Origins of Myc Proteins - Using Intrinsic Protein Disorder to Trace Distant Relatives

PLoS ONE

Volumn 8, Issue 9, 2013, Pages

  Mahani, Amir ^a   Henriksson, Johan ^a   Wright, Anthony P H ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

INTRINSIC PROTEIN; MEMBRANE PROTEIN; MYC PROTEIN; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; ARTICLE; DIMERIZATION; ENERGY METABOLISM; HUMAN; HUMAN CELL; MONOSIGA BREVICOLLIS; NONHUMAN; PHYLOGENETIC TREE; PROTEIN ANALYSIS; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEIN DEFICIENCY; PROTEIN DOMAIN; PROTEIN FUNCTION; PROTEIN MOTIF; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; PROTEIN SYNTHESIS; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; CONSERVED SEQUENCE; HUMANS; INTRINSICALLY DISORDERED PROTEINS; MOLECULAR SEQUENCE DATA; NEOPLASMS; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; PROTO-ONCOGENE PROTEINS C-MYC; SEQUENCE ALIGNMENT;

EID: 84884570252     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0075057     Document Type: Article

References (69)

1. Eilers M, Eisenman RN, (2008) Myc's broad reach. Genes & Development 22: 2755-2766.
2. Lüscher B, Vervoorts J, (2012) Regulation of gene transcription by the oncoprotein MYC. Gene 494: 145-160.
3. Sodir NM, Evan GI (2011) Finding cancer's weakest link.
4. Albihn A, Johnsen JI, Arsenian Henriksson M (2010) Chapter 6- MYC in Oncogenesis and as a Target for Cancer Therapies. In: George FVW, George K, editors. Advances in Cancer Research: Academic Press. 163-224.
5. Soucek L, Whitfield J, Martins CP, Finch AJ, Murphy DJ, et al. (2008) Modelling Myc inhibition as a cancer therapy. Nature 455: 679-683.
6. Smith K, Dalton S, (2010) Myc transcription factors: key regulators behind establishment and maintenance of pluripotency. Regen Med 5: 947-959.
7. Morton CC, Nussenzweig MC, Sousa R, Sorenson GD, Pettengill OS, et al. (1989) Mapping and characterization of an X-linked processed gene related to MYCL1. Genomics 4: 367-375.
8. Robertson NG, Pomponio RJ, Mutter GL, Morton CC, (1991) Testis-specific expression of the human MYCL2 gene. Nucleic Acids Res 19: 3129-3137.
9. Takahashi K, Yamanaka S, (2006) Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors. Cell 126: 663-676.
10. Evan GI, Wyllie AH, Gilbert CS, Littlewood TD, Land H, et al. (1992) Induction of apoptosis in fibroblasts by c-myc protein. Cell 69: 119-128.
11. Luscher B, Larsson LG, (1999) The basic region/helix-loop-helix/leucine zipper domain of Myc proto-oncoproteins: function and regulation. Oncogene 18: 2955-2966.
12. Arabi A, Wu S, Ridderstrale K, Bierhoff H, Shiue C, et al. (2005) c-Myc associates with ribosomal DNA and activates RNA polymerase I transcription. Nat Cell Biol 7: 303-310.
13. Gomez-Roman N, Grandori C, Eisenman RN, White RJ, (2003) Direct activation of RNA polymerase III transcription by c-Myc. Nature 421: 290-294.
14. Grandori C, Gomez-Roman N, Felton-Edkins ZA, Ngouenet C, Galloway DA, et al. (2005) c-Myc binds to human ribosomal DNA and stimulates transcription of rRNA genes by RNA polymerase I. Nat Cell Biol. 7: 311-318.
15. van Riggelen J, Yetil A, Felsher DW, (2010) MYC as a regulator of ribosome biogenesis and protein synthesis. Nat Rev Cancer 10: 301-309.
16. Dang CV, Le A, Gao P, (2009) MYC-induced cancer cell energy metabolism and therapeutic opportunities. Clin Cancer Res 15: 6479-6483.
17. Hydbring P, Larsson LG, (2010) Cdk2: a key regulator of the senescence control function of Myc. Aging (Albany NY) 2: 244-250.
18. Gallant P, (2006) Myc/Max/Mad in invertebrates: the evolution of the Max network. Curr Top Microbiol Immunol 302: 235-253.
19. Marandel L, Labbe C, Bobe J, Le Bail PY, (2012) Evolutionary history of c-myc in teleosts and characterization of the duplicated c-myca genes in goldfish embryos. Molecular reproduction and development 79: 85-96.
20. Johnston LA, Prober DA, Edgar BA, Eisenman RN, Gallant P, (1999) Drosophila myc regulates cellular growth during development. Cell 98: 779-790.
21. Iritani BM, Eisenman RN, (1999) c-Myc enhances protein synthesis and cell size during B lymphocyte development. Proc Natl Acad Sci U S A 96: 13180-13185.
22. Trumpp A, Refaeli Y, Oskarsson T, Gasser S, Murphy M, et al. (2001) c-Myc regulates mammalian body size by controlling cell number but not cell size. Nature 414: 768-773.
23. Flinn EM, Busch CM, Wright AP, (1998) myc boxes, which are conserved in myc family proteins, are signals for protein degradation via the proteasome. Mol Cell Biol 18: 5961-5969.
24. Salghetti SE, Kim SY, Tansey WP, (1999) Destruction of Myc by ubiquitin-mediated proteolysis: cancer-associated and transforming mutations stabilize Myc. Embo J 18: 717-726.
25. Smith-Sorensen B, Hijmans EM, Beijersbergen RL, Bernards R, (1996) Functional analysis of Burkitt's lymphoma mutant c-Myc proteins. The Journal of biological chemistry 271: 5513-5518.
26. Nair SK, Burley SK, (2003) X-ray structures of Myc-Max and Mad-Max recognizing DNA. Molecular bases of regulation by proto-oncogenic transcription factors. Cell 112: 193-205.
27. McEwan IJ, Dahlman-Wright K, Ford J, Wright AP, (1996) Functional interaction of the c-Myc transactivation domain with the TATA binding protein: evidence for an induced fit model of transactivation domain folding. Biochemistry 35: 9584-9593.
28. Liu J, Perumal NB, Oldfield CJ, Su EW, Uversky VN, et al. (2006) Intrinsic disorder in transcription factors. Biochemistry 45: 6873-6888.
29. Xue B, Oldfield CJ, Van YY, Dunker AK, Uversky VN, (2012) Protein intrinsic disorder and induced pluripotent stem cells. Mol Biosyst 8: 134-150.
30. Nilsson J, Grahn M, Wright AP, (2011) Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins. Genome biology 12: R65.
31. King N, Westbrook MJ, Young SL, Kuo A, Abedin M, et al. (2008) The genome of the choanoflagellate Monosiga brevicollis and the origin of metazoans. Nature 451: 783-788.
32. McFerrin LG, Atchley WR, (2011) Evolution of the Max and Mlx networks in animals. Genome biology and evolution 3: 915-937.
33. Young SL, Diolaiti D, Conacci-Sorrell M, Ruiz-Trillo I, Eisenman RN, et al. (2011) Premetazoan ancestry of the Myc-Max network. Mol Biol Evol 28: 2961-2971.
34. Mulder N, Apweiler R, (2007) InterPro and InterProScan: tools for protein sequence classification and comparison. Methods Mol Biol 396: 59-70.
35. Hartl M, Mitterstiller AM, Valovka T, Breuker K, Hobmayer B, et al. (2010) Stem cell-specific activation of an ancestral myc protooncogene with conserved basic functions in the early metazoan Hydra. Proceedings of the National Academy of Sciences of the United States of America 107: 4051-4056.
36. Yada M, Hatakeyama S, Kamura T, Nishiyama M, Tsunematsu R, et al. (2004) Phosphorylation-dependent degradation of c-Myc is mediated by the F-box protein Fbw7. Embo J 23: 2116-2125.
37. Andresen C, Helander S, Lemak A, Fares C, Csizmok V, et al. (2012) Transient structure and dynamics in the disordered c-Myc transactivation domain affect Bin1 binding. Nucleic Acids Res 40: 6353-6366.
38. Daughdrill GW, Borcherds WM, Wu H, (2011) Disorder predictors also predict backbone dynamics for a family of disordered proteins. PloS one 6: e29207.
39. Dinkel H, Michael S, Weatheritt RJ, Davey NE, Van Roey K, et al. (2012) ELM-the database of eukaryotic linear motifs. Nucleic Acids Res 40: D242-251.
40. Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, et al. (2009) Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature biotechnology 27: 829-839.
41. Meszaros B, Simon I, Dosztanyi Z, (2009) Prediction of protein binding regions in disordered proteins. PLoS Comput Biol 5: e1000376.
42. Chang DW, Claassen GF, Hann SR, Cole MD, (2000) The c-Myc transactivation domain is a direct modulator of apoptotic versus proliferative signals. Molecular and cellular biology 20: 4309-4319.
43. Srivastava M, Begovic E, Chapman J, Putnam NH, Hellsten U, et al. (2008) The Trichoplax genome and the nature of placozoans. Nature 454: 955-960.
44. Ferreira ME, Hermann S, Prochasson P, Workman JL, Berndt KD, et al. (2005) Mechanism of transcription factor recruitment by acidic activators. J Biol Chem 280: 21779-21784.
45. Hermann S, Berndt KD, Wright AP, (2001) How transcriptional activators bind target proteins. J Biol Chem 276: 40127-40132.
46. Fuxreiter M, Simon I, Bondos S, (2011) Dynamic protein-DNA recognition: beyond what can be seen. Trends Biochem Sci 36: 415-423.
47. Toth-Petroczy A, Oldfield CJ, Simon I, Takagi Y, Dunker AK, et al. (2008) Malleable machines in transcription regulation: the mediator complex. PLoS Comput Biol 4: e1000243.
48. Hsu W-L, Oldfield CJ, Xue B, Meng J, Huang F, et al. (2013) Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding. Protein Science 22: 258-273.
49. Brown CJ, Johnson AK, Daughdrill GW, (2010) Comparing models of evolution for ordered and disordered proteins. Mol Biol Evol 27: 609-621.
50. Brown CJ, Johnson AK, Dunker AK, Daughdrill GW, (2011) Evolution and disorder. Current Opinion in Structural Biology 21: 441-446.
51. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. Journal of molecular biology 215: 403-410.
52. Suzek BE, Huang H, McGarvey P, Mazumder R, Wu CH, (2007) UniRef: comprehensive and non-redundant UniProt reference clusters. Bioinformatics 23: 1282-1288.
53. Skinner MK, Rawls A, Wilson-Rawls J, Roalson EH, (2010) Basic helix-loop-helix transcription factor gene family phylogenetics and nomenclature. Differentiation 80: 1-8.
54. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, et al. (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
55. Notredame C, Higgins DG, Heringa J, (2000) T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol 302: 205-217.
56. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
57. Peng K, Radivojac P, Vucetic S, Dunker AK, Obradovic Z, (2006) Length-dependent prediction of protein intrinsic disorder. BMC bioinformatics 7: 208.
58. Bordoli L, Kiefer F, Schwede T, (2007) Assessment of disorder predictions in CASP7. Proteins 69Suppl 8: 129-136.
59. Walsh I, Martin AJ, Di Domenico T, Tosatto SC, (2012) ESpritz: accurate and fast prediction of protein disorder. Bioinformatics 28: 503-509.
60. Dosztanyi Z, Csizmok V, Tompa P, Simon I, (2005) IUPred: web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21: 3433-3434.
61. Dosztanyi Z, Csizmok V, Tompa P, Simon I, (2005) The pairwise energy content estimated from amino acid composition discriminates between folded and intrinsically unstructured proteins. Journal of molecular biology 347: 827-839.
62. Xue B, Dunbrack RL, Williams RW, Dunker AK, Uversky VN, (2010) PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochimica et biophysica acta 1804: 996-1010.
63. Romero Obradovic, Dunker K, (1997) Sequence Data Analysis for Long Disordered Regions Prediction in the Calcineurin Family. Genome Inform Ser Workshop Genome Inform 8: 110-124.
64. Romero P, Obradovic Z, Li X, Garner EC, Brown CJ, et al. (2001) Sequence complexity of disordered protein. Proteins 42: 38-48.
65. Radivojac P, Obradovic Z, Brown CJ, Dunker AK (2003) Prediction of boundaries between intrinsically ordered and disordered protein regions. Pac Symp Biocomput: 216-227.
66. Dosztanyi Z, Meszaros B, Simon I, (2009) ANCHOR: web server for predicting protein binding regions in disordered proteins. Bioinformatics 25: 2745-2746.
67. Wickham H (2009) ggplot2: Elegant Graphics for Data Analysis: Springer.
68. Suzuki R, Shimodaira H, (2006) Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics 22: 1540-1542.
69. Grothendieck G (2012) sqldf: Perform SQL Selects on R Data Frames. R package version 04-64 http://CRAN.R-project.org/package=sqldf. Accessed August 15, 2013.