Molecular and in silico analyses of the full-length isoform of usherin identify new pathogenic alleles in Usher type II patients †
David Baux
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
David Baux and Lise Larrieu contributed equally to this work.
Search for more papers by this authorLise Larrieu
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
David Baux and Lise Larrieu contributed equally to this work.
Search for more papers by this authorCatherine Blanchet
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorChristian Hamel
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorSafouane Ben Salah
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorAnne Vielle
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
Search for more papers by this authorBrigitte Gilbert-Dussardier
Centre Hospitalier Universitaire (CHU) de Poitiers, Service de Génétique Médicale, Poitiers, France
Search for more papers by this authorMuriel Holder
Centre Hospitalier Universitaire (CHU) de Lille, Service de Génétique Clinique, Lille, France
Search for more papers by this authorPatrick Calvas
Hôpital Purpan, Service de Génétique Médicale, Toulouse, France
Search for more papers by this authorNicole Philip
Hôpital d'enfants de la Timone, Département de Génétique Médicale, Marseille, France
Search for more papers by this authorPatrick Edery
Hôpital Debrousse, Unité de Génétique Médicale, Lyon, France
Search for more papers by this authorDominique Bonneau
Centre Hospitalier Universitaire (CHU), Angers, Service de Génétique, Angers, France
Search for more papers by this authorMireille Claustres
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
INSERM, U827, Montpellier, France
Université Montpellier I, Montpellier, France
Search for more papers by this authorSue Malcolm
Clinical and Molecular Genetics, Institute of Child Health, London, United Kingdom
Search for more papers by this authorCorresponding Author
Anne-Françoise Roux
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
INSERM, U827, Montpellier, France
Laboratoire de Génétique Moléculaire, CHU Montpellier, IURC, 641 Avenue du Doyen Gaston Giraud, F-34093 Montpellier cedex 5, FranceSearch for more papers by this authorDavid Baux
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
David Baux and Lise Larrieu contributed equally to this work.
Search for more papers by this authorLise Larrieu
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
David Baux and Lise Larrieu contributed equally to this work.
Search for more papers by this authorCatherine Blanchet
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorChristian Hamel
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorSafouane Ben Salah
Centre Hospitalier Universitaire (CHU) Montpellier, Centre National de Référence Maladies Rares “Affections Sensorielles Génétiques,” Montpellier, France
Search for more papers by this authorAnne Vielle
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
Search for more papers by this authorBrigitte Gilbert-Dussardier
Centre Hospitalier Universitaire (CHU) de Poitiers, Service de Génétique Médicale, Poitiers, France
Search for more papers by this authorMuriel Holder
Centre Hospitalier Universitaire (CHU) de Lille, Service de Génétique Clinique, Lille, France
Search for more papers by this authorPatrick Calvas
Hôpital Purpan, Service de Génétique Médicale, Toulouse, France
Search for more papers by this authorNicole Philip
Hôpital d'enfants de la Timone, Département de Génétique Médicale, Marseille, France
Search for more papers by this authorPatrick Edery
Hôpital Debrousse, Unité de Génétique Médicale, Lyon, France
Search for more papers by this authorDominique Bonneau
Centre Hospitalier Universitaire (CHU), Angers, Service de Génétique, Angers, France
Search for more papers by this authorMireille Claustres
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
INSERM, U827, Montpellier, France
Université Montpellier I, Montpellier, France
Search for more papers by this authorSue Malcolm
Clinical and Molecular Genetics, Institute of Child Health, London, United Kingdom
Search for more papers by this authorCorresponding Author
Anne-Françoise Roux
Centre Hospitalier Universitaire (CHU) Montpellier, Laboratoire de Génétique Moléculaire, Montpellier, France
INSERM, U827, Montpellier, France
Laboratoire de Génétique Moléculaire, CHU Montpellier, IURC, 641 Avenue du Doyen Gaston Giraud, F-34093 Montpellier cedex 5, FranceSearch for more papers by this authorCommunicated by Garry Cutting
Abstract
The usherin gene (USH2A) has been screened for mutations causing Usher syndrome type II (USH2). Two protein isoforms have been identified: a short isoform of 1,546 amino acids and a more recently recognized isoform extending to 5,202 amino acids. We have screened the full length by genomic sequencing. We confirm that many mutations occur in the exons contributing solely to the longer form. USH2 is an autosomal recessive disorder and, in contrast to previous studies, both mutations were identified in 23 patients and a single mutation in 2 out of 33 patients. A total of 34 distinct mutated alleles were identified, including one complex allele with three variants and another with two. A total of 27 of these are novel, confirming that most mutations in usherin are private. Many of the mutations will lead to prematurely truncated protein but as there are a substantial number of missense variants, we have used in silico analysis to assess their pathogenicity. Evidence that they are disease-causing has been produced by protein alignments and three-dimensional (3D) structural predictions when possible. We have identified a previously unrecognized cysteine rich structural domain, containing 12 dicysteine repeats, and show that three missense mutations result in the loss of one of a pair of the defining cysteine-cysteine pairs. Hum Mutat 28(8), 781–789, 2007. © 2007 Wiley-Liss, Inc.
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REFERENCES
- Adato A, Weston MD, Berry A, Kimberling WJ, Bonne-Tamir A. 2000. Three novel mutations and twelve polymorphisms identified in the USH2A gene in Israeli USH2 families. Hum Mutat 15: 388.
10.1002/(SICI)1098-1004(200004)15:4<388::AID-HUMU27>3.0.CO;2-N CAS PubMed Web of Science® Google Scholar
- Adato A, Lefevre G, Delprat B, Michel V, Michalski N, Chardenoux S, Weil D, El-Amraoui A, Petit C. 2005. Usherin, the defective protein in Usher syndrome type IIA, is likely to be a component of interstereocilia ankle links in the inner ear sensory cells. Hum Mol Genet 14: 3921–3932.
- Ahmed ZM, Riazuddin S, Wilcox ER. 2003. The molecular genetics of Usher syndrome. Clin Genet 63: 431–444.
- Aller E, Jaijo T, Beneyto M, Najera C, Oltra S, Ayuso C, Baiget M, Carballo M, Antinolo G, Valverde D, Moreno F, Vilela C, Collado D, Perez-Garrigues H, Navea A, Millan JM. 2006. Identification of 14 novel mutations in the long isoform of USH2A in Spanish patients with Usher syndrome type II. J Med Genet 43: e55.
- Bernal S, Ayuso C, Antinolo G, Gimenez A, Borrego S, Trujillo MJ, Marcos I, Calaf M, Del Rio E, Baiget M. 2003. Mutations in USH2A in Spanish patients with autosomal recessive retinitis pigmentosa: high prevalence and phenotypic variation. J Med Genet 40: e8.
- Chenna R, Sugawara H, Koike T, Lopez R, Gibson TJ, Higgins DG, Thompson JD. 2003. Multiple sequence alignment with the Clustal series of programs. Nucleic Acids Res 31: 3497–3500.
- Contreras-Moreira B, Bates PA. 2002. Domain fishing: a first step in protein comparative modelling. Bioinformatics 18: 1141–1142.
- Creighton TE. 1983. An empirical approach to protein conformation stability and flexibility. Biopolymers 22: 49–58.
- Cremers FP, Kimberling WJ, Kulm M, de Brouwer A, van Wijk E, Te Brinke H, Cremers CW, Hoefsloot LH, Banfi S, Simonelli F, Fleischhauer JC, Berger W, Kelley PM, Haralambous E, Bitner-Glindzicz M, Webster AR, Saihan Z, Debaere E, Leroy BP, Silvestri G, McKay G, Koenekoop RK, Millan JM, Rosenberg T, Joensuu T, Sankila EM, Weil D, Weston MD, Wissinger B, Kremer H. 2007. Development of a genotyping microarray for usher syndrome. J Med Genet 44: 153–160.
- Doig AJ, Errington N, Iqbalsyah TM. 2005. Stability and design of alpha-helices. In: T Kiefhaber, J Buchner, editors. Protein folding handbook. Weinheim: Wiley-VCH. p 247–299.
- Dreyer B, Tranebjaerg L, Rosenberg T, Weston MD, Kimberling WJ, Nilssen O. 2000. Identification of novel USH2A mutations: implications for the structure of USH2A protein. Eur J Hum Genet 8: 500–506.
- Dreyer B, Tranebjaerg L, Brox V, Rosenberg T, Moller C, Beneyto M, Weston MD, Kimberling WJ, Cremers CW, Liu XZ, Nilssen O. 2001. A common ancestral origin of the frequent and widespread 2299delG USH2A mutation. Am J Hum Genet 69: 228–234.
- Ebermann I, Scholl HP, Charbel Issa P, Becirovic E, Lamprecht J, Jurklies B, Millan JM, Aller E, Mitter D, Bolz H. A novel gene for Usher syndrome type 2: mutations in the long isoform of whirlin are associated with retinitis pigmentosa and sensorineural hearing loss. Hum Genet (in press).
- Eisenberg D, Luthy R, Bowie JU. 1997. VERIFY3D: assessment of protein models with three-dimensional profiles. Methods Enzymol 277: 396–404.
- Eudy JD, Weston MD, Yao S, Hoover DM, Rehm HL, Ma-Edmonds M, Yan D, Ahmad I, Cheng JJ, Ayuso C, Cremers C, Davenport S, Moller C, Talmadge CB, Beisel KW, Tamayo M, Morton CC, Swaroop A, Kimberling WJ, Sumegi J. 1998. Mutation of a gene encoding a protein with extracellular matrix motifs in Usher syndrome type IIa. Science 280: 1753–1757.
- Frishman D, Argos P. 1996. Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 9: 133–142.
- Fukuda I, Ooki S, Fujita T, Murayama E, Nagasawa H, Isa Y, Watanabe T. 2003. Molecular cloning of a cDNA encoding a soluble protein in the coral exoskeleton. Biochem Biophys Res Commun 304: 11–17.
10.1016/S0006-291X(03)00527-8 Google Scholar
- Hohenester E, Tisi D, Talts JF, Timpl R. 1999. The crystal structure of a laminin G-like module reveals the molecular basis of alpha-dystroglycan binding to laminins, perlecan, and agrin. Mol Cell 4: 783–792.
- Leroy BP, Aragon-Martin JA, Weston MD, Bessant DA, Willis C, Webster AR, Bird AC, Kimberling WJ, Payne AM, Bhattacharya SS. 2001. Spectrum of mutations in USH2A in British patients with Usher syndrome type II. Exp Eye Res 72: 503–509.
- Liff MI, Zimmerman MN. 1998. NMR study of crosslinking by oxidation of four-cysteine polypeptide models of the elastic network phase of wool fibre. Polym Int 47: 375–385.
- Marti-Renom MA, Stuart AC, Fiser A, Sanchez R, Melo F, Sali A. 2000. Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 29: 291–325.
- Pennings RJ, Te Brinke H, Weston MD, Claassen A, Orten DJ, Weekamp H, Van Aarem A, Huygen PL, Deutman AF, Hoefsloot LH, Cremers FP, Cremers CW, Kimberling WJ, Kremer H. 2004. USH2A mutation analysis in 70 Dutch families with Usher syndrome type II. Hum Mutat 24: 185.
- Reiners J, van Wijk E, Marker T, Zimmermann U, Jurgens K, Te Brinke H, Overlack N, Roepman R, Knipper M, Kremer H, Wolfrum U. 2005. Scaffold protein harmonin (USH1C) provides molecular links between Usher syndrome type 1 and type 2. Hum Mol Genet 14: 3933–3943.
- Rivolta C, Sweklo EA, Berson EL, Dryja TP. 2000. Missense mutation in the USH2A gene: association with recessive retinitis pigmentosa without hearing loss. Am J Hum Genet 66: 1975–1978.
- Roux AF, Faugere V, Le Guedard S, Pallares-Ruiz N, Vielle A, Chambert S, Marlin S, Hamel C, Gilbert B, Malcolm S, Claustres M. 2006. Survey of the frequency of USH1 gene mutations in a cohort of Usher patients shows the importance of cadherin 23 and protocadherin 15 genes and establishes a detection rate of above 90%. J Med Genet 43: 763–768.
- Senapathy P, Shapiro MB, Harris NL. 1990. Splice junctions, branch point sites, and exons: sequence statistics, identification, and applications to genome project. Methods Enzymol 183: 252–278.
- Seyedahmadi BJ, Rivolta C, Keene JA, Berson EL, Dryja TP. 2004. Comprehensive screening of the USH2A gene in Usher syndrome type II and non-syndromic recessive retinitis pigmentosa. Exp Eye Res 79: 167–173.
- Sippl MJ. 1993. Recognition of errors in three-dimensional structures of proteins. Proteins 17: 355–362.
- Smith RJ, Berlin CI, Hejtmancik JF, Keats BJ, Kimberling WJ, Lewis RA, Moller CG, Pelias MZ, Tranebjaerg L. 1994. Clinical diagnosis of the Usher syndromes. Usher syndrome consortium. Am J Med Genet 50: 32–38.
- Stetefeld J, Mayer U, Timpl R, Huber R. 1996. Crystal structure of three consecutive laminin-type epidermal growth factor-like (LE) modules of laminin gamma1 chain harboring the nidogen binding site. J Mol Biol 257: 644–657.
- Strickler SS, Gribenko AV, Gribenko AV, Keiffer TR, Tomlinson J, Reihle T, Loladze VV, Makhatadze GI. 2006. Protein stability and surface electrostatics: a charged relationship. Biochemistry 45: 2761–2766.
- Thusberg J, Vihinen M. 2006. Bioinformatic analysis of protein structure-function relationships: case study of leukocyte elastase (ELA2) missense mutations. Hum Mutat 27: 1230–1243.
- van Wijk E, Pennings RJ, te Brinke H, Claassen A, Yntema HG, Hoefsloot LH, Cremers FP, Cremers CW, Kremer H. 2004. Identification of 51 novel exons of the Usher syndrome type 2A (USH2A) gene that encode multiple conserved functional domains and that are mutated in patients with Usher syndrome type II. Am J Hum Genet 74: 738–744.
- Weston MD, Eudy JD, Fujita S, Yao S, Usami S, Cremers C, Greenberg J, Ramesar R, Martini A, Moller C, Smith RJ, Sumegi J, Kimberling WJ, Greenburg J. 2000. Genomic structure and identification of novel mutations in usherin, the gene responsible for Usher syndrome type IIa. Am J Hum Genet 66: 1199–1210.
- Weston MD, Luijendijk MW, Humphrey KD, Moller C, Kimberling WJ. 2004. Mutations in the VLGR1 gene implicate G-protein signaling in the pathogenesis of Usher syndrome type II. Am J Hum Genet 74: 357–366.
