Publications

Publications are arranged under the following topics:

Cytoplasm to vacuole targeting/autophagy
Reviews
Vacuolar ATPase
Trehalase and miscellaneous
Teaching/Learning

Cytoplasm to vacuole targeting/autophagy

Kanki, T., K. Wang, Y. Cao, M. Baba and D.J. Klionsky. 2009. Atg32 is a mitochondrial protein that confers selectivity during mitophagy. Dev. Cell, 17: 98-109.

Cao, Y., U. Nair, K. Yasumura-Yorimitsu and D.J. Klionsky. 2009. A multiple ATG gene knockout strain for yeast two-hybrid analysis. Autophagy, 5: 699-705.

Yorimitsu, T., C. He., K. Wang and D.J. Klionsky. 2009. Tap42-associated protein phosphatase type 2A negatively regulates induction of autophagy. Autophagy, 5: 616-624.

He, C., C. Bartholomew, W. Zhou and D.J. Klionsky. 2009. Assaying autophagic activity in transgenic GFP-Lc3 and GFP-gabarap zebrafish embryos. Autophagy, 5: 520-526.

Xie, Z., U. Nair, J. Geng, M.B. Szefler, E.D. Rothman and D.J. Klionsky. 2009. Indirect estimation of the area density of Atg8 on the phagophore. Autophagy, 5: 217-220.

He, C., M. Baba, Y. Cao and D.J. Klionsky. 2008. Self-interaction is critical for Atg9 transport and function at the phagophore assembly site during autophagy. Mol. Biol. Cell, 19: 5506-5516.

Kanki, T. and D.J. Klionsky. 2008. Mitophagy in yeast occurs through a selective mechanism. J. Biol. Chem., 283: 32386-32393.

Cao, Y., H. Cheong, H. Song and D.J. Klionsky. 2008. In vivo reconstitution of autophagy in Saccharomyces cerevisiae. J. Cell Biol., 182: 703-713.

Xie, Z., U. Nair and D.J. Klionsky. Atg8 controls phagophore expansion during autophagosome formation. Mol. Biol. Cell, 19: 3290-3298.

Geng, J., M. Baba, U. Nair and D.J. Klionsky. 2008. Quantitative analysis of autophagy-related protein stoichiometry by fluorescence microscopy. J. Cell Biol., 182: 129-140.

Monastyrska, I., C. He, J. Geng, A.D. Hoppe and D.J. Klionsky. 2008. The actin-related protein Arp2 is required for Atg9 movement during autophagy. Mol. Biol. Cell, 19: 1962-1975.

Cheong, H., U. Nair, J. Geng and D.J. Klionsky. 2008. The Atg1 kinase complex is involved in the regulation of protein recruitment to initiate sequestering vesicle formation for nonspecific autophagy in Saccharomyces cerevisiae. Mol. Biol. Cell, 19: 668-681.

Yorimitsu, T., S. Zaman, J.R. Broach and D.J. Klionsky. 2007. Protein kinase A and Sch9 cooperatively regulate induction of autophagy in Saccharomyces cerevisiae. Mol. Biol. Cell, 18: 4180-4189.

Huang, J., F. Reggiori and D.J. Klionsky. 2007. The transmembrane domain of acid trehalase mediates ubiquitin-independent Multivesicular body pathway sorting. Mol. Biol. Cell, 18: 2511-2524.

Legakis, J.E., W.-L. Yen and D.J. Klionsky. 2007. A cycling protein complex required for selective autophagy. Autophagy, 3: 422-432.

Tal, R., G. Winter, N. Ecker, D.J. Klionsky and H. Abeliovich. 2007. Aup1p, a yeast mitochondrial protein phosphatase homolog, is required for efficient stationary phase mitophagy and cell survival. J. Biol. Chem., 282: 5617-5624.

Yen, W.-L., J.E. Legakis, U. Nair and D.J. Klionsky. 2007. Atg27 is required for autophagy-dependent cycling of Atg9. Mol. Biol. Cell. 18: 581-593.

Cao, Y. and D.J. Klionsky. 2007. Atg26 is not involved in autophagy-related pathways in Saccharomyces cerevisiae . Autophagy, 3: 17-20.

He , C., H. Song, T. Yorimitsu, I. Monastyrska, W.-L. Yen, J.E. Legakis and D.J. Klionsky. 2006. Recruitment of Atg9 to the pre-autophagosomal structure by Atg11 is essential for selective autophagy in budding yeast. J. Cell Biol., 175: 925-935.

Yang, Z., J. Huang, J. Geng, U. Nair and D.J. Klionsky. 2006. Atg22 recycles amino acids to link the degradative and recycling functions of autophagy. Mol. Biol. Cell, 17: 5094-5104.

Yorimitsu, T., U. Nair, Z. Yang and D.J. Klionsky. 2006. Endoplasmic reticulum stress triggers autophagy. J. Biol. Chem., 281: 30299-30304.

Reggiori, F., I. Monastyrska, T. Shintani and D.J. Klionsky. 2006. The actin cytoskeleton is essential for selective autophagy in the yeast Saccharomyces cerevisiae. Mol. Biol. Cell, 16: 5843-5856.

Towns, R., Y. Kabeya, T. Yoshimori, C. Guo, Y. Shangguan, S. Hong, M. Kaplan, D.J. Klionsky, and J.W. Wiley. 2005. Sera from patients with type 2 diabetes and neuropathy induce autophagy and colocalization with mitochondria in SY5Y cells. Autophagy, 1: 163-170.

Cheong, H., T. Yorimitsu, F. Reggiori, J.E. Legakis, C.-W. Wang, and D.J. Klionsky. 2005. Atg17 regulates the magnitude of the autophagic response. Mol. Biol. Cell, 16: 3438-3453.

Reggiori, F., T. Shintani, U. Nair, and D.J. Klionsky. 2005. Atg9 cycles between mitochondria and the pre-autophagosomal structure in yeasts. Autophagy, 2: 101-109.

Nazarko, T.Y., J. Huang, J.-M. Nicaud, D.J. Klionsky, and A.A. Sibirny. 2005. Trs85 is required for macroautophagy, pexophagy and cytoplasm to vacuole targeting in Yarrowia lipolytica and Saccharomyces cerevisiae . Autophagy, 1: 37-45.

Yorimitsu, T., and D.J. Klionsky. 2005. Atg11 links cargo to the vesicle-forming machinery in the cytoplasm to vacuole targeting pathway. Mol. Biol. Cell, 16: 1593-1605.

Stromhaug, P.E., F. Reggiori, J. Guan, C.-W. Wang and D.J. Klionsky. 2004. Atg21 is a phosphoinositide binding protein required for efficient lipidation and localization of Atg8 during uptake of aminopeptidase I by selective autophagy. Mol. Biol. Cell, 15: 3553-3566.

Shintani, T. and D.J. Klionsky. 2004. Cargo proteins facilitate the formation of transport vesicles in the cytoplasm to vacuole targeting pathway. J. Biol. Chem., 279: 29889-29894.

Reggiori, F., C.-W. Wang, U. Nair, H. Abeliovich and D.J. Klionsky. 2004. Early stages of the secretory pathway, but not endosomes, are required for Cvt vesicle and autophagosome assembly in Saccharomyces cerevisiae. Mol. Biol. Cell, 15: 2189-2204.

Budovskaya, Y.V., J.S. Stephan, F. Reggiori, D.J. Klionsky and P.K. Herman. 2004. The Ras/PKA signaling pathway regulates an early step of the autophagy process in Saccharomyces cerevisiae. J. Biol. Chem., 279: 20663-20671.

Reggiori, F., K.A. Tucker, P.E. Stromhaug and D.J. Klionsky. 2004. The Atg1-Atg13 complex regulates Atg9 and Atg23 retrieval transport from the pre-autophagosomal structure. Dev. Cell, 6: 79-90.

Wang, C.-W., P.E. Stromhaug, E.J. Kauffman, L.S. Weisman and D.J. Klionsky. 2003. Yeast homotypic vacuole fusion requires the Ccz1-Mon1 complex during the tethering/docking stage. J. Cell Biol., 163: 973-985.

Tucker, K.A., F. Reggiori, W.A. Dunn Jr. and D.J. Klionsky. 2003. Atg23 is essential for the cytoplasm to vacuole targeting pathway and efficient autophagy but not pexophagy. J. Biol. Chem., 278: 48455-48452.

Reggiori, F., C.-W. Wang, P.E. Stromhaug, T. Shintani and D.J. Klionsky. 2003. Vps51 is part of the yeast Vps Fifty-three tethering complex essential for retrograde traffic from the early endosome and Cvt vesicle completion. J. Biol. Chem., 278: 5009-5020.

Abeliovich, H., C. Zhang, W.A. Dunn, Jr., K.M. Shokat and D.J. Klionsky. 2003. Chemical genetic analysis of Apg1 reveals a non-kinase role in the induction of autophagy. Mol. Biol. Cell, 14: 477-490.

Shintani, T., W.-P. Huang, P.E. Stromhaug and D.J. Klionsky. 2002. Mechanism of cargo selection in the cytoplasm to vacuole targeting pathway. Dev. Cell, 3: 825-837.

Wang, C.-W., P.E. Stromhaug, J. Shima, and D.J. Klionsky. 2002. The Ccz1-Mon1 protein complex is required for the late step of multiple vacuole delivery pathways. J. Biol. Chem., 277: 47917-47927.

Nice, D.C., III, T.K. Sato, P.E. Stromhaug, S.D. Emr and D.J. Klionsky. 2002. Cooperative binding of the cytoplasm to vacuole targeting pathway proteins, Cvt13 and Cvt20, to phosphatidylinositol 3-phosphate at the pre-autophagosomal structure is required for selective autophagy. J. Biol. Chem., 277: 30198-30207.

Kim, J., W.-P. Huang, P.E. Stromhaug. 2002. Convergence of multiple autophagy and cytoplasm to vacuole targeting components to a perivacuolar membrane compartment prior to de novo vesicle formation. J. Biol. Chem., 277: 763-773.

Guan, J., P.E. Stromhaug, M.D. George, P. Habibzadegah-Tari, A. Bevan, W.A. Dunn Jr. and D.J. Klionsky. 2001. CVT18/GSA12 is required for cytoplasm to vacuole transport, pexophagy and autophagy in Saccharomyces cerevisiae and Pichia pastoris. Mol. Biol. Cell, 12: 3821-3838.

Wang, C.-W., J. Kim, W.-P. Huang, H. Abeliovich, P.E. Stromhaug, W.A. Dunn Jr. and D.J. Klionsky. 2001. Apg2 is a novel protein required for the cytoplasm to vacuole targeting, autophagy, and pexophagy pathways. J. Biol. Chem., 276: 30442-30451.

Scott, S.V., J. Guan, M.U. Hutchins, J. Kim and D.J. Klionsky. 2001. Cvt19 is a receptor for the cytoplasm to vacuole targeting pathway. Mol. Cell, 7: 1131-1141.

Hutchins, M.U. and D.J. Klionsky. 2001. Vacuolar localization of oligomeric α-mannosidase requires the cytoplasm to vacuole targeting and autophagy pathway components in Saccharomyces cerevisiae. J. Biol. Chem., 276: 20491-20498.

Kim, J., Y. Kamada, P.E. Stromhaug, J. Guan, A. Hefner-Gravink, M. Baba, S.V. Scott, Y. Ohsumi, W.A. Dunn Jr. and D.J. Klionsky. 2001. Cvt9/Gsa9 functions in sequestering selective cytosolic cargo destined for the vacuole. J. Cell Biol., 153: 381-396.

Teter, S.A., K.P. Eggerton, S.V. Scott, J. Kim, A.M. Fischer and D.J. Klionsky. 2001. Degradation of lipid vesicles in the yeast vacuole requires function of CVT17, a putative lipase. J. Biol. Chem., 276: 2083-2087.

Kim, J., W.-P. Huang and D.J. Klionsky. 2001. Membrane recruitment of Aut7p in the autophagy and Cvt pathways requires Aut1p, Aut2p and the Apg conjugation complex. J. Cell Biol., 152: 51-64.

Abeliovich, H., W.A. Dunn Jr., J. Kim and D.J. Klionsky. 2000. Dissection of autophagosome biogenesis into distinct nucleation and expansion steps. J. Cell Biol., 151: 1025-1034.

Scott, S.V., D.C. Nice III, J.J. Nau, L.S.Weisman, Y. Kamada, I. Keizer-Gunnink, T. Funakoshi, M. Veenhuis, Y. Ohsumi and D.J. Klionsky. 2000. Apg13p and Vac8p are part of a complex of phosphoproteins that are required for cytoplasm to vacuole targeting. J. Biol. Chem., 275: 25840-25849.

George, M.D., M. Baba, S.V. Scott, N. Mizushima, B.S. Garrison, Y. Ohsumi and D.J. Klionsky. 2000. Apg5p functions in the sequestration step in the cytoplasm to vacuole targeting and macroautophagy pathways. Mol. Bio. Cell., 11: 969-982.

Huang, W.-P., S.V. Scott, J. Kim and D.J. Klionsky. 2000. The itinerary of a vesicle component, Aut7p/Cvt5p, terminates in the yeast vacuole via the autophagy/Cvt pathways. J. Biol. Chem., 275: 5845-5851.

Noda, T., J. Kim, W.-P. Huang, M. Baba, C. Tokunaga, Y. Ohsumi and D.J. Klionsky. 2000. Apg9/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways. J. Cell Biol., 148: 465-480.

Hutchins, M.U., M. Veenhuis and D.J. Klionsky. 1999. Peroxisome degradation in Saccharomyces cerevisiae is dependent on machinery of macroautophagy and the Cvt pathway. J. Cell Sci., 112: 4079-4087.

Kim, J., V.M. Dalton, K.P. Eggerton, S.V. Scott and D.J. Klionsky. 1999. Apg7p/Cvt2p is required for the Cvt, macroautophagy, and peroxisomal degradation pathways. Mol. Biol. Cell, 10: 1337-1351.

Fleckenstein, D., M. Rohde, D.J. Klionsky and M. Rudiger. 1998. Yel013p (Vac8p), an armadillo repeat protein related to plakoglobin and importin a, is associated with the yeast vacuole membrane. J. Cell Sci., 111: 3109-3118.

Mizushima, N., T. Noda, T. Yoshimori, Y. Tanaka, T. Ishii, M.D. George, D.J. Klionsky, M. Ohsumi and Y. Ohsumi. 1998. A protein conjugation system essential for autophagy. Nature, 395: 395-398.

Baba, M., M. Osumi, S.V. Scott, D.J. Klionsky, and Y. Ohsumi. 1997 Two distinct pathways for targeting proteins from the cytoplasm to the vacuole/lysosome. J. Cell Biol., 139: 1687-1695.

Scott, S.V., M. Baba, Y. Ohsumi, and D.J. Klionsky. 1997. Aminopeptidase I is targeted to the vacuole by a nonclassical vesicular mechanism. J. Cell Biol., 138: 37-44.

Kim, J., S.V. Scott, M.N. Oda and D.J. Klionsky. 1997. Transport of a large oligomeric protein by the cytoplasm to vacuole protein targeting pathway. J. Cell Biol., 137:609-618.

Scott, S.V., A. Hefner-Gravink, K.A. Morano, T. Noda, Y. Ohsumi and D.J. Klionsky. 1996. Cytoplasm to vacuole targeting and autophagy employ the same machinery to deliver proteins to the yeast vacuole. Proc. Natl. Acad. Sci. USA., 93: 12304-12308.

Wang, Y.-X., H. Zhao, T.M. Harding, D.S. Gomes de Mesquita, C.L. Woldringh, D.J. Klionsky, A.L. Munn and L.S. Weisman. 1996. Multiple classes of yeast mutants are defective in vacuole partitioning yet target vacuole proteins correctly. Mol. Biol. Cell, 7: 1375-1389.

Harding, T.M., A. Hefner-Gravink, M. Thumm and D.J. Klionsky. 1996. Genetic and phenotypic overlap between autophagy and the cytoplasm to vacuole protein targeting pathway. J. Biol. Chem., 271: 17621-17624.

Oda, M.N., S.V. Scott, A. Hefner-Gravink, A.D. Caffarelli and D.J. Klionsky. 1996. Identification of a cytoplasm to vacuole targeting determinant in aminopeptidase I. J. Cell Biol., 132: 999-1010.

Scott, S.V. and D.J. Klionsky. 1995. In vitro reconstitution of cytoplasm to vacuole protein targeting in yeast. J. Cell Biol., 131: 1727-1735.

Harding, T.M., K.A. Morano, S.V. Scott and D.J. Klionsky. 1995. Isolation and characterization of yeast mutants in the cytoplasm to vacuole protein targeting pathway. J. Cell Biol., 131: 591-602.

Klionsky, D.J., R. Cueva and D.S. Yaver. 1992. Aminopeptidase I of Saccharomyces cerevisiae is localized to the vacuole independent of the secretory pathway. J. Cell Biol., 119: 287-299.

Reviews

Klionsky, D.J. 2009. Crohn's disease, autophagy, and the Paneth cell. New Engl. J. Med. 360: 1785-1786.

Yen, W.-L. and D.J. Klionsky. 2008. How to Live Long and Prosper: Autophagy, Mitochondria, and Aging. Physiol., 23: 248-262.

Geng, J. and D.J. Klionsky. 2008. The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. EMBO Rep. 9: 859-864.

Deretic, V. and D.J. Klionsky. 2008. How cells clean house. Sci. American, 298: 74-81.

Mizushima, N., B. Levine, A.M. Cuervo and D.J. Klionsky. 2008. Autophagy fights disease through cellular self-digestion. Nature, 451: 1069-1075.

Legakis, J.E. and D.J. Klionsky. 2008. Analysis of autophagosome membrane cycling by fluorescence microscopy. In Autophagosome and Phagosome (Deretic, V. ed). Humana, 135-145.

Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, Baba M, Baehrecke EH, Bahr BA, Ballabio A, Bamber BA, Bassham DC, Bergamini E, Bi X, Biard-Piechaczyk M, Blum JS, Bredesen DE, Brodsky JL, Brumell JH, Brunk UT, Bursch W, Camougrand N, Cebollero E, Cecconi F, Chen Y, Chin L-S, Choi A, Chu CT, Chung J, Clark RSB, Clarke PGH, Clarke SG, Clave C, Cleveland JL, Codogno P, Colombo MI, Coto-Montes A, Cregg JM, Cuervo AM, Debnath J, Dennis PB, Dennis PA, Demarchi F, Deretic V, Devenish RJ, Di Sano F, Dice JF, Distelhorst CW, Dinesh-Kumar S, DiFiglia M, Djavaheri-Mergny M, Dorsey FC, Droge W, Dron M, Dunn WAJ, Duszenko M, Eissa NT, Elazar Z, Esclatine A, Eskelinen E-L, Fesus L, Finley K, Fuentes JM, Fueyo J, Fujisaki K, Galliot B, Gao F-B, Gewirtz DA, Gibson SB, Gohla A, Goldberg AL, Gonzalez R, Gonzalez-Estevez C, Gorski S, Gottlieb RA, Haussinger D, He Y-W, Heidenreich K, Hill JA, Hoyer-Hansen M, Hu X, Huang W-P, Iwasaki A, Jaattela M, Jackson WT, Jiang X, Jin S, Johansen T, Jung JU, Kadowaki M, Kang C, Kelekar A, Kessel DH, Kiel JAKW, Kim HP, Kimchi A, Kinsella TJ, Kiselyov K, Kitamoto K, Knecht E, Komatsu M, Kominami E, Kondo S, Kovacs AL, Kroemer G, Kuan C-Y, Kumar R, Kundu M, Landry J, Laporte M, Le W, Lei H-Y, Levine B, Lieberman A, Lim K-L, Lin F-C, Liou W, Liu LF, Lopez-Berestein G, Lopez-Otin C, Lu B, Macleod KF, Malorni W, Martinet W, Matsuoka K, Mautner J, Meijer AJ, Melendez A, Michels P, Miotto G, Mistiaen WP, Mizushima N, Mograbi B, Moore MN, Moreira PI, Moriyasu Y, Motyl T, Munz C, Murphy LO, Naqvi NI, Neufeld TP, Nishino I, Nixon RA, Noda T, Nurnberg B, Ogawa M, Oleinick NL, Olsen LJ, Ozpolat B, Paglin S, Palmer GE, Papassideri IS, Parkes M, Perlmutter DH, Perry G, Piacentini M, Pinkas-Kramarski R, Prescott M, Proikas-Cezanne T, Raben N, Rami A, Reggiori F, Rohrer B, Rubinsztein DC, Ryan KM, Sadoshima J, Sakagami H, Sakai Y, Sandri M, Sasakawa C, Sass M, Schneider C, Seglen PO, Seleverstov O, Settleman J, Shacka JJ, Shapiro IM, Sibirny A, Silva-Zacarin ECM, Simon H-U, Simone C, Simonsen A, Smith MA, Spanel-Borowski K, Srinivas V, Steeves M, Stenmark H, Stromhaug PE, Subauste CS, Sugimoto S, Sulzer D, Suzuki T, Swanson MS, Tabas I, Takeshita F, Talbot NJ, Talloczy Z, Tanaka K, Tanaka K, Tanida I, Taylor GS, Taylor JP, Terman A, Tettamanti G, Thompson CB, Thumm M, Tolkovsky AM, Tooze SA, Truant R, Tumanovska LV, Uchiyama Y, Ueno T, Uzcategui NL, van der Klei IJ, Vaquero EC, Vellai T, Vogel MW, Wang H-G, Webster P, Xi Z, Xiao G, Yahalom J, Yang J-M, Yap GS, Yin X-M, Yoshimori T, Yue Z, Yuzaki M, Zabirnyk O, Zheng X, Zhu X, Deter RL. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4: 151-175.

Klionsky, D.J. 2007. Autophagy: from phenomenology to molecular understanding in less than a decade. Nat. Rev. Mol. Cell Biol., 8: 931-937.

Cao, Y. and D.J. Klionsky. 2007. Physiological functions of Atg6/Beclin 1: a unique autophagy-related protein. Cell Res. 17: 839-849.

Xie, Z. and D.J. Klionsky. 2007. Autophagosome formation: core machinery and adaptations. Nat. Cell Biol., 9: 1102-1109.

Huang, J. and D.J. Klionsky. 2007. Autophagy and Human Disease. Cell Cycle, 6: 1837-1849.

Mijaljica, D., M. Prescott, D.J. Klionsky and R.J. Devenish. 2007. Autophagy and vacuole homeostasis: a case for self-degradation? Autophagy, 3: 417-421.

Yorimitsu, T. and D.J. Klionsky. 2007. Eating the endoplasmic reticulum: Quality control by autophagy. Trends Cell Biol., 17:279-285.

Rubinsztein, D.C., J.E. Gestwicki, L.O. Murphy and D.J. Klionsky. 2007. Potential therapeutic applications of autophagy. Nat. Rev. Drug Disc., 6: 304-312.

Klionsky, D.J., A.M. Cuervo, and P.O. Seglen. 2007. Methods for monitoring autophagy from yeast to human. Autophagy, 3: 181-206.

He, C. and D.J. Klionsky. 2007. Atg9 trafficking in autophagy-related pathways. Autophagy, 3: 271-274.

Yen, W-L. and D.J. Klionsky. 2007. Atg27 is a second transmembrane cycling protein. Autophagy, 3: 254-256.

Mizushima, N. and D.J. Klionsky. 2007. Protein turnover via autophagy: implications for metabolism. Annu. Rev. Nutr., 27: 19-39.

Yorimitsu, T. and D.J. Klionsky. 2007. Endoplasmic reticulum stress: a new pathway to induce autophagy. Autophagy, 3: 160-162.

Yang, Z. and D.J. Klionsky. 2007. Permeases recycle amino acids resulting from autophagy. Autophagy, 3: 149-150.

Klionsky, D.J. 2007. Monitoring autophagy in yeast: The Pho8Ģ60 assay. In Methods in Molecular Biology: Protein Targeting Protocols, 2 nd ed. (M. van der Giezen, ed.) The Humana Press Inc., Totowa, NJ. 390: 363-371.

Monastyrska , I. and D.J. Klionsky. 2006. Autophagy in organelle homeostasis: Peroxisome turnover. Mol. Aspects Med., 27: 483-494.

Legakis, J.E. and D.J. Klionsky. 2006. Overview of autophagy. In Autophagy in Immunity and Infection. A Novel Immune Effector (Deretic, V. ed). Wiley-VCH, Weinheim, pp. 3-17.

Klionsky, D.J. 2006. Good riddance to bad rubbish. Nature, 441: 819-820.

He, C. and D.J. Klionsky. 2006. Autophagy and neurodegeneration. ACS Chem. Biol., 1: 211-213.

Nair, U. and D.J. Klionsky. 2005. Molecular mechanisms and regulation of specific and nonspecific autophagy pathways in yeast. J. Biol. Chem., in press.

Yorimitsu, T., and D.J. Klionsky. 2005. Autophagy: molecular machinery for self-eating. Cell Death Diff., 12: 1542-1552.

Klionsky, D.J. 2005. Autophagy. Current Biology, 15: R282-283.

Klionsky, D.J. 2005. The molecular machinery of autophagy: Unanswered questions. J. Cell Sci., 118: 7-18.

Shintani, T., and D.J. Klionsky. 2004. Autophagy in health and disease: a double-edged sword. Science, 306: 990-995.

Klionsky, D.J. 2004 Regulated self-cannibalism. Nature, 431: 31-32.

Klionsky, D.J. and J. Guan. 2004. Autophagy in fungi and mammals. Encyclopedia of Biological Chemistry, Academic Press/Elsevier Science, 1: 138-144.

Klionsky, D.J. 2004. Autophagy. 2004 McGraw-Hill Yearbook of Science & Technology, New York, NY, McGraw-Hill, pp. 23-26.

Levine, B. and D.J. Klionsky. 2004. Development by self-digestion: Molecular mechanisms and biological functions of autophagy. Dev. Cell, 6: 463-477.

D.J. Klionsky (ed.) 2004. Autophagy. Landes Bioscience, Georgetown, TX.

Stromhaug, P.E. and D.J. Klionsky. 2004. Cytoplasm to vacuole targeting. D.J. Klionsky (ed.) Autophagy. Landes Bioscience, Georgetown, TX, pp. 84-106.

Wang, C.-W. and D.J. Klionsky. 2004. Microautophagy. D.J. Klionsky (ed.) Autophagy. Landes Bioscience, Georgetown, TX, pp. 107-114.

Moriyasu, Y. and D.J. Klionsky. 2003. Autophagy in plants. D.J. Klionsky (ed.) Autophagy. Landes Bioscience, Georgetown, TX, pp. 208-215.

Klionsky, D.J. 2004. Autophagy: An overview. D.J. Klionsky (ed.) Autophagy. Landes Bioscience, Georgetown, TX.

Klionsky, D.J., J.M. Cregg, W.A. Dunn Jr., S.D. Emr, Y. Sakai, I.V. Sandoval, A. Sibirny, S. Subramani, M. Thumm, M. Veenhuis and Y. Ohsumi. 2003. A unified nomenclature for yeast autophagy-related genes. Dev. Cell, 5: 539-545.

Wang, C.-W. and D.J. Klionsky. 2003. The molecular mechanism of autophagy. Mol. Med., 9: 65-76.

Huang, W.-P. and D.J. Klionsky. 2002. Autophagy in yeast: A review of the molecular machinery. Cell Struct. Funct. 27: 409-420.

Khalfan, W.A. and D.J. Klionsky. 2002. Molecular machinery required for autophagy and the cytoplasm to vacuole targeting (Cvt) pathway in S. cerevisiae. Curr. Opin. Cell Biol. 14: 468-475.

Reggiori, F. and D.J. Klionsky. 2002. Autophagy in the eukaryotic cell. Euk. Cell, 1: 11-21.

Abeliovich, H. and D.J. Klionsky. 2001. Autophagy in yeast: Mechanistic insights and physiological function. Micro. Molec. Biol. Rev., 65: 463-479.

Stromhaug, P.E. and D.J. Klionsky. 2001. Approaching the molecular mechanism of autophagy. Traffic, 2: 524-531.

Noda, T., Y. Ohsumi and D.J. Klionsky. 2000. The Yeast Vacuole: A Paradigm for Plant Cell Biologists? In: Vacuolar Compartments, Annual Plant Reviews, Vol. 5, D.G. Robinson, and J.C. Rogers (Eds.), Sheffield Academic Press Ltd., Sheffield, England, pp 1-19.

Klionsky, D.J. and S.D. Emr. 2000. Autophagy as a regulated pathway of cellular degradation. Science, 290: 1717-1721.

Kim, J. and D.J. Klionsky. 2000. Autophagy, cytoplasm-to-vacuole targeting pathway, and pexophagy in yeast and mammalian cells. Annu. Rev. Biochem., 69: 303-342.

Teter, S.A. and D.J. Klionsky. 2000. Transport of proteins to the yeast vacuole: Autophagy, Cytoplasm to vacuole targeting, and role of the vacuole in degradation. Sem. Cell and Dev. Biol., 11: 173-179.

Kim, J., S.V. Scott and D.J. Klionsky. 2000. Alternative protein sorting pathways. Intl. Rev. Cytol., 198: 153-201.

Teter, S.A. and D.J. Klionsky. 1999. New lessons in protein targeting: How to get a folded protein across a membrane. Trends Cell Biol., 11: 428-431.

Klionsky, D.J. and Y. Ohsumi. 1999. Cytoplasm to vacuole protein transport. Annu. Rev. Cell Dev. Biol., 15: 1-32.

Scott, S.V. and D.J. Klionsky. 1998. Delivery of proteins and organelles to the vacuole from the cytoplasm. Curr. Opin. Cell Biol., 10: 523-529.

Klionsky, D.J. 1998. Nonclassical protein sorting to the yeast vacuole. J. Biol. Chem., 273: 10807-10810.

Klionsky, D.J. 1997. Protein transport from the cytoplasm into the vacuole. J. Memb. Biol., 157:105-115.

Scott, S.V. and D.J. Klionsky. 1997. Nonclassical protein sorting. Trends Cell Biol., 7:225-229.

Nelson, N. and D.J. Klionsky. 1996. Vacuolar H+-ATPase-From mammals to yeast and back. Experientia, 52: 1101-1110.

Vacuolar ATPase

Tomashek, J.J., L.A. Graham, M.U. Hutchins, and D.J. Klionsky. 1997. V1-situated stalk subunits of the yeast vacuolar proton-translocating ATPase. J. Biol. Chem., 272: 26787-26793.

Tomashek, J.J., B.S. Garrison, and D.J. Klionsky. 1997. Reconstitution in vitro of the V1 complex from the yeast vacuolar proton-translocating ATPase - Assembly recapitulates mechanism. J. Biol. Chem., 272:16618-16623.

Tomashek, J.J., J.L. Sonnenburg, J.M. Artimovich and D.J. Klionsky. 1996. Resolution of subunit interactions and cytoplasmic sub-complexes of the yeast vacuolar proton-translocating ATPase. J. Biol. Chem., 271: 10397-10404.

Morano, K.A. and D.J. Klionsky. 1994. Differential effects of compartment deacidification on the targeting of membrane and soluble proteins to the vacuole in yeast. J. Cell Science, 107: 2813-2824.

Yaver, D.S., H. Nelson, N. Nelson and D.J. Klionsky. 1993. Vacuolar ATPase mutants accumulate precursor proteins in a pre-vacuolar compartment. J. Biol. Chem., 268: 10564-10572.

Klionsky, D.J., H. Nelson, N. Nelson and D.S. Yaver. 1992. Mutations in the yeast vacuolar ATPase result in the mislocalization of vacuolar proteins. J. Exp. Biol., 172: 83-92.

Klionsky, D.J., H. Nelson, and N. Nelson. 1992. Compartment acidification is required for efficient sorting of proteins to the vacuole in Saccharomyces cerevisiae. J. Biol. Chem., 267: 3416-3422

Trehalase and miscellaneous

Huang, J., F. Reggiori and D.J. Klionsky. 2007. The transmembrane domain of acid trehalase mediates ubiquitin-independent Multivesicular body pathway sorting. Mol. Biol. Cell, 18: 2511-2524.

Matoba, S., K.A. Morano, D.J. Klionsky, K. Kim, and D.M. Ogrydziak. 1997. Dipeptidyl aminopeptidase processing and biosynthesis of alkaline extracellular protease from Yarrowia lipolytica. Microbiology., 143: 3263-3272.

Alizadeh, P. and D.J. Klionsky. 1996. Purification and biochemical characterization of the ATH1 gene product, vacuolar acid trehalase, from Saccharomyces cerevisiae. FEBS Lett., 391: 273-278.

Kim, J., P. Alizadeh, T. Harding, A. Hefner-Gravink and D.J. Klionsky. 1996. Disruption of the yeast ATH1 gene confers better survival after dehydration, freezing and ethanol shock: potential commercial applications. Appl. Environ. Microbiol., 62: 1563-1569.

Destruelle, M., H. Holzer and D.J. Klionsky. 1995. Isolation and characterization of a novel yeast gene, ATH1, that is required for vacuolar acid trehalase activity. Yeast, 11: 1015-1025.

Destruelle, M., H. Holzer and D. J. Klionsky. 1994. Identification and characterization of a novel yeast gene: the YGP1 gene product is a highly glycosylated secreted protein that is synthesized in response to nutrient limitation. Mol. Cell. Biol., 14: 2740-2754.

Teaching/Learning

Sirum, K.L., D. Madigan and D.J. Klionsky. 2009. Enabling a culture of change: A life sciences faculty learning community promotes scientific teaching. J. Coll. Sci. Teach., 38: 24-30.

Klionsky, D.J. 2008. The quiz factor. Cell Biol. Ed., 7: 265-266.

Klionsky, D.J. 2007. From the Future: A Brief History of Pedagogy. Teaching Prof., 21: 5.

Klionsky, D.J. 2007. Malpractice insurance for university professors? Teach. Prof, 21: 6.

Klionsky, D.J. and A. Kumar. 2006. A systems biology approach to learning autophagy. Autophagy, 2: 12-23.

Klionsky, D.J. 2006. Why don't we teach the telephone book? Teach. Prof. 20:7.

Klionsky, D.J. 2004. Talking biology: Teaching outside the textbook, and the lecture. Cell Biol. Ed., 3: 204-211.

Klionsky, D.J. 2003. Why the scientific method matters: A cautionary tale. Teach. Prof., 17: 4

Klionsky, D.J. 2001/2002. Constructing knowledge in the lecture hall. J. Coll. Sci. Teach., 31: 246-251.

Klionsky, D.J., and J.J. Tomashek. 1999. An interactive exercise to learn eukaryotic cell structure and organelle function. Amer. Biol. Teacher, 61: 539-542.

Klionsky, D.J. 1999. Tips for using questions in large classes. The Teaching Professor, 13: 1,3.

Klionsky, D.J. 1998. A cooperative learning approach to teaching introductory biology. J. Coll. Sci. Teach., 27: 334-338.

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