The pea seedling mitochondrial Nε-lysine acetylome

Mitochondrion

Volumn 19, Issue PB, 2014, Pages 154-165

  Smith Hammond, Colin L ^a,b   Hoyos, Elizabeth ^a,b   Miernyk, Ján A ^a,b  

^a University of Missouri   (United States)

^b UNIVERSITY OF MISSOURI   (United States)

Author keywords

Lysine acetylation; Mass spectrometry; Pisum sativum; Proteomics

Indexed keywords

LYSINE; MITOCHONDRIAL PROTEIN; PROTEOME; VEGETABLE PROTEIN;

ACETYLATION; CHEMISTRY; ISOLATION AND PURIFICATION; METABOLISM; MITOCHONDRION; PEA; PROTEIN PROCESSING; SEEDLING;

ACETYLATION; LYSINE; MITOCHONDRIA; MITOCHONDRIAL PROTEINS; PEAS; PLANT PROTEINS; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEOME; SEEDLING;

EID: 84914115224     PISSN: 15677249     EISSN: 18728278     Source Type: Journal    
DOI: 10.1016/j.mito.2014.04.012     Document Type: Article

References (98)

1. Allfrey V.G., Faulkner R., Mirsky A.E. Acetylation and methylation of histones and their possible role in the regulation of RNA synthesis. Proc. Natl. Acad. Sci. U. S. A. 1964, 51:786-794.
2. Altman-Price N., Mevarech M. Genetic evidence for the importance of protein acetylation and protein deacetylation in the halophilic archaeon Haloferax volcanii. J. Bacteriol. 2009, 191:1610-1617.
3. Altschul S.F., Wootton J.C., Gertz E.M., Agarwala R., Morgulis A., Schäffer A.A., Yu Y.-K. Protein database searches using compositionally adjusted substitution matrices. FEBS J. 2005, 272:5101-5109.
4. Arnon D.I. Copper enzymes in isolated chloroplasts. Polyphenoloxidase in Beta vulgaris. Plant Physiol. 1949, 24:1-15.
5. Biomatters Ltd, 2013. Geneious 6.1.6 Available from. http://www.geneious.com/.
6. Bunkenborg J., Espadas G., Molina H. Cutting edge proteomics: benchmarking of six commercial trypsins. J. Proteome Res. 2013, 12. (130619070701000).
7. Cannon S.B., May G.D., Jackson S.A. Three sequenced legume genomes and many crop species: rich opportunities for translational genomics. Plant Physiol. 2009, 151:970-977.
8. Cham B.E., Knowles B.R. A solvent system for delipidation of plasma or serum without protein precipitation. J. Lipid Res. 1976, 17:176-181.
9. Chambers M.C., MacLean B., Burke R., Amodei D., Ruderman D.L., Neumann S., Gatto L., Fischer B., Pratt B., Egertson J., Hoff K., Kessner D., Tasman N., Shulman N., Frewen B., Baker T.A., Brusniak M.-Y., Paulse C., Creasy D., Flashner L., Kani K., Moulding C., Seymour S.L., Nuwaysir L.M., Lefebvre B., Kuhlmann F., Roark J., Rainer P., Detlev S., Hemenway T., Huhmer A., Langridge J., Connolly B., Chadick T., Holly K., Eckels J., Deutsch E.W., Moritz R.L., Katz J.E., Agus D.B., MacCoss M., Tabb D.L., Mallick P. A cross-platform toolkit for mass spectrometry and proteomics. Nat. Biotechnol. 2012, 30:918-920.
10. Chen J., Ghazawi F.M., Li Q. Interplay of bromodomain and histone acetylation in the regulation of p300-dependent genes. Epigenetics 2010, 5:509-515.
11. Pisum sativum Cool Season Food Legume Database 2012, C.-H. Cheng, D. Main (Eds.).
12. 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, 325:834-840.
13. 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, 26:1367-1372.
14. MaxQuant Contaminants Database 2013, Max Planck Institute of Biochemistry, (URL http://www.maxquant.org/contaminants.zip (accessed 5.5.13)). J. Cox, M. Mann (Eds.).
15. 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, 10:1794-1805.
16. Delieu T., Walker D.A. An improved cathode for the measurement of photosynthetic oxygen evolution by isolated chloroplasts. New Phytol. 1972, 71:201-225.
17. Ellis R.J. The most abundant protein in the world. Trends Biochem. Sci. 1979, 4:241-244.
18. Eng J.K., McCormack A.L., Yates J.R. An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994, 5:976-989.
19. Fang T.K., David N.R., Miernyk J.A., Randall D.D. Isolation and purification of functional pea mitochondria free of chlorophyll contamination. Curr. Top. Plant Biochem. Physiol. 1987, 175:543.
20. Feldman J.L., Dittenhafer-Reed K.E., Denu J.M. Sirtuin catalysis and regulation. J. Biol. Chem. 2012, 287:42419-42427.
21. Finkemeier I., Laxa M., Miguet L., Howden A.J.M., Sweetlove L.J. Proteins of diverse function and subcellular location are lysine acetylated in Arabidopsis. Plant Physiol. 2011, 155:1779-1790.
22. Giegé P., Heazlewood J.L., Roessner-Tunali U., Millar A.H., Fernie A.R., Leaver C.J., Sweetlove L.J. Enzymes of glycolysis are functionally associated with the mitochondrion in Arabidopsis cells. Plant Cell 2003, 15:2140-2151.
23. Global Proteome Machine Organization cRAP Protein Sequences [WWW Document]. thegpm.org. URL, (accessed 11.20.11). http://www.thegpm.org/crap/index.html.
24. Goodstein D.M., Shu S., Howson R., Neupane R., Hayes R.D., Fazo J., Mitros T., Dirks W., Hellsten U., Putnam N., Rokhsar D.S. Phytozome: a comparative platform for green plant genomics. Nucleic Acids Res. 2011, 40:D1178-D1186.
25. Graham J.W.A., Williams T.C.R., Morgan M., Fernie A.R., Ratcliffe R.G., Sweetlove L.J. Glycolytic enzymes associate dynamically with mitochondria in response to respiratory demand and support substrate channeling. Plant Cell 2007, 19:3723-3738.
26. Hahne K., Haucke V., Ramage L., Schatz G. Incomplete arrest in the outer membrane sorts NADH-cytochrome b 5 reductase to two different submitochondrial compartments. Cell 1994, 79:829-839.
27. Hebert A.S., Dittenhafer-Reed K.E., Yu W., Bailey D.J., Selen E.S., Boersma M.D., Carson J.J., Tonelli M., Balloon A.J., Higbee A.J., Westphall M.S., Pagliarini D.J., Prolla T.A., Assadi-Porter F., Roy S., Denu J.M., Coon J.J. Calorie restriction and SIRT3 trigger global reprogramming of the mitochondrial protein acetylome. Mol. Cell 2012, 49:186-199.
28. Henriksen P., Wagner S.A., Weinert B.T., Sharma S., Bacinskaja G., Rehman M., Juffer A.H., Walther T.C., Lisby M., Choudhary C. Proteome-wide analysis of lysine acetylation suggests its broad regulatory scope in Saccharomyces cerevisiae. Mol. Cell. Proteomics 2012, 11:1510-1522.
29. Hiller S., Garces R.G., Malia T.J., Orekhov V.Y., Colombini M., Wagner G. Solution structure of the integral human membrane protein VDAC-1 in detergent micelles. Science 2008, 321:1206-1210.
30. Hirschey M.D., Shimazu T., Huang J.-Y., Verdin E. Acetylation of mitochondrial proteins. Methods Enzymol. 2009, 457:137-147.
31. Homblé F., Krammer E.-M., Prévost M. Plant VDAC: facts and speculations. Biochim. Biophys. Acta Biomembr. 2012, 1818:1486-1501.
32. Hornbeck P.V., Kornhauser J.M., Tkachev S., Zhang B., Skrzypek E., Murray B., Latham V., Sullivan M. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012, 40:D261-D270.
33. Huang L.-S., Sun G., Cobessi D., Wang A.C., Shen J.T., Tung E.Y., Anderson V.E., Berry E.A. 3-Nitropropionic acid is a suicide inhibitor of mitochondrial respiration that, upon oxidation by complex II, forms a covalent adduct with a catalytic base arginine in the active site of the enzyme. J. Biol. Chem. 2006, 281:5965-5972.
34. Humphrey W., Dalke A., Schulten K. VMD: visual molecular dynamics. J. Mol. Graph. 1996, 14(33):27-28.
35. Jain M., Misra G., Patel R.K., Priya P., Jhanwar S., Khan A.W., Shah N., Singh V.K., Garg R., Jeena G., Yadav M., Kant C., Sharma P., Yadav G., Bhatia S., Tyagi A.K., Chattopadhyay D. A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 2013, 74:715-729.
36. Käll L., Canterbury J.D., Weston J., Noble W.S., MacCoss M.J. Semi-supervised learning for peptide identification from shotgun proteomics datasets. Nat. Methods 2007, 4:923-925.
37. Käll L., Storey J.D., MacCoss M.J., Noble W.S. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. J. Proteome Res. 2008, 7:29-34.
38. Kim S., Pevzner P.A. MS-GF+: universal database search tool for mass spectrometry. 8th Annual US HUPO Conference, San Francisco, USA 2012.
39. Kim S.C., Sprung R., Chen Y., Xu Y., Ball H., Pei J., Cheng T., Kho Y., Xiao H., Xiao L., Grishin N.V., White M., Yang X.-J., Zhao Y. Substrate and functional diversity of lysine acetylation revealed by a proteomics survey. Mol. Cell 2006, 23:607-618.
40. Kim S., Suga M., Ogasahara K., Ikegami T., Minami Y., Yubisui T., Tsukihara T. Structure of Physarum polycephalum cytochrome b5 reductase at 1.56Å resolution. Acta Crystallogr. Sect. F: Struct. Biol. Cryst. Commun. 2007, 63:274-279.
41. Kim S., Mischerikow N., Bandeira N., Navarro J.D., Wich L., Mohammed S., Heck A.J.R., Pevzner P.A. The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search. Mol. Cell. Proteomics 2010, 9:2840-2852.
42. Kleczkowski L.A., Randall D.D., Blevins D.G. Purification and characterization of a novel NADPH(NADH)-dependent glyoxylate reductase from spinach leaves. Comparison of immunological properties of leaf glyoxylate reductase and hydroxypyruvate reductase. Biochem. J. 1986, 239:653-659.
43. Korolev N., Vorontsova O.V., Nordenskiöld L. Physicochemical analysis of electrostatic foundation for DNA-protein interactions in chromatin transformations. Prog. Biophys. Mol. Biol. 2007, 95:23-49.
44. Kouzarides T. Acetylation: a regulatory modification to rival phosphorylation?. EMBO J. 2000, 19:1176-1179.
45. Kruft V., Eubel H., Jansch L., Werhahn W., Braun H.P. Proteomic approach to identify novel mitochondrial proteins in Arabidopsis. Plant Physiol. 2001, 127:1694-1710.
46. Lavin M., Herendeen P.S., Wojciechowski M.F. Evolutionary rates analysis of Leguminosae implicates a rapid diversification of lineages during the tertiary. Syst. Biol. 2005, 54:575-594.
47. Lee C.P., Taylor N.L., Millar A.H. Recent advances in the composition and heterogeneity of the Arabidopsis mitochondrial proteome. Front. Plant Sci. 2013, 4:4.
48. Lomize M.A., Pogozheva I.D., Joo H., Mosberg H.I., Lomize A.L. OPM database and PPM web server: resources for positioning of proteins in membranes. Nucleic Acids Res. 2012, 40:D370-D376.
49. Lundby A., Lage K., Weinert B.T., Bekker-Jensen D.B., Secher A., Skovgaard T., Kelstrup C.D., Dmytriyev A., Choudhary C., Lundby C., Olsen J.V. Proteomic analysis of lysine acetylation sites in rat tissues reveals organ specificity and subcellular patterns. Cell Rep. 2012, 2:419-431.
50. Maglott D., Ostell J., Pruitt K.D., Tatusova T. Entrez gene: gene-centered information at NCBI. Nucleic Acids Res. 2011, 39:D52-D57.
51. Melo-Braga M.N., Verano-Braga T., León I.R., Antonacci D., Nogueira F.C.S., Thelen J.J., Larsen M.R., Palmisano G. Modulation of protein phosphorylation, N-glycosylation and Lys-acetylation in grape (Vitis vinifera) mesocarp and exocarp owing to Lobesia botrana infection. Mol. Cell. Proteomics 2012, 11:945-956.
52. Michishita E., Park J.Y., Burneskis J.M., Barrett J.C., Horikawa I. Evolutionarily conserved and nonconserved cellular localizations and functions of human SIRT proteins. Mol. Biol. Cell 2005, 16:4623-4635.
53. Miernyk J.A., Hajduch M. Seed proteomics. J. Proteomics 2011, 74:389-400.
54. Miernyk J.A., Randall D.D. Some kinetic and regulatory properties of the pea mitochondrial pyruvate dehydrogenase complex. Plant Physiol. 1987, 83:306-310.
55. Miernyk J.A., Pretová A., Olmedilla A., Klubicová K., Obert B., Hajduch M. Using proteomics to study sexual reproduction in angiosperms. Sex. Plant Reprod. 2011, 24:9-22.
56. Moreno J.I., David N.R., Miernyk J.A., Randall D.D. Pisum sativum mitochondrial pyruvate dehydrogenase can be assembled as a functional α2β2 heterotetramer in the cytoplasm of Pichia pastoris. Protein Expr. Purif. 2000, 19:276-283.
57. Mullen R.T., Lisenbee C.S., Miernyk J.A., Trelease R.N. Peroxisomal membrane ascorbate peroxidase is sorted to a membranous network that resembles a subdomain of the endoplasmic reticulum. Plant Cell 1999, 11:2167-2185.
58. Nguyen T.H.N., Brechenmacher L., Aldrich J., Clauss T., Gritsenko M., Hixson K., Libault M., Tanaka K., Yang F., Yao Q., Pasa-Tolic L., Xu D., Nguyen H.T., Stacey G. Quantitative phosphoproteomic analysis of soybean root hairs inoculated with Bradyrhizobium japonicum. Mol. Cell. Proteomics 2012, 11:1140-1155.
59. Olsen J.V., Ong S.-E., Mann M. Trypsin cleaves exclusively C-terminal to arginine and lysine residues. Mol. Cell. Proteomics 2004, 3:608-614.
60. O'Shea J.P., Chou M.F., Quader S.A., Ryan J.K., Church G.M., Schwartz D. pLogo: a probabilistic approach to visualizing sequence motifs. Nat. Methods 2013, 10:1211-1214.
61. Pandey R., Müller A., Napoli C.A., Selinger D.A., Pikaard C.S., Richards E.J., Bender J., Mount D.W., Jorgensen R.A. Analysis of histone acetyltransferase and histone deacetylase families of Arabidopsis thaliana suggests functional diversification of chromatin modification among multicellular eukaryotes. Nucleic Acids Res. 2002, 30:5036-5055.
62. Piques M., Schulze W.X., hne M.H.O., Usadel B., Gibon Y., Rohwer J., Stitt M. Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis. Mol. Syst. Biol. 2009, 5:1-17.
63. Quevillon E., Silventoinen V., Pillai S., Harte N., Mulder N., Apweiler R., Lopez R. InterProScan: protein domains identifier. Nucleic Acids Res. 2005, 33:W116-W120.
64. Rao J., Bhattacharya D., Banerjee B., Sarin A., Shivashankar G.V. Trichostatin-A induces differential changes in histone protein dynamics and expression in HeLa cells. Biochem. Biophys. Res. Commun. 2007, 363:263-268.
65. Rardin M.J., Newman J.C., Held J.M. Label-free quantitative proteomics of the lysine acetylome in mitochondria identifies substrates of SIRT3 in metabolic pathways. Proc. Natl. Acad. Sci. U. S. A. 2013, 110:6601-6606.
66. Sato S., Nakamura Y., Kaneko T., Asamizu E., Kato T., Nakao M., Sasamoto S., Watanabe A., Ono A., Kawashima K., Fujishiro T., Katoh M., Kohara M., Kishida Y., Minami C., Nakayama S., Nakazaki N., Shimizu Y., Shinpo S., Takahashi C., Wada T., Yamada M., Ohmido N., Hayashi M., Fukui K., Baba T., Nakamichi T., Mori H., Tabata S. Genome structure of the legume, Lotus japonicus. DNA Res. 2008, 15:227-239.
67. Schmutz J., Cannon S.B., Schlueter J., Ma J., Mitros T., Nelson W., Hyten D.L., Song Q., Thelen J.J., Cheng J., Xu D., Hellsten U., May G.D., Yu Y., Sakurai T., Umezawa T., Bhattacharyya M.K., Sandhu D., Valliyodan B., Lindquist E., Peto M., Grant D., Shu S., Goodstein D., Barry K., Futrell-Griggs M., Abernathy B., Du J., Tian Z., Zhu L., Gill N., Joshi T., Libault M., Sethuraman A., Zhang X.-C., Shinozaki K., Nguyen H.T., Wing R.A., Cregan P., Specht J., Grimwood J., Rokhsar D., Stacey G., Shoemaker R.C., Jackson S.A. Genome sequence of the palaeopolyploid soybean. Nature 2010, 463:178-183.
68. Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., Chen W., Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.
69. Scott I., Webster B.R., Li J.H., Sack M.N. Identification of a molecular component of the mitochondrial acetyltransferase programme: a novel role for GCN5L1. Biochem. J. 2012, 443:655-661.
70. ε-acetylome. J. Proteomics 2014, 96:56-66.
71. Smýkal P., Aubert G., Burstin J., Coyne C.J., Ellis N.T.H., Flavell A.J., Ford R., Hýbl M., Macas J., Neumann P., McPhee K.E., Redden R.J., Rubiales D., Weller J.L., Warkentin T.D. Pea (Pisum sativum L.) in the genomic era. Agronomy 2012, 2:74-115.
72. Song C., Saxena R.K., Azam S., Yu S., Sharpe A.G., Cannon S., Baek J., Rosen B.D., Tar'an B., Millan T., Zhang X., Ramsay L.D., Iwata A., Wang Y., Nelson W., Farmer A.D., Gaur P.M., Soderlund C., Penmetsa R.V., Xu C., Bharti A.K., He W., Winter P., Zhao S., Hane J.K., Carrasquilla-Garcia N., Condie J.A., Upadhyaya H.D., Luo M.-C., Thudi M., Gowda C.L.L., Singh N.P., Lichtenzveig J., Gali K.K., Rubio J., Nadarajan N., Dolezel J., Bansal K.C., Xu X., Edwards D., Zhang G., Kahl G., Gil J., Singh K.B., Datta S.K., Jackson S.A., Varshney R.K., Wang J., Cook D.R. Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 2013, 31:240-246.
73. Stajich J.E., Block D., Boulez K., Brenner S.E., Chervitz S.A., Dagdigian C., Fuellen G., Gilbert J.G.R., Korf I., Lapp H., Lehväslaiho H., Matsalla C., Mungall C.J., Osborne B.I., Pocock M.R., Schattner P., Senger M., Stein L.D., Stupka E., Wilkinson M.D., Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002, 12:1611-1618.
74. Stilger K.L., Sullivan W.J. Elp3 lysine acetyltransferase is a tail-anchored mitochondrial protein in Toxoplasma gondii. J. Biol. Chem. 2013, 288:25318-25329.
75. Still A.J., Floyd B.J., Hebert A.S., Bingman C.A., Carson J.J., Gunderson D.R., Dolan B.K., Grimsrud P.A., Dittenhafer-Reed K.E., Stapleton D.S., Keller M.P., Westphall M.S., Denu J.M., Attie A.D., Coon J.J., Pagliarini D.J. Quantification of mitochondrial acetylation dynamics highlights prominent sites of metabolic regulation. J. Biol. Chem. 2013, 288:26209-26219.
76. Stone J.E. An efficient library for parallel ray tracing and animation. Intel Supercomputer Users Group Proc 1998, (http://citeseerx.ist.psu.edu/viewdoc/ summary?doi = 10.1.1.49.7193).
77. Syntichaki P., Topalidou I., Thireos G. The Gcn5 bromodomain co-ordinates nucleosome remodelling. Nature 2000, 404:414-417.
78. Thimm O., Bläsing O., Gibon Y., Nagel A., Meyer S., Krüger P., Selbig J., Müller L.A., Rhee S.Y., Stitt M. MapMan: a user driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004, 37:914-939.
79. Ujwal R., Cascio D., Colletier J.-P., Faham S., Zhang J., Toro L., Ping P., Abramson J. The crystal structure of mouse VDAC1 at 2.3Å resolution reveals mechanistic insights into metabolite gating. Proc. Natl. Acad. Sci. U. S. A. 2008, 105:17742-17747.
80. UniProt Consortium Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40:D71-D75.
81. Phytozome v9.1: Phaseolus vulgaris v1.0 2013, US Department of Energy Joint Genome Institute (Ed.).
82. van Noort V., Seebacher J., Bader S., Mohammed S., Vonkova I., Betts M.J., hner S.K.U., Kumar R., Maier T., Flaherty M.O.A., Rybin V., Schmeisky A., Yus E., lke J.O.R.S.U., Serrano L., Russell R.B., Heck A.J., Bork P., Gavin A.-C. Cross-talk between phosphorylation and lysine acetylation in a genome-reduced bacterium. Mol. Syst. Biol. 2012, 8:1-16.
83. Villén J., Gygi S.P. The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry. Nat. Protoc. 2008, 3:1630-1638.
84. Vizcaíno J.A., CÔté R.G., Csordas A., Dianes J.A., Fabregat A., Foster J.M., Griss J., Alpi E., Birim M., Contell J., O'Kelly G., Schoenegger A., Ovelleiro D., Perez-Riverol Y., Reisinger F., Ríos D., Wang R., Hermjakob H. The Proteomics Identifications (PRIDE) database and associated tools: status in 2013. Nucleic Acids Res. 2013, 41:D1063-D1069.
85. Vogelauer M., Krall A.S., McBrian M.A., Li J.-Y., Kurdistani S.K. Stimulation of histone deacetylase activity by metabolites of intermediary metabolism. J. Biol. Chem. 2012, 287:32006-32016.
86. Wagner G.R., Payne R.M. Widespread and enzyme-independent N-acetylation and N-succinylation in the chemical conditions of the mitochondrial matrix. J. Biol. Chem. 2013, 288:29036-29045.
87. Wang Q., Zhang Y., Yang C., Xiong H., Lin Y., Yao J., Li H., Xie L., Zhao W., Yao Y., Ning Z.-B., Zeng R., Xiong Y., Guan K.-L., Zhao S., Zhao G.-P. Acetylation of metabolic enzymes coordinates carbon source utilization and metabolic flux. Science 2010, 327:1004-1007.
88. Weinert B.T., Wagner S.A., Horn H., Henriksen P., Liu W.R., Olsen J.V., Jensen L.J., Choudhary C. Proteome-wide mapping of the Drosophila acetylome demonstrates a high degree of conservation of lysine acetylation. Sci. Signal. 2011, 4:ra48.
89. Wenger C.D., Phanstiel D.H., Lee M.V., Bailey D.J., Coon J.J. COMPASS: a suite of pre- and post-search proteomics software tools for OMSSA. Proteomics 2011, 11:1064-1074.
90. Wirtz M., Beard K.F.M., Lee C.P., Boltz A., Schwarzländer M., Fuchs C., Meyer A.J., Heeg C., Sweetlove L.J., Ratcliffe R.G., Hell R. Mitochondrial cysteine synthase complex regulates O-acetylserine biosynthesis in plants. J. Biol. Chem. 2012, 287:27941-27947.
91. Wu X., Oh M.H., Schwarz E.M., Larue C.T., Sivaguru M., Imai B.S., Yau P.M., Ort D.R., Huber S.C. Lysine acetylation is a widespread protein modification for diverse proteins in Arabidopsis. Plant Physiol. 2011, 155:1769-1778.
92. Xiong Y., Guan K.-L. Mechanistic insights into the regulation of metabolic enzymes by acetylation. J. Cell Biol. 2012, 198:155-164.
93. Yao Q., Bollinger C., Gao J., Xu D., Thelen J.J. P(3)DB: an integrated database for plant protein phosphorylation. Front. Plant Sci. 2012, 3:206.
94. Young N.D., Debellé F., Oldroyd G.E.D., Geurts R., Cannon S.B., Udvardi M.K., Benedito V.A., Mayer K.F.X., Gouzy J., Schoof H., van de Peer Y., Proost S., Cook D.R., Meyers B.C., Spannagl M., Cheung F., De Mita S., Krishnakumar V., Gundlach H., Zhou S., Mudge J., Bharti A.K., Murray J.D., Naoumkina M.A., Rosen B., Silverstein K.A.T., Tang H., Rombauts S., Zhao P.X., Zhou P., Barbe V., Bardou P., Bechner M., Bellec A., Berger A., Bergès H., Bidwell S., Bisseling T., Choisne N., Couloux A., Denny R., Deshpande S., Dai X., Doyle J.J., Dudez A.-M., Farmer A.D., Fouteau S., Franken C., Gibelin C., Gish J., Goldstein S., González A.J., Green P.J., Hallab A., Hartog M., Hua A., Humphray S.J., Jeong D.-H., Jing Y., Jöcker A., Kenton S.M., Kim D.-J., Klee K., Lai H., Lang C., Lin S., Macmil S.L., Magdelenat G., Matthews L., McCorrison J., Monaghan E.L., Mun J.-H., Najar F.Z., Nicholson C., Noirot C., O'Bleness M., Paule C.R., Poulain J., Prion F., Qin B., Qu C., Retzel E.F., Riddle C., Sallet E., Samain S., Samson N., Sanders I., Saurat O., Scarpelli C., Schiex T., Segurens B., Severin A.J., Sherrier D.J., Shi R., Sims S., Singer S.R., Sinharoy S., Sterck L., Viollet A., Wang B.-B., Wang K., Wang M., Wang X., Warfsmann J., Weissenbach J., White D.D., White J.D., Wiley G.B., Wincker P., Xing Y., Yang L., Yao Z., Ying F., Zhai J., Zhou L., Zuber A., Dénarié J., Dixon R.A., May G.D., Schwartz D.C., Rogers J., Quétier F., Town C.D., Roe B.A. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 2011, 480:520-524.
95. Yuan H., Marmorstein R. Histone acetyltransferases: rising ancient counterparts to protein kinases. Biopolymers 2012, 99:98-111.
96. Zhang J., Sprung R., Pei J., Tan X., Kim S., Zhu H., Liu C.-F., Grishin N.V., Zhao Y. Lysine acetylation is a highly abundant and evolutionarily conserved modification in Escherichia coli. Mol. Cell. Proteomics 2009, 8:215-225.
97. Zhang T., Wang S., Lin Y., Xu W., Ye D., Xiong Y., Zhao S., Guan K.-L. Acetylation negatively regulates glycogen phosphorylase by recruiting protein phosphatase 1. Cell Metab. 2012, 15:75-87.
98. Zippo A., Serafini R., Rocchigiani M., Pennacchini S., Krepelova A., Oliviero S. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 2009, 138:1122-1136.