Quantitative chemical proteomics profiling of de novo protein synthesis during starvation-mediated autophagy

References

• Bauvy C, Meijer AJ, Codogno P. Assaying of autophagic protein degradation. Methods Enzymol 2009; 452:47-61; PMID:19200875; http://dx.doi.org/10.1016/S0076-6879(08)03604-5
   PubMed Web of Science ®Google Scholar
• Levine B, Klionsky DJ. Development by self-digestion: molecular mechanisms and biological functions of autophagy. Dev Cell 2004; 6:463-77; PMID:15068787; http://dx.doi.org/10.1016/S1534-5807(04)00099-1
   PubMed Web of Science ®Google Scholar
• Mizushima N, Komatsu M. Autophagy: renovation of cells and tissues. Cell 2011; 147:728-41; PMID:22078875; http://dx.doi.org/10.1016/j.cell.2011.10.026
   PubMed Web of Science ®Google Scholar
• Shen HM, Mizushima N. At the end of the autophagic road: an emerging understanding of lysosomal functions in autophagy. Trends Biochem Sci 2014; 39:61-71; PMID:24369758; http://dx.doi.org/10.1016/j.tibs.2013.12.001
   PubMed Web of Science ®Google Scholar
• He C, Klionsky DJ. Regulation mechanisms and signaling pathways of autophagy. Annu Rev Genet 2009; 43:67-93; PMID:19653858; http://dx.doi.org/10.1146/annurev-genet-102808-114910
   PubMed Web of Science ®Google Scholar
• Kroemer G, Marino G, Levine B. Autophagy and the integrated stress response. Mol Cell 2010; 40:280-93; PMID:20965422; http://dx.doi.org/10.1016/j.molcel.2010.09.023
   PubMed Web of Science ®Google Scholar
• Chen Y, Klionsky DJ. The regulation of autophagy - unanswered questions. J Cell Sci 2011; 124:161-70; PMID:21187343; http://dx.doi.org/10.1242/jcs.064576
   PubMed Web of Science ®Google Scholar
• Mizushima N, Klionsky DJ. Protein turnover via autophagy: implications for metabolism. Annu Rev Nutr 2007; 27:19-40; PMID:17311494; http://dx.doi.org/10.1146/annurev.nutr.27.061406.093749
   PubMed Web of Science ®Google Scholar
• Wirawan E, Vanden Berghe T, Lippens S, Agostinis P, Vandenabeele P. Autophagy: for better or for worse. Cell Res 2012; 22:43-61; PMID:21912435; http://dx.doi.org/10.1038/cr.2011.152
   PubMed Web of Science ®Google Scholar
• Kuma A, Hatano M, Matsui M, Yamamoto A, Nakaya H, Yoshimori T, Ohsumi Y, Tokuhisa T, Mizushima N. The role of autophagy during the early neonatal starvation period. Nature 2004; 432:1032-6; PMID:15525940; http://dx.doi.org/10.1038/nature03029
   PubMed Web of Science ®Google Scholar
• Lum JJ, DeBerardinis RJ, Thompson CB. Autophagy in metazoans: cell survival in the land of plenty. Nat Rev Mol Cell Biol 2005; 6:439-48; PMID:15928708; http://dx.doi.org/10.1038/nrm1660
   PubMed Web of Science ®Google Scholar
• Mizushima N. The pleiotropic role of autophagy: from protein metabolism to bactericide. Cell Death Differ 2005; 12 (Suppl 2):1535-41; PMID:16247501; http://dx.doi.org/10.1038/sj.cdd.4401728
   PubMed Web of Science ®Google Scholar
• Watanabe-Asano T, Kuma A, Mizushima N. Cycloheximide inhibits starvation-induced autophagy through mTORC1 activation. Biochem Biophys Res Commun 2014; 445:334-9; PMID:24525133; http://dx.doi.org/10.1016/j.bbrc.2014.01.180
   PubMed Web of Science ®Google Scholar
• Desai S, Liu Z, Yao J, Patel N, Chen J, Wu Y, Ahn EE, Fodstad O, Tan M. Heat shock factor 1 (HSF1) controls chemoresistance and autophagy through transcriptional regulation of autophagy-related protein 7 (ATG7). J Biol Chem 2013; 288:9165-76; PMID:23386620; http://dx.doi.org/10.1074/jbc.M112.422071
   PubMed Web of Science ®Google Scholar
• Guerriero JL, Ditsworth D, Zong WX. Non-apoptotic routes to defeat cancer. Oncoimmunology 2012; 1:94-6; PMID:22720222; http://dx.doi.org/10.4161/onci.1.1.17885
   PubMed Web of Science ®Google Scholar
• Sengupta A, Molkentin JD, Yutzey KE. FoxO transcription factors promote autophagy in cardiomyocytes. J Biol Chem 2009; 284:28319-31; PMID:19696026; http://dx.doi.org/10.1074/jbc.M109.024406
   PubMed Web of Science ®Google Scholar
• Jiang L, Sheikh MS, Huang Y. Decision Making by p53: Life versus Death. Mol Cell Pharmacol 2010; 2:69-77; PMID:20514355
   PubMedGoogle Scholar
• Kreuzaler PA, Staniszewska AD, Li W, Omidvar N, Kedjouar B, Turkson J, Poli V, Flavell RA, Clarkson RW, Watson CJ. Stat3 controls lysosomal-mediated cell death in vivo. Nat Cell Biol 2011; 13:303-9; PMID:21336304; http://dx.doi.org/10.1038/ncb2171
   PubMed Web of Science ®Google Scholar
• Martinez-Outschoorn UE, Trimmer C, Lin Z, Whitaker-Menezes D, Chiavarina B, Zhou J, Wang C, Pavlides S, Martinez-Cantarin MP, Capozza F, et al. Autophagy in cancer associated fibroblasts promotes tumor cell survival: Role of hypoxia, HIF1 induction and NFkappaB activation in the tumor stromal microenvironment. Cell Cycle 2010; 9:3515-33; PMID:20855962; http://dx.doi.org/10.4161/cc.9.17.12928
   PubMed Web of Science ®Google Scholar
• Dunlop EA, Tee AR. mTOR and autophagy: a dynamic relationship governed by nutrients and energy. Semin Cell Dev Biol 2014; 36:121-9; PMID:25158238; http://dx.doi.org/10.1016/j.semcdb.2014.08.006
   PubMed Web of Science ®Google Scholar
• Russell RC, Yuan HX, Guan KL. Autophagy regulation by nutrient signaling. Cell Res 2014; 24:42-57; PMID:24343578; http://dx.doi.org/10.1038/cr.2013.166
   PubMed Web of Science ®Google Scholar
• Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM. Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT). Proc Natl Acad Sci U S A 2006; 103:9482-7; PMID:16769897; http://dx.doi.org/10.1073/pnas.0601637103
   PubMed Web of Science ®Google Scholar
• Dieterich DC, Lee JJ, Link AJ, Graumann J, Tirrell DA, Schuman EM. Labeling, detection and identification of newly synthesized proteomes with bioorthogonal non-canonical amino-acid tagging. Nat Protoc 2007; 2:532-40; PMID:17406607; http://dx.doi.org/10.1038/nprot.2007.52
   PubMed Web of Science ®Google Scholar
• Ngo JT, Tirrell DA. Noncanonical amino acids in the interrogation of cellular protein synthesis. Acc Chem Res 2011; 44:677-85; PMID:21815659; http://dx.doi.org/10.1021/ar200144y
   PubMed Web of Science ®Google Scholar
• Kiick KL, Saxon E, Tirrell DA, Bertozzi CR. Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation. Proc Natl Acad Sci U S A 2002; 99:19-24; PMID:11752401; http://dx.doi.org/10.1073/pnas.012583299
   PubMed Web of Science ®Google Scholar
• Tornoe CW, Christensen C, Meldal M. Peptidotriazoles on solid phase: [1,2,3]-triazoles by regiospecific copper(i)-catalyzed 1,3-dipolar cycloadditions of terminal alkynes to azides. J Org Chem 2002; 67:3057-64; PMID:11975567; http://dx.doi.org/10.1021/jo011148j
   PubMed Web of Science ®Google Scholar
• Rostovtsev VV, Green LG, Fokin VV, Sharpless KB. A stepwise huisgen cycloaddition process: copper(I)-catalyzed regioselective “ligation” of azides and terminal alkynes. Angew Chem Int Ed Engl 2002; 41:2596-9; PMID:12203546; http://dx.doi.org/10.1002/1521-3773(20020715)41:14%3c2596::AID-ANIE2596%3e3.0.CO;2-4
   PubMed Web of Science ®Google Scholar
• 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; PMID:24675368; http://dx.doi.org/10.4161/auto.28267
   PubMed Web of Science ®Google Scholar
• Wang J, Tan XF, Nguyen VS, Yang P, Zhou J, Gao M, Li Z, Lim TK, He Y, Ong CS, et al. A quantitative chemical proteomics approach to profile the specific cellular targets of andrographolide, a promising anticancer agent that suppresses tumor metastasis. Mol Cell Proteomics 2014; 13:876-86; PMID:24445406; http://dx.doi.org/10.1074/mcp.M113.029793
   PubMed Web of Science ®Google Scholar
• Wang J, Zhang CJ, Zhang J, He Y, Lee YM, Chen S, Lim TK, Ng S, Shen HM, Lin Q. Mapping sites of aspirin-induced acetylations in live cells by quantitative acid-cleavable activity-based protein profiling (QA-ABPP). Sci Rep 2015; 5:7896; PMID:25600173; http://dx.doi.org/10.1038/srep07896
   PubMed Web of Science ®Google Scholar
• Bhatia VN, Perlman DH, Costello CE, McComb ME. Software tool for researching annotations of proteins: open-source protein annotation software with data visualization. Anal Chem 2009; 81:9819-23; PMID:19839595; http://dx.doi.org/10.1021/ac901335x
   PubMed Web of Science ®Google Scholar
• Galluzzi L, Kepp O, Kroemer G. Mitochondrial dynamics: a strategy for avoiding autophagy. Curr Biol 2011; 21:R478-80; PMID:21683905; http://dx.doi.org/10.1016/j.cub.2011.05.002
   PubMed Web of Science ®Google Scholar
• Scherz-Shouval R, Shvets E, Fass E, Shorer H, Gil L, Elazar Z. Reactive oxygen species are essential for autophagy and specifically regulate the activity of Atg4. EMBO J 2007; 26:1749-60; PMID:17347651; http://dx.doi.org/10.1038/sj.emboj.7601623
   PubMed Web of Science ®Google Scholar
• Gomes LC, Di Benedetto G, Scorrano L. During autophagy mitochondria elongate, are spared from degradation and sustain cell viability. Nat Cell Biol 2011; 13:589-98; PMID:21478857; http://dx.doi.org/10.1038/ncb2220
   PubMed Web of Science ®Google Scholar
• Dengjel J, Hoyer-Hansen M, Nielsen MO, Eisenberg T, Harder LM, Schandorff S, Farkas T, Kirkegaard T, Becker AC, Schroeder S, et al. Identification of autophagosome-associated proteins and regulators by quantitative proteomic analysis and genetic screens. Mol Cell Proteomics 2012; 11:M111 014035; PMID:22311637; http://dx.doi.org/10.1074/mcp.M111.014035
   PubMed Web of Science ®Google Scholar
• Zhao Y, Wang Q, Qiu G, Zhou S, Jing Z, Wang J, Wang W, Cao J, Han K, Cheng Q, et al. RACK1 Promotes Autophagy by Enhancing the Atg14L-Beclin 1-Vps34-Vps15 Complex Formation upon Phosphorylation by AMPK. Cell Rep 2015; 13:1407-17; PMID:26549445; http://dx.doi.org/10.1016/j.celrep.2015.10.011
   PubMed Web of Science ®Google Scholar
• Lapierre LR, Kumsta C, Sandri M, Ballabio A, Hansen M. Transcriptional and epigenetic regulation of autophagy in aging. Autophagy 2015; 11:867-80; PMID:25836756; http://dx.doi.org/10.1080/15548627.2015.1034410
   PubMed Web of Science ®Google Scholar
• Fullgrabe J, Klionsky DJ, Joseph B. The return of the nucleus: transcriptional and epigenetic control of autophagy. Nat Rev Mol Cell Biol 2014; 15:65-74; PMID:24326622; http://dx.doi.org/10.1038/nrm3716
   PubMed Web of Science ®Google Scholar
• Alvarez-Castelao B, Ruiz-Rivas C, Castano JG. A critical appraisal of quantitative studies of protein degradation in the framework of cellular proteostasis. Biochem Res Int 2012; 2012:823597; PMID:23119163; http://dx.doi.org/10.1155/2012/823597
   PubMedGoogle Scholar
• Yewdell JW, Lacsina JR, Rechsteiner MC, Nicchitta CV. Out with the old, in with the new? Comparing methods for measuring protein degradation. Cell Biol Int 2011; 35:457-62; PMID:21476986; http://dx.doi.org/10.1042/CBI20110055
   PubMed Web of Science ®Google Scholar
• de Godoy LM, Olsen JV, de Souza GA, Li G, Mortensen P, Mann M. Status of complete proteome analysis by mass spectrometry: SILAC labeled yeast as a model system. Genome Biol 2006; 7:R50; PMID:16784548
   PubMed Web of Science ®Google Scholar
• Eichelbaum K, Winter M, Berriel Diaz M, Herzig S, Krijgsveld J. Selective enrichment of newly synthesized proteins for quantitative secretome analysis. Nat Biotechnol 2012; 30:984-90; PMID:23000932; http://dx.doi.org/10.1038/nbt.2356
   PubMed Web of Science ®Google Scholar
• Levine B, Yuan J. Autophagy in cell death: an innocent convict? J Clin Invest 2005; 115:2679-88; PMID:16200202; http://dx.doi.org/10.1172/JCI26390
   PubMed Web of Science ®Google Scholar
• Levine B, Mizushima N, Virgin HW. Autophagy in immunity and inflammation. Nature 2011; 469:323-35; PMID:21248839; http://dx.doi.org/10.1038/nature09782
   PubMed Web of Science ®Google Scholar
• Kristensen AR, Schandorff S, Hoyer-Hansen M, Nielsen MO, Jaattela M, Dengjel J, Andersen JS. Ordered organelle degradation during starvation-induced autophagy. Mol Cell Proteomics 2008; 7:2419-28; PMID:18687634; http://dx.doi.org/10.1074/mcp.M800184-MCP200
   PubMed Web of Science ®Google Scholar
• Neckelmann N, Warner CK, Chung A, Kudoh J, Minoshima S, Fukuyama R, Maekawa M, Shimizu Y, Shimizu N, Liu JD, et al. The human ATP synthase beta subunit gene: sequence analysis, chromosome assignment, and differential expression. Genomics 1989; 5:829-43; PMID:2687158; http://dx.doi.org/10.1016/0888-7543(89)90125-0
   PubMed Web of Science ®Google Scholar
• Davies KM, Anselmi C, Wittig I, Faraldo-Gomez JD, Kuhlbrandt W. Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae. Proc Natl Acad Sci U S A 2012; 109:13602-7; PMID:22864911; http://dx.doi.org/10.1073/pnas.1204593109
   PubMed Web of Science ®Google Scholar
• Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, et al. Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents. Mol Cell Proteomics 2004; 3:1154-69; PMID:15385600; http://dx.doi.org/10.1074/mcp.M400129-MCP200
   PubMed Web of Science ®Google Scholar
• Wang J, Zhang CJ, Chia WN, Loh CC, Li Z, Lee YM, He Y, Yuan LX, Lim TK, Liu M, et al. Haem-activated promiscuous targeting of artemisinin in Plasmodium falciparum. Nat Commun 2015; 6:10111; PMID:26694030; http://dx.doi.org/10.1038/ncomms10111
   PubMed Web of Science ®Google Scholar
• Tan HT, Tan S, Lin Q, Lim TK, Hew CL, Chung MC. Quantitative and temporal proteome analysis of butyrate-treated colorectal cancer cells. Mol Cell Proteomics 2008; 7:1174-85; PMID:18344232; http://dx.doi.org/10.1074/mcp.M700483-MCP200
   PubMed Web of Science ®Google Scholar
• Higuchi S, Lin Q, Wang J, Lim TK, Joshi SB, Anand GS, Chung MC, Sheetz MP, Fujita H. Heart extracellular matrix supports cardiomyocyte differentiation of mouse embryonic stem cells. J Biosci Bioeng 2013; 115:320-5; PMID:23168383; http://dx.doi.org/10.1016/j.jbiosc.2012.10.004
   PubMed Web of Science ®Google Scholar
• Wang J, Zhang J, Zhang CJ, Wong YK, Lim TK, Hua ZC, Liu B, Tannenbaum SR, Shen HM, Lin Q. In situ Proteomic Profiling of Curcumin Targets in HCT116 Colon Cancer Cell Line. Sci Rep 2016; 6:22146; PMID:26915414; http://dx.doi.org/10.1038/srep22146
   PubMed Web of Science ®Google Scholar