Homeodomain revisited: A lesson from disease-causing mutations

Human Genetics

Volumn 116, Issue 6, 2005, Pages 433-444

  Chi, Young In ^a  

^a UNIVERSITY OF KENTUCKY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARGININE; HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HOMEODOMAIN PROTEIN; NUCLEAR FACTOR I; TRANSCRIPTION FACTOR; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; AMINO TERMINAL SEQUENCE; AUTOSOMAL DOMINANT DISORDER; BIOINFORMATICS; COMPUTER SYSTEM; CONGENITAL MALFORMATION; CRYSTALLOGRAPHY; DATA BASE; DEVELOPMENTAL DISORDER; DNA BINDING; DNA BINDING MOTIF; FRAMESHIFT MUTATION; GENE MAPPING; GENE MUTATION; GENE SEQUENCE; GENE STRUCTURE; GENE TARGETING; GENETIC CODE; GENETIC CONSERVATION; GENETIC DISORDER; GENETIC VARIABILITY; HUMAN; INFORMATION RETRIEVAL; MISSENSE MUTATION; MUTATIONAL ANALYSIS; NONHUMAN; NONSENSE MUTATION; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN DEGRADATION; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN STABILITY; REVIEW; SEQUENCE ANALYSIS; TRANSCRIPTION REGULATION; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; GENETICS; MOLECULAR GENETICS; MUTATION; NUCLEOTIDE SEQUENCE;

AMINO ACID SEQUENCE; CONSERVED SEQUENCE; GENETIC DISEASES, INBORN; HOMEODOMAIN PROTEINS; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MUTATION; TRANSCRIPTION FACTORS;

EID: 21444446875     PISSN: 03406717     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00439-004-1252-1     Document Type: Review

References (64)

1. Acton TB, Mead J, Steiner AM, Vershon AK (2000) Scanning mutagenesis of Mcm1: Residues required for DNA binding, DNA bending, and transcriptional activation by a MADS-box protein. Mol Cell Biol 20:1-11
2. Ades SE, Sauer RT (1994) Differential DNA-binding specificity of the engrailed homeodomain: The role of residue 50. Biochemistry 33:9187-9194 1:CAS:528:DyaK2cXlt1Krs7Y%3D
3. Aishima J, Wolberger C (2003) Insights into nonspecific binding of homeodomains from a structure of MATalpha2 bound to DNA. Proteins 51:544-551
4. Antonarakis SE, Krawczak M, Cooper DN (2000) Disease-causing mutations in the human genome. Eur J Pediatr 159 (Suppl 3):S173-S178
5. Billeter M (1996) Homeodomain-type DNA recognition. Prog Biophys Mol Biol 66:211-225
6. Bullock AN, Fersht AN (2001) Rescuing the function of mutant p53. Nat Rev Cancer 1:68-76
7. Chi YI, Frantz JD, Oh BC, Hansen L, Dhe-Paganon S, Shoelson SE (2002) Diabetes mutations delineate an atypical POU domain in HNF-1alpha. Mol Cell 10:1129-1137
8. Choo Y, Isalan M (2000) Advances in zinc finger engineering. Curr Opin Struct Biol 10:411-416
9. Connolly JP, Augustine JG, Francklyn C (1999) Mutational analysis of the engrailed homeodomain recognition helix by phage display. Nucleic Acids Res 27:1182-1189
10. DJ Cooper M Krawczak SE Antonarakis 1997 The nature and mechanisms of human gene mutation In: CD Scriver AL Beaudet WS Sly D Valle (eds) The metabolic and molecular basis of inherited disease 7th edn McGraw-Hill New York 259-291
11. Dattani MT, Martinez-Barbera JP, Thomas PQ, Brickman JM, Gupta R, Martensson IL, Toresson H, Fox M, Wales JK, Hindmarsh PC, Krauss S, Beddington RS, Robinson IC (1998) Mutations in the homeobox gene HESX1/ Hesx1 associated with septo-optic dysplasia in human and mouse. Nat Genet 19:125-133
12. D'Elia AV, Tell G, Paron I, Pellizzari L, Lonigro R, Damante G (2001) Missense mutations of human homeoboxes: A review. Hum Mutat 18:361-374
13. Di Palma T, Nitsch R, Mascia A, Nitsch L, Di Lauro R, Zannini M (2003) The paired domain-containing factor Pax8 and the homeodomain-containing factor TTF-1 directly interact and synergistically activate transcription. J Biol Chem 278:3395-3402
14. D Duboule 1994 Guidebook to the homeodomain genes Oxford University Press Oxford
15. Engelkamp D, Heyningen V van (1996) Transcription factors in disease. Curr Opin Genet Dev 6:334-342
16. Ferrer-Costa C, Orozco M, Cruz X de la (2002) Characterization of disease-associated single amino acid polymorphisms in terms of sequence and structure properties. J Mol Biol 315:771-786
17. Gehring W (1966) Cell heredity and changes of determination in cultures of imaginal discs in Drosophila melanogaster. J Embryol Exp Morphol 15:77-111
18. Gehring WJ, Qian YQ, Billeter M, Furukubo-Tokunaga K, Schier AF, Resendez-Perez D, Affolter M, Otting G, Wuthrich K (1994) Homeodomain-DNA recognition. Cell 78:211-223 10.1016/0092-8674(94)90292-5
19. Goodman FR, Scambler PJ (2001) Human HOX gene mutations. Clin Genet 59:1-11
20. Grant RA, Rould MA, Klemm JD, Pabo CO (2000) Exploring the role of glutamine 50 in the homeodomain-DNA interface: Crystal structure of engrailed (Gln50 → ala) complex at 2.0 Å. Biochemistry 39:8187-8192
21. Harada R, Dufort D, Denis-Larose C, Nepveu A (1994) Conserved cut repeats in the human cut homeodomain protein function as DNA binding domains. J Biol Chem 269:2062-2067
22. Hobert O, Westphal H (2000) Functions of LIM-homeobox genes. Trends Genet 16:75-83
23. Jacobson EM, Li P, Leon-del-Rio AM, Rosenfeld MG, Aggarwal AK (1997) Structure of Pit-1 POU domain bound to DNA as a dimer: Unexpected arrangement and flexibility. Genes Dev 11:198-212
24. Jamieson AC, Miller JC, Pabo CO (2003) Drug discovery with engineered zinc-finger proteins. Nat Rev Drug Discov 2:361-368
25. Jimenez-Sanchez G, Childs B, Valle D (2001) Human disease genes. Nature 409:853-855
26. Kalodimos CG, Biris N, Bonvin AMJJ, Levandoski MM, Guennuegues M, Boelens R, Kaptein R (2004) Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes. Science 305:386-389
27. Krawczak M, Chuzhanova NA, Stenson PD, Johansen BN, Ball EV, Cooper DN (2000) Changes in primary DNA sequence complexity influence the phenotypic consequences of mutations in human gene regulatory regions. Hum Genet 107:362-365
28. Lewis EB (1978) A gene complex controlling segmentation in Drosophila. Nature 276:565-570
29. McGinnis W, Levine MS, Hafen E, Kuroiwa A, Gehring WJ (1984) A conserved DNA sequence in homoeotic genes of the Drosophila antennapedia and bithorax complexes. Nature 308:428-433
30. McIntosh I, Dreyer SD, Clough MV, Dunston JA, Eyaid W, Roig CM, Montgomery T, Ala-Mello S, Kaitila I, Winterpacht A, Zabel B, Frydman M, Cole WG, Francomano CA, Lee B(1998) Mutation analysis of LMX1B gene in nail-patella syndrome patients. Am J Hum Genet 63:1651-1658
31. Morrison KL, Weiss GA (2001) Combinatorial alanine-scanning. Curr Opin Chem Biol 5:302-307
32. Ogata K, Sato K, Tahirov TH, Tahirov T (2003) Eukaryotic transcriptional regulatory complexes: Cooperativity from near and afar. Curr Opin Struct Biol 13:40-48
33. Okada Y, Nagai R, Sato T, Matsuura E, Minami T, Morita I, Doi T (2003) Homeodomain proteins MEIS1 and PBXs regulate the lineage-specific transcription of the platelet factor 4 gene. Blood 101:4748-4756
34. Pabo CO, Peisach E, Grant RA (2001) Design and selection of novel Cys2His2 zinc finger proteins. Annu Rev Biochem 70:313-340
35. Pfeifer GP (2000) p53 mutational spectra and the role of methylated CpG sequences. Mutat Res 450:155-166
36. Pomerantz JL, Sharp PA (1994) Homeodomain determinants of major groove recognition. Biochemistry 33:10851-10858
37. Qu S, Tucker SC, Ehrlich JS, Levorse JM, Flaherty LA, Wisdom R, Vogt TF (1998) Mutations in mouse aristaless-like4 cause Strong's luxoid polydactyly. Development 125:2711-2721
38. Quentien M-H, Pitoia F, Gunz G, Guillet M-P, Enjalbert A, Pellegrini I (2002) Regulation of prolactin, GH, and Pit-1 gene expression in anterior pituitary by Pitx2: An approach using Pitx2 mutants. Endocrinology 143:2839-2851
39. Ryan AK, Rosenfeld MG (1997) POU domain family values: Flexibility, partnerships, and developmental codes. Genes Dev 11:1207-1225 1:CAS:528:DyaK2sXjsFaitb8%3D
40. Sato K, Simon MD, Levin AM, Shokat KM, Weiss GA (2004) Dissecting the engrailed homeodomain-DNA interaction by phage-displayed shotgun scanning. Chem Biol 11:1017-1023
41. 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 USA 81:4115-4119
42. Seidman JG, Seidman C (2002) Transcription factor haploinsufficiency: when half a loaf is not enough. J Clin Invest 109:451-455
43. GL Semenza 1989 Transcription factors and human disease Oxford University Press Oxford
44. Shang Z, Isaac VE, Li H, Patel L, Catron KM, Curran T, Montelione GT, Abate C (1994) Design of a "minimA1" homeodomain: The N-terminal arm modulates DNA binding affinity and stabilizes homeodomain structure. Proc Natl Acad Sci USA 91:8373-8377
45. Simon MD, Shokat KM (2004) Adaptability at a protein-DNA interface: re-engineering the engrailed homeodomain to recognize an unnatural nucleotide. J Am Chem Soc 126:8078-8079
46. Simon MD, Sato K, Weiss GA, Shokat KM (2004) A phage display selection of engrailed homeodomain mutants and the importance of residue Q50. Nucleic Acids Res 32:3623-3631
47. Swaroop A, Wang Q, Wu W, Cook J, Coats C, Xu S, Chen S, Zack D, Sieving P (1999) Leber congenital amaurosis caused by a homozygous mutation (R90W) in the homeodomain of the retinal transcription factor CRX: direct evidence for the involvement of CRX in the development of photoreceptor function. Hum Mol Genet 8:299-305
48. Treisman J, Gonczy P, Vashishtha M, Harris E, Desplan C (1989) A single amino acid can determine the DNA binding specificity of homeodomain proteins. Cell 59:553-562
49. Tucker-Kellogg L, Rould MA, Chambers KA, Ades SE, Sauer RT, Pabo CO (1997) Engrailed (Gln50 → Lys) homeodomain-DNA complex at 1.9 A resolution: Structural basis for enhanced affinity and altered specificity. Structure 5:1047-1054
50. Vaxillaire M, Abderrahmani A, Boutin P, Bailleul B, Froguel P, Yaniv M, Pontoglio M (1999) Anatomy of a homeoprotein revealed by the analysis of human MODY3 mutations. J Biol Chem 274:35639-35646
51. Vitkup D, Sander C, Church GM (2003) The amino-acid mutational spectrum of human genetic disease. Genome Biol 4:R72
52. Wang Z, Moult J (2001) SNPs, protein structure, and disease. Hum Mutat 17:263-270
53. Weiler S, Gruschus JM, Tsao DH, Yu L, Wang LH, Nirenberg M, Ferretti JA (1998) Site-directed mutations in the vnd/NK-2 homeodomain. Basis of variations in structure and sequence-specific DNA binding. J Biol Chem 273:10994-11000
54. Wilkie AO, Tang Z, Elanko N, Walsh S, Twigg SR, Hurst JA, Wall SA, Chrzanowska KH, Maxson RE Jr (2000) Functional haploinsufficiency of the human homeobox gene MSX2 causes defects in skull ossification. Nat Genet 24:387-390
55. Wilson DS, Guenther B, Desplan C, Kuriyan J (1995) High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell 82:709-719
56. Wolberger C (1996) Homeodomain interactions. Curr Opin Struct Biol 6:62-68
57. Wolfe SA (2004) Mapping key elements of a protein motif. Chem Biol 11:889-891
58. Wolfe SA, Nekludova L, Pabo CO (2000) DNA recognition by Cys2His2 zinc finger proteins. Annu Rev Biophys Biomol Struct 29:183-212
59. Wu W, Cogan JD, Pfaffle RW, Dasen JS, Frisch H, O'Connell SM, Flynn SE, Brown MR, Mullis PE, Parks JS, Phillips JA 3rd, Rosenfeld MG (1998) Mutations in PROP1 cause familial combined pituitary hormone deficiency. Nat Genet 18:147-149
60. Xu HE, Rould MA, Xu W, Epstein JA, Maas RL, Pabo CO (1999) Crystal structure of the human Pax6 paired domain-DNA complex reveals specific roles for the linker region and carboxy-terminal subdomain in DNA binding. Genes Dev 13:1263-1275
61. Yamada S, Tomura H, Nishigori H, Sho K, Mabe H, Iwatani N, Takumi T, Kito Y, Moriya N, Muroya K, Ogata T, Onigata K, Morikawa A, Inoue I, Takeda J (1999) Identification of mutations in the hepatocyte nuclear factor-1alpha gene in Japanese subjects with early-onset NIDDM and functional analysis of the mutant proteins. Diabetes 48:645-648
62. Yoshiuchi I, Yamagata K, Yang Q, Iwahashi H, Okita K, Yamamoto K, Oue T, Imagawa A, Hamaguchi T, Yamasaki T, Horikawa Y, Satoh T, Nakajima H, Miyazaki J, Higashiyama S, Miyagawa J, Namba M, Hanafusa T, Matsuzawa Y (1999) Three new mutations in the hepatocyte nuclear factor-1alpha gene in Japanese subjects with diabetes mellitus: Clinical features and functional characterization. Diabetologia 42:621-626
63. Zhang Z, Gerstein M (2003) Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes. Nucleic Acids Res 31:5338-5348
64. Zhao Y, Westphal H (2002) Homeobox genes and human genetic disorders. Curr Mol Med 2:13-23