A mechanism for the evolution of phosphorylation sites

Cell

Volumn 147, Issue 4, 2011, Pages 934-946

  Pearlman, Samuel M ^a   Serber, Zach ^a   Ferrell Jr , James E ^a  

^a STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; ASPARTIC ACID; DNA TOPOISOMERASE (ATP HYDROLYSING); ELONGATION FACTOR 2; ENOLASE; G PROTEIN COUPLED RECEPTOR; GLUTAMIC ACID; RAF PROTEIN; SERINE; THREONINE; TYROSINE;

AMINO ACID SUBSTITUTION; ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; EUKARYOTE EVOLUTION; HUMAN; MOLECULAR EVOLUTION; PHYLOGENY; PRIORITY JOURNAL; PROKARYOTE; PROTEIN ANALYSIS; PROTEIN FAMILY; PROTEIN PHOSPHORYLATION; PROTEIN STRUCTURE; SEQUENCE HOMOLOGY;

EID: 81055129599     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2011.08.052     Document Type: Article

References (46)

1. F. Abascal, R. Zardoya, and D. Posada ProtTest: selection of best-fit models of protein evolution Bioinformatics 21 2005 2104 2105
2. A. Alonso, J. Sasin, N. Bottini, I. Friedberg, A. Osterman, A. Godzik, T. Hunter, J. Dixon, and T. Mustelin Protein tyrosine phosphatases in the human genome Cell 117 2004 699 711
3. S.F. Altschul, W. Gish, W. Miller, E.W. Myers, and D.J. Lipman Basic local alignment search tool J. Mol. Biol. 215 1990 403 410
4. B.A. Ballif, J. Villen, S.A. Beausoleil, D. Schwartz, and S.P. Gygi Phosphoproteomic analysis of the developing mouse brain Mol. Cell. Proteomics 3 2004 1093 1101
5. S.A. Beausoleil, M. Jedrychowski, D. Schwartz, J.E. Elias, J. Villen, J. Li, M.A. Cohn, L.C. Cantley, and S.P. Gygi Large-scale characterization of HeLa cell nuclear phosphoproteins Proc. Natl. Acad. Sci. USA 101 2004 12130 12135
6. N. Blom, S. Gammeltoft, and S. Brunak Sequence and structure-based prediction of eukaryotic protein phosphorylation sites J. Mol. Biol. 294 1999 1351 1362
7. N.R. Brown, M.E. Noble, J.A. Endicott, and L.N. Johnson The structural basis for specificity of substrate and recruitment peptides for cyclin-dependent kinases Nat. Cell Biol. 1 1999 438 443
8. F.D. Ciccarelli, T. Doerks, C. von Mering, C.J. Creevey, B. Snel, and P. Bork Toward automatic reconstruction of a highly resolved tree of life Science 311 2006 1283 1287
9. P. Cohen The regulation of protein function by multisite phosphorylation-a 25 year update Trends Biochem. Sci. 25 2000 596 601
10. J.A. Cooper, B.M. Sefton, and T. Hunter Detection and quantification of phosphotyrosine in proteins Methods Enzymol. 99 1983 387 402
11. M.O. Dayhoff Atlas of Protein Sequence and Structure 1978 National Biomedical Research Foundation Silver Springs M.D.
12. C.B. Do, M.S. Mahabhashyam, M. Brudno, and S. Batzoglou ProbCons: Probabilistic consistency-based multiple sequence alignment Genome Res. 15 2005 330 340
13. R.C. Edgar MUSCLE: multiple sequence alignment with high accuracy and high throughput Nucleic Acids Res. 32 2004 1792 1797
14. N. Essoussi, K. Boujenfa, and M. Limam A comparison of MSA tools Bioinformation 2 2008 452 455
15. J.R. Fabian, I.O. Daar, and D. Morrison Critical tyrosine residues regulate the enzymatic and biological activity of Raf-1 kinase Mol. Cell. Biol. 13 1993 7170 7179
16. S.B. Ficarro, M.L. McCleland, P.T. Stukenberg, D.J. Burke, M.M. Ross, J. Shabanowitz, D.F. Hunt, and F.M. White Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae Nat. Biotechnol. 20 2002 301 305
17. S. Guindon, and O. Gascuel A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst. Biol. 52 2003 696 704
18. L.J. Holt, B.B. Tuch, J. Villen, A.D. Johnson, S.P. Gygi, and D.O. Morgan Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution Science 325 2009 1682 1686
19. J.H. Hurley, A.M. Dean, P.E. Thorsness, D.E. Koshland Jr.; and R.M. Stroud Regulation of isocitrate dehydrogenase by phosphorylation involves no long-range conformational change in the free enzyme J. Biol. Chem. 265 1990 3599 3602
20. J.H. Hurley, P.E. Thorsness, V. Ramalingam, N.H. Helmers, D.E. Koshland Jr.; and R.M. Stroud Structure of a bacterial enzyme regulated by phosphorylation, isocitrate dehydrogenase Proc. Natl. Acad. Sci. USA 86 1989 8635 8639
21. R. Jorgensen, A.R. Merrill, and G.R. Andersen The life and death of translation elongation factor 2 Biochem. Soc. Trans. 34 2006 1 6
22. P. Kunapuli, V.V. Gurevich, and J.L. Benovic Phospholipid-stimulated autophosphorylation activates the G protein-coupled receptor kinase GRK5 J. Biol. Chem. 269 1994 10209 10212
23. Y.Z. Kurmangaliyev, A. Goland, and M.S. Gelfand Evolutionary patterns of phosphorylated serines Biol. Direct 6 2011 8
24. M.T. Laub, and M. Goulian Specificity in two-component signal transduction pathways Annu. Rev. Genet. 41 2007 121 145
25. G. Manning, G.D. Plowman, T. Hunter, and S. Sudarsanam Evolution of protein kinase signaling from yeast to man Trends Biochem. Sci. 27 2002 514 520
26. G. Manning, D.B. Whyte, R. Martinez, T. Hunter, and S. Sudarsanam The protein kinase complement of the human genome Science 298 2002 1912 1934
27. R. Marais, Y. Light, H.F. Paterson, and C.J. Marshall Ras recruits Raf-1 to the plasma membrane for activation by tyrosine phosphorylation EMBO J. 14 1995 3136 3145
28. S. Miller, J. Janin, A.M. Lesk, and C. Chothia Interior and surface of monomeric proteins J. Mol. Biol. 196 1987 641 656
29. D.O. Morgan Principles of CDK regulation Nature 374 1995 131 134
30. A.M. Moses, J.K. Heriche, and R. Durbin Clustering of phosphorylation site recognition motifs can be exploited to predict the targets of cyclin-dependent kinase Genome Biol. 8 2007 R23
31. J.V. Olsen, B. Blagoev, F. Gnad, B. Macek, C. Kumar, P. Mortensen, and M. Mann Global, in vivo, and site-specific phosphorylation dynamics in signaling networks Cell 127 2006 635 648
32. N.R. Pace Mapping the tree of life: progress and prospects Microbiol. Mol. Biol. Rev. 73 2009 565 576
33. K. Palczewski, J. Buczylko, P. Van Hooser, S.A. Carr, M.J. Huddleston, and J.W. Crabb Identification of the autophosphorylation sites in rhodopsin kinase J. Biol. Chem. 267 1992 18991 18998
34. T. Pawson, G.D. Gish, and P. Nash SH2 domains, interaction modules and cellular wiring Trends Cell Biol. 11 2001 504 511
35. E.F. Pettersen, T.D. Goddard, C.C. Huang, G.S. Couch, D.M. Greenblatt, E.C. Meng, and T.E. Ferrin UCSF Chimera-a visualization system for exploratory research and analysis J. Comput. Chem. 25 2004 1605 1612
36. J. Posada, and J.A. Cooper Requirements for phosphorylation of MAP kinase during meiosis in Xenopus oocytes Science 255 1992 212 215
37. T. Pupko, I. Pe'er, M. Hasegawa, D. Graur, and N. Friedman A branch-and-bound algorithm for the inference of ancestral amino-acid sequences when the replacement rate varies among sites: Application to the evolution of five gene families Bioinformatics 18 2002 1116 1123
38. A.J. Schoeffler, and J.M. Berger DNA topoisomerases: harnessing and constraining energy to govern chromosome topology Q. Rev. Biophys. 41 2008 41 101
39. Z. Serber, and J.E. Ferrell Jr. Tuning bulk electrostatics to regulate protein function Cell 128 2007 441 444
40. S.C. Strickfaden, M.J. Winters, G. Ben-Ari, R.E. Lamson, M. Tyers, and P.M. Pryciak A mechanism for cell-cycle regulation of MAP kinase signaling in a yeast differentiation pathway Cell 128 2007 519 531
41. J.W. Taylor, and M.L. Berbee Dating divergences in the Fungal Tree of Life: review and new analyses Mycologia 98 2006 838 849
42. P.E. Thorsness, and D.E. Koshland Jr. Inactivation of isocitrate dehydrogenase by phosphorylation is mediated by the negative charge of the phosphate J. Biol. Chem. 262 1987 10422 10425
43. H. Tjong, S. Qin, and H.X. Zhou PI2PE: protein interface/interior prediction engine Nucleic Acids Res. 35 2007 W357-362
44. G. Vogt, S. Woell, and P. Argos Protein thermal stability, hydrogen bonds, and ion pairs J. Mol. Biol. 269 1997 631 643
45. P.T. Wan, M.J. Garnett, S.M. Roe, S. Lee, D. Niculescu-Duvaz, V.M. Good, C.M. Jones, C.J. Marshall, C.J. Springer, and D. Barford Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF Cell 116 2004 855 867
46. Z. Wang, N.D. Udeshi, C. Slawson, P.D. Compton, K. Sakabe, W.D. Cheung, J. Shabanowitz, D.F. Hunt, and G.W. Hart Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis Sci. Signal. 3 2010 ra2