Hippo Pathway Phylogenetics Predicts Monoubiquitylation of Salvador and Merlin/Nf2

PLoS ONE

Volumn 7, Issue 12, 2012, Pages

  Wisotzkey, Robert G ^a   Konikoff, Charlotte E ^b   Newfeld, Stuart J ^c  

^a NextBio   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c ARIZONA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HIPPO KINASE; MERLIN; PHOSPHOTRANSFERASE; SALVADOR PROTEIN; TRANSFORMING GROWTH FACTOR BETA; TUMOR SUPPRESSOR PROTEIN; UNCLASSIFIED DRUG; WNT PROTEIN;

ARTICLE; INTRACELLULAR SIGNALING; MONOUBIQUITINATION; PHYLOGENY; PREDICTION; PROTEIN DEGRADATION; REGULATORY MECHANISM; UBIQUITINATION;

ANIMALS; BAYES THEOREM; CELL CYCLE PROTEINS; DROSOPHILA MELANOGASTER; DROSOPHILA PROTEINS; HUMANS; INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS; LIKELIHOOD FUNCTIONS; LYSINE; NEUROFIBROMIN 2; PHOSPHORYLATION; PHYLOGENY; PROTEIN-SERINE-THREONINE KINASES; SIGNAL TRANSDUCTION; SMAD4 PROTEIN; TRANSFORMING GROWTH FACTOR BETA; UBIQUITIN;

ANURA; MAMMALIA;

EID: 84871332284     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0051599     Document Type: Article

References (43)

1. Sebé-Pedrós A, Zheng Y, Ruiz-Trillo I, Pan D, (2012) Premetazoan origin of the Hippo signaling pathway. Cell Reports 1: 13-20.
2. Hilman D, Gat U, (2011) The evolutionary history of Yap and the Hippo/Yap pathway. Mol Biol Evol 28: 2403-2417.
3. Newfeld SJ, Wisotzkey R (2006) Molecular Evolution of Smad Proteins. In Smad Signal Transduction, eds. Heldin C, ten Dijke P, Springer, Dordrecht, Netherlands, 15-35.
4. Konikoff C, Wisotzkey R, Newfeld S, (2008) Lysine conservation and context in TGF-ß and Wnt signaling suggests new targets and general themes for post-translational modification. J Mol Evol 67: 323-333.
5. Dupont S, Inui M, Newfeld S, (2012) Regulation of TGF-β signal transduction by mono- and deubiquitylation of Smads. FEBS Letters 586: 1913-1920.
6. Fuentealba L, Eivers E, Ikeda C, Hurtado H, Kuroda H, et al. (2007) Integrating patterning signals: Wnt/GSK3 regulates the duration of the BMP/Smad1 signal. Cell 131: 980-993.
7. Quijano J, Stinchfield M, Newfeld S, (2011) Wg signaling via Zw3 and Mad restricts self-renewal of sensory organ precursor cells in Drosophila. Genetics 189: 809-824.
8. Dupont S, Mamidi A, Cordenonsi M, Montagner M, Zacchigna L, et al. (2009) FAM/USP9x a deubiquitinating enzyme essential for TGF-β signaling controls Smad4 monoubiquitination. Cell 136: 123-135.
9. Stinchfield M, Takaesu N, Quijano J, Castillo A, Tiusanen N, et al. (2012) Fat facets deubiquitylation of Medea/Smad4 modulates interpretation of a Dpp morphogen gradient. Development 139: 2721-2729.
10. Konikoff C, Wisotzkey R, Stinchfield M, Newfeld S, (2010) Distinct molecular evolutionary mechanisms underlie the functional diversification of the Wnt and TGF-β pathways. J Mol Evol 70: 303-312.
11. Halder G, Johnson R, (2001) Hippo signaling: growth control and beyond. Development 138: 9-22.
12. Shaw R, Kohlmaier A, Polesello C, Veelken C, Edgar B, et al. (2010) The Hippo pathway regulates intestinal stem cell proliferation during Drosophila adult midgut regeneration. Development 137: 4147-4158.
13. Zhao B, Li L, Lei Q, Guan K, (2010) The Hippo-Yap pathway in organ size control and tumorigenesis: an updated version. Genes Dev 24: 862-874.
14. Morén A, Hellman U, Inada Y, Imamura T, Heldin C, (2003) Differential ubiquitination defines the functional status of Smad4. J Biol Chem 278: 33571-33582.
15. Cai Y, Huang T, Hu L, Shi X, Xie L, et al. (2012) Prediction of lysine ubiquitination with mRMR feature selection and analysis. Amino Acids 42: 1387-1395.
16. Tung C, Ho S, (2008) Computational identification of ubiquitylation sites from protein sequences. BMC Bioinformatics 9: 310.
17. Radivojac P, Vacic V, Haynes C, Cocklin R, Mohan A, et al. (2010) Identification, analysis, and prediction of protein ubiquitination sites. Proteins 78: 365-380.
18. Hedges S, Kumar K (2009) Time tree of life. Oxford University Press, New York, New York.
19. Record C, Chaikuad A, Rellos P, Das S, Pike A, et al. (2010) Structural comparison of human mammalian Ste20-like kinases. PLoS One 5: e11905.
20. Hwang E, Ryu K, Pääkkönen K, Güntert P, Cheong H, et al. (2007) Structural insight into dimeric interaction of the SARAH domains from Mst and RASSF proteins in apoptosis. Proc Natl Acad Sci USA 104: 9236-9241.
21. Poy F, Lepourcelet M, Shivdasani R, Eck M, (2001) Structure of a humanTcf4-ß-catenin complex. Nature Struct Biol 8: 1053-1057.
22. Yang J, Cron P, Good V, Thompson V, Hemmings B, et al. (2002) Crystal structure of an activated Akt/Protein kinase B ternary complex with GSK3-peptide and AMP-PNP. Nat Struct Biol 9: 940-944.
23. Mrkobrada S, Boucher L, Ceccarelli D, Tyers M, Sicheri F, (2006) Structural and functional analysis of S. cerevisiae Mob1. J Mol Biol 362: 430-440.
24. Lapi E, DiAgostino S, Donzelli S, Gal H, Domany E, et al. (2008) PML, YAP and p73 are components of a proapoptotic autoregulatory feedback loop. Mol Cell 32: 803-814.
25. Zhao B, Li L, Tumaneng K, Wang C, Guan K, (2010) A coordinated phosphorylation by Lats and CK1 regulates YAP stability through SCFβ-TRCP. Genes Dev 24: 72-85.
26. Burglin T, (1991) The TEA domain: a highly conserved DNA binding motif. Cell 66: 11-12.
27. Yogesha S, Sharff A, Giovannini M, Bricogne G, Izard T, (2011) Unfurling of the FERM domain of the Merlin tumor suppressor. Protein Sci 20: 2113-2120.
28. Hirano Y, Hatano T, Takahashi A, Toriyama M, Inagaki N, et al. (2011) Structural basis of cargo recognition by the myosin-XMyTH4-FERM domain. EMBO J 30: 2734-2747.
29. Tang X, Jang S, Wang X, Liu Z, Bahr S, et al. (2007) Akt phosphorylation regulates tumor-suppressor Merlin through ubiquitination and degradation. Nat Cell Biol 9: 1199-1207.
30. Jukam D, Desplan C, (2010) Binary regulation of Hippo pathway by Merlin/NF2, Kibra, Lgl, and Melted specifies and maintains postmitotic neuronal fate. Dev Cell 21: 874-887.
31. Sidow A, (1996) Genome duplication in the evolution of vertebrates. Curr Opin Genet Dev 6: 715-722.
32. Amores A, Force A, Yan Y, Joly L, Amemiya C, et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-1714.
33. Gray R, Bayly R, Green S, Agarwala S, Lowe C, et al. (2009) Diversification of the expression patterns and developmental functions of the Dishevelled family during chordate evolution. Dev Dynamics 238: 2044-2057.
34. Huminiecki L, Goldovsky L, Freilich S, Moustakas A, Ouzounis C, et al. (2009) Emergence, development and diversification of TGF-β signaling in animals. BMC Evol Biol 9: 28.
35. Capra E, Perchuk B, Skerker J, Laub M, (2012) Adaptive mutations that prevent crosstalk enable the expansion of paralogous signaling protein families. Cell 150: 222-232.
36. Takaesu N, Hyman-Walsh C, Ye S, Wisotzkey R, Stinchfield M, et al. (2006) dSno facilitates Baboon signaling in the Drosophila brain by switching the affinity of Medea away from Mad and toward dSmad2. Genetics 174: 1299-1313.
37. Ponte I, Vidal-Taboada J, Suau P, (1998) Evolution of the vertebrate H1 histone class: evidence for the functional differentiation of the subtypes. Mol Biol Evol 15: 702-708.
38. Delport W, Scheffler K, Botha G, Gravenor M, Muse S, et al. (2010) Codon test: modeling amino acid substitution preferences in coding sequences. PLoS Comp Biol 6: e1000885.
39. Newfeld S, Wisotzkey R, Kumar S, (1999) Molecular evolution of a developmental pathway: Phylogenetic analyses of TGF-β family ligands, receptors and Smad signal transducers. Genetics 152: 783-795.
40. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, et al. (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28: 2731-2739.
41. Edgar R, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
42. Ronquist F, Huelsenbeck J, (2003) MrBayes3: bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
43. Abascal F, Zardoya R, Posada D, (2005) ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21: 2104-5.