klionsky DJ. Atg11 Links Cargo to the Vesicle-forming Machinery in the Cytoplasm to Vacuole Targeting Pathway. 2005; 16:1593 - 605
   Google Scholar
• He C, Song H, Yorimitsu T, Monastyrska I, Yen W-L, Legakis JE, Klionsky DJ. Recruitment of Atg9 to the preautophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J Cell Biol 2006; 175:925 - 35; http://dx.doi.org/10.1083/jcb.200606084; PMID: 17178909
   PubMed Web of Science ®Google Scholar
• Suvorova ES, Duden R, Lupashin VV. The Sec34/Sec35p complex, a Ypt1p effector required for retrograde intra-Golgi trafficking, interacts with Golgi SNAREs and COPI vesicle coat proteins. J Cell Biol 2002; 157:631 - 43; http://dx.doi.org/10.1083/jcb.200111081; PMID: 12011112
   PubMed Web of Science ®Google Scholar
• Huang J, Birmingham CL, Shahnazari S, Shiu J, Zheng YT, Smith AC, Campellone KG, Heo WD, Gruenheid S, Meyer T, et al. Antibacterial autophagy occurs at PI(3)P-enriched domains of the endoplasmic reticulum and requires Rab1 GTPase. Autophagy 2011; 7:17 - 26; http://dx.doi.org/10.4161/auto.7.1.13840; PMID: 20980813
   PubMed Web of Science ®Google Scholar
• Winslow AR, Chen C, Corrochano S, Acevedo-arozena A, Gordon DE, Peden AA, Lichtenberg M, Menzies FM, Ravikumar B, Imarisio S, et al. Alpha-Synuclein impairs macroautophagy: implications for Parkinson’s disease. 2010; 190:1023 - 37
   Google Scholar
• Lipatova Z, Tokarev AA, Jin Y, Mulholland J, Weisman LS, Segev N. Direct Interaction between a Myosin V Motor and the Rab GTPases Ypt31 / 32 Is Required for Polarized Secretion. 2008; 19:4177 - 87
   Google Scholar
• Hsu VW, Prekeris R. Transport at the recycling endosome. Curr Opin Cell Biol 2010; 22:528 - 34; http://dx.doi.org/10.1016/j.ceb.2010.05.008; PMID: 20541925
   PubMed Web of Science ®Google Scholar
• Jones S, Newman C, Liu F, Segev N. The TRAPP complex is a nucleotide exchanger for Ypt1 and Ypt31/32. Mol Biol Cell 2000; 11:4403 - 11; http://dx.doi.org/10.1091/mbc.11.12.4403; PMID: 11102533
   PubMed Web of Science ®Google Scholar
• Morozova N, Liang Y, Tokarev AA, Chen SH, Cox R, Andrejic J, Lipatova Z, Sciorra VA, Emr SD, Segev N. TRAPPII subunits are required for the specificity switch of a Ypt-Rab GEF. Nat Cell Biol 2006; 8:1263 - 9; http://dx.doi.org/10.1038/ncb1489; PMID: 17041589
   PubMed Web of Science ®Google Scholar
• Wang W, Ferro-Novick S. A. Ypt32p Exchange Factor Is a Putative Effector of Ypt1p. 2002; 13:3336 - 43
   Google Scholar
• Rivera-Molina FE, Novick PJ. A Rab GAP cascade defines the boundary between two Rab GTPases on the secretory pathway. Proc Natl Acad Sci U S A 2009; 106:14408 - 13; http://dx.doi.org/10.1073/pnas.0906536106; PMID: 19666511
   PubMed Web of Science ®Google Scholar
• Barbero P, Bittova L, Pfeffer SR. Visualization of Rab9-mediated vesicle transport from endosomes to the trans-Golgi in living cells. J Cell Biol 2002; 156:511 - 8; http://dx.doi.org/10.1083/jcb.200109030; PMID: 11827983
   PubMed Web of Science ®Google Scholar
• Yoshimura S, Gerondopoulos A, Linford A, Rigden DJ, Barr FA. Family-wide characterization of the DENN domain Rab GDP-GTP exchange factors. J Cell Biol 2010; 191:367 - 81; http://dx.doi.org/10.1083/jcb.201008051; PMID: 20937701
   PubMed Web of Science ®Google Scholar
• Valsdottir R, Hashimoto H, Ashman K, Koda T, Storrie B, Nilsson T. Identification of rabaptin-5, rabex-5, and GM130 as putative effectors of rab33b, a regulator of retrograde traffic between the Golgi apparatus and ER. FEBS Lett 2001; 508:201 - 9; http://dx.doi.org/10.1016/S0014-5793(01)02993-3; PMID: 11718716
   PubMed Web of Science ®Google Scholar
• Bravo-Cordero JJ, Marrero-Diaz R, Megías D, Genís L, García-Grande A, García MA, Arroyo AG, Montoya MC. MT1-MMP proinvasive activity is regulated by a novel Rab8-dependent exocytic pathway. EMBO J 2007; 26:1499 - 510; http://dx.doi.org/10.1038/sj.emboj.7601606; PMID: 17332756
   PubMed Web of Science ®Google Scholar
• Henry L, Sheff DR. Rab8 regulates basolateral secretory, but not recycling, traffic at the recycling endosome. Mol Biol Cell 2008; 19:2059 - 68; http://dx.doi.org/10.1091/mbc.E07-09-0902; PMID: 18287531
   PubMed Web of Science ®Google Scholar
• Roland JT, Kenworthy AK, Peranen J, Caplan S, Goldenring JR. Myosin Vb interacts with Rab8a on a tubular network containing EHD1 and EHD3. Mol Biol Cell 2007; 18:2828 - 37; http://dx.doi.org/10.1091/mbc.E07-02-0169; PMID: 17507647
   PubMed Web of Science ®Google Scholar
• Olkkonen VM, Dupree P, Killisch I, Lütcke A, Zerial M, Simons K. Molecular cloning and subcellular localization of three GTP-binding proteins of the rab subfamily. J Cell Sci 1993; 106:1249 - 61; PMID: 8126105
   PubMed Web of Science ®Google Scholar
• Bultema JJ, Di Pietro SM. Cell type-specific Rab32 and Rab38 cooperate with the ubiquitous lysosome biogenesis machinery to synthesize specialized lysosome-related organelles. Small GTPases 2013; 4:16 - 21; http://dx.doi.org/10.4161/sgtp.22349; PMID: 23247405
   PubMedGoogle Scholar
• Bui M, Gilady SY, Fitzsimmons REB, Benson MD, Lynes EM, Gesson K, Alto NM, Strack S, Scott JD, Simmen T. Rab32 modulates apoptosis onset and mitochondria-associated membrane (MAM) properties. J Biol Chem 2010; 285:31590 - 602; http://dx.doi.org/10.1074/jbc.M110.101584; PMID: 20670942
   PubMed Web of Science ®Google Scholar
• Hamasaki M, Furuta N, Matsuda A, Nezu A, Yamamoto A, Fujita N, Oomori H, Noda T, Haraguchi T, Hiraoka Y, et al. Autophagosomes form at ER-mitochondria contact sites. Nature 2013; 495:389 - 93; http://dx.doi.org/10.1038/nature11910; PMID: 23455425
   PubMed Web of Science ®Google Scholar
• Chua CEL, Gan BQ, Tang BL. Involvement of members of the Rab family and related small GTPases in autophagosome formation and maturation. Cell Mol Life Sci 2011; 68:3349 - 58; http://dx.doi.org/10.1007/s00018-011-0748-9; PMID: 21687989
   PubMed Web of Science ®Google Scholar
• Cooper AA, Gitler AD, Cashikar A, Haynes CM, Hill KJ, Bhullar B, Liu K, Xu K, Strathearn KE, Liu F, et al. Alpha-synuclein blocks ER-Golgi traffic and Rab1 rescues neuron loss in Parkinson’s models. Science 2006; 313:324 - 8; http://dx.doi.org/10.1126/science.1129462; PMID: 16794039
   PubMed Web of Science ®Google Scholar
• Rendón WO, Martínez-Alonso E, Tomás M, Martínez-Martínez N, Martínez-Menárguez JA. Golgi fragmentation is Rab and SNARE dependent in cellular models of Parkinson’s disease. Histochem Cell Biol 2013; 139:671 - 84; http://dx.doi.org/10.1007/s00418-012-1059-4; PMID: 23212845
   PubMed Web of Science ®Google Scholar
• Gitler AD, Bevis BJ, Shorter J, Strathearn KE, Hamamichi S, Su LJ, Caldwell KA, Caldwell GA, Rochet JC, McCaffery JM, et al. The Parkinson’s disease protein alpha-synuclein disrupts cellular Rab homeostasis. Proc Natl Acad Sci U S A 2008; 105:145 - 50; http://dx.doi.org/10.1073/pnas.0710685105; PMID: 18162536
   PubMed Web of Science ®Google Scholar
• Li X, Sapp E, Valencia A, Kegel KB, Qin Z-H, Alexander J, Masso N, Reeves P, Ritch JJ, Zeitlin S, et al. A function of huntingtin in guanine nucleotide exchange on Rab11. Neuroreport 2008; 19:1643 - 7; http://dx.doi.org/10.1097/WNR.0b013e328315cd4c; PMID: 18845944
   PubMed Web of Science ®Google Scholar
• Li X, Standley C, Sapp E, Valencia A, Qin Z-H, Kegel KB, Yoder J, Comer-Tierney LA, Esteves M, Chase K, et al. Mutant huntingtin impairs vesicle formation from recycling endosomes by interfering with Rab11 activity. Mol Cell Biol 2009; 29:6106 - 16; http://dx.doi.org/10.1128/MCB.00420-09; PMID: 19752198
   PubMed Web of Science ®Google Scholar
• Li X, Valencia A, Sapp E, Masso N, Alexander J, Reeves P, Kegel KB, Aronin N, Difiglia M. Aberrant Rab11-dependent trafficking of the neuronal glutamate transporter EAAC1 causes oxidative stress and cell death in Huntington’s disease. J Neurosci 2010; 30:4552 - 61; http://dx.doi.org/10.1523/JNEUROSCI.5865-09.2010; PMID: 20357106
   PubMed Web of Science ®Google Scholar
• Li X, Valencia A, McClory H, Sapp E, Kegel KB, Difiglia M. Deficient Rab11 activity underlies glucose hypometabolism in primary neurons of Huntington’s disease mice. Biochem Biophys Res Commun 2012; 421:727 - 30; http://dx.doi.org/10.1016/j.bbrc.2012.04.070; PMID: 22542623
   PubMed Web of Science ®Google Scholar
• Steinert JR, Campesan S, Richards P, Kyriacou CP, Forsythe ID, Giorgini F. Rab11 rescues synaptic dysfunction and behavioural deficits in a Drosophila model of Huntington’s disease. Hum Mol Genet 2012; 21:2912 - 22; http://dx.doi.org/10.1093/hmg/dds117; PMID: 22466800
   PubMed Web of Science ®Google Scholar
• Toro D, Alberch J, La F, Xifro X, Egea G, Canals JM. Mutant Huntingtin Impairs Post-Golgi Trafficking to Lysosomes by Delocalizing Optineurin / Rab8 Complex from the Golgi Apparatus. 2009; 20:1478 - 92
   Google Scholar
• Martinez-Vicente M, Tallóczy Z, Wong E, Tang G, Koga H, Kaushik S, de Vries R, Arias E, Harris S, Sulzer D, et al. Cargo recognition failure is responsible for inefficient autophagy in Huntington’s disease. Nat Neurosci 2010; 13:567 - 76; http://dx.doi.org/10.1038/nn.2528; PMID: 20383138
   PubMed Web of Science ®Google Scholar
• Ko DC, Milenkovic L, Beier SM, Manuel H, Buchanan J, Scott MP. Cell-autonomous death of cerebellar purkinje neurons with autophagy in Niemann-Pick type C disease. PLoS Genet 2005; 1:81 - 95; PMID: 16103921
   PubMed Web of Science ®Google Scholar
• Sarkar S, Carroll B, Buganim Y, Maetzel D, Ng AHM, Cassady JP, Cohen MA, Chakraborty S, Wang H, Spooner E, et al. Impaired autophagy in the lipid-storage disorder Niemann-Pick type C1 disease. Cell Rep 2013; 5:1302 - 15; http://dx.doi.org/10.1016/j.celrep.2013.10.042; PMID: 24290752
   PubMed Web of Science ®Google Scholar
• Linder MD, Uronen R, Ho M, Sluijs P, Van Der, Pera J, Ikonen E. Rab8-dependent Recycling Promotes Endosomal Cholesterol Removal in Normal and Sphingolipidosis Cells. 2007; 18:47 - 56
   Google Scholar
• Narita K, Choudhury A, Dobrenis K, Sharma DK, Holicky EL, Marks DL, Walkley SU, Pagano RE, Clinic M, Neuroscience M, et al. Protein transduction of Rab9 in Niemann-Pick C cells reduces cholesterol storage. 2005; 17:1 - 17
   Google Scholar
• Kaptzan T, West SA, Holicky EL, Wheatley CL, Marks DL, Wang T, Peake KB, Vance J, Walkley SU, Pagano RE. Development of a Rab9 transgenic mouse and its ability to increase the lifespan of a murine model of Niemann-Pick type C disease. Am J Pathol 2009; 174:14 - 20; http://dx.doi.org/10.2353/ajpath.2009.080660; PMID: 19056848
   PubMed Web of Science ®Google Scholar
• Popovic D, Akutsu M, Novak I, Harper JW, Behrends C, Dikic I. Rab GTPase-activating proteins in autophagy: regulation of endocytic and autophagy pathways by direct binding to human ATG8 modifiers. Mol Cell Biol 2012; 32:1733 - 44; http://dx.doi.org/10.1128/MCB.06717-11; PMID: 22354992
   PubMed Web of Science ®Google Scholar