Evolution of hedgehog and hedgehog-related genes, their origin from Hog proteins in ancestral eukaryotes and discovery of a novel Hint motif

BMC Genomics

Volumn 9, Issue , 2008, Pages

  Bürglin, Thomas R ^a  

^a KAROLINSKA INSTITUTE   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; INTEIN; PROTEIN HINT; SONIC HEDGEHOG PROTEIN; VON WILLEBRAND FACTOR;

AMINO TERMINAL SEQUENCE; ARTICLE; BRUGIA MALAYI; CAENORHABDITIS ELEGANS; COELENTERATE; CONTROLLED STUDY; EUKARYOTE EVOLUTION; GENETIC CODE; GENETIC IDENTIFICATION; MERCENARIA; MULTIGENE FAMILY; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN MOTIF; PROTEIN SECRETION; TRICHINELLA SPIRALIS; AMINO ACID SEQUENCE; ANIMAL; BIOLOGICAL MODEL; BIOLOGY; COMPARATIVE STUDY; GENETICS; GENOMICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; PROTEIN TERTIARY STRUCTURE; SEA ANEMONE; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SPECIES DIFFERENCE; STATISTICAL MODEL;

ANIMALIA; BRUGIA MALAYI; CAENORHABDITIS ELEGANS; CNIDARIA; DEUTEROSTOMIA; ENOPLEA; ERINACEIDAE; EUKARYOTA; NEMATODA; NEMATOSTELLA VECTENSIS; PROTISTA; PROTOSTOMIA; TRICHINELLA SPIRALIS; XIPHINEMA;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOMICS; HEDGEHOG PROTEINS; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MOLECULAR SEQUENCE DATA; NEMATODA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEA ANEMONES; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY;

EID: 42949083286     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-9-127     Document Type: Article

References (71)

1. Cohen MM Jr. The hedgehog signaling network Am J Med Genet A 2003, 123(1):5-28. 10.1002/ajmg.a.20495 14556242
2. Hooper JE Scott MP Communicating with Hedgehogs Nature reviews 2005, 6(4):306-317. 10.1038/nrm1622 15803137
3. Huangfu D Anderson KV Signaling from Smo to Ci/Gli: Conservation and divergence of Hedgehog pathways from Drosophila to vertebrates Development (Cambridge, England) 2006, 133(1):3-14. 16339192
4. Wang Y McMahon AP Allen BL Shifting paradigms in Hedgehog signaling Current opinion in cell biology 2007, 19(2):159-165. 10.1016/ j.ceb.2007.02.005 17303409
5. Beachy PA Karhadkar SS Berman DM Tissue repair and stem cell renewal in carcinogenesis Nature 2004, 432(7015):324-331. 10.1038/nature03100 15549094
6. Briscoe J Thérond P Hedgehog Signaling: From the Drosphila cuticle to anti-cancer drugs Dev Cell 2005, 8:143-151. 10.1016/ j.devcel.2005.01.008 15736317
7. McMahon AP Ingham PW Tabin CJ Developmental roles and clinical significance of hedgehog signaling Current topics in developmental biology 2003, 53:1-114. 12509125
8. Rubin LL de Sauvage FJ Targeting the Hedgehog pathway in cancer Nature reviews 2006, 5(12):1026-1033. 10.1038/nrd2086 17139287
9. Zardoya R Abouheif E Meyer A Evolution and orthology of hedgehog genes. Trends Genet 1996. 12(12):496-497. 10.1016/S0168-9525(96)20014-9 9257526
10. Avaron F Hoffman L Guay D Akimenko MA Characterization of two new zebrafish members of the hedgehog family: Atypical expression of a zebrafish indian hedgehog gene in skeletal elements of both endochondral and dermal origins Dev Dyn 2006, 235(2):478-489. 10.1002/dvdy.20619 16292774
11. Meyer A Schartl M Gene and genome duplications in vertebrates: The one-to-four (-to-eight in fish) rule and the evolution of novel gene functions Current opinion in cell biology 1999, 11(6):699-704. 10.1016/ S0955-0674(99)00039-3 10600714
12. Hall TMT Porter JA Young KE Koonin EV Beachy PA Leahy DJ Crystal structure of a Hedgehog autoprocessing domain: Homology between Hedgehog and self-splicing proteins. Cell 1997, 91:85-97. 10.1016/ S0092-8674(01)80011-8 9335337
13. Porter JA Young KE Beachy PA Cholesterol modification of Hedgehog signaling proteins in animal development. Science 1996, 274:255-259. 10.1126/science.274.5285.255 8824192
14. Bijlsma MF Spek CA Peppelenbosch MP Hedgehog: An unusual signal transducer. Bioessays 2004, 26(4):387-394. 10.1002/bies.20007 15057936
15. Gallet A Rodriguez R Ruel L Therond PP Cholesterol modification of hedgehog is required for trafficking and movement, revealing an asymmetric cellular response to hedgehog Dev Cell 2003, 4(2):191-204. 10.1016/S1534-5807(03)00031-5 12586063
16. Gallet A Ruel L Staccini-Lavenant L Therond PP Cholesterol modification is necessary for controlled planar long-range activity of Hedgehog in Drosophila epithelia Development (Cambridge, England) 2006, 133(3):407-418. 16396912
17. Aspöck G Kagoshima H Niklaus G Bürglin TR Caenorhabditis elegans has scores of hedgehog-related genes: Sequence and expression analysis. Genome Res 1999, 9(10):909-923. 10.1101/gr.9.10.909 10523520
18. Bürglin TR Kuwabara PE Homologs of the Hh signalling network in C. elegans WormBook 2006:1-14. 18050469 10.1895/wormbook.1.76.1
19. Hao L Mukherjee K Liegeois S Baillie D Labouesse M Bürglin TR The hedgehog-related gene qua-1 is required for molting in Caenorhabditis elegans Dev Dyn 2006, 235(6):1469-1481. 10.1002/dvdy.20721 16502424
20. Beachy PA Cooper MK Young KE von Kessler DP Park WJ Hall TMT Leahy DJ Porter JA Multiple roles of cholesterol in hedgehog protein biogenesis and signaling. Cold Spring Harb Symp Quant Biol 1997, 62:191-204. 9598352
21. Dassa B Pietrokovski S Origin and evolution of inteins and other Hint domains Homing Endonucleases and Inteins Springer Belfort M, Stoddard BL, Wood DW, Derbyshire V Nucleic Acids and Molecular Biology 2005.
22. Snell EA Brooke NM Taylor WR Casane D Philippe H Holland PW An unusual choanoflagellate protein released by Hedgehog autocatalytic processing Proc Biol Sci 2006, 273(1585):401-407. 1560198 16615205 10.1098/ rspb.2005.3263
23. Philippe H Snell EA Bapteste E Lopez P Holland PW Casane D Phylogenomics of eukaryotes: Impact of missing data on large alignments Mol Biol Evol 2004, 21(9):1740-1752. 10.1093/molbev/msh182 15175415
24. James TY Kauff F Schoch CL Matheny PB Hofstetter V Cox CJ Celio G Gueidan C Fraker E Miadlikowska J Lumbsch HT Rauhut A Reeb V Arnold AE Amtoft A Stajich JE Hosaka K Sung GH Johnson D O'Rourke B Crockett M Binder M Curtis JM Slot JC Powell MJ Taylor JW McLaughlin DJ Spatafora JW Vilgalys R Reconstructing the early evolution of Fungi using a six-gene phylogeny Nature 2006, 443(7113):818-822. 10.1038/nature05110 17051209
25. Technau U Rudd S Maxwell P Gordon PM Saina M Grasso LC Hayward DC Sensen CW Saint R Holstein TW Ball EE Miller DJ Maintenance of ancestral complexity and non-metazoan genes in two basal cnidarians Trends Genet 2005, 21(12):633-639. 10.1016/j.tig.2005.09.007 16226338
26. Walton KD Croce JC Glenn TD Wu SY McClay DR Genomics and expression profiles of the Hedgehog and Notch signaling pathways in sea urchin development Developmental biology 2006, 300(1):153-164. 1880897 17067570 10.1016/j.ydbio.2006.08.064
27. Nichols SA Dirks W Pearse JS King N Early evolution of animal cell signaling and adhesion genes Proceedings of the National Academy of Sciences of the United States of America 2006, 103(33):12451-12456. 1567900 16891419 10.1073/pnas.0604065103
28. Sullivan JC Ryan JF Watson JA Webb J Mullikin JC Rokhsar D Finnerty JR StellaBase: The Nematostella vectensis Genomics Database Nucleic Acids Res 2006, 34: Database issue D495-9. 1347383 16381919 10.1093/nar/gkj020
29. Requena N Mann P Hampp R Franken P Early developmentally regulated genes in the arbuscular mycorrhizal fungus Glomus mosseae: Identification of GmGIN1, a novel gene with homology to the C-terminus of metazoan hedgehog proteins Plant Soil 2002, 244:129-139. 10.1023/A:1020249932310
30. Perler FB InBase: The Intein Database Nucleic Acids Res 2002, 30(1):383-384. 99080 11752343 10.1093/nar/30.1.383
31. Poulter RT Goodwin TJ Butler MI The nuclear-encoded inteins of fungi Fungal Genet Biol 2007, 44(3):153-179. 10.1016/j.fgb.2006.07.012 17046294
32. Pietrokovski S Intein spread and extinction in evolution Trends Genet 2001, 17(8):465-472. 10.1016/S0168-9525(01)02365-4 11485819
33. Amitai G Belenkiy O Dassa B Shainskaya A Pietrokovski S Distribution and function of new bacterial intein-like protein domains Molecular microbiology 2003, 47(1):61-73. 10.1046/j.1365-2958.2003.03283.x 12492854
34. Pietrokovski S Conserved sequence features of inteins (protein introns) and their use in identifying new inteins and related proteins. Protein Science 1994, 3:2340-2350. 2142770 7756989
35. Dalgaard JZ Moser MJ Hughey R Mian IS Statistical modeling, phylogenetic analysis and structure prediction of a protein splicing domain common to Inteins and Hedgehog proteins. Journal of Computational Biology 1997, 4(2):193-214. 9228618
36. Perler FB Olsen GJ Adam E Compilation and analysis of intein sequences. Nucl Acids Res 1997, 25(6):1087-1093. 146560 9092614 10.1093/nar/ 25.6.1087
37. Saleh L Perler FB Protein splicing in cis and in trans Chemical record 2006, 6(4):183-193. 10.1002/tcr.20082 16900466
38. Hao L Johnsen R Lauter G Baillie D Bürglin TR Comprehensive analysis of gene expression patterns of hedgehog-related genes BMC Genomics 2006, 7:280. 1636047 17076889 10.1186/1471-2164-7-280
39. De Ley P A quick tour of nematode diversity and the backbone of nematode phylogeny WormBook WormBook Community TCR 2006. http://www.wormbook.org 10.1895/wormbook.1.41.1 18050465
40. Huang G Gao B Maier T Allen R Davis EL Baum TJ Hussey RS A profile of putative parasitism genes expressed in the esophageal gland cells of the root-knot nematode Meloidogyne incognita Mol Plant Microbe Interact 2003, 16(5):376-381. 10.1094/MPMI.2003.16.5.376 12744507
41. Genome Sequencing Center, Washington University School of Medicine http://genome.wustl.edu/
42. Varjosalo M Li SP Taipale J Divergence of hedgehog signal transduction mechanism between Drosophila and mammals Dev Cell 2006, 10(2):177-186. 10.1016/j.devcel.2005.12.014 16459297
43. Svard J Heby-Henricson K Persson-Lek M Rozell B Lauth M Bergstrom A Ericson J Toftgard R Teglund S Genetic elimination of Suppressor of fused reveals an essential repressor function in the mammalian Hedgehog signaling pathway Dev Cell 2006, 10(2):187-197. 10.1016/ j.devcel.2005.12.013 16459298
44. Colombatti A Bonaldo P Doliana R Type A modules: Interacting domains found in several non-fibrillar collagens and in other extracellular matrix proteins Matrix 1993, 13(4):297-306. 8412987
45. Perkins SJ Smith KF Williams SC Haris PI Chapman D Sim RB The secondary structure of the von Willebrand factor type A domain in factor B of human complement by Fourier transform infrared spectroscopy. Its occurrence in collagen types VI, VII, XII and XIV, the integrins and other proteins by averaged structure predictions J Mol Biol 1994, 238(1):104-119. 10.1006/jmbi.1994.1271 8145250
46. Baldauf SL The deep roots of eukaryotes Science 2003, 300(5626):1703-1706. 10.1126/science.1085544 12805537
47. Ryan JF Burton PM Mazza ME Kwong GK Mullikin JC Finnerty JR The cnidarian-bilaterian ancestor possessed at least 56 homeoboxes. Evidence from the starlet sea anemone, Nematostella vectensis Genome Biol 2006, 7(7):R64. 1779571 16867185 10.1186/gb-2006-7-7-r64
48. Mukherjee K Bürglin TR Comprehensive Analysis of Animal TALE Homeobox Genes: New Conserved Motifs and Cases of Accelerated Evolution Journal of molecular evolution 2007, 65(2):137-153. 10.1007/ s00239-006-0023-0 17665086
49. J. Craig Venter Institute http://www.tigr.org
50. BLAST: Basic Local Alignment and Search Tool http://www.ncbi.nlm.nih.gov/ blast/
51. Wylie T Martin JC Dante M Mitreva MD Clifton SW Chinwalla A Waterston RH Wilson RK McCarter JP Nematode.net: A tool for navigating sequences from parasitic and free-living nematodes Nucleic Acids Res 2004, 32: Database issue D423-6. 308745 14681448 10.1093/nar/gkh010
52. O'Brien EA Koski LB Zhang Y Yang L Wang E Gray MW Burger G Lang BF TBestDB: A taxonomically broad database of expressed sequence tags (ESTs) Nucleic Acids Res 2007, 35: Database issue D445-51. 1899108 17202165 10.1093/nar/gkl770
53. GSC: BLAST Server http://genome.wustl.edu/tools/blast/
54. StellaBase: Nematostella vectensis Database http://evodevo.bu.edu/ stellabase/
55. DOE Joint Genome Institute http://www.jgi.doe.gov/
56. ZFIN: The Zebrafish Model Organism Database http://zfin.org/
57. Sprague J Bayraktaroglu L Clements D Conlin T Fashena D Frazer K Haendel M Howe DG Mani P Ramachandran S Schaper K Segerdell E Song P Sprunger B Taylor S Van Slyke CE Westerfield M The Zebrafish Information Network: the zebrafish model organism database Nucleic Acids Res 2006, 34: Database issue D581-5. 1347449 16381936 10.1093/nar/gkj086
58. NEB Intein Database http://www.neb.com/neb/inteins.html
59. SoftBerry http://www.softberry.com
60. Bürglin TR PPCMatrix: A PowerPC dotmatrix program to compare large genomic sequences against protein sequences. Bioinformatics 1998, 14(8):751-752. 9789102
61. Sequence Assembly at Iowa State University http://deepc2.psi.iastate.edu/ aat/cap/cap.html
62. Thompson JD Gibson TJ Plewniak F Jeanmougin F Higgins DG The CLUSTAL_X windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucl Acids Res 1997, 25(24):4876-4882. 147148 9396791 10.1093/nar/25.24.4876
63. MUSCLE http://phylogenomics.berkeley.edu/cgi-bin/muscle/input_muscle.py
64. Edgar RC MUSCLE: A multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics 2004, 5(1):113. 517706 15318951 10.1186/1471-2105-5-113
65. Galtier N Gouy M Gautier C SEAVIEW and PHYLO_WIN: Two graphic tools for sequence alignment and molecular phylogeny. Comput Appl Biosci 1996, 12(6):543-548. 9021275
66. Guindon S Gascuel O A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood Syst Biol 2003, 52(5):696-704. 10.1080/10635150390235520 14530136
67. SignalP 3.0 Server http://www.cbs.dtu.dk/services/SignalP/
68. Bendtsen JD Nielsen H von Heijne G Brunak S Improved prediction of signal peptides: SignalP 3.0 J Mol Biol 2004, 340(4):783-795. 10.1016/ j.jmb.2004.05.028 15223320
69. LogoBar - Java application for protein sequence Logos http://www.biosci.ki.se/groups/tbu/logobar/
70. Pérez-Bercoff Koch J Bürglin TR LogoBar: Bar graph visualization of protein logos with gaps Bioinformatics 2006, 22(1):112-114. 10.1093/bioinformatics/bti761 16269415
71. Letunic I Copley RR Schmidt S Ciccarelli FD Doerks T Schultz J Ponting CP Bork P SMART 4.0: Towards genomic data integration Nucleic Acids Res 2004, 32: Database issue D142-4. 308822 14681379 10.1093/nar/gkh088