1 |
Kim, B.W., Jung, Y.O., Kim, M.K., Kwon, D.H., Park, S.H., Kim, J.H., Kuk, Y.B., Oh, S.J., Kim, L., Kim, B.H., et al. (2017). ACCORD: an assessment tool to determine the orientation of homodimeric coiledcoils. Sci. Rep. 7, 43318.
DOI
|
2 |
Klionsky, D.J., and Schulman, B.A. (2014). Dynamic regulation of macroautophagy by distinctive ubiquitin-like proteins. Nat. Struct. Mol. Biol. 21, 336-345.
DOI
|
3 |
Klionsky, D.J., Abdelmohsen, K., Abe, A., Abedin, M.J., Abeliovich, H., Acevedo Arozena, A., Adachi, H., Adams, C.M., Adams, P.D., Adeli, K., et al. (2016). Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition). Autophagy 12, 1-222.
DOI
|
4 |
Kwon, D.H., Kim, L., Kim, B.W., Kim, J.H., Roh, K.H., Choi, E.J., and Song, H.K. (2017a). A novel conformation of the LC3-interacting region motif revealed by the structure of a complex between LC3B and RavZ. Biochem. Biophys. Res. Commun. 490, 1093-1099.
DOI
|
5 |
Kwon, D.H., Kim, S., Jung, Y.O., Roh, K.H., Kim, L., Kim, B.W., Hong, S.B., Lee, I.Y., Song, J.H., Lee, W.C., et al. (2017b). The 1:2 complex between RavZ and LC3 reveals a mechanism for deconjugation of LC3 on the phagophore membrane. Autophagy 13, 70-81.
DOI
|
6 |
Levine, B. (2005). Eating oneself and uninvited guests: autophagyrelated pathways in cellular defense. Cell 120, 159-162.
|
7 |
Thurston, T.L., Wandel, M.P., von Muhlinen, N., Foeglein, A., and Randow, F. (2012). Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion. Nature 482, 414-418.
DOI
|
8 |
Wen, X., and Klionsky, D.J. (2016). An overview of macroautophagy in yeast. J. Mol. Biol. 428, 1681-1699.
DOI
|
9 |
Yang, A., Pantoom, S., and Wu, Y.W. (2017). Elucidation of the antiautophagy mechanism of the Legionella effector RavZ using semisynthetic LC3 proteins. Elife 6, e23905.
|
10 |
Yoshii, S.R., and Mizushima, N. (2017). Monitoring and Measuring Autophagy. Int. J. Mol. Sci. 18, 1865.
DOI
|
11 |
Chen, W., Biswas, T., Porter, V.R., Tsodikov, O.V., and Garneau-Tsodikova, S. (2011). Unusual regioversatility of acetyltransferase Eis, a cause of drug resistance in XDR-TB. Proc. Natl. Acad. Sci. USA 108, 9804-9808.
DOI
|
12 |
Zaffagnini, G., and Martens, S. (2016). Mechanisms of selective autophagy. J. Mol. Biol. 428, 1714-1724.
DOI
|
13 |
Zhang, R.G., Scott, D.L., Westbrook, M.L., Nance, S., Spangler, B.D., Shipley, G.G., and Westbrook, E.M. (1995). The three-dimensional crystal structure of cholera toxin. J. Mol. Biol. 251, 563-573.
DOI
|
14 |
Behrends, C., and Fulda, S. (2012). Receptor proteins in selective autophagy. Int. J. Cell Biol. 2012, 673290.
|
15 |
Boyle, K.B., and Randow, F. (2013). The role of 'eat-me' signals and autophagy cargo receptors in innate immunity. Curr. Opin. Microbiol. 16, 339-348.
DOI
|
16 |
Celli, J. (2012). LRSAM1, an E3 Ubiquitin ligase with a sense for bacteria. Cell Host. Microbe 12, 735-736.
DOI
|
17 |
Choy, A., Dancourt, J., Mugo, B., O'Connor, T.J., Isberg, R.R., Melia, T.J., and Roy, C.R. (2012). The Legionella effector RavZ inhibits host autophagy through irreversible Atg8 deconjugation. Science 338, 1072-1076.
DOI
|
18 |
Davis, J., Wang, J., Tropea, J.E., Zhang, D., Dauter, Z., Waugh, D.S., and Wlodawer, A. (2008). Novel fold of VirA, a type III secretion system effector protein from Shigella flexneri. Protein Sci. 17, 2167-2173.
DOI
|
19 |
Levine, B., and Klionsky, D.J. (2017). Autophagy wins the 2016 Nobel Prize in Physiology or Medicine: Breakthroughs in baker's yeast fuel advances in biomedical research. Proc. Natl. Acad. Sci. USA 114, 201-205.
DOI
|
20 |
Fan, E., O'Neal, C.J., Mitchell, D.D., Robien, M.A., Zhang, Z., Pickens, J.C., Tan, X.J., Korotkov, K., Roach, C., Krumm, B., et al. (2004). Structural biology and structure-based inhibitor design of cholera toxin and heat-labile enterotoxin. Int. J. Med. Microbiol. 294, 217-223.
DOI
|
21 |
Levine, B., Mizushima, N., and Virgin, H.W. (2011). Autophagy in immunity and inflammation. Nature 469, 323-335.
DOI
|
22 |
Li, S., Wandel, M.P., Li, F., Liu, Z., He, C., Wu, J., Shi, Y., and Randow, F. (2013). Sterical hindrance promotes selectivity of the autophagy cargo receptor NDP52 for the danger receptor galectin-8 in antibacterial autophagy. Sci. Signal. 6, ra9.
DOI
|
23 |
Liu, X.M., and Du, L.L. (2015). A selective autophagy pathway takes an unconventional route. Autophagy 11, 2381-2382.
DOI
|
24 |
Liu, L., Sakakibara, K., Chen, Q., and Okamoto, K. (2014). Receptormediated mitophagy in yeast and mammalian systems. Cell Res. 24, 787-795.
DOI
|
25 |
Manzanillo, P.S., Ayres, J.S., Watson, R.O., Collins, A.C., Souza, G., Rae, C.S., Schneider, D.S., Nakamura, K., Shiloh, M.U., and Cox, J.S. (2013). The ubiquitin ligase parkin mediates resistance to intracellular pathogens. Nature 501, 512-516.
DOI
|
26 |
Maruyama, T., and Noda, N.N. (2018). Autophagy-regulating protease Atg4: structure, function, regulation and inhibition. J. Antibiot. (Tokyo). 71, 72-78.
DOI
|
27 |
Merritt, E.A., Sarfaty, S., van den Akker, F., L'Hoir, C., Martial, J.A., and Hol, W.G. (1994). Crystal structure of cholera toxin B-pentamer bound to receptor GM1 pentasaccharide. Protein Sci. 3, 166-175.
|
28 |
Mizushima, N. (2011). Autophagy in protein and organelle turnover. Cold Spring Harb. Symp. Quant. Biol. 76, 397-402.
|
29 |
Farre, J.C., and Subramani, S. (2016). Mechanistic insights into selective autophagy pathways: lessons from yeast. Nat. Rev. Mol. Cell Biol. 17, 537-552.
|
30 |
Mizushima, N., Noda, T., Yoshimori, T., Tanaka, Y., Ishii, T., George, M.D., Klionsky, D.J., Ohsumi, M., and Ohsumi, Y. (1998). A protein conjugation system essential for autophagy. Nature 395, 395-398.
DOI
|
31 |
Gangwer, K.A., Mushrush, D.J., Stauff, D.L., Spiller, B., McClain, M.S., Cover, T.L., and Lacy, D.B. (2007). Crystal structure of the Helicobacter pylori vacuolating toxin p55 domain. Proc. Natl. Acad. Sci. USA 104, 16293-16298.
DOI
|
32 |
Germane, K.L., Ohi, R., Goldberg, M.B., and Spiller, B.W. (2008). Structural and functional studies indicate that Shigella VirA is not a protease and does not directly destabilize microtubules. Biochemistry 47, 10241-10243.
DOI
|
33 |
He, H., Dang, Y., Dai, F., Guo, Z., Wu, J., She, X., Pei, Y., Chen, Y., Ling, W., Wu, C., et al. (2003). Post-translational modifications of three members of the human MAP1LC3 family and detection of a novel type of modification for MAP1LC3B. J. Biol. Chem. 278, 29278-29287.
DOI
|
34 |
Heckmann, B.L., Boada-Romero, E., Cunha, L.D., Magne, J., and Green, D.R. (2017). LC3-Associated Phagocytosis and Inflammation. J. Mol. Biol. 429, 3561-3576.
DOI
|
35 |
Neves, D., Job, V., Dortet, L., Cossart, P., and Dessen, A. (2013). Structure of internalin InlK from the human pathogen Listeria monocytogenes. J. Mol. Biol. 425, 4520-4529.
DOI
|
36 |
Holmner, A., Lebens, M., Teneberg, S., Angstrom, J., Okvist, M., and Krengel, U. (2004). Novel binding site identified in a hybrid between cholera toxin and heat-labile enterotoxin: 1.9 crystal structure reveals the details. Structure 12, 1655-1667.
DOI
|
37 |
Hong, S.B., Kim, B.W., Lee, K.E., Kim, S.W., Jeon, H., Kim, J., and Song, H.K. (2011). Insights into noncanonical E1 enzyme activation from the structure of autophagic E1 Atg7 with Atg8. Nat. Struct. Mol. Biol. 18, 1323-1330.
DOI
|
38 |
Hong, S.B., Kim, B.W., Kim, J.H., and Song, H.K. (2012). Structure of the autophagic E2 enzyme Atg10. Acta Crystallogr. D Biol. Crystallogr. 68, 1409-1417.
DOI
|
39 |
Nah, J., Yuan, J., and Jung, Y.K. (2015). Autophagy in neurodegenerative diseases: from mechanism to therapeutic approach. Mol. Cells 38, 381-389.
DOI
|
40 |
Nakatogawa, H., Suzuki, K., Kamada, Y., and Ohsumi, Y. (2009). Dynamics and diversity in autophagy mechanisms: lessons from yeast. Nat. Rev. Mol. Cell Biol. 10, 458-467.
DOI
|
41 |
Ng, A., and Xavier, R.J. (2011). Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity. Autophagy 7, 1082-1084.
DOI
|
42 |
Ng, A.C., Eisenberg, J.M., Heath, R.J., Huett, A., Robinson, C.M., Nau, G.J., and Xavier, R.J. (2011). Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Proc. Natl. Acad. Sci. USA 108 Suppl 1, 4631-4638.
DOI
|
43 |
Noad, J., von der Malsburg, A., Pathe, C., Michel, M.A., Komander, D., and Randow, F. (2017). LUBAC-synthesized linear ubiquitin chains restrict cytosol-invading bacteria by activating autophagy and NF-kappaB. Nat. Microbiol. 2, 17063.
DOI
|
44 |
Ogawa, M., Yoshimori, T., Suzuki, T., Sagara, H., Mizushima, N., and Sasakawa, C. (2005). Escape of intracellular Shigella from autophagy. Science 307, 727-731.
DOI
|
45 |
Pantoom, S., Yang, A., and Wu, Y.W. (2017). Lift and cut: Anti-host autophagy mechanism of Legionella pneumophila. Autophagy 13, 1467-1469.
DOI
|
46 |
Huang, J., and Brumell, J.H. (2014). Bacteria-autophagy interplay: a battle for survival. Nat. Rev. Microbiol. 12, 101-114.
DOI
|
47 |
Perrin, A.J., Jiang, X., Birmingham, C.L., So, N.S., and Brumell, J.H. (2004). Recognition of bacteria in the cytosol of Mammalian cells by the ubiquitin system. Curr. Biol. 14, 806-811.
DOI
|
48 |
Rahighi, S., and Dikic, I. (2012). Selectivity of the ubiquitin-binding modules. FEBS Lett. 586, 2705-2710.
DOI
|
49 |
Horenkamp, F.A., Kauffman, K.J., Kohler, L.J., Sherwood, R.K., Krueger, K.P., Shteyn, V., Roy, C.R., Melia, T.J., and Reinisch, K.M. (2015). The Legionella anti-autophagy effector RavZ targets the autophagosome via PI3P- and curvature-sensing motifs. Dev. Cell 34, 569-576.
DOI
|
50 |
Huang, J., and Klionsky, D.J. (2007). Autophagy and human disease. Cell Cycle 6, 1837-1849.
DOI
|
51 |
Huett, A., Heath, R.J., Begun, J., Sassi, S.O., Baxt, L.A., Vyas, J.M., Goldberg, M.B., and Xavier, R.J. (2012). The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular Salmonella Typhimurium. Cell Host Microbe 12, 778-790.
DOI
|
52 |
Ji, C.H., and Kwon, Y.T. (2017). Crosstalk and Interplay between the Ubiquitin-Proteasome System and Autophagy. Mol. Cells 40, 441-449.
|
53 |
Kim, K.H., An, D.R., Yoon, H.J., Yang, J.K., and Suh, S.W. (2014). Structure of Mycobacterium smegmatis Eis in complex with paromomycin. Acta Crystallogr. F Struct. Biol. Commun. 70, 1173-1179.
|
54 |
Kim, J.H., and Song, H.K. (2015). Swapping of interaction partners with ATG5 for autophagosome maturation. BMB Rep. 48, 129-130.
DOI
|
55 |
Kim, K.H., An, D.R., Song, J., Yoon, J.Y., Kim, H.S., Yoon, H.J., Im, H.N., Kim, J., Kim do, J., Lee, S.J., et al. (2012). Mycobacterium tuberculosis Eis protein initiates suppression of host immune responses by acetylation of DUSP16/MKP-7. Proc. Natl. Acad. Sci. USA 109, 7729-7734.
DOI
|
56 |
Kim, B.W., Hong, S.B., Kim, J.H., Kwon, D.H., and Song, H.K. (2013). Structural basis for recognition of autophagic receptor NDP52 by the sugar receptor galectin-8. Nat. Commun. 4, 1613.
DOI
|
57 |
Shen, Y., Guo, Q., Zhukovskaya, N.L., Drum, C.L., Bohm, A., and Tang, W.J. (2004). Structure of anthrax edema factor-calmodulinadenosine 5'-(alpha,beta-methylene)-triphosphate complex reveals an alternative mode of ATP binding to the catalytic site. Biochem. Biophys. Res. Commun. 317, 309-314.
DOI
|
58 |
Renshaw, P.S., Lightbody, K.L., Veverka, V., Muskett, F.W., Kelly, G., Frenkiel, T.A., Gordon, S.V., Hewinson, R.G., Burke, B., Norman, J., et al. (2005). Structure and function of the complex formed by the tuberculosis virulence factors CFP-10 and ESAT-6. EMBO J. 24, 2491-2498.
DOI
|
59 |
Santelli, E., Bankston, L.A., Leppla, S.H., and Liddington, R.C. (2004). Crystal structure of a complex between anthrax toxin and its host cell receptor. Nature 430, 905-908.
DOI
|
60 |
Satoo, K., Noda, N.N., Kumeta, H., Fujioka, Y., Mizushima, N., Ohsumi, Y., and Inagaki, F. (2009). The structure of Atg4B-LC3 complex reveals the mechanism of LC3 processing and delipidation during autophagy. EMBO J. 28, 1341-1350.
DOI
|
61 |
Tattoli, I., Sorbara, M.T., Philpott, D.J., and Girardin, S.E. (2012). Bacterial autophagy: the trigger, the target and the timing. Autophagy 8, 1848-1850.
DOI
|
62 |
Shin, D.M., Jeon, B.Y., Lee, H.M., Jin, H.S., Yuk, J.M., Song, C.H., Lee, S.H., Lee, Z.W., Cho, S.N., Kim, J.M., et al. (2010). Mycobacterium tuberculosis eis regulates autophagy, inflammation, and cell death through redox-dependent signaling. PLoS Pathog. 6, e1001230.
DOI
|
63 |
Sorbara, M.T., and Girardin, S.E. (2015). Emerging themes in bacterial autophagy. Curr. Opin. Microbiol. 23, 163-170.
DOI
|
64 |
Svenning, S., and Johansen, T. (2013). Selective autophagy. Essays Biochem. 55, 79-92.
DOI
|
65 |
Thurston, T.L., Ryzhakov, G., Bloor, S., von Muhlinen, N., and Randow, F. (2009). The TBK1 adaptor and autophagy receptor NDP52 restricts the proliferation of ubiquitin-coated bacteria. Nat. Immunol. 10, 1215-1221.
DOI
|
66 |
Kim, B.-W., Kwon, D.H., and Song, H.K. (2016). Structure biology of selective autophagy receptors. BMB Rep. 49, 73-80.
DOI
|
67 |
Kim, J.H., Hong, S.B., Lee, J.K., Han, S., Roh, K.H., Lee, K.E., Kim, Y.K., Choi, E.J., and Song, H.K. (2015). Insights into autophagosome maturation revealed by the structures of ATG5 with its interacting partners. Autophagy 11, 75-87.
DOI
|