Gene fishing: The use of a simple protocol to isolate multiple homeodomain classes from diverse invertebrate taxa

Journal of Molecular Evolution

Volumn 56, Issue 4, 2003, Pages 509-516

  Lee, Shannon E ^a   Gates, Ruth D ^a   Jacobs, David K ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Homeobox genes; HOX; Invertebrate; Lophotrochozoa; Metazoa; PAIRED; ParaHOX; PCR

Indexed keywords

COMPLEMENTARY DNA; GENOMIC DNA; RNA;

AMINO ACID SEQUENCE; ARTICLE; CONTROLLED STUDY; GENE SEQUENCE; HOMEOBOX; INVERTEBRATE; LOPHOTROCHOZOA; METAZOON; NONHUMAN; POLYMERASE CHAIN REACTION; REGULATOR GENE; RNA TRANSLATION;

ACOELA; ANNELIDA; CNIDARIA; ECHIURA; INVERTEBRATA; LOPHOTROCHOZOA; METAZOA; MOLLUSCA; PLATYHELMINTHES; PORIFERA;

EID: 0037381766     PISSN: 00222844     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00239-002-2421-2     Document Type: Article

References (65)

1. Abzhanov A, Kaufman TC (2000) Homologs of Drosophila appendage genes in the patterning of arthropod limbs. Dev Biol 227:673-689
2. Agosti D, Jacobs D, DeSalle R (1996) On combining protein sequences and nucleic acid sequences in phylogenetic analysis: The homeobox protein case. Cladistics 12:65-82
3. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic Local Alignment Search Tool. J Mol Biol 215:403-410
4. Barrels JL, Murtha MT, Ruddle FH (1993) Multiple Hox/HOM-class homeoboxes in platyhelminthes. Mol Phylogenet Evol 2:143-151
5. Bastianello A, Ronco M, Burato PA, Minelli A (2002) Hox gene sequences from the geophilomorph centipede Pachymerium ferrugineum (CL Koch, 1835) (Chilopoda: Geophilomorpha: Geophilidae): Implications for the evolution of the Hox class genes of arthropods. Mol Phylogenet Evol 22:155-161
6. Berney C, Pawlowski J, Zanietti, L (2000) Elongation factor 1-alpha sequences do not support an early divergence of the acoela. Mol Biol Evol 17:1032-1039
7. Bogue CW, Ganea GR, Sturm E, Ianucci R, Jacobs HC (2000) Hex expression suggests a role in the development and function of organs derived from foregut endoderm. Dev Dyn 219:84-89
8. Bonicelli E, Gulisano M, Broccoli V (1993) Emx and Otx homeobox genes in the developing mouse brain. J Neurobiol 24:1356-1366
9. Bulfone A, Puelles L, Porteus MH, Frohman MA, Martin GR, Rubenstein JLR (1993) Spatially restricted expression of Dlx-1, Dlx-2 (Tes-1), Gbx-2, and Wnt-3 in the embryonic day 12.5 mouse forebrain defines potential transverse and longitudinal segmental boundaries. J Neurosci 13:3156-3172
10. Bulfone A, Menguzzato E, Vani B, Marchitiello A, Gattuso C, Mariani M, Consalez GG, Martinez S, Ballabio A, Banfi S (2000) Barh 11, a gene belonging to a new subfamily of mammalian homeobox genes, is expressed in migrating neurons of the CNS. Hum Mol Genet 9:1443-1452
11. Carranza S, Baguña J, Riutort M (1997) Are platyhelminthes a monophyletic primitive group? An assessment using 18S rDNA sequences. Mol Biol Evol 14:485-497
12. Cartwright P, Dick M, Buss LW (1993) HOM/Hox type homeoboxes in the chelicerate Limulus polyphemus. Mol Phylogenet Evol 2:185-192
13. Chen F, Liu KC, Epstein JA (1999) Lbx2, a novel murine homeobox gene related to the Drosophila ladybird genes, is expressed in the developing urogenital system, eye, and brian. Mech Dev 84:181-184
14. Chiang C, Young KE, Beachy PA (1995) Control of Drosophila tracheal branching by the novel homeodomain gene unplugged, a regulatory target for genes of the bithorax complex. Development 121:3901-3912
15. Dalton D, Chadwick R, McGinnis W (1989) Expression and embryonic function of empty spiracles: A Drosophila homeobox gene with two patterning functions on the anterior-posterior axis of the embryo. Genes Dev 3:1940-1956
16. DeRosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, Akam M, Carroll SB, Balavoine G (1998) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399:772-776
17. Dick MH, Buss LW (1994) A PCR-based survey of homeobox genes in Ctenodrilus serratus (Annelida:Polychaeta). Mol Phylogenet Evol 3:146-158
18. Dohrmann C, Azpiazo N, Frasch M (1990) A new Drosophila homeobox gene is expressed in mesodermal precursor cells of distinct muscles during embryogenesis. Genes Dev 4:2098-2111
19. Farris JS, Albert VA, Kallersjo M, Lipscomb D, Kluge AG (1996) Parsimony jackknifing outperforms neighbor-joining. Cladistics 12:99-124
20. Finnerty JR, Master VA, Irvine S, Kourakis MJ, Warriner S, Martindale MQ (1996) Homeobox genes in the Ctenophora: Identification of paired-type and Hox homologues in the atentaculate ctenophore, Beroë ovata. Mol Mar Bio Biotech 5:249-258
21. Galliot B, de Vargas C, Miller D (1999) Evolution of homeobox genes: Q50 Paired-like genes founded the Paired class. Dev Genes Evol 209:186-197
22. Hayashi T, Kojima T, Saigo K (1998) Specification of primary pigment cell and outer photoreceptor fates by BarH1 homeobox gene in the developing Drosophila eye. Dev Biol 200:131-145
23. Hirth F, Therianos S, Loop T, Gehring W, Reichert H, Furukubo-Tokunaga, K (1995) Developmental defects in brain segmentation caused by mutations of the homeobox genes orthodenticle and empty spiracles in Drosophila. Neuron 15:769-778
24. Jacobs DK, Lee SE, Dawson MN, Staton JL, Raskoff KA (1998) The history of development through the evolution of molecules: gene tress, hearts, eyes and dorsoventral inversion. In: R DeSalle, B Schierwater (eds) Molecular approaches to ecology and evolution. Birkhauser Verlag, Basel
25. Jagla K, Frasch M, Jagla T, Dretzen G, Bellard F, Bellard M (1997a) Ladybird, a new component of the cardiogenic pathway in Drosophila required for diversification of the heart precursors. Development 124:3471-3479
26. Jagla K, Jagla T, Heitzler P, Dretzen G, Bellard F, Bellard M (1997b) ladybird, a tandem of homeobox genes that maintain late wingless expression in terminal and dorsal epidermis of the Drosophila embryo. Development 124:91-100
27. Jagla T, Bellard F, Lutz Y, Dretzen G, Bellard M, Jagla K (1998) Ladybird determines cell fate decisions during diversification of Drosophila somatic muscles. Development 125:3699-3708
28. Jagla T, Bellard F, Vonesch J-L, Bellard M, Dastugue B, Jagla K (1999) Plasticity within the lateral somatic mesoderm of Drosophila embryos. Int Dev Biol 43:571-573
29. Jones B, McGinnis W (1993a) The regulation of empty spiracles by Abdominal-B mediates an abdominal segment identity function. Genes Dev 7:229-240
30. Jones B, McGinnis W (1993b) A new Drosophila homeobox gene, bsh, is expressed in a subset of brain cells during embryogenesis. Development 117:793-806
31. Katayama T, Yamamoto M, Wada H, Satoh N (1993) Phylogenetic position of acoel turbellarians inferred from partial 18S rDNA sequences. Zool Sci 10:529-536
32. Keng VW, Yagi H, Ikawa M, Nagano T, Myint Z, Yamada K, Tanaka T, Sato A, Muramatsu I, Okabe M, Sato M, Noguchi T (2000) Homeobox gene Hex is essential for onset of mouse embryonic liver development and differentiation of the monocyte lineage. Biochem Biophys Res Commun 276:1155-1161
33. Kim CB, Bailey W, Amemiya C, Miller W, Shimizu N, Ruddle FH (2000) Hox gene organization of horn shark, Heterodontus francisci. Am Zool 39:78A
34. Kmita-Cunisse M, Loosli F, Bièrne J, Gehring WJ (1998) Homeobox genes in the ribbonworm Lineus sanguineus: Evolutionary implications. Proc Natl Acad Sci USA 95:3030-3035
35. Knirr S, Azpiazu N, Frasch M (1999) The role of the NK-homeobox gene slouch (S59) in somatic muscle patterning. Development 126:4525-4535
36. Kojima T, Sato M, Kaoru S (2000) Formation and specification of distal leg elements in Drosophila by dual Bar homeobox genes, BarH1 and BarH2. Development 127:769-778
37. Littlewood DTJ, Rohde K, Clough KA (1999) The interrelationships of all major groups of Platyhelminthes: Phylogenetic evidence from morphology and molecules. Biol J Linn Soc 66:75-114
38. Martinez B, Pedro J, Clements M, Thomas P, Rodriguez T, Meloy D, Kioussis D, Beddington RSP (2000) The homeobox gene Hex is required in definitive endodermal tissues for normal forebrain, liver, and thyroid formation. Development 127:2433-2445
39. Milewski WM, Duguay SJ, Chan SJ, Steiner DF (1998) Conservation of PDX-1 structure, function, and expression in zebrafish. Endocrinology 139:1440-1449
40. Mokady O, Dick MH, Lackschewitz D, Schierwater B, Buss LW (2000) Over one-half billion years of head conservation? Expression of an ems class gene in Hydractinia symbiolongicarpus (Cnidaria:Hydrozoa). Proc Natl Acad Sci USA 95:3673-3678
41. Mouchel-Viehl E, Rigolot C, Gibert J-M, Deutsch JS (1998) Molecules and the body plan: The Hox genes of cirripedes (Crustacea). Mol Phylogenet Evol 9:382-389
42. Murtha MT, Leckman JF, Ruddle FH (1991) Detection of homeobox genes in development and evolution. Proc Natl Acad Sci USA 88:10711-10715
43. Neyt C, Jagla K, Thisse C, Thisse B, Haines L, Currie PD (2000) Evolutionary origins of vertebrate appendicular muscle. Nature 408:82-86
44. Oliver G, Vispo M, Mailhos A, Martinez C, Sosa-Pineda B, Fielitz W, Ehrlich R (1992) Homeoboxes in flatworms. Gene 121:337-342
45. Patterson KD, Cleaver O, Gerber WV, White FG, Krieg PA (2000) Distinct expression patterns for two Xenopus Bar homeobox genes. Dev Gene Evol 210:140-144
46. Pattyn A, Morin X, Cremer H, Goridis C, Brunet J-F (1997) Expression and interactions of the two closely related homeobox genes Phox2a and Phox2b during neurogenesis. Development 124:4065-4075
47. Pellegrini M, Mansouri A, Simeone A, Boncinelli E, Gruss P (1996) Dentate gyrus formation requires Emx2. Development 122:3893-3898
48. Pendleton JW, Nagai BK, Murtha MT, Ruddle FH (1993) Expansion of the Hox gene family and the evolution of chordates. Proc Natl Acad Sci USA 90:6300-6304
49. Qui M, Anderson S, Chen S, Menese JJ, Hevner R, Kuwana E, Pedersen RA, Rubenstein JLR (1996) Mutation of the Emx-1 homeobox gene disrupts the corpus callosum. Dev Biol 178:174-178
50. Ruiz-Trillo I, Riutort M, Littlewood TJ, Herniou EA, Baguña J (1999) Acoel flatworms: earliest extant bilaterian metazoans, not members of the Platyhelminthes. Science 283:1919-1923
51. Ruiz-Trillo I, Paps J, Loukota M, Ribera C, Jondelius U, Baguna J, Riutort M (2002) A phylogenetic analysis of myosin heavy chain type II sequences corroborates that Acoela and Nemertodermatida are basal bilaterians. Proc Natl Acad Sci USA 9:11246-11251
52. Saito T, Greenwood A, Qi S, Anderson DJ (1995) Identification by differential RT-PCR of a novel Paired homeodomain protein specifically expressed in sensory neurons and a subset of their CNS targets. Mol Cell NeuroSci 6:280-292
53. Schierwater B, Murtha M, Dick M, Ruddle FH, Buss LW (1991) Homeoboxes in cnidarians. J Exp Zool 260:413-416
54. Schubert FR, Fainsod A, Gruenbaum Y, Gruss P (1995) Expression of the novel murine homeobox gene Sax-1 in the developing nervous system. Mech Dev 51:99-114
55. Schubert M, Holland LZ, Holland ND, Jacobs DK (2000) A phylogenetic tree of the Wnt genes based on all available full-length sequences, including five from the cephalochordate amphioxus. Mol Biol Evol 17:1896-1903
56. Semina EV, Mintz-Hittner HA, Murray JC (2000) Isolation and characterization of a novel human paired-like homeodomain-containing transcription factor gene, VSXI, expressed in ocular tissues. Genomics 63:289-293
57. Shamim H, Mason I (1998) Expression of Gbx-2 during early development of the chick embryo. Mech Dev 76:157-159
58. Snow P, Buss LW (1994) Hox-type homeoboxes from Stylaria lacustris (Annelida:Oligochaeta). Mol Phylogenet Evol 3:360-364
59. Uchiyama A, Hanaoka K (2000) Expression of Lbx1 involved in the hypaxial musculature formation of the mouse embryo. J Exp Zool 286:270-279
60. Von Bubnoff, A, Schmidt JE, Kimelman D (1996) The Xenopus laevis homeobox gene Xgbx-2 is an early marker of anteroposterior patterning in the ectoderm. Mech Dev 54:149.160
61. Waldorf U, Gehring, WJ (1992) Empty spiracles, a gap gene containing a homeobox involved in Drosophila head development. EMBO J 11:2247-2259
62. Weiss JB, Von Ohlen T, Mellerick DM, Dressler G, Doe CQ, Scott MP (1998) Dorsoventral patterning in the Drosophila central nervous system: The intermediate neuroblasts defective homeobox gene specifies intermediate column identity. Genes Dev 12:3591-3602
63. Wright CVE, Schnegelsberg P, De Robertis EM (1989) XLHbox8: A novel Xenopus homeoprotein restricted to a narrow band of endoderm. Development 105:787-794
64. Xiong W-C, Okano H, Patel NH, Blendy JA, Montell C (1994) Repo encodes a glial-specific homeodomain protein required in the Drosophila nervous system. Genes Dev 8:981-994
65. Yoshida M, Suda Y, Matsuo I, Miyamoto N, Takeda N, Kuratani S, Aizawa S (1997) Emx1 and Emx2 functions in development of dorsal telecephalon. Development 124:101-111