Improving Hox protein classification across the major model organisms

PLoS ONE

Volumn 5, Issue 5, 2010, Pages

  Hueber, Stefanie D ^a   Weiller, Georg F ^a   Djordjevic, Michael A ^a   Frickey, Tancred ^a  

^a AUSTRALIAN NATIONAL UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

HOMEODOMAIN PROTEIN; HOX PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; CAENORHABDITIS ELEGANS; CLASSIFICATION; CONTROLLED STUDY; DNA FLANKING REGION; DROSOPHILA MELANOGASTER; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PHYLOGENY; PREDICTION; PROTEIN ANALYSIS; PROTEIN DATABASE; PROTEIN FUNCTION; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SYNTENY; UNINDEXED SEQUENCE; ZEBRA FISH; ANIMAL; ANIMAL MODEL; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; GENETICS; METABOLISM; MULTIGENE FAMILY;

BRANCHIOSTOMA FLORIDAE; CAENORHABDITIS ELEGANS; DANIO RERIO; DROSOPHILA MELANOGASTER; MUS MUSCULUS;

ANIMALS; CLUSTER ANALYSIS; HOMEODOMAIN PROTEINS; MODELS, ANIMAL; MODELS, MOLECULAR; MULTIGENE FAMILY;

EID: 77956294348     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010820     Document Type: Article

References (57)

1. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276: 565-70.
2. Schneuwly S, Klemenz R, Gehring WJ (1987) Redesigning the body plan of Drosophila by ectopic expression of the homoeotic gene Antennapedia. Nature 325: 816-8.
3. Goodman FR (2002) Limb malformations and the human HOX genes. Am J Hum Genet 112: 256-65.
4. Wellik DM (2007) Hox patterning of the vertebrate axial skeleton. Dev Dyn 236: 2454-63.
5. Harding K, Wedeen C, McGinnis W, Levine M (1985) Spatially regulated expression of homeotic genes in Drosophila. Science 229: 1236-42.
6. Duboule D, Dollé P (1989) The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes. EMBO J 8: 1497-505.
7. McGinnis W, Garber RL, Wirz J, Kuroiwa A, Gehring WJ (1984) A homologous protein-coding sequence in Drosophila homeotic genes and its conservation in other metazoans. Cell 37: 403-8.
8. Scott MP, Weiner AJ (1984) Structural relationships among genes that control development: sequence homology between the Antennapedia, Ultrabithorax, and fushi tarazu loci of Drosophila. Proc Natl Acad Sci 81: 4115-9.
9. Gehring WJ, Affolter M, Burglin T (1994) Homeodomain proteins. Annu Rev Biochem 63: 487-526.
10. Garcia-Fernandez J, (2005) The genesis and evolution of homeobox gene clusters. Nat Rev Genet 6: 881-92.
11. Garcia-Fernandez J, Holland PWH, (1994) Archetypal organization of the amphioxus Hox gene cluster. Nature 370: 563-6.
12. Carroll SB (1995) Homeotic genes and the evolution of arthropods and chordates. Nature 376: 479-85.
13. Putnam NH, Butts T, Ferrier DEK, Furlong RF, Hellsten U, et al. (2008) The amphioxus genome and the evolution of the chordate karyotype. Nature 453: 1064-71.
14. de Rosa R, Grenier JK, Andreeva T, Cook CE, Adoutte A, et al. (1999) Hox genes in brachiopods and priapulids and protostome evolution. Nature 399: 772-6.
15. Minguillon C, Gardenyes J, Serra E, Castro LFC, Hill-Force A, et al. (2005) No more than 14: the end of the amphioxus Hox cluster. Int J Biol Sci 1: 19-23.
16. Duboule D (2007) The rise and fall of Hox gene clusters. Development 134: 2549-60.
17. Amores A, Force A, Yan YL, Joly L, Amemiya C, et al. (1998) Zebrafish hox clusters and vertebrate genome evolution. Science 282: 1711-4.
18. Heuer JG, Kaufman TC (1992) Homeotic genes have specific functional roles in the establishment of the Drosophila embryonic peripheral nervous system. Development 115: 35-47.
19. Chauvet S, Merabet S, Bilder D, Scott MP, Pradel J, et al. (2000) Distinct hox protein sequences determine specificity in different tissues. Proc Natl Acad Sci 97: 4064-9.
20. Hueber SD, Bezdan D, Henz SR, Blank M, Wu H, et al. (2007) Comparative analysis of Hox downstream genes in Drosophila. Development 134: 381-92.
21. Krumlauf R (1992) Evolution of the vertebrate Hox homeobox genes. Bioessays 14: 245-52.
22. Gehring WJ, Kloter U, Suga H (2009) Evolution of the Hox Gene Complex from an Evolutionary Ground State. Curr Top Dev Biol 88: 35-61.
23. Monteiro AS, Ferrier DEK (2006) Hox genes are not always Colinear. Int J Biol Sci 2: 95-103.
24. Veraksa A, Del Campo M, McGinnis W (2000) Developmental patterning genes and their conserved functions: from model organisms to humans. Mol Genet Metab 69: 85-100.
25. Prince VE (2002) The Hox Paradox: More complex (es) than imagined. Dev Biol 249: 1-15.
26. Garcia-Fernandez J, (2004) Hox, ParaHox, ProtoHox: facts and guesses. Heredity 94: 145-52.
27. Lemons D, McGinnis W (2006) Genomic evolution of Hox gene clusters. Science 313: 1918-22.
28. McGinnis W, Kuziora M (1994) The molecular architects of body design. Sci Am 270: 58-61, 64-6.
29. Pearson JC, Lemons D, McGinnis W (2005) Modulating Hox gene functions during animal body patterning. Nat Rev Genet 6: 893-904.
30. Foronda D, de Navas LF, Garaulet DL, Sanchez-Herrero E (2008) Function and specificity of Hox genes. Int J Dev Biol 53: 1404-19.
31. Hueber SD, Lohmann I (2008) Shaping segments: Hox gene function in the genomic age. Bioessays 30: 965-79.
32. De Robertis EM (2008) Evo-Devo: Variations on Ancestral Themes. Cell 132: 185-95.
33. Lewis EB, Pfeiffer BD, Mathog DR, Celniker SE (2003) Evolution of the homeobox complex in the Diptera. Curr Biol 13: 587-8.
34. Lutz B, Lu HC, Eichele G, Miller D, Kaufman TC (1996) Rescue of Drosophila labial null mutant by the chicken ortholog Hoxb-1 demonstrates that the function of Hox genes is phylogenetically conserved. Genes Dev 10: 176-84.
35. McGinnis N, Kuziora MA, McGinnis W (1990) Human Hox-4.2 and Drosophila deformed encode similar regulatory specificities in Drosophila embryos and larvae. Cell 63: 969-76.
36. Zhao JJ, Lazzarini RA, Pick L (1993) The mouse Hox-1.3 gene is functionally equivalent to the Drosophila Sex combs reduced gene. Genes Dev 7: 343-54.
37. Zakany J, Gerard M, Favier B, Potter SS, Duboule D (1996) Functional equivalence and rescue among group 11HoxGene products in vertebral patterning. Dev Biol 176: 325-8.
38. Greer JM, Puetz J, Thomas KR, Capecchi MR (2000) Maintenance of functional equivalence during paralogous Hox gene evolution. Nature 403: 661-5.
39. Tvrdik P, Capecchi MR (2006) Reversal of Hox1 gene subfunctionalization in the mouse. Developmental cell 11: 239-50.
40. Malicki J, Schughart K, McGinnis W (1990) Mouse Hox-2.2 specifies thoracic segmental identity in Drosophila embryos and larvae. Cell 63: 961-7.
41. Malicki J, Bogarad LD, Martin MM, Ruddle FH, McGinnis W (1993) Functional analysis of the mouse homeobox gene HoxB9 in Drosophila development. Mech Dev 42: 139-50.
42. Hunter CP, Kenyon C (1995) Specification of anteroposterior cell fates in Caenorhabditis elegans by Drosophila Hox proteins. Nature 377: 229-32.
43. Percival-Smith A, Teft WA, Barta JL (2005) Tarsus determination in Drosophila melanogaster. Genome 48: 712-21.
44. Biggin MD, McGinnis (1997) Regulation of segmentation and segmental identity by Drosophila homeoproteins: the role of DNA binding in functional activity and specificity. 124: 4425-33.
45. Ferrier DEK, Minguillón C, Holland PWH, Garcia-Fernandez J, (2000) The amphioxus Hox cluster: deuterostome posterior flexibility and Hox14. Evolution and Development 2: 284-93.
46. Ruddle FH, Bartels JL, Bentley KL, Kappen C, Murtha MT, et al. (1994) Evolution of Hox genes. Annu Rev Genet 28: 423-42.
47. Ruvkun G, Hobert O (1998) The taxonomy of developmental control in Caenorhabditis elegans. Science 282: 2033-41.
48. Ali N, Bienz M (1991) Functional dissection of Drosophila abdominal-B protein. Mech Dev 35: 55-64.
49. Joshi R, Passner JM, Rohs R, Jain R, Sosinsky A, et al. (2007) Functional specificity of a Hox protein mediated by the recognition of minor groove structure. Cell 131: 530-43.
50. Reed HC, Hoare T, Thomsen S, Weaver TA, White RAH, et al. (2009) Alternative Splicing Modulates Ubx Protein Function in Drosophila melanoga-ster. Genetics.
51. Merabet S, Hudry B, Saadaoui M, Graba Y (2009) Classification of sequence signatures: a guide to Hox protein function. Bioessays 31: 500-11.
52. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-402.
53. Frickey T, (2009) AlnEdit at the RSBS Bioinformatics Server: Available at: http://www.webcitation.org/query.php?url=http://bioinfoserver.rsbs.anu.edu. au/programs/alnedit/&refdoi=10.1186/1471-2229-8-1. Accessed 23 December 2009.
54. Edgar RC (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32: 1792-7.
55. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14: 755-63.
56. Frickey T, Lupas A (2004) CLANS: a Java application for visualizing protein families based on pairwise similarity. Bioinformatics 20: 3702-4.
57. Frickey T, Weiller G (2007) Analyzing microarray data using CLANS. Bioinformatics 23: 1170-1.