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Volumn 15, Issue 3, 2016, Pages 1103-1113

Site-Specific Identification of Lysine Acetylation Stoichiometries in Mammalian Cells

Author keywords

lysine acetylation; quantitative proteomics; stoichiometry

Indexed keywords

BUTYRIC ACID; ESTER; HISTONE H3; HISTONE H4; LYSINE; PROTEOME; STABLE ISOTOPE; SYNTHETIC PEPTIDE; HISTONE;

EID: 84960375649     PISSN: 15353893     EISSN: 15353907     Source Type: Journal    
DOI: 10.1021/acs.jproteome.5b01097     Document Type: Article
Times cited : (35)

References (55)
  • 1
    • 28044433451 scopus 로고    scopus 로고
    • Protein posttranslational modifications: The chemistry of proteome diversifications
    • Walsh, C. T.; Garneau-Tsodikova, S.; Gatto, G. J., Jr. Protein posttranslational modifications: the chemistry of proteome diversifications Angew. Chem., Int. Ed. 2005, 44 (45) 7342-72 10.1002/anie.200501023
    • (2005) Angew. Chem., Int. Ed. , vol.44 , Issue.45 , pp. 7342-7372
    • Walsh, C.T.1    Garneau-Tsodikova, S.2    Gatto, G.J.3
  • 2
    • 0014430407 scopus 로고
    • Chemical studies of histone acetylation. The distribution of epsilon-N-acetyllysine in calf thymus histones
    • Vidali, G.; Gershey, E. L.; Allfrey, V. G. Chemical studies of histone acetylation. The distribution of epsilon-N-acetyllysine in calf thymus histones J. Biol. Chem. 1968, 243 (24) 6361-6
    • (1968) J. Biol. Chem. , vol.243 , Issue.24 , pp. 6361-6366
    • Vidali, G.1    Gershey, E.L.2    Allfrey, V.G.3
  • 3
    • 0030797585 scopus 로고    scopus 로고
    • Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain
    • Gu, W.; Roeder, R. G. Activation of p53 sequence-specific DNA binding by acetylation of the p53 C-terminal domain Cell 1997, 90 (4) 595-606 10.1016/S0092-8674(00)80521-8
    • (1997) Cell , vol.90 , Issue.4 , pp. 595-606
    • Gu, W.1    Roeder, R.G.2
  • 5
    • 35648935529 scopus 로고    scopus 로고
    • N-lysine propionylation controls the activity of propionyl-CoA synthetase
    • Garrity, J.; Gardner, J. G.; Hawse, W.; Wolberger, C.; Escalante-Semerena, J. C. N-lysine propionylation controls the activity of propionyl-CoA synthetase J. Biol. Chem. 2007, 282 (41) 30239-45 10.1074/jbc.M704409200
    • (2007) J. Biol. Chem. , vol.282 , Issue.41 , pp. 30239-30245
    • Garrity, J.1    Gardner, J.G.2    Hawse, W.3    Wolberger, C.4    Escalante-Semerena, J.C.5
  • 6
    • 78650516004 scopus 로고    scopus 로고
    • Identification of lysine succinylation as a new post-translational modification
    • Zhang, Z.; Tan, M.; Xie, Z.; Dai, L.; Chen, Y.; Zhao, Y. Identification of lysine succinylation as a new post-translational modification Nat. Chem. Biol. 2011, 7 (1) 58-63 10.1038/nchembio.495
    • (2011) Nat. Chem. Biol. , vol.7 , Issue.1 , pp. 58-63
    • Zhang, Z.1    Tan, M.2    Xie, Z.3    Dai, L.4    Chen, Y.5    Zhao, Y.6
  • 8
    • 84925832609 scopus 로고    scopus 로고
    • Quantitative proteomic analysis of histone modifications
    • Huang, H.; Lin, S.; Garcia, B. A.; Zhao, Y. Quantitative proteomic analysis of histone modifications Chem. Rev. 2015, 115 (6) 2376-418 10.1021/cr500491u
    • (2015) Chem. Rev. , vol.115 , Issue.6 , pp. 2376-2418
    • Huang, H.1    Lin, S.2    Garcia, B.A.3    Zhao, Y.4
  • 9
    • 84939203943 scopus 로고    scopus 로고
    • Metabolic regulation by lysine malonylation, succinylation and glutarylation
    • Hirschey, M. D.; Zhao, Y. Metabolic regulation by lysine malonylation, succinylation and glutarylation Mol. Cell. Proteomics 2015, 14, 2308-15 10.1074/mcp.R114.046664
    • (2015) Mol. Cell. Proteomics , vol.14 , pp. 2308-2315
    • Hirschey, M.D.1    Zhao, Y.2
  • 10
    • 0035839136 scopus 로고    scopus 로고
    • Translating the histone code
    • Jenuwein, T.; Allis, C. D. Translating the histone code Science 2001, 293 (5532) 1074-80 10.1126/science.1063127
    • (2001) Science , vol.293 , Issue.5532 , pp. 1074-1080
    • Jenuwein, T.1    Allis, C.D.2
  • 13
    • 84867594869 scopus 로고    scopus 로고
    • Mitochondrial protein acetylation regulates metabolism
    • Anderson, K. A.; Hirschey, M. D. Mitochondrial protein acetylation regulates metabolism Essays Biochem. 2012, 52, 23-35 10.1042/bse0520023
    • (2012) Essays Biochem. , vol.52 , pp. 23-35
    • Anderson, K.A.1    Hirschey, M.D.2
  • 14
    • 0032030770 scopus 로고    scopus 로고
    • Histone acetylation and transcriptional regulatory mechanisms
    • Struhl, K. Histone acetylation and transcriptional regulatory mechanisms Genes Dev. 1998, 12 (5) 599-606 10.1101/gad.12.5.599
    • (1998) Genes Dev. , vol.12 , Issue.5 , pp. 599-606
    • Struhl, K.1
  • 15
    • 34547890019 scopus 로고    scopus 로고
    • Functions of site-specific histone acetylation and deacetylation
    • Shahbazian, M. D.; Grunstein, M. Functions of site-specific histone acetylation and deacetylation Annu. Rev. Biochem. 2007, 76, 75-100 10.1146/annurev.biochem.76.052705.162114
    • (2007) Annu. Rev. Biochem. , vol.76 , pp. 75-100
    • Shahbazian, M.D.1    Grunstein, M.2
  • 16
    • 22444448143 scopus 로고    scopus 로고
    • A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response
    • Masumoto, H.; Hawke, D.; Kobayashi, R.; Verreault, A. A role for cell-cycle-regulated histone H3 lysine 56 acetylation in the DNA damage response Nature 2005, 436 (7048) 294-8 10.1038/nature03714
    • (2005) Nature , vol.436 , Issue.7048 , pp. 294-298
    • Masumoto, H.1    Hawke, D.2    Kobayashi, R.3    Verreault, A.4
  • 17
    • 84904872156 scopus 로고    scopus 로고
    • The growing landscape of lysine acetylation links metabolism and cell signalling
    • Choudhary, C.; Weinert, B. T.; Nishida, Y.; Verdin, E.; Mann, M. The growing landscape of lysine acetylation links metabolism and cell signalling Nat. Rev. Mol. Cell Biol. 2014, 15 (8) 536-50 10.1038/nrm3841
    • (2014) Nat. Rev. Mol. Cell Biol. , vol.15 , Issue.8 , pp. 536-550
    • Choudhary, C.1    Weinert, B.T.2    Nishida, Y.3    Verdin, E.4    Mann, M.5
  • 18
    • 17844385784 scopus 로고    scopus 로고
    • Regulatory cross-talk between lysine acetylation and ubiquitination: Role in the control of protein stability
    • Caron, C.; Boyault, C.; Khochbin, S. Regulatory cross-talk between lysine acetylation and ubiquitination: role in the control of protein stability BioEssays 2005, 27 (4) 408-15 10.1002/bies.20210
    • (2005) BioEssays , vol.27 , Issue.4 , pp. 408-415
    • Caron, C.1    Boyault, C.2    Khochbin, S.3
  • 19
    • 68949212379 scopus 로고    scopus 로고
    • Lysine acetylation targets protein complexes and co-regulates major cellular functions
    • Choudhary, C.; Kumar, C.; Gnad, F.; Nielsen, M. L.; Rehman, M.; Walther, T. C.; Olsen, J. V.; Mann, M. Lysine acetylation targets protein complexes and co-regulates major cellular functions Science 2009, 325 (5942) 834-40 10.1126/science.1175371
    • (2009) Science , vol.325 , Issue.5942 , pp. 834-840
    • Choudhary, C.1    Kumar, C.2    Gnad, F.3    Nielsen, M.L.4    Rehman, M.5    Walther, T.C.6    Olsen, J.V.7    Mann, M.8
  • 23
    • 79960979428 scopus 로고    scopus 로고
    • A large-scale method tmeasure absolute protein phospxorylation stoichiometries
    • Wu, R.; Haas, W.; Dephoure, N.; Huttlin, E. L.; Zhai, B.; Sowa, M. E.; Gygi, S. P. A large-scale method to measure absolute protein phosphorylation stoichiometries Nat. Methods 2011, 8 (8) 677-83 10.1038/nmeth.1636
    • (2011) Nat. Methods , vol.8 , Issue.8 , pp. 677-683
    • Wu, R.1    Haas, W.2    Dephoure, N.3    Huttlin, E.L.4    Zhai, B.5    Sowa, M.E.6    Gygi, S.P.7
  • 24
    • 0037402422 scopus 로고    scopus 로고
    • Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4
    • Smith, C. M.; Gafken, P. R.; Zhang, Z.; Gottschling, D. E.; Smith, J. B.; Smith, D. L. Mass spectrometric quantification of acetylation at specific lysines within the amino-terminal tail of histone H4 Anal. Biochem. 2003, 316 (1) 23-33 10.1016/S0003-2697(03)00032-0
    • (2003) Anal. Biochem. , vol.316 , Issue.1 , pp. 23-33
    • Smith, C.M.1    Gafken, P.R.2    Zhang, Z.3    Gottschling, D.E.4    Smith, J.B.5    Smith, D.L.6
  • 25
    • 84857043850 scopus 로고    scopus 로고
    • Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms
    • Hersman, E.; Nelson, D. M.; Griffith, W. P.; Jelinek, C.; Cotter, R. J. Analysis of Histone Modifications from Tryptic Peptides of Deuteroacetylated Isoforms Int. J. Mass Spectrom. 2012, 312, 5-16 10.1016/j.ijms.2011.04.006
    • (2012) Int. J. Mass Spectrom. , vol.312 , pp. 5-16
    • Hersman, E.1    Nelson, D.M.2    Griffith, W.P.3    Jelinek, C.4    Cotter, R.J.5
  • 26
    • 84924875114 scopus 로고    scopus 로고
    • Global and specific responses of the histone acetylome to systematic perturbation
    • Feller, C.; Forne, I.; Imhof, A.; Becker, P. B. Global and specific responses of the histone acetylome to systematic perturbation Mol. Cell 2015, 57 (3) 559-71 10.1016/j.molcel.2014.12.008
    • (2015) Mol. Cell , vol.57 , Issue.3 , pp. 559-571
    • Feller, C.1    Forne, I.2    Imhof, A.3    Becker, P.B.4
  • 27
    • 34548130666 scopus 로고    scopus 로고
    • A quantitative study on the in vitro and in vivo acetylation of high mobility group A1 proteins
    • Zhang, Q.; Zhang, K.; Zou, Y.; Perna, A.; Wang, Y. A quantitative study on the in vitro and in vivo acetylation of high mobility group A1 proteins J. Am. Soc. Mass Spectrom. 2007, 18 (9) 1569-78 10.1016/j.jasms.2007.05.020
    • (2007) J. Am. Soc. Mass Spectrom. , vol.18 , Issue.9 , pp. 1569-1578
    • Zhang, Q.1    Zhang, K.2    Zou, Y.3    Perna, A.4    Wang, Y.5
  • 29
  • 31
    • 84895538371 scopus 로고    scopus 로고
    • Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells
    • Kulak, N. A.; Pichler, G.; Paron, I.; Nagaraj, N.; Mann, M. Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells Nat. Methods 2014, 11 (3) 319-24 10.1038/nmeth.2834
    • (2014) Nat. Methods , vol.11 , Issue.3 , pp. 319-324
    • Kulak, N.A.1    Pichler, G.2    Paron, I.3    Nagaraj, N.4    Mann, M.5
  • 32
    • 57449099865 scopus 로고    scopus 로고
    • MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification
    • Cox, J.; Mann, M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification Nat. Biotechnol. 2008, 26 (12) 1367-72 10.1038/nbt.1511
    • (2008) Nat. Biotechnol. , vol.26 , Issue.12 , pp. 1367-1372
    • Cox, J.1    Mann, M.2
  • 33
    • 79953701087 scopus 로고    scopus 로고
    • Andromeda: A peptide search engine integrated into the MaxQuant environment
    • Cox, J.; Neuhauser, N.; Michalski, A.; Scheltema, R. A.; Olsen, J. V.; Mann, M. Andromeda: a peptide search engine integrated into the MaxQuant environment J. Proteome Res. 2011, 10 (4) 1794-805 10.1021/pr101065j
    • (2011) J. Proteome Res. , vol.10 , Issue.4 , pp. 1794-1805
    • Cox, J.1    Neuhauser, N.2    Michalski, A.3    Scheltema, R.A.4    Olsen, J.V.5    Mann, M.6
  • 34
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang; da, W.; Sherman, B. T.; Lempicki, R. A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources Nat. Protoc. 2009, 4 (1) 44-57 10.1038/nprot.2008.211
    • (2009) Nat. Protoc. , vol.4 , Issue.1 , pp. 44-57
    • Huang1    Da, W.2    Sherman, B.T.3    Lempicki, R.A.4
  • 35
    • 84867186480 scopus 로고    scopus 로고
    • Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways
    • Chen, Y.; Zhao, W.; Yang, J. S.; Cheng, Z.; Luo, H.; Lu, Z.; Tan, M.; Gu, W.; Zhao, Y. Quantitative acetylome analysis reveals the roles of SIRT1 in regulating diverse substrates and cellular pathways Mol. Cell. Proteomics 2012, 11 (10) 1048-62 10.1074/mcp.M112.019547
    • (2012) Mol. Cell. Proteomics , vol.11 , Issue.10 , pp. 1048-1062
    • Chen, Y.1    Zhao, W.2    Yang, J.S.3    Cheng, Z.4    Luo, H.5    Lu, Z.6    Tan, M.7    Gu, W.8    Zhao, Y.9
  • 38
    • 84874032401 scopus 로고    scopus 로고
    • Specific and efficient N-propionylation of histones with propionic acid N-hydroxysuccinimide ester for histone marks characterization by LC-MS
    • Liao, R.; Wu, H.; Deng, H.; Yu, Y.; Hu, M.; Zhai, H.; Yang, P.; Zhou, S.; Yi, W. Specific and efficient N-propionylation of histones with propionic acid N-hydroxysuccinimide ester for histone marks characterization by LC-MS Anal. Chem. 2013, 85 (4) 2253-9 10.1021/ac303171h
    • (2013) Anal. Chem. , vol.85 , Issue.4 , pp. 2253-2259
    • Liao, R.1    Wu, H.2    Deng, H.3    Yu, Y.4    Hu, M.5    Zhai, H.6    Yang, P.7    Zhou, S.8    Yi, W.9
  • 39
    • 79851496150 scopus 로고    scopus 로고
    • Histone H4 lysine 12 acetylation regulates telomeric heterochromatin plasticity in Saccharomyces cerevisiae
    • Zhou, B. O.; Wang, S. S.; Zhang, Y.; Fu, X. H.; Dang, W.; Lenzmeier, B. A.; Zhou, J. Q. Histone H4 lysine 12 acetylation regulates telomeric heterochromatin plasticity in Saccharomyces cerevisiae PLoS Genet. 2011, 7 (1) e1001272 10.1371/journal.pgen.1001272
    • (2011) PLoS Genet. , vol.7 , Issue.1 , pp. e1001272
    • Zhou, B.O.1    Wang, S.S.2    Zhang, Y.3    Fu, X.H.4    Dang, W.5    Lenzmeier, B.A.6    Zhou, J.Q.7
  • 41
    • 0038676409 scopus 로고    scopus 로고
    • Inhibition of histone deacetylase activity by butyrate
    • Davie, J. R. Inhibition of histone deacetylase activity by butyrate J. Nutr. 2003, 133 (7 Suppl) 2485S-2493S
    • (2003) J. Nutr. , vol.133 , Issue.7 , pp. 2485S-2493S
    • Davie, J.R.1
  • 42
    • 27744453898 scopus 로고    scopus 로고
    • Comprehensive analysis of dynamics of histone H4 acetylation in mitotic barley cells
    • Wako, T.; Murakami, Y.; Fukui, K. Comprehensive analysis of dynamics of histone H4 acetylation in mitotic barley cells Genes Genet. Syst. 2005, 80 (4) 269-76 10.1266/ggs.80.269
    • (2005) Genes Genet. Syst. , vol.80 , Issue.4 , pp. 269-276
    • Wako, T.1    Murakami, Y.2    Fukui, K.3
  • 43
    • 54949117927 scopus 로고    scopus 로고
    • Differential acetylation of histone H4 lysine during development of in vitro fertilized, cloned and parthenogenetically activated bovine embryos
    • Maalouf, W. E.; Alberio, R.; Campbell, K. H. Differential acetylation of histone H4 lysine during development of in vitro fertilized, cloned and parthenogenetically activated bovine embryos Epigenetics 2008, 3 (4) 199-209 10.4161/epi.3.4.6497
    • (2008) Epigenetics , vol.3 , Issue.4 , pp. 199-209
    • Maalouf, W.E.1    Alberio, R.2    Campbell, K.H.3
  • 44
    • 0022365083 scopus 로고
    • Deposition-related histone acetylation in micronuclei of conjugating Tetrahymena
    • Allis, C. D.; Chicoine, L. G.; Richman, R.; Schulman, I. G. Deposition-related histone acetylation in micronuclei of conjugating Tetrahymena Proc. Natl. Acad. Sci. U. S. A. 1985, 82 (23) 8048-52 10.1073/pnas.82.23.8048
    • (1985) Proc. Natl. Acad. Sci. U. S. A. , vol.82 , Issue.23 , pp. 8048-8052
    • Allis, C.D.1    Chicoine, L.G.2    Richman, R.3    Schulman, I.G.4
  • 45
    • 0028356458 scopus 로고
    • Non-random acetylation of histone H4 by a cytoplasmic histone acetyltransferase as determined by novel methodology
    • Sobel, R. E.; Cook, R. G.; Allis, C. D. Non-random acetylation of histone H4 by a cytoplasmic histone acetyltransferase as determined by novel methodology J. Biol. Chem. 1994, 269 (28) 18576-82
    • (1994) J. Biol. Chem. , vol.269 , Issue.28 , pp. 18576-18582
    • Sobel, R.E.1    Cook, R.G.2    Allis, C.D.3
  • 46
    • 0028847955 scopus 로고
    • Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4
    • Sobel, R. E.; Cook, R. G.; Perry, C. A.; Annunziato, A. T.; Allis, C. D. Conservation of deposition-related acetylation sites in newly synthesized histones H3 and H4 Proc. Natl. Acad. Sci. U. S. A. 1995, 92 (4) 1237-41 10.1073/pnas.92.4.1237
    • (1995) Proc. Natl. Acad. Sci. U. S. A. , vol.92 , Issue.4 , pp. 1237-1241
    • Sobel, R.E.1    Cook, R.G.2    Perry, C.A.3    Annunziato, A.T.4    Allis, C.D.5
  • 47
    • 84881163383 scopus 로고    scopus 로고
    • Genome-wide analysis of H4K5 acetylation associated with fear memory in mice
    • Park, C. S.; Rehrauer, H.; Mansuy, I. M. Genome-wide analysis of H4K5 acetylation associated with fear memory in mice BMC Genomics 2013, 14, 539 10.1186/1471-2164-14-539
    • (2013) BMC Genomics , vol.14 , pp. 539
    • Park, C.S.1    Rehrauer, H.2    Mansuy, I.M.3
  • 52
    • 84890673317 scopus 로고    scopus 로고
    • Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli
    • Colak, G.; Xie, Z.; Zhu, A. Y.; Dai, L.; Lu, Z.; Zhang, Y.; Wan, X.; Chen, Y.; Cha, Y. H.; Lin, H.; Zhao, Y.; Tan, M. Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in Escherichia coli Mol. Cell. Proteomics 2013, 12 (12) 3509-20 10.1074/mcp.M113.031567
    • (2013) Mol. Cell. Proteomics , vol.12 , Issue.12 , pp. 3509-3520
    • Colak, G.1    Xie, Z.2    Zhu, A.Y.3    Dai, L.4    Lu, Z.5    Zhang, Y.6    Wan, X.7    Chen, Y.8    Cha, Y.H.9    Lin, H.10    Zhao, Y.11    Tan, M.12
  • 53
    • 84883307077 scopus 로고    scopus 로고
    • Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation
    • Weinert, B. T.; Scholz, C.; Wagner, S. A.; Iesmantavicius, V.; Su, D.; Daniel, J. A.; Choudhary, C. Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation Cell Rep. 2013, 4 (4) 842-51 10.1016/j.celrep.2013.07.024
    • (2013) Cell Rep. , vol.4 , Issue.4 , pp. 842-851
    • Weinert, B.T.1    Scholz, C.2    Wagner, S.A.3    Iesmantavicius, V.4    Su, D.5    Daniel, J.A.6    Choudhary, C.7
  • 54
    • 84915822556 scopus 로고    scopus 로고
    • Systematic identification of the lysine succinylation in the protozoan parasite Toxoplasma gondii
    • Li, X.; Hu, X.; Wan, Y.; Xie, G.; Chen, D.; Cheng, Z.; Yi, X.; Liang, S.; Tan, F. Systematic identification of the lysine succinylation in the protozoan parasite Toxoplasma gondii J. Proteome Res. 2014, 13 (12) 6087-95 10.1021/pr500992r
    • (2014) J. Proteome Res. , vol.13 , Issue.12 , pp. 6087-6095
    • Li, X.1    Hu, X.2    Wan, Y.3    Xie, G.4    Chen, D.5    Cheng, Z.6    Yi, X.7    Liang, S.8    Tan, F.9
  • 55
    • 84926431871 scopus 로고    scopus 로고
    • Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis
    • Yang, M.; Wang, Y.; Chen, Y.; Cheng, Z.; Gu, J.; Deng, J.; Bi, L.; Chen, C.; Mo, R.; Wang, X.; Ge, F. Succinylome analysis reveals the involvement of lysine succinylation in metabolism in pathogenic Mycobacterium tuberculosis Mol. Cell. Proteomics 2015, 14 (4) 796-811 10.1074/mcp.M114.045922
    • (2015) Mol. Cell. Proteomics , vol.14 , Issue.4 , pp. 796-811
    • Yang, M.1    Wang, Y.2    Chen, Y.3    Cheng, Z.4    Gu, J.5    Deng, J.6    Bi, L.7    Chen, C.8    Mo, R.9    Wang, X.10    Ge, F.11


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