메뉴 건너뛰기




Volumn 14, Issue 10, 2016, Pages 2426-2439

Global Analysis of Cellular Protein Flux Quantifies the Selectivity of Basal Autophagy

Author keywords

[No Author keywords available]

Indexed keywords

CELL PROTEIN; CHAPERONIN CONTAINING TCP1; PROTEASOME; AUTOPHAGY RELATED PROTEIN 5; AUTOPHAGY RELATED PROTEIN 7; CARBON; CHAPERONIN; P62 PROTEIN, HUMAN; PEPTIDE; PROTEIN; RIBOSOME PROTEIN; RNA BINDING PROTEIN; RPS11 PROTEIN, HUMAN; TRYPSIN;

EID: 84960391342     PISSN: None     EISSN: 22111247     Source Type: Journal    
DOI: 10.1016/j.celrep.2016.02.040     Document Type: Article
Times cited : (53)

References (61)
  • 1
    • 84927130414 scopus 로고    scopus 로고
    • Surfactant-aided precipitation/on-pellet-digestion (SOD) procedure provides robust and rapid sample preparation for reproducible, accurate and sensitive LC/MS quantification of therapeutic protein in plasma and tissues
    • An B., Zhang M., Johnson R.W., Qu J. Surfactant-aided precipitation/on-pellet-digestion (SOD) procedure provides robust and rapid sample preparation for reproducible, accurate and sensitive LC/MS quantification of therapeutic protein in plasma and tissues. Anal. Chem. 2015, 87:4023-4029.
    • (2015) Anal. Chem. , vol.87 , pp. 4023-4029
    • An, B.1    Zhang, M.2    Johnson, R.W.3    Qu, J.4
  • 4
    • 50549185027 scopus 로고
    • Total carbon turnover measured by feeding a uniformly labeled diet
    • Buchanan D.L. Total carbon turnover measured by feeding a uniformly labeled diet. Arch. Biochem. Biophys. 1961, 94:500-511.
    • (1961) Arch. Biochem. Biophys. , vol.94 , pp. 500-511
    • Buchanan, D.L.1
  • 5
    • 82755184981 scopus 로고    scopus 로고
    • Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover
    • Cambridge S.B., Gnad F., Nguyen C., Bermejo J.L., Krüger M., Mann M. Systems-wide proteomic analysis in mammalian cells reveals conserved, functional protein turnover. J. Proteome Res. 2011, 10:5275-5284.
    • (2011) J. Proteome Res. , vol.10 , pp. 5275-5284
    • Cambridge, S.B.1    Gnad, F.2    Nguyen, C.3    Bermejo, J.L.4    Krüger, M.5    Mann, M.6
  • 6
    • 11244309014 scopus 로고    scopus 로고
    • Proteolysis: from the lysosome to ubiquitin and the proteasome
    • Ciechanover A. Proteolysis: from the lysosome to ubiquitin and the proteasome. Nat. Rev. Mol. Cell Biol. 2005, 6:79-87.
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 79-87
    • Ciechanover, A.1
  • 8
    • 84870676972 scopus 로고    scopus 로고
    • Proteome dynamics: revisiting turnover with a global perspective
    • Claydon A.J., Beynon R. Proteome dynamics: revisiting turnover with a global perspective. Mol. Cell. Proteomics 2012, 11:1551-1565.
    • (2012) Mol. Cell. Proteomics , vol.11 , pp. 1551-1565
    • Claydon, A.J.1    Beynon, R.2
  • 9
    • 0029664461 scopus 로고    scopus 로고
    • Requirement of p27Kip1 for restriction point control of the fibroblast cell cycle
    • Coats S., Flanagan W.M., Nourse J., Roberts J.M. Requirement of p27Kip1 for restriction point control of the fibroblast cell cycle. Science 1996, 272:877-880.
    • (1996) Science , vol.272 , pp. 877-880
    • Coats, S.1    Flanagan, W.M.2    Nourse, J.3    Roberts, J.M.4
  • 11
    • 0030016595 scopus 로고    scopus 로고
    • Structure and functions of the 20S and 26S proteasomes
    • Coux O., Tanaka K., Goldberg A.L. Structure and functions of the 20S and 26S proteasomes. Annu. Rev. Biochem. 1996, 65:801-847.
    • (1996) Annu. Rev. Biochem. , vol.65 , pp. 801-847
    • Coux, O.1    Tanaka, K.2    Goldberg, A.L.3
  • 15
    • 67049119810 scopus 로고    scopus 로고
    • A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome
    • Duan X., Young R., Straubinger R.M., Page B., Cao J., Wang H., Yu H., Canty J.M., Qu J. A straightforward and highly efficient precipitation/on-pellet digestion procedure coupled with a long gradient nano-LC separation and Orbitrap mass spectrometry for label-free expression profiling of the swine heart mitochondrial proteome. J. Proteome Res. 2009, 8:2838-2850.
    • (2009) J. Proteome Res. , vol.8 , pp. 2838-2850
    • Duan, X.1    Young, R.2    Straubinger, R.M.3    Page, B.4    Cao, J.5    Wang, H.6    Yu, H.7    Canty, J.M.8    Qu, J.9
  • 16
    • 60849139395 scopus 로고    scopus 로고
    • GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists
    • Eden E., Navon R., Steinfeld I., Lipson D., Yakhini Z. GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 2009, 10:48.
    • (2009) BMC Bioinformatics , vol.10 , pp. 48
    • Eden, E.1    Navon, R.2    Steinfeld, I.3    Lipson, D.4    Yakhini, Z.5
  • 19
    • 0343875425 scopus 로고
    • A metabolic inhomogeneity of glycine in vivo. I. Experimental determination
    • Garfinkel D., Lajtha A. A metabolic inhomogeneity of glycine in vivo. I. Experimental determination. J. Biol. Chem. 1963, 238:2429-2434.
    • (1963) J. Biol. Chem. , vol.238 , pp. 2429-2434
    • Garfinkel, D.1    Lajtha, A.2
  • 20
    • 0016908233 scopus 로고
    • Intracellular protein degradation in mammalian and bacterial cells: Part 2
    • Goldberg A.L., St John A.C. Intracellular protein degradation in mammalian and bacterial cells: Part 2. Annu. Rev. Biochem. 1976, 45:747-803.
    • (1976) Annu. Rev. Biochem. , vol.45 , pp. 747-803
    • Goldberg, A.L.1    St John, A.C.2
  • 21
    • 83055163797 scopus 로고    scopus 로고
    • A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling
    • Guan S., Price J.C., Prusiner S.B., Ghaemmaghami S., Burlingame A.L. A data processing pipeline for mammalian proteome dynamics studies using stable isotope metabolic labeling. Mol. Cell. Proteomics 2011, 10:010728.
    • (2011) Mol. Cell. Proteomics , vol.10 , pp. 010728
    • Guan, S.1    Price, J.C.2    Prusiner, S.B.3    Ghaemmaghami, S.4    Burlingame, A.L.5
  • 23
    • 0026448766 scopus 로고
    • Mass isotopomer distribution analysis: a technique for measuring biosynthesis and turnover of polymers
    • Hellerstein M.K., Neese R.A. Mass isotopomer distribution analysis: a technique for measuring biosynthesis and turnover of polymers. Am. J. Physiol. 1992, 263:E988-E1001.
    • (1992) Am. J. Physiol. , vol.263 , pp. E988-E1001
    • Hellerstein, M.K.1    Neese, R.A.2
  • 24
    • 74249095519 scopus 로고    scopus 로고
    • CRISPR/Cas, the immune system of bacteria and archaea
    • Horvath P., Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010, 327:167-170.
    • (2010) Science , vol.327 , pp. 167-170
    • Horvath, P.1    Barrangou, R.2
  • 27
    • 84876916040 scopus 로고    scopus 로고
    • Structural biology of the proteasome
    • Kish-Trier E., Hill C.P. Structural biology of the proteasome. Annu. Rev. Biophys. 2013, 42:29-49.
    • (2013) Annu. Rev. Biophys. , vol.42 , pp. 29-49
    • Kish-Trier, E.1    Hill, C.P.2
  • 28
    • 0034537290 scopus 로고    scopus 로고
    • Autophagy as a regulated pathway of cellular degradation
    • Klionsky D.J., Emr S.D. Autophagy as a regulated pathway of cellular degradation. Science 2000, 290:1717-1721.
    • (2000) Science , vol.290 , pp. 1717-1721
    • Klionsky, D.J.1    Emr, S.D.2
  • 30
    • 60549093730 scopus 로고    scopus 로고
    • Autophagy inhibition compromises degradation of ubiquitin-proteasome pathway substrates
    • Korolchuk V.I., Mansilla A., Menzies F.M., Rubinsztein D.C. Autophagy inhibition compromises degradation of ubiquitin-proteasome pathway substrates. Mol. Cell 2009, 33:517-527.
    • (2009) Mol. Cell , vol.33 , pp. 517-527
    • Korolchuk, V.I.1    Mansilla, A.2    Menzies, F.M.3    Rubinsztein, D.C.4
  • 31
    • 43049138051 scopus 로고    scopus 로고
    • Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease
    • Kraft C., Deplazes A., Sohrmann M., Peter M. Mature ribosomes are selectively degraded upon starvation by an autophagy pathway requiring the Ubp3p/Bre5p ubiquitin protease. Nat. Cell Biol. 2008, 10:602-610.
    • (2008) Nat. Cell Biol. , vol.10 , pp. 602-610
    • Kraft, C.1    Deplazes, A.2    Sohrmann, M.3    Peter, M.4
  • 34
    • 0030941458 scopus 로고    scopus 로고
    • P53, the cellular gatekeeper for growth and division
    • Levine A.J. p53, the cellular gatekeeper for growth and division. Cell 1997, 88:323-331.
    • (1997) Cell , vol.88 , pp. 323-331
    • Levine, A.J.1
  • 35
    • 84899746695 scopus 로고    scopus 로고
    • Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy
    • Mancias J.D., Wang X., Gygi S.P., Harper J.W., Kimmelman A.C. Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy. Nature 2014, 509:105-109.
    • (2014) Nature , vol.509 , pp. 105-109
    • Mancias, J.D.1    Wang, X.2    Gygi, S.P.3    Harper, J.W.4    Kimmelman, A.C.5
  • 36
    • 84937574462 scopus 로고    scopus 로고
    • Autophagic degradation of the 26S proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis
    • Marshall R.S., Li F., Gemperline D.C., Book A.J., Vierstra R.D. Autophagic degradation of the 26S proteasome is mediated by the dual ATG8/ubiquitin receptor RPN10 in Arabidopsis. Mol. Cell 2015, 58:1053-1066.
    • (2015) Mol. Cell , vol.58 , pp. 1053-1066
    • Marshall, R.S.1    Li, F.2    Gemperline, D.C.3    Book, A.J.4    Vierstra, R.D.5
  • 37
    • 84907994253 scopus 로고    scopus 로고
    • Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity
    • Mathew R., Khor S., Hackett S.R., Rabinowitz J.D., Perlman D.H., White E. Functional role of autophagy-mediated proteome remodeling in cell survival signaling and innate immunity. Mol. Cell 2014, 55:916-930.
    • (2014) Mol. Cell , vol.55 , pp. 916-930
    • Mathew, R.1    Khor, S.2    Hackett, S.R.3    Rabinowitz, J.D.4    Perlman, D.H.5    White, E.6
  • 38
    • 36249025723 scopus 로고    scopus 로고
    • Autophagy: process and function
    • Mizushima N. Autophagy: process and function. Genes Dev. 2007, 21:2861-2873.
    • (2007) Genes Dev. , vol.21 , pp. 2861-2873
    • Mizushima, N.1
  • 40
    • 81055144784 scopus 로고    scopus 로고
    • Autophagy: renovation of cells and tissues
    • Mizushima N., Komatsu M. Autophagy: renovation of cells and tissues. Cell 2011, 147:728-741.
    • (2011) Cell , vol.147 , pp. 728-741
    • Mizushima, N.1    Komatsu, M.2
  • 42
    • 34447099450 scopus 로고    scopus 로고
    • Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion
    • Nakatogawa H., Ichimura Y., Ohsumi Y. Atg8, a ubiquitin-like protein required for autophagosome formation, mediates membrane tethering and hemifusion. Cell 2007, 130:165-178.
    • (2007) Cell , vol.130 , pp. 165-178
    • Nakatogawa, H.1    Ichimura, Y.2    Ohsumi, Y.3
  • 43
    • 56449094841 scopus 로고    scopus 로고
    • Autophagy and the ubiquitin-proteasome system: collaborators in neuroprotection
    • Nedelsky N.B., Todd P.K., Taylor J.P. Autophagy and the ubiquitin-proteasome system: collaborators in neuroprotection. Biochim. Biophys. Acta 2008, 1782:691-699.
    • (2008) Biochim. Biophys. Acta , vol.1782 , pp. 691-699
    • Nedelsky, N.B.1    Todd, P.K.2    Taylor, J.P.3
  • 44
    • 84882254367 scopus 로고    scopus 로고
    • The role of autophagy in neurodegenerative disease
    • Nixon R.A. The role of autophagy in neurodegenerative disease. Nat. Med. 2013, 19:983-997.
    • (2013) Nat. Med. , vol.19 , pp. 983-997
    • Nixon, R.A.1
  • 45
    • 0036583926 scopus 로고    scopus 로고
    • Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
    • Ong S.E., Blagoev B., Kratchmarova I., Kristensen D.B., Steen H., Pandey A., Mann M. Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Mol. Cell. Proteomics 2002, 1:376-386.
    • (2002) Mol. Cell. Proteomics , vol.1 , pp. 376-386
    • Ong, S.E.1    Blagoev, B.2    Kratchmarova, I.3    Kristensen, D.B.4    Steen, H.5    Pandey, A.6    Mann, M.7
  • 46
    • 84896265496 scopus 로고    scopus 로고
    • Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy
    • Ossareh-Nazari B., Niño C.A., Bengtson M.H., Lee J.W., Joazeiro C.A., Dargemont C. Ubiquitylation by the Ltn1 E3 ligase protects 60S ribosomes from starvation-induced selective autophagy. J. Cell Biol. 2014, 204:909-917.
    • (2014) J. Cell Biol. , vol.204 , pp. 909-917
    • Ossareh-Nazari, B.1    Niño, C.A.2    Bengtson, M.H.3    Lee, J.W.4    Joazeiro, C.A.5    Dargemont, C.6
  • 47
  • 50
    • 84892859905 scopus 로고    scopus 로고
    • Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy
    • Rogov V., Dötsch V., Johansen T., Kirkin V. Interactions between autophagy receptors and ubiquitin-like proteins form the molecular basis for selective autophagy. Mol. Cell 2014, 53:167-178.
    • (2014) Mol. Cell , vol.53 , pp. 167-178
    • Rogov, V.1    Dötsch, V.2    Johansen, T.3    Kirkin, V.4
  • 51
    • 0016205753 scopus 로고
    • Turnover of myelin and other structural proteins in the developing rat brain
    • Sabri M.I., Bone A.H., Davison A.N. Turnover of myelin and other structural proteins in the developing rat brain. Biochem. J. 1974, 142:499-507.
    • (1974) Biochem. J. , vol.142 , pp. 499-507
    • Sabri, M.I.1    Bone, A.H.2    Davison, A.N.3
  • 52
    • 84905262730 scopus 로고    scopus 로고
    • Improved vectors and genome-wide libraries for CRISPR screening
    • Sanjana N.E., Shalem O., Zhang F. Improved vectors and genome-wide libraries for CRISPR screening. Nat. Methods 2014, 11:783-784.
    • (2014) Nat. Methods , vol.11 , pp. 783-784
    • Sanjana, N.E.1    Shalem, O.2    Zhang, F.3
  • 54
    • 79955631150 scopus 로고    scopus 로고
    • Autophagy in the cellular energetic balance
    • Singh R., Cuervo A.M. Autophagy in the cellular energetic balance. Cell Metab. 2011, 13:495-504.
    • (2011) Cell Metab. , vol.13 , pp. 495-504
    • Singh, R.1    Cuervo, A.M.2
  • 55
    • 79960610118 scopus 로고    scopus 로고
    • REVIGO summarizes and visualizes long lists of gene ontology terms
    • Supek F., Bošnjak M., Škunca N., Šmuc T. REVIGO summarizes and visualizes long lists of gene ontology terms. PLoS ONE 2011, 6:e21800.
    • (2011) PLoS ONE , vol.6 , pp. e21800
    • Supek, F.1    Bošnjak, M.2    Škunca, N.3    Šmuc, T.4
  • 56
    • 0035503594 scopus 로고    scopus 로고
    • The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation
    • Suzuki K., Kirisako T., Kamada Y., Mizushima N., Noda T., Ohsumi Y. The pre-autophagosomal structure organized by concerted functions of APG genes is essential for autophagosome formation. EMBO J. 2001, 20:5971-5981.
    • (2001) EMBO J. , vol.20 , pp. 5971-5981
    • Suzuki, K.1    Kirisako, T.2    Kamada, Y.3    Mizushima, N.4    Noda, T.5    Ohsumi, Y.6
  • 58
    • 50849129599 scopus 로고    scopus 로고
    • Autophagy is activated, but is not required for the G0 function of BCL-2 or BCL-xL
    • Valentin M., Yang E. Autophagy is activated, but is not required for the G0 function of BCL-2 or BCL-xL. Cell Cycle 2008, 7:2762-2768.
    • (2008) Cell Cycle , vol.7 , pp. 2762-2768
    • Valentin, M.1    Yang, E.2
  • 59
    • 0032567967 scopus 로고    scopus 로고
    • Reconstitution of telomerase activity in normal human cells leads to elongation of telomeres and extended replicative life span
    • Vaziri H., Benchimol S. Reconstitution of telomerase activity in normal human cells leads to elongation of telomeres and extended replicative life span. Curr. Biol. 1998, 8:279-282.
    • (1998) Curr. Biol. , vol.8 , pp. 279-282
    • Vaziri, H.1    Benchimol, S.2
  • 60
    • 69249086611 scopus 로고    scopus 로고
    • Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches
    • Voskarides K., Deltas C. Screening for mutations in kidney-related genes using SURVEYOR nuclease for cleavage at heteroduplex mismatches. J. Mol. Diagn. 2009, 11:311-318.
    • (2009) J. Mol. Diagn. , vol.11 , pp. 311-318
    • Voskarides, K.1    Deltas, C.2
  • 61


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.