Molecular evolution of a developmental pathway: Phylogenetic analyses of transforming growth factor-β family ligands, receptors and Smad signal transducers

Genetics

Volumn 152, Issue 2, 1999, Pages 783-795

  Newfeld, Stuart J ^a   Wisotzkey, Robert G ^a   Kumar, Sudhir ^b  

^a ARIZONA STATE UNIVERSITY   (United States)

^b AXYS Phannaceulicals Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN; RECEPTOR SUBTYPE; TRANSFORMING GROWTH FACTOR BETA; TRANSFORMING GROWTH FACTOR BETA RECEPTOR;

AMINO ACID SEQUENCE; ARTICLE; DEVELOPMENT; GENETIC ASSOCIATION; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PRIORITY JOURNAL; SIGNAL TRANSDUCTION; UNINDEXED SEQUENCE;

AMINO ACID SEQUENCE; ANIMALS; BINDING SITES; CONSERVED SEQUENCE; DROSOPHILA; EVOLUTION, MOLECULAR; GENE EXPRESSION REGULATION, DEVELOPMENTAL; LIGANDS; PHYLOGENY; RECEPTORS, TRANSFORMING GROWTH FACTOR BETA; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; SIGNAL TRANSDUCTION; TRANS-ACTIVATORS; TRANSFORMING GROWTH FACTOR BETA; VARIATION (GENETICS);

ANIMALIA; ARTHROPODA; CAENORHABDITIS ELEGANS; FUNGI; MAMMALIA; NEMATODA;

EID: 0032979875     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article

References (72)

1. AGUINALDO, A., J. TURBEVILLK, I.. LiXFORn, M. RIVKRA, J. GARKV el al., 1997 Evidence for a clade of ncmatodcs, arthropods and other moulting animals. Nature 387: -489-493.
2. BRUMMKI., TJ., V. TWOXIHIY, G. MARQUKS, J. WRANA, SJ. NIVHID et al., 1994 Cliaracterization and relationship ofDpp receptors encoded by the saxophone und thickveins genes in Drosophila. Cell 78: 251-262.
3. BRUMMEL, TJ., S. AIîDOIIAII, T. HAKKRY, M. SIIIMKIJ., J. MKRRIAM el al., 1999 The Drosophila activin receptor Baboon signals through DSmad2 and controls cell proliferation but not patterning during larval development. Genes Dcv. 13: 98-111.
4. BüRGE, C., and S. KARIIN, 1997 Prediction of complete gene structures in human gcnomic DNAJ. Mol. Biol. 268: 78-91.
5. BUKT, D., and A. Luv, 1994 Evolution of the TGF-β superfamily. Prog. Growth Factor Res. 5: 99-118.
6. CiiEN,Y.,A. BHUSHAN and W. VALE, 1997 SmadS mediates the signaling of the receptor serine kinase. Proc. Natl. Acad. Sei. USA 94: 12938-12943.
7. Cmins, S.,J. WRANA, K. ARORA, L. ATTISANO, M. O'CONNOR et al., 1993 Identification of a Drosophila aclivin receptor. Proc. Natl. Acad. Sei. USA 90: 9475-9479.
8. COLLIGNON, J., I. VARIET and E. ROHKRTSOX, 1996 Relationship between asymmetric orfn/expression and the direction of embryonic turning. Nature 381: 155-158.
9. DKRVNCK, R., Y. ZIIANG and X. FENG, 1998 Smads: transcriptional activators of TGF-β responses. Cell 95: 737-740.
10. DOPAZO, J., 1994 Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach. J. Mol. Evol. 38: 300-304.
11. ElTKRT, K., S. SCHKRER, H. O/CKIIK, R. PlROXK, P. HOODI.ESS et al., 1996 MADR2 maps to 18q21 and encodes a TGF-β regulated MAD-rclated protein that is functionally mutated in colorcctal carcinoma: Cell 86: 543-552.
12. ESTEVEZ, M., L. ATTISANO, J. WRANA, P. ALBERT, J. MASSAGUé et al., 1993 The rfn/4 gene encodes a BMP receptor controlling C. elegans daucr lar-a development. Nature 365: 644-649.
13. FEISENSTEIN, J., 1985 Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39: 783-791.
14. FEI-SENSTKINJ., 1993 PHYLIP version 3.5c. University of Washington, Seattle.
15. FITCH, W., and E. MARGOIIASII, 1970 The usefulness of amino acid and nucleotide sequences in evolutionär)' studies. Evol. Biol. 4: 67-109.
16. FRISCH, A., and C. WRIGHT, 1998 XBMPR-II, a novel Xcnopus Type II receptor mediating BMP signaling in embryonic tissues. Development 125: 431-142.
17. GEORC-I, I.., P. ALBERT and D. RIDDLE, 1990 dafl: a C. elegans gene controlling dauer larva development encodes a novel receptor protein kinase. Cell 61: 635-645.
18. GRAFFJ., R. TiiiESJ. SONG, A. CELESTE and D. MELTON, 1994 Studies with a Xcnopus BMP receptor suggest that ventral mesoderminducing signals override dorsal signals in vivo. Cell 79: 169-179.
19. GRAFT, J., A. BANSAI. and D. MELTON, 1996 Xcnopus MAD proteins transduce distinct subsets of signals for the TGF-β family. Cell 85: 479-487.
20. HAERRV, T., O. KIIAISA, M. O'CONNOR and K. WIIARTON, 1998 Synergistic signaling by two BMP ligands through the SAX and TKV receptors controls wing growth and patterning in Drosophila. Development 125: 3977-3987.
21. HAHN, S., M. SCHUTTE, A. HOQUE, C. MOSKAIUK, L. DA COSTA et al., 1996 DPC4, a candidate tumor suppressor gene at human chromosome 18q21.1. Science 271: 350-353.
22. I IICGINS, D., A. BLEASBY and R. FUCHS, 1992 CIUSTAL V: improved software for multiple sequence alignment. Comput. Appl. Biosci. 8: 189-191.
23. In.iis, D., anclj. BULL, 1993 An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis. Syst. Biol. 42: 182-192.
24. HOODIESS. P., T. HAERRY, S. AüDOII.MI, M. STAH.KTOX, M. O'CONNOR el al, 1996 MAORI, a A/nrf-related protein that functions in BMP2 signaling pathways. Cell 85: 489-500.
25. IMAMURA, T., M. TAKASK, A. NISIIIIIARA, E. OKDA, J. HANAI et ni, 1997 Smadβ inhibits signaling by the TGF-β superfamily. Nature 389: 622-626.
26. JACKSON, S., H. NAKATO, M. SUGIURA, A. JANNUJI, R. OAKES el al, 1997 dally, a Drosophila glypican controls cellular responses to the TGF-β related morphogen Dpp. Development 124: 41134120.
27. JIS-G, S., D. WEN, Y. Yu, P. HOLST, Y. Iuo et al, 1996 GDN'F-induced activation of the ret protein lyrosine kinase is mediated by a novel receptor for GDXF. Cell 85: 1113-1124.
28. JONES, C., M. KUKIIN, B. HOGAN, J. SMITH and C. WRIGHT, 1995 Nodal-related signals induce axial mesodcrni and dorsalizc mesoderm in gastnilation. Development 121: 3651-3662.
29. KINGSIKV, D., 1994 The TGF-β superfamily: new members, new receptors, and new genetic tests of function in different organisms. Genes Dcv. 8: 133-146.
30. KOKNIG, B., J. COOK, D. WOISING, J. TING, J. TIESMAN et al, 1994 Characterization and cloning of a receptor for BMP2 and BMP4 from NTH 3T3 cells. Mol. Cell. Biol. 14: 5961-5974.
31. KRISHNA, S., I.. MADUZIA and R. PADGKTT, 1999 Spécifiât)' of TGF-β signaling is conferred by distinct Type I receptors and their associated Smacl proteins in C. elegans. Development 126: 251-260.
32. KUMAR, S., K. TAMURA and M. NEI, 1993 MEGA: Molecular Evolutionary Genetic Analysis. Pennsylvania State University Press, University Park, PA.
33. KUTTY, G., R. KUTTY, W. SAMUKI, T. DUNCAN, C. JAWORSKI et ni., 1998 Identification of a new member of the TGF-β family in Drosophila: the first invertebrate activin gene. Biochem. Biopliys. Res. Commun. 246: 644-649.
34. LEVIN, M., R. JOHNSON, R. STERN, M. KUKIIN and C. TABIN, 1995 A molecular pathway determining left-right asymmetry in chick embryogenesis. Cell 82: 803-814.
35. LIN, L., D. DOIIERTY, J. LIIK, S. BEKTESH and F. COIIINS, 1993 GDN'F: a glial cell line derived ncurotrophic factor for midbrain dopaminergic neurons. Science 260: 1130-1132.
36. Liu, F., F. VENTURA, J. Doonv andj. MASSAGUK, 1995 Human type II receptor for BMPs: extension of the two-kinasc receptor model to the BMPs. Mol. Cell. Biol. 15: 3479-3486.
37. MASSAGUK, J., L. ATTISANO and J. WRANA, 1994 The TGF-β family and its composite receptors. Trends Cell Biol. 4: 172-178.
38. MIYA, T., K. MORITA, A. SUZUKI, N. UKNO and N. SATOII, 1997 Functional analysis of an ascidian homolog of vertebrate BMP2/BMP4 suggests its role in the inhibition of nenralfate specification. Development 124: 5149-5159.
39. NAKAVAMA, T., M. SNYDKR, S. GRKWKI., K. TSUNKIZUMI, T. TAIîATA et al., 1998 Xenopus SmadS acts downstream of BMP4 to modulate its activity during vertebrate embryonic patterning. Development 125: 857-867.
40. NEI, M., S. KUMAR and K. TAKAIIASHI, 1998 The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nuclcotides or amino acids used is small. Proc. Nail. Acad. Sei. USA 95: 12390-12397.
41. NEWFELD, S. J., and W. M. GKIBART, 1995 Identification of tvo Drosophila TGF-β family members in the grasshopper Scfiislocerca americana.]. Mol. Evol. 41: 155-160.
42. NEWFEIH, SJ., E. CIIARTOKFJ. GRAKK, D. MKITON and W. GKIBART, 1996 Mothers against djiji encodes a conserved cytoplasmic protein required in DPP/TGF-β responsive cells. Development 122: 2099-2108.
43. NGUYKN, M., S. PARK, G. MARQUES and K. ARORA, 1998 Interpretation of a BMP activity gradient in Drosophila embryos depends on synergystic signaling by two Type I receptors, SAX and TKV. Cell 95: 495-506.
44. PADGETT, R., J. WOZNEY and W. GEIBART, 1993 Human BMP sequences confer normal dorsal ventral patterning in the Drosophila embryo. Proc. Natl. Acad. Sei. USA 90: 2905-2909.
45. PATTKRSON, G., A. KOWKKK, A. WONG, Y. Liu and G. RUVKUN, 1997 The daf-3 Smad protein antagonizes TGF-β related receptor signaling in the C. elegansdaucr pathway. Genes Dev. 11:2679-2690.
46. POSAKONY, L. G., L. A. RAFTKRY and W. M. GKIBART, 1991 Wing formation in Drosophila requires decapentaplegic function along the anterior-posterior compartment boundary. Mech. Dcv. 33: 69-82.
47. RUHKRTK, E., T. MARI Y, D. NKII.KN, M. AFFOI.TKR and K. BASIKR, 1995 An absolute requirement for both the Type II and Type I receptors Punt and Thickveins for Dpp signaling in vivo. Cell 80: 889-897.
48. RZIIETSKY, A., and M. NEI, 1993 A simple method for estimating and testing minimum-evolution trees. Mol. Biol. Evol. 9:945-967.
49. SAITOU, N., and M. NEI, 1987 The neighborjoining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
50. SAMPATII, T., K. RASHKAJ. DOCTOR, R. TUCKKR and F. M. HOFFMANN, 1993 Drosophila TGF-β superfamily proteins induce endochon-drial bone formation in mammals. Proc. Natl. Acacl. Sei. USA 790: 6004-0008.
51. SAVAGE, C., P. DAS, A. FINKIII, S. TOWNSKND, G. SUN et al, 1996 C. elegans genes sma-2, sma-3, and sma-4 define a conserved family of TGF-β pathway components. Proc. Natl. Acad. Sei. USA 93: 790-794.
52. SINGER, M., A. PENTON, V. TWOMBLY, F. M. HOFFMANN and W. GELBART, 1996 Signaling through both Type I Dpp receptors is required for anterior-posterior patterning of the entire Drosophilaing. Development 124: 79-89.
53. SITNIKOVA, T., 1996 Bootstrap method of interior-branch test for phylogenetic trees. Mol. Biol. Evol. 13: 605-611.
54. SMITH, W., R. MCüKNURV, S. RimsijR. and R. HARIAND, 1995 A norfrtArelated gene defines a physical and functional domain within the Spemann organizer. Cell 82: 37-46.
55. SOIOVVEV, V., and A. SAIAMOV, 1997 The GeneFindcr computer tools for analysis of human and model organism genome sequences. Intel. Sys. Mol. Biol. 5: 294-302.
56. STRIMMER, K., and A. VON HAFSFIER, 1997 Likelihood-mapping: a simple method to visualize phylogenetic content of a sequence alignment. Proc. Natl. Acad. Sei. USA 94: 6815-6819.
57. SUZUKI, A., R. TIIIES, N. YAMAJI, J. So.c.,J. WOZNEY et al., 1994 A truncated BMP receptor affects dorsal-ventral patterning in the early Xcnopns embryo. Proc. Natl. Acad. Sei. USA 91: 1025510259.
58. SWOFFORD, D. L., 1998 PAVP: Phylogenetic Analysis Using Parsimony (and Other Methods). Sinauer Associates, Sunderland, MA.
59. SZUTS, D., S. ERESII and M. BIENZ, 1998 Functional intertwining of Dpp and EGFR signaling during Drosophila cndoderm induction. Genes Dev. 12: 2022-2035.
60. TEN DIJKE, P., H. YAMASIIITA, T. SAMTATH, A. REDDI, M. ESTEVEZ et al, 1994a Identification of Type I receptors for Osteogenic Proteinl and BMP4.J. Biol. Chem. 269: 16985-16988.
61. TEN DIJKE, P., H. YAMASIIITA, H. Icmjo, P. FRAN/KN, M. LAIIIO et al., 1994b Characterization of Type I receptors for TGF-β and activin. Science 264: 101-104.
62. TIIATCHERJ., C. HAUN and P. OKKEMA, 1999 The Daf-3 Smad binds DMA and represses gene expression in the C. elegans pharynx. Development 126: 97-107.
63. TlIIAGAIINGAM, S., C. LENGAUKR, F. LEACH, M. SCHUTTE, S. HAHN et al., 1996 Evaluation of candidate tumor suppressor genes in colorectal cancer. Nat. Genet. 13: 343-346.
64. TSUKAZAKI, T., T. Ci HANG, A. DAVisoN, L. AiTisANO and J. WRANA, 1998 SARA, a FWE domain protein that recruits Smad2 to the TGF-β receptor. Cell 95: 779-791.
65. WANG, D., S. KUMAR and S. B. HEDGES, 1999 Divergence time estimates for the early history of animal phyla: the origin of plants, animals and fungi. Proc. R. Soc. Lond. Ser B 266: 163-171.
66. WFIS-GARCIA, F., andj. MASSAGUé, 1996 Complementation between kinase defective and activation defective TGF-β receptors reveals a novel form of receptor cooperativity essential for signaling. EMBOJ. 15: 276-289.
67. WHITMAN, M., 1998 Smads and early developmental signaling by thc TGF-β snperfamily. Genes Dev. 12: 2445-2462.
68. Wiso TJKKY, R. G., A. MFHRA, D. SUTHERIAND, L. DOIIKNS, X. Liu et al., 1998 Medea is a Drosophila Smad4 homolog that is differentially required to potentiate Dpp responses. Development 125: 14331445.
69. WRANA, J., H. TRAN, L. ATTISANO, K. ARORA, S. GUILDS et al., 1994 Two distinct transmembrane serine-threonine kinases from Drosophila form an activin receptor complex. Mol. Cell. Biol. 14: 994-950.
70. YINGUNG, J., P. DAS, C. SAVAGE, M. ZIIANC, R. PADGETT el al, 1996 Mammalian dwarfins arc phosphor) latcd in response to TGF-β and are implicated in control of cell growth. Proc. Natl. Acad. Sei. USA 93: 8940-8944.
71. ZHOU, X., H. SASAKI, L. LöWE, B. HOGAN and M. KUFIIN, 1993 nodal is a novel TGF-β-likc gene expressed in the mouse node during gastrulation. Nature 361: 543-547.
72. Zou, H., R. WIESER, J. MASSAGUé and L. NISWANüER, 1997 Distinct roles of Type I BMP receptors in the formation and differentiation of cartilage. Genes Dev. II: 2191-2203.