Parallel Evolution of Nacre Building Gene Sets in Molluscs

Addadi, 2006, Mollusk shell formation: a source of new concepts for understanding biomineralization processes, Chemistry, 12, 980, 10.1002/chem.200500980

Addadi, 1987, A chemical-model for the cooperation of sulfates and carboxylates in calcite crystal nucleation— relevance to biomineralization, Proc Natl Acad Sci USA, 84, 2732, 10.1073/pnas.84.9.2732

Addadi, 1992, Control and design principles in biological mineralization, Angew Chem, 31, 153, 10.1002/anie.199201531

Amore, 2006, cis-Regulatory control of cyclophilin, a member of the ETS-DRI skeletogenic gene battery in the sea urchin embryo, Dev Biol, 293, 555, 10.1016/j.ydbio.2006.02.024

Bedouet, 2006, Identification of low molecular weight molecules as new components of the nacre organic matrix, Comp Biochem Physiol B, 144, 532, 10.1016/j.cbpb.2006.05.012

Belcher, 1996, Control of crystal phase switching and orientation by soluble mollusc-shell proteins, Nature, 381, 56, 10.1038/381056a0

Benson, 1990, The synthesis and secretion of collagen by cultured sea urchin micromeres, Exp Cell Res, 188, 141, 10.1016/0014-4827(90)90289-M

Blank, 2003, The nacre protein perlucin nucleates growth of calcium carbonate crystals, J Microsc, 212, 280, 10.1111/j.1365-2818.2003.01263.x

Burke, 1986, The silkmoth late chorion locus. I. Variation within two paired multigene families, J Mol Biol, 190, 343, 10.1016/0022-2836(86)90006-9

Butler, 1995, The nature and functional significance of dentin extracellular matrix proteins, Int J Dev Biol, 39, 169

Castresana, 2000, Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis, Mol Biol Evol, 17, 540, 10.1093/oxfordjournals.molbev.a026334

Chao, 2006, (20 co-authors). Use of a large-scale Triticeae expressed sequence tag resource to reveal gene expression profiles in hexaploid wheat (Triticum aestivum L.), Genome, 49, 531, 10.1139/G06-003

Chateigner, 2000, Mollusc shell microstructures and crystallographic textures, J Struct Geol, 22, 1723, 10.1016/S0191-8141(00)00088-2

Checa, 2009, Nacre and false nacre (foliated aragonite) in extant monoplacophorans (= Tryblidiida: Mollusca), Naturwissenschaften, 96, 111, 10.1007/s00114-008-0461-1

Chen, 2006, GO-Diff: mining functional differentiation between EST-based transcriptomes, BMC Bioinform, 7, 72, 10.1186/1471-2105-7-72

Colgan, 2000, Gastropod evolutionary rates and phylogenetic relationships assessed using partial 28S rDNA and histone H3 sequences, Zool Scripta, 29, 29, 10.1046/j.1463-6409.2000.00021.x

Cusack, 2008, Biomineralization: elemental and organic influence in carbonate systems, Chem Rev, 108, 4433, 10.1021/cr078270o

Edgar, 2004, MUSCLE: a multiple sequence alignment method with reduced time and space complexity, BMC Bioinform, 5, 113, 10.1186/1471-2105-5-113

Eisenhaber, 1999, Prediction of potential GPI-modification sites in proprotein sequences, J Mol Biol, 292, 741, 10.1006/jmbi.1999.3069

Emanuelsson, 2007, Locating proteins in the cell using TargetP, SignalP and related tools, Nat Prot, 2, 953, 10.1038/nprot.2007.131

Ewing, 1999, Large-scale statistical analyses of rice ESTs reveal correlated patterns of gene expression, Genome Res, 9, 950, 10.1101/gr.9.10.950

Falini, 2003, Chitin-silk fibroin interactions: relevance to calcium carbonate formation in invertebrates, Cal Tiss Int, 72, 548, 10.1007/s00223-002-1055-0

Fu, 2005, CaCO3 biomineralization: acidic 8-kDa proteins isolated from aragonitic abalone shell nacre can specifically modify calcite crystal morphology, Biomacromolecules, 6, 1289, 10.1021/bm049314v

Furuhashi, 2009, Pyrolysis GC/MS and IR spectroscopy in chitin analysis of molluscan shells, Biosci Biotechnol Biochem, 73, 93, 10.1271/bbb.80498

Gatesy, 2001, Extreme diversity, conservation, and convergence of spider silk fibroin sequences, Science, 291, 2603, 10.1126/science.1057561

Gilbert, 2008, Gradual ordering in red abalone nacre, J Am Chem Soc, 130, 17519, 10.1021/ja8065495

Gong, 2008, Immunolocalization of matrix proteins in nacre lamellae and their in vivo effects on aragonitic tablet growth, J Struct Biol, 164, 33, 10.1016/j.jsb.2008.05.009

Gosline, 1999, The mechanical design of spider silks: from fibroin sequence to mechanical function, J Exp Biol, 202, 3295, 10.1242/jeb.202.23.3295

Gotliv, 2003, Mollusk shell acidic proteins: in search of individual functions, Chem Biochem, 4, 522

Hayashi, 2000, Molecular architecture and evolution of a modular spider silk protein gene, Science, 287, 1477, 10.1126/science.287.5457.1477

Hedegaard, 1997, Shell structures of the recent Vetigastropoda, J Moll Stud, 63, 369, 10.1093/mollus/63.3.369

Hedegaard, 1998, Microstructure and texture patterns of mollusc shells, J Moll Stud, 64, 133, 10.1093/mollus/64.1.133

Horne, 2002, Carbonic anhydrase in mineralization of the crayfish cuticle, Crustaceana, 75, 1067, 10.1163/156854002763270473

Hotz-Wagenblatt, 2003, ESTAnnotator: a tool for high throughput EST annotation, Nucleic Acid Res, 31, 3716, 10.1093/nar/gkg566

Huang, 1999, CAP3: a DNA sequence assembly program, Genome Res, 9, 868, 10.1101/gr.9.9.868

Jackson, 2007, Sponge paleogenomics reveals an ancient role for carbonic anhydrase in skeletogenesis, Science, 316, 1893, 10.1126/science.1141560

Jackson, 2006, A rapidly evolving secretome builds and patterns a sea shell, BMC Evol Biol, 4, 40, 10.1186/1741-7007-4-40

Jackson, 2007, Dynamic expression of ancient and novel molluscan shell genes during ecological transitions, BMC Evol Biol, 7, 160, 10.1186/1471-2148-7-160

Jolly, 2004, Zonal localization of shell matrix proteins in mantle of Haliotis tuberculata (Mollusca, Gastropoda), Mar Biotech, 6, 541, 10.1007/s10126-004-3129-7

Kawasaki, 2004, Genetic basis for the evolution of vertebrate mineralized tissue, Proc Natl Acad Sci USA, 101, 11356, 10.1073/pnas.0404279101

Kawasaki, 2006, Evolutionary genetics of vertebrate tissue mineralization: the origin and evolution of the secretory calcium-binding phosphoprotein family, J Exp Biol, 306, 295

Keith, 1993, Comparative analysis of macromolecules in mollusc shells, Comp Biochem Physiol B, 105, 487, 10.1016/0305-0491(93)90078-J

Leu, 2007, Comparative analysis of differentially expressed genes in normal and white spot syndrome virus infected Penaeus monodon, BMC Gen, 8, 120, 10.1186/1471-2164-8-120

Levi-Kalisman, 2001, Structure of the nacreous organic matrix of a bivalve mollusk shell examined in the hydrated state using cryo-TEM, J Struct Biol, 135, 8, 10.1006/jsbi.2001.4372

Livingston, 2006, A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus, Dev Biol, 300, 335, 10.1016/j.ydbio.2006.07.047

Ma, 2007, A novel extrapallial fluid protein controls the morphology of nacre lamellae in the pearl oyster, Pinctada fucata, J Biol Chem, 282, 23253, 10.1074/jbc.M700001200

Marchler-Bauer, 2009, (28 co-authors) CDD: specific functional annotation with the Conserved Domain Database, Nuc Acid Res, 37, D205, 10.1093/nar/gkn845

Marin, 2004, Molluscan shell proteins, Comptes Rendus Palevol, 3, 469, 10.1016/j.crpv.2004.07.009

Marxen, 1998, Carbohydrates of the organic shell matrix and the shell-forming tissue of the snail Biomphalaria glabrata (Say), Biol Bull, 194, 231, 10.2307/1543052

Meldrum, 2008, Controlling mineral morphologies and structures in biological and synthetic systems, Chem Rev, 108, 4332, 10.1021/cr8002856

Metzler, 2007, Architecture of columnar nacre, and implications for its formation mechanism, Phys Rev Lett, 98, 268102, 10.1103/PhysRevLett.98.268102

Mita, 1994, Highly repetitive structure and its organization of the silk fibroin gene, J Mol Evol, 38, 583, 10.1007/BF00175878

Miyamoto, 1996, A carbonic anhydrase from the nacreous layer in oyster pearls, Proc Natl Acad Sci USA, 93, 9657, 10.1073/pnas.93.18.9657

Miyamoto, 2005, The carbonic anhydrase domain protein nacrein is expressed in the epithelial cells of the mantle and acts as a negative regulator in calcification in the mollusc Pinctada fucata, Zool Sci, 22, 311, 10.2108/zsj.22.311

Miyamoto, 2003, Similarities in the structure of nacrein, the shell-matrix protein, in a bivalve and a gastropod, J Moll Stud, 69, 87, 10.1093/mollus/69.1.87

Moya, 2008, Carbonic anhydrase in the scleractinian coral Stylophora pistillata: characterization, localization, and role in biomineralization, J Biol Chem, 283, 25475, 10.1074/jbc.M804726200

Newman, 2007, XSTREAM: a practical algorithm for identification and architecture modeling of tandem repeats in protein sequences, BMC Bioinform, 8, 382, 10.1186/1471-2105-8-382

Nishikata, 2001, Profiles of maternally expressed genes in fertilized eggs of Ciona intestinalis, Dev Biol, 238, 315, 10.1006/dbio.2001.0370

Nudelman, 2006, Mollusk shell formation: mapping the distribution of organic matrix components underlying a single aragonitic tablet in nacre, J Struct Biol, 153, 176, 10.1016/j.jsb.2005.09.009

Parkhaev, 2008, The early Cambrian radiation of Mollusca, Phylogeny and evolution of the Mollusca, 33, 10.1525/california/9780520250925.003.0003

Perina, 2006, The complete set of ribosomal proteins from the marine sponge Suberites domuncula, Gene, 366, 275, 10.1016/j.gene.2005.08.015

Peters, 1972, Occurrence of chitin in Mollusca, Comp Biochem Physiol B, 41, 541, 10.1016/0305-0491(72)90117-4

Ponder, 2008, Phylogeny and evolution of the Mollusca, 10.1525/california/9780520250925.001.0001

Poulicek, 1986, Chitinoproteic complexes and mineralization in mollusk skeletal structures, Chitin in nature and technology, 7, 10.1007/978-1-4613-2167-5_2

Qin, 1997, Tough tendons. Mussel byssus has collagen with silk-like domains, J Biol Chem, 272, 32623, 10.1074/jbc.272.51.32623

Satoh, 2003, Ciona intestinalis: an emerging model for whole-genome analyses, Trends Genet, 19, 376, 10.1016/S0168-9525(03)00144-6

Schmid, 2008, annot8r: gO, EC and KEGG annotation of EST datasets, BMC Bioinform, 9, 180, 10.1186/1471-2105-9-180

Shen, 1997, Molecular cloning and characterization of lustrin A, a matrix protein from shell and pearl nacre of Haliotis rufescens, J Biol Chem, 272, 32472, 10.1074/jbc.272.51.32472

Shen, 1998, A type I peritrophic matrix protein from the malaria vector Anopheles gambiae binds to chitin, J Biol Chem, 273, 17665, 10.1074/jbc.273.28.17665

Sigwart, 2007, Deep molluscan phylogeny: synthesis of palaeontological and neontological data, Proc Biol Sci, 274, 2413, 10.1098/rspb.2007.0701

Suzuki, 2007, Identification of chitin in the prismatic layer of the shell and a chitin synthase gene from the Japanese pearl oyster, Pinctada fucata, Biosci Biotechnol Biochem, 71, 1735, 10.1271/bbb.70140

Takahashi, 2009, An EST screen from the annelid Pomatoceros lamarckii reveals patterns of gene loss and gain in animals, BMC Evol Biol, 9, 240, 10.1186/1471-2148-9-240

Vera, 2008, Rapid transcriptome characterization for a nonmodel organism using 454 pyrosequencing, Mol Ecol, 17, 1636, 10.1111/j.1365-294X.2008.03666.x

Waring, 1990, Multiple proteins are produced from the dec-1 eggshell gene in Drosophila by alternative RNA splicing and proteolytic cleavage events, Dev Biol, 142, 1, 10.1016/0012-1606(90)90146-A

Weiner, 1980, X-ray diffraction study of the insoluble organic matrix of mollusk shells, FEBS Lett, 111, 311, 10.1016/0014-5793(80)80817-9

Weiner, 1984, Macromolecules in mollusk shells and their functions in biomineralization, Philos Trans R Soc Lond B, 304, 425, 10.1098/rstb.1984.0036

Weiss, 2006, The distribution of chitin in larval shells of the bivalve mollusk Mytilus galloprovincialis, J Struct Biol, 153, 264, 10.1016/j.jsb.2005.11.006

Weiss, 2006, The chitin synthase involved in marine bivalve mollusk shell formation contains a myosin domain, FEBS Lett, 580, 1846, 10.1016/j.febslet.2006.02.044

Wessel, 1991, Primary mesenchyme cells of the sea urchin embryo require an autonomously produced, nonfibrillar collagen for spiculogenesis, Dev Biol, 148, 261, 10.1016/0012-1606(91)90335-Z

Wilson, 2009, Assessing the molluscan hypothesis Serialia (Monoplacophora + Polyplacophora) using novel molecular data, Mol Phylo Evol

Yamasu, 1999, Functional organization of DNA elements regulating SM30alpha, a spicule matrix gene of sea urchin embryos, Dev Growth Differ, 41, 81, 10.1046/j.1440-169x.1999.00407.x

Yano, 2006, Shematrin: a family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata, Comp Biochem Physiol B, 144, 254, 10.1016/j.cbpb.2006.03.004

Zhang, 2006, A novel matrix protein family participating in the prismatic layer framework formation of pearl oyster, Pinctada fucata, Biochem Biophys Res Commun, 344, 735, 10.1016/j.bbrc.2006.03.179

Zhao, 1996, Crystal structure implies that cyclophilin predominantly catalyzes the trans to cis isomerization, Biochemistry, 35, 7356, 10.1021/bi9602775