Repeated evolution of identical domain architecture in metazoan netrin domain-containing proteins

Genome Biology and Evolution

Volumn 4, Issue 9, 2012, Pages 883-899

  Leclère, Lucas ^a   Rentzsch, Fabian ^a  

^a UNIVERSITY OF BERGEN   (Norway)

Author keywords

Convergence; Domain architecture; Multidomain protein; Netrin; Phylogeny; SFRP

Indexed keywords

ANIMALIA; EUKARYOTA; EUMETAZOA; METAZOA;

FRZB PROTEIN; GLYCOPROTEIN; LAMININ; NERVE GROWTH FACTOR;

ANIMAL; ARTICLE; CHEMISTRY; CLASSIFICATION; DROSOPHILA; GENETICS; MOLECULAR EVOLUTION; MOUSE; PHYLOGENY; PROTEIN DOMAIN; SEQUENCE ALIGNMENT; STRONGYLOCENTROTUS;

ANIMALS; DROSOPHILA; EVOLUTION, MOLECULAR; GLYCOPROTEINS; LAMININ; MICE; NERVE GROWTH FACTOR; PHYLOGENY; PROTEIN INTERACTION DOMAINS AND MOTIFS; SEQUENCE ALIGNMENT; STRONGYLOCENTROTUS;

EID: 84873192706     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs061     Document Type: Article

References (77)

1. Abascal F, Zardoya R, Posada D. 2005. ProtTest: selection of best-fit models of protein evolution. Bioinformatics 21:2104-2105.
2. AdamskaM, et al. 2010. Structure and expression of conservedWnt pathway components in the demosponge Amphimedon queenslandica. Evol Dev. 12:494-518.
3. Adell T, Thakur AN, Muller WE. 2007. Isolation and characterization of Wnt pathway-related genes from Porifera. Cell Biol Int. 31:939-949.
4. Banyai L, Patthy L. 1999. The NTR module: domains of netrins, secreted frizzled related proteins, and type I procollagen C-proteinase enhancer protein are homologous with tissue inhibitors of metalloproteases. Protein Sci. 8:1636-1642.
5. Bashton M, Chothia C. 2007. The generation of new protein functions by the combination of domains. Structure 15:85-99.
6. BasuMK, Carmel L, Rogozin IB, Koonin. 2008. Evolution of protein domain promiscuity in eukaryotes. Genome Res. 18:449-461.
7. Bergsten J. 2005. A review of long-branch attraction. Cladistics 21: 163-193.
8. Bhat RA, Stauffer B, Komm BS, Bodine PV. 2007. Structure-function analysis of secreted frizzled-related protein-1 for its Wnt antagonist function. J Cell Biochem. 102:1519-1528.
9. Bovolenta P, Esteve P, Ruiz JM, Cisneros E, Lopez-Rios J. 2008. Beyond Wnt inhibition: new functions of secreted frizzled-related proteins in development and disease. J Cell Sci. 121:737-746.
10. Bramham J, et al. 2005. Functional insights from the structure of the multifunctional C345C domain of C5 of complement. J Biol Chem. 280:10636-10645.
11. Brew K, Nagase H. 2010. The tissue inhibitors of metalloproteinases (TIMPs): an ancient family with structural and functional diversity. Biochim Biophys Acta. 1803:55-71.
12. Brinkmann H, Philippe H. 1999. Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies. Mol Biol Evol. 16:817-825.
13. Brinkmann H, van der Giezen M, Zhou Y, Poncelin de Raucourt G, Philippe H. 2005. An empirical assessment of long-branch attraction artefacts in deep eukaryotic phylogenomics. Syst Biol. 54:743-757.
14. Buljan M, Frankish A, Bateman A. 2010. Quantifying the mechanisms of domain gain in animal proteins. Genome Biol. 11:R74.
15. Chong JM, Uren A, Rubin JS, Speicher DW. 2002. Disulfide bond assignments of secreted frizzled-related protein-1 provide insights about frizzled homology and netrin modules. J Biol Chem. 277: 5134-5144.
16. Delsuc F, Brinkmann H, Philippe H. 2005. Phylogenomics and the reconstruction of the tree of life. Nat Rev Genet. 6:361-375.
17. Edgar RC. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32:1792-1797.
18. Fahey B, Degnan BM. 2012. Origin and evolution of laminin gene family diversity. Mol Biol Evol. 29:1823-1836.
19. Felsenstein J. 1985. Confidence-limits on phylogenies-an approach using the bootstrap. Evolution 39:783-791.
20. Forslund K, Henricson A, Hollich V, Sonnhammer EL. 2008. Domain tree-based analysis of protein architecture evolution. Mol Biol Evol. 25:254-264.
21. Foster PG, Hickey DA. 1999. Compositional bias may affect both DNA-based and protein-based phylogenetic reconstructions. J Mol Evol. 48:284-290.
22. Gatesy J, DeSalle R, Wahlberg N. 2007. How many genes should a systematist sample? Conflicting insights from a phylogenomic matrix characterized by replicated incongruence. Syst Biol. 56:355-363.
23. Goldman N, Anderson JP, Rodrigo AG. 2000. Likelihood-based tests of topologies in phylogenetics. Syst Biol. 49:652-670.
24. Gough J. 2005. Convergent evolution of domain architectures (is rare). Bioinformatics 21:1464-1471.
25. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
26. Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows 95/98/NT. Nucleic Acids Symp. 41: 95-98.
27. Jeffroy O, Brinkmann H, Delsuc F, Philippe H. 2006. Phylogenomics: the beginning of incongruence? Trends Genet. 22:225-231.
28. Jordan IK, Henze K, Fedorova ND, Koonin EV, Galperin MY. 2003. Phylogenomic analysis of the Giardia intestinalis transcarboxylase revealsmultiple instances of domain fusion and fission in the evolution of biotin-dependent enzymes. JMol Microbiol Biotechnol. 5:172-189.
29. Kasahara M. 2007. The 2R hypothesis: an update. Curr Opin Immunol. 19: 547-552.
30. Koch M, et al. 2000. A novel member of the netrin family, beta-netrin, shares homology with the beta chain of laminin: identification, expression, and functional characterization. J Cell Biol. 151:221-234.
31. Koonin EV. 2005. Orthologs, paralogs, and evolutionary genomics. Annu Rev Genet. 39:309-338.
32. Koonin EV, Wolf YI, Karev GP. 2002. The structure of the protein universe and genome evolution. Nature 420:218-223.
33. Kummerfeld SK, Teichmann SA. 2005. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet. 21:25-30.
34. Lai Wing Sun K, Correia JP, Kennedy TE. 2011. Netrins: versatile extracellular cues with diverse functions. Development 138:2153-2169.
35. Lejmi E, et al. 2008. Netrin-4 inhibits angiogenesis via binding to neogenin and recruitment of Unc5B. Proc Natl Acad Sci U S A. 105: 12491-12496.
36. Li Y, Liu Z, Shi P, Zhang J. 2010. The hearing gene Prestin unites echolocating bats and whales. Curr Biol. 20:R55-R56.
37. Liepinsh E, Banyai L, Pintacuda G, Trexler M, Patthy L, Otting G. 2003. NMR structure of the netrin-like domain (NTR) of human type I procollagen C-proteinase enhancer defines structural consensus of NTR domains and assesses potential proteinase inhibitory activity and ligand binding. J Biol Chem. 278:25982-25989.
38. Lin K, et al. 1997. The cysteine-rich frizzled domain of Frzb-1 is required and sufficient for modulation of Wnt signaling. Proc Natl Acad Sci U S A. 94:11196-11200.
39. Lopez-Rios J, Esteve P, Ruiz JM, Bovolenta P. 2008. The netrin-related domain of Sfrp1 interacts with Wnt ligands and antagonizes their activity in the anterior neural plate. Neural Dev. 3:19.
40. Lopez P, Casane D, Philippe H. 2002. Heterotachy, an important process of protein evolution. Mol Biol Evol. 19:1-7.
41. Mii Y, Taira M. 2011. Secreted Wnt "inhibitors" are not just inhibitors: regulation of extracellular Wnt by secreted frizzled-related proteins. Dev Growth Differ. 53:911-923.
42. Moore AD, Bjorklund AK, Ekman D, Bornberg-Bauer E, Elofsson A. 2008. Arrangements in the modular evolution of proteins. Trends Biochem Sci. 33:444-451.
43. Moore SW, Tessier-Lavigne M, Kennedy TE. 2007. Netrins and their receptors. Adv Exp Med Biol. 621:17-31.
44. Nakashiba T, et al. 2000. Netrin-G1: a novel glycosyl phosphatidylinositol-linked mammalian netrin that is functionally divergent from classical netrins. J Neurosci. 20:6540-6550.
45. Page RDM. 1996. TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci. 12:357-358.
46. Pang K, Ryan JF, Mullikin JC, Baxevanis AD, Martindale MQ. 2010. Genomic insights into Wnt signaling in an early diverging metazoan, the ctenophore Mnemiopsis leidyi. Evodevo 1:10.
47. Petersen CP, Reddien PW. 2009. Wnt signaling and the polarity of the primary body axis. Cell 139:1056-1068.
48. Philippe H, Zhou Y, Brinkmann H, Rodrigue N, Delsuc F. 2005. Heterotachy and long-branch attraction in phylogenetics. BMC Evol Biol. 5:50.
49. Qin S, Yu L, Gao Y, Zhou R, Zhang C. 2007. Characterization of the receptors for axon guidance factor netrin-4 and identification of the binding domains. Mol Cell Neurosci. 34:243-250.
50. Rajasekharan S, Kennedy TE. 2009. The netrin protein family. Genome Biol. 10:239.
51. Rambaut A, Grassly NC. 1997. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput Appl Biosci. 13:235-238.
52. Ronquist F, Huelsenbeck JP. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574.
53. Salbaum JM, Kappen C. 2000. Cloning and expression of nope, a new mouse gene of the immunoglobulin superfamily related to guidance receptors. Genomics 64:15-23.
54. SatohW, Gotoh T, Tsunematsu Y, Aizawa S, Shimono A. 2006. Sfrp1 and Sfrp2 regulate anteroposterior axis elongation and somite segmentation during mouse embryogenesis. Development 133:989-999.
55. Seiradake E, et al. 2011. Structural basis for cell surface patterning through NetrinG-NGL interactions. EMBO J. 30:4479-4488.
56. Seo DW, et al. 2003. TIMP-2 mediated inhibition of angiogenesis: an MMP-independent mechanism. Cell 114:171-180.
57. Serafini T, et al. 1996. Netrin-1 is required for commissural axon guidance in the developing vertebrate nervous system. Cell 87: 1001-1014.
58. Sheffield NC, Song H, Cameron SL, Whiting MF. 2009. Nonstationary evolution and compositional heterogeneity in beetle mitochondrial phylogenomics. Syst Biol. 58:381-394.
59. Shimodaira H. 2002. An approximately unbiased test of phylogenetic tree selection. Syst Biol. 51:492-508.
60. Shimodaira H, Hasegawa M. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246-1247.
61. Srivastava M, et al. 2010. The Amphimedon queenslandica genome and the evolution of animal complexity. Nature 466:720-726.
62. Stamatakis A. 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688-2690.
63. Stanco A, et al. 2009. Netrin-1-alpha3beta1 integrin interactions regulate themigration of interneurons through the corticalmarginal zone. Proc Natl Acad Sci U S A. 106:7595-7600.
64. Staquicini FI, et al. 2009. Discovery of a functional protein complex of netrin-4, laminin gamma1 chain, and integrin alpha6beta1 in mouse neural stem cells. Proc Natl Acad Sci U S A. 106:2903-2908.
65. Swofford DL. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods), version 4.0b10 (Alvitec). Sunderland (MA): Sinauer Associates.
66. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739.
67. Toyoda R, Nakamura H,Watanabe Y. 2005. Identification of protogenin, a novel immunoglobulin superfamily gene expressed during early chick embryogenesis. Gene Expr Patterns. 5:778-785.
68. Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA. 2004. Supra-domains: evolutionary units larger than single protein domains. J Mol Biol. 336:809-823.
69. Vogel C, Teichmann SA, Pereira-Leal J. 2005. The relationship between domain duplication and recombination. J Mol Biol. 346:355-365.
70. Wang R, et al. 2009. Autoinhibition of UNC5b revealed by the cytoplasmic domain structure of the receptor. Mol Cell. 33:692-703.
71. Weiner J III, Beaussart F, Bornberg-Bauer E. 2006. Domain deletions and substitutions in the modular protein evolution. FEBS J. 273: 2037-2047.
72. Wu B, Huan T, Gong J, Zhou P, Bai Z. 2011. Domain combination of the vertebrate-like TLR gene family: implications for their origin and evolution. J Genet. 90:401-408.
73. Yanai I, Wolf YI, Koonin EV. 2002. Evolution of gene fusions: horizontal transfer versus independent events. Genome Biol. 3:research0024.
74. Yebra M, et al. 2003. Recognition of the neural chemoattractant Netrin-1 by integrins alpha6beta4 and alpha3beta1 regulates epithelial cell adhesion and migration. Dev Cell. 5:695-707.
75. Yebra M, et al. 2011. Endothelium-derived Netrin-4 supports pancreatic epithelial cell adhesion and differentiation through integrins alpha2-beta1 and alpha3beta1. PLoS One. 6:e22750
76. Yin Y, Miner JH, Sanes JR. 2002. Laminets: laminin- and netrin-related genes expressed in distinct neuronal subsets. Mol Cell Neurosci. 19: 344-358.
77. Zhang Q, Zmasek CM, Godzik A. 2010. Domain architecture evolution of pattern-recognition receptors. Immunogenetics 62:263-272.