A fish-specific member of the TPPP protein family?

Journal of Molecular Evolution

Volumn 75, Issue 1-2, 2012, Pages 55-72

  Orosz, Ferenc ^a  

^a INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Fish evolution; Paralogon; Phylogenetic analysis; Synteny analysis; Whole genome duplication

Indexed keywords

FISH PROTEIN; MICROTUBULE ASSOCIATED PROTEIN;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; DNA SEQUENCE; FISH; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; ANIMALS; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; FISH PROTEINS; FISHES; MICROTUBULE-ASSOCIATED PROTEINS; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID;

EUKARYOTA; MAMMALIA; TELEOSTEI; VERTEBRATA;

EID: 84868554224     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-012-9521-4     Document Type: Article

References (64)

1. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W et al (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 25:3389-3402
2. Aparicio S, Chapman J, Stupka E, Putnam N, Chia JM, Dehal P et al (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science 297:1301-1310
3. Ari E, Ittzés P, Podani J, Thi QC, Jakó E (2012) Comparison of Boolean analysis and standard phylogenetic methods using artificially evolved and natural mt-tRNA sequences from great apes. Mol Phylogenet Evol 63:193-202
4. Bishop MJ, Friday AE (1987) Tetrapod relationships: the molecular evidence. In: Patterson C (ed) Molecules and morphology in evolution: conflict or compromise?. Cambridge University Press, Cambridge, pp 1123-139
5. Bork P, Dandekar T, Diaz-Lazcoz Y, Eisenhaber F, Huynen M, Yuan Y (1998) Predicting function: from genes to genomes and back. J Mol Biol 283:707-725
6. Catchen JM, Conery JS, Postlethwait JH (2009) Automated identification of conserved synteny after whole genome duplication. Genome Res 19:1497-1505
7. Chen JW, Romero P, Uversky VN, Dunker AK (2006) Conservation of intrinsic disorder in protein domains and families: II. Functions of conserved disorder. J Proteome Res 5:888-898
8. Christoffels A, Koh EG, Chia JM, Brenner S, Aparicio S, Venkatesh B (2004) Fugu genome analysis provides evidence for a wholegenome duplication early during the evolution of ray-finned fishes. Mol Biol Evol 21:1146-1151
9. Dehal P, Boore JL (2005) Two rounds of whole genome duplication in the ancestral vertebrate. PLoS Biol 3:e314
10. Feiner N, Begemann G, Renz AJ, Meyer A, Kuraku S (2009) The origin of bmp16, a novel Bmp2/4 relative, retained in teleost fish genomes. BMC Evol Biol 9:277
11. Felsenstein J (2008) PHYLIP (Phylogeny Inference Package), version 3.68. Department of Genome Sciences and Department of Biology, University of Washington, Seattle, WA
12. Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y et al (2011) Ensembl 2011. Nucl Acids Res 39:D800-D806
13. Hlavanda E, Kovács J, Oláh J, Orosz F, Medzihradszky KF, Ovádi J (2002) Brain-specific p25 protein binds to tubulin and microtubules and induces aberrant microtubule assemblies at substoichiometric concentrations. Biochemistry 417:8657-8664
14. Hlavanda E, Klement E, Kókai E, Kovács J, Vincze O, Tokési N et al (2007) Phosphorylation blocks the activity of tubulin polymerization-promoting protein (TPPP): identification of sites targeted by different kinases. J Biol Chem 282:29531-29539
15. Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E et al (2004) Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature 431:946-957
16. Jakó E, Ari E, Ittzés P, Horváth A, Podani J (2009) BOOL-AN: a method for comparative sequence analysis and phylogenetic reconstruction. Mol Phylogenet Evol 52:887-897
17. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275-282
18. Jun. J, Mandoiu II, Nelson CE (2009) Identification of mammalian orthologs using local synteny. BMC Genomics 10:630
19. Kasahara M (2007) The 2R hypothesis: an update. Curr Opin Immunol 19:547-552
20. Kasahara M, Naruse K, Sasaki S, Nakatani Y, Qu W, Ahsan B et al (2007) The medaka draft genome and insights into vertebrate genome evolution. Nature 447:714-719
21. Kishino H, Miyata T, Hasegawa M (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. J Mol Evol 30:151-160
22. Koonin EV, Wolf YI (2010) Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet 11:487-498
23. Kovács GG, László L, Kovács J, Jensen PH, Lindersson E, Botond G et al (2004) Natively unfolded tubulin polymerization promoting protein TPPP/p25 is a common marker of alpha-synucleinopathies. Neurobiol Dis 17:155-162
24. Kuraku S (2008) Insights into cyclostome phylogenomics: pre-2R or post-2R. Zool Sci 25:960-968
25. Kuraku S, Meyer A, Kuratani S (2009) Timing of genome duplications relative to the origin of the vertebrates: did cyclostomes diverge before or after? Mol Biol Evol 26:47-59
26. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948
27. Lavoué S, Miya M, Inoue JG, Saitoh K, Ishiguro NB, Nishida M (2005) Molecular systematics of the gonorynchiform fishes (Teleostei) based on whole mitogenome sequences: implications for higher-level relationships within the Otocephala. Mol Phylogenet Evol 37:165-177
28. Lehotzky A, Tirián L, Tokési N, Lénárt P, Szabó B, Kovács J et al (2004) Dynamic targeting of microtubules by TPPP/p25 affects cell survival. J Cell Sci 117:6249-6259
29. Lehotzky A, Tokési N, Gonzalez-Alvarez I, Merino V, Bermejo M, Orosz F et al (2008) Progress in the development of early diagnosis and a drug with unique pharmacology to improve cancer therapy. Philos Trans A Math Phys Eng Sci 366:3599-3617
30. Lehotzky A, Lau P, Tokési N, Muja N, Hudson LD, Ovádi J (2010) Tubulin polymerization-promoting protein (TPPP/p25) is critical for oligodendrocyte differentiation. Glia 58:157-168
31. Muffato M, Louis A, Poisnel C-E, Roest Crollius H (2010) Genomicus: a database and a browser to study gene synteny in modern and ancestral genomes. Bioinformatics 26:1119-1121
32. Nakatani Y, Takeda H, Kohara Y, Morishita S (2007) Reconstruction of the vertebrate ancestral genome reveals dynamic genome reorganization in early vertebrates. Genome Res 17:1254-1265
33. Ohno S (1970) Evolution by gene duplication. Springer, Berlin
34. Orosz F (2009) Apicortin, a unique protein, with a putative cytoskeletal role, shared only by apicomplexan parasites and the placozoan Trichoplax adhaerens. Infect Genet Evol 9:1275-1286
35. Orosz F, Ovádi J (2008) TPPP orthologs are ciliary proteins. FEBS Lett 582:3757-3764
36. Orosz F, Kovács GG, Lehotzky A, Oláh J, Vincze O, Ovádi J (2004) TPPP/p25: from unfolded protein to misfolding disease, prediction and experiments. Biol Cell 96:701-711
37. Orosz F, Lehotzky A, Oláh J, Ovádi J (2009) TPPP/p25: a new unstructured protein hallmarking synucleinopathies, In: Ovádi J, Orosz F (eds) Protein folding and misfolding: neurodegenerative diseases, Focus on structural biology, vol 7. Springer, New York, pp 225-250
38. Ovádi J, Orosz F (2009) An unstructured protein with destructive potential: TPPP/p25 in neurodegeneration. BioEssays 31:676-686
39. Panopoulou G, Hennig S, Groth D, Krause A, Poustka AJ, Herwig R et al (2003) New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes. Genome Res 13:1056-1066
40. Pébusque MJ, Coulier F, Birnbaum D, Pontarotti P (1998) Ancient large-scale genome duplications, phylogenetic and linkage analyses shed light on chordate genome evolution. Mol Biol Evol 15:1145-1159
41. Podani J (2000) Introduction to the exploration of multivariate biological data. Backhuys Publishers, Leiden
42. Postlethwait JH (2007) The zebrafish genome in context: ohnologues gone missing. J Exp Zool B Mol Dev Evol 308:563-577
43. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixture models. Bioinformatics 19:1572-1574
44. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
45. Sato Y, Hashiguchi Y, Nishida M (2009) Temporal pattern of loss/persistence of duplicate genes involved in signal transduction and metabolic pathways after teleost-specific genome duplication. BMC Evol Biol 9:127
46. Schmidt HA (2009) Testing tree topologies. In: Lemey P, Salemi M, Vandamme AM (eds) The phylogenetic handbook: a practical approach to phylogenetic analysis and hypothesis testing, 2nd edn. Cambridge University Press, Cambridge, pp 381-404
47. Schmidt HA, Strimmer K, Vingron M, von Haeseler A (2002) TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing. Bioinformatics 18:502-504
48. Shimodaira H (2002) An approximately unbiased test of phylogenetic tree selection. Syst Biol 51:492-508
49. Shimodaira H, Hasegawa M (1999) Multiple comparisons of loglikelihoods with applications to phylogenetic inference. Mol Biol Evol 16:1114-1116
50. Shimodaira H, Hasegawa M (2001) CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247
51. Skjoerringe T, Lundvig DMS, Jensen PH, Moos T (2006) P25 alpha/tubulin polymerization promoting protein expression by myelinating oligodendrocytes of the developing rat brain. J Neurochem 99:333-342
52. Staverosky JA, Pryce BA, Watson SS, Schweitzer R (2009) Tubulin polymerization-promoting protein family member 3, Tpp p3, is a specific marker of the differentiating tendon sheath and synovial joints. Dev Dyn 238:685-692
53. Strimmer K, Rambaut A (2002) Inferring confidence sets of possibly misspecified gene trees. Proc R Soc Lond B 269:137-142
54. Takahashi M, Tomizawa K, Ishiguro K, Sato K, Omori A, Sato S et al (1991) A novel brainspecific 25 kDa protein (p25) is phosphorylated by a Ser/Thr-Pro kinase (TPK II) from tau protein kinase fractions. FEBS Lett 289:37-43
55. Takahashi M, Tomizawa K, Fujita SC, Sato K, Uchida T, Imahori K (1993) A brain-specific protein p25 is localized and associated with oligodendrocytes, neuropil, and fiber-like structures of the CA hippocampal region in the rat brain. J Neurochem 60:228-235
56. Tatusov RL, Koonin EV, Lipman DJ (1997) A genomic perspective on protein families. Science 278:631-637
57. Tirián L, Hlavanda E, Oláh J, Horváth I, Orosz F, Szabó B et al (2003) TPPP/p25 promotes tubulin assemblies and blocks mitotic spindle formation. Proc Natl Acad Sci USA 100:13976-13981
58. Tokési N, Lehotzky A, Horváth I, Szabó B, Oláh J, Lau P et al (2010) TPPP/p25 promotes tubulin acetylation by inhibiting histone deacetylase 6. J Biol Chem 285:17896-17906
59. Vincze O, Tokési N, Oláh J, Hlavanda E, Zotter A, Horváth I et al (2006) TPPP proteins, members of a new family with distinct structures and functions. Biochemistry 45:13818-13826
60. Wolfe K (2000) Robustness-it's not where you think it is. Nat Genet 25:3-4
61. Zhang Z, Wu CC, Huang W-N, Wang S, Zhao E, Huang Q et al (2002) A novel human gene whose product shares homology with bovine brain-specific protein p25 is expressed in fetal brain but not in adult brain. J Hum Genet 47:266-268
62. Zhou W, Li J, Wang X, Hu R (2010a) Stable knockdown of TPPP3 by RNA interference in Lewis lung carcinoma cell inhibits tumor growth and metastasis. Mol Cell Biochem 343:231-238
63. Zhou W, Wang X, Li L, Feng X, Yang Z, Zhang W et al (2010b) Depletion of tubulin polymerization promoting protein family member 3 suppresses HeLa cell proliferation. Mol Cell Biochem 333:91-98
64. Zhou RM, Jing YY, Guo Y, Gao C, Zhang BY, Chen C et al (2011) Molecular interaction of TPPP with PrP antagonized the CytoPrP-induced disruption of microtubule structures and cytotoxicity. PLoS ONE 6:e23079