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#  Complete Reference information for:
#  "Carbonate Organic Matrix (COM) proteins from coral, mollusk, and sea urchin" dataset
#  PI: Paul Falkowski (Rutgers)
#  Co-PIs: Y. Rosenthal, R. Sherrell, & O. Schofield (Rutgers)
#  Version: 29 October 2014
#  Go back to the dataset
=========================
abbrev                            full_reference  
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Alvares 2009                      Alvares, K., Dixit, S. N., Lux, E. & Veis, A. 2009. Echinoderm Phosphorylated Matrix Proteins UTMP16 and UTMP19 Have Different Functions in Sea Urchin Tooth Mineralization. J Biol Chem 284(38): 26149-26160.  
Azizur 2005                       Azizur Rahman, M. & Isa, Y. 2005. Characterization of proteins from the matrix of spicules from the alcyonarian, Lobophytum crassum. J Exp Mar Biol Ecol 321(1): 71-82.  
Bedouet 2001                      Bedouet, L., Jose Schuller, M., Marin, F., Milet, C., Lopez, E. & Giraud, M. 2001. Soluble proteins of the nacre of the giant oyster Pinctada maxima and of the abalone Haliotis tuberculata:: extraction and partial analysis of nacre proteins. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 128(3): 389-400.  
Bertucci 2011                     Bertucci, A., Tambutte, S., Supuran, C., Allemand, D. & Zoccola, D. 2011. A new coral carbonic anhydrase in Stylophora pistillata. Mar Biotechnol 13(5): 992-1002.  
Bowen & Tang 1996                 Bowen, C. E. & Tang, H. 1996. Conchiolin-protein in aragonite shells of mollusks. Comparative Biochemistry and Physiology Part A: Physiology 115(4): 269-275.  
Costa 2012                        Costa, C., Karakostis, K., Zito, F. & Matranga, V. 2012. Phylogenetic analysis and expression patterns of p16 and p19 in Paracentrotus lividus embryos. Dev Genes Evol 222(4): 245-251.  
Drake 2013                        Drake, J. L., Mass, T., Haramaty, L., Zelzion, E., Bhattacharya, D. & Falkowski, P. G. 2013. Proteomic analysis of skeletal organic matrix from the stony coral Stylophora pistillata. Proceedings of the National Academy of Sciences 110(10): 3788-3793.  
Evans 2012                        Evans, J. S. 2012. Aragonite-associated biomineralization proteins are disordered and contain interactive motifs. Bioinformatics 28(24): 3182-3185.  
Fang 2012 J Biol Chem             Fang, D., Pan, C., Lin, H., Lin, Y., Zhang, G., Wang, H., He, M., Xie, L. & Zhang, R. 2012. Novel Basic Protein, PfN23, Functions as Key Macromolecule during Nacre Formation. J Biol Chem 287(19): 15776-15785.  
Fang 2012 PlusOne                 Fang et al 2012 PlusOne  
Fukuda 2003                       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(1): 11-17.  
Gotliv 2005                       Gotliv, B.-A., Kessler, N., Sumerel, J. L., Morse, D. E., Tuross, N., Addadi, L. & Weiner, S. 2005. Asprich: A novel aspartic acid-rich protein family from the prismatic shell matrix of the bivalve Atrina rigida. ChemBioChem 6(2): 304-314.  
Hasegawa 2005                     Hasegawa, Y. & Uchiyama, K. 2005. cDNA clonings of shell matrix proteins from scallop shell. Fish Sci 71(5): 1174-1178.  
Hattan 2001                       Hattan, S. J., Laue, T. M. & Chasteen, N. D. 2001. Purification and Characterization of a Novel Calcium-binding Protein from the Extrapallial Fluid of the Mollusc, Mytilus edulis. J Biol Chem 276(6): 4461-4468.  
Hayward 2011                      Hayward, D. C., Hetherington, S., Behm, C. A., Grasso, L. C., Foret, S., Miller, D. J. & Ball, E. E. 2011. Differential gene expression at coral settlement and metamorphosis - a subtractive hybridization study. PLoS ONE 6(10): e26411.  
Huang 2007                        Huang, J., Zhang, C., Ma, Z., Xie, L. & Zhang, R. 2007. A novel extracellular EF-hand protein involved in the shell formation of pearl oyster. Biochimica et Biophysica Acta (BBA) - General Subjects 1770(7): 1037-1044.  
Illies & Ettensohn 2002           Illies, M., Peeler, M., Dechtiaruk, A. & Ettensohn, C. 2002. Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus. Dev Genes Evol 212(9): 419-431.  
Joubert 2010                      Joubert, C., Piquemal, D., Marie, B., Manchon, L., Pierrat, F., Zanella-Cleon, I., Cochennec-Laureau, N., Gueguen, Y. & Montagnani, C. 2010. Transcriptome and proteome analysis of Pinctada margaritifera calcifying mantle and shell: Focus on biomineralization. BMC Genomics 11(1): 613.  
Kaniewska 2012                    Kaniewska, P., Campbell, P. R., Kline, D. I., Rodriguez-Lanetty, M., Miller, D. J., Dove, S. & Hoegh-Guldberg, O. 2012. Major cellular and physiological impacts of ocean acidification on a reef building coral. PLoS ONE 7(4): e34659.  
Keith 1993                        Keith, J., Stockwell, S., Ball, D., Remillard, K., Kaplan, D., Thannhauser, T. & Sherwood, R. 1993. Comparative analysis of macromolecules in mollusc shells. Comparative Biochemistry and Physiology Part B: Comparative Biochemistry 105(3): 487-496.  
Kinoshita 2011                    Kinoshita, S., Wang, N., Inoue, H., Maeyama, K., Okamoto, K., Nagai, K., Kondo, H., Hirono, I., Asakawa, S. & Watabe, S. 2011. Deep Sequencing of ESTs from Nacreous and Prismatic Layer Producing Tissues and a Screen for Novel Shell Formation-Related Genes in the Pearl Oyster. PLoS ONE 6(6): e21238.  
Kong 2009                         Kong, Y., Jing, G., Yan, Z., Li, C., Gong, N., Zhu, F., Li, D., Zhang, Y., Zheng, G., Wang, H., et al. 2009. Cloning and Characterization of Prisilkin-39, a Novel Matrix Protein Serving a Dual Role in the Prismatic Layer Formation from the Oyster Pinctada fucata. J Biol Chem 284(16): 10841-10854.  
Kono 2000                         Kono, M., Hayashi, N. & Samata, T. 2000. Molecular Mechanism of the Nacreous Layer Formation in Pinctada maxima. Biochem Biophys Res Commun 269(1): 213-218.  
Lee 2006                          Lee, S., Kim, Y., Choi, H., Yang, J. & Choi, C. 2006. Primary Structure of Myostracal Prism Soluble Protein (MPSP) in Oyster Shell, Crassostrea gigas. The Protein Journal 25(4): 288-294.  
Li et al 2005                     Li, S., Xie, L., Ma, Z. & Zhang, R. 2005. cDNA cloning and characterization of a novel calmodulin-like protein from pearl oyster Pinctada fucata. FEBS J 272(19): 4899-4910.  
Liu 2006                          Liu, H.-L., Liu, S.-F., Ge, Y.-J., Liu, J., Wang, X.-Y., Xie, L.-P., Zhang, R.-Q. & Wang, Z. 2006. Identification and Characterization of a Biomineralization Related Gene PFMG1 Highly Expressed in the Mantle of Pinctada fucata. Biochemistry 46(3): 844-851.  
Ma 2007                           Ma, Z., Huang, J., Sun, J., Wang, G., Li, C., Xie, L. & Zhang, R. 2007. A novel extrapallial fluid protein controls the morphology of nacre lamellae in the pearl oyster, Pinctada fucata. J Biol Chem 282(32): 23253-23263.  
Mann 2012                         Mann, K., Edsinger-Gonzales, E. & Mann, M. 2012. In-depth proteomic analysis of a mollusc shell: acid-soluble and acid-insoluble matrix of the limpet Lottia gigantea. Proteome science 10(1): 1-18.  
Mann 2008                         Mann, K., Poustka, A. & Mann, M. 2008. In-depth, high-accuracy proteomics of sea urchin tooth organic matrix. Proteome science 6(1): 33.  
Mann 2008b                        Mann, K., Poustka, A. & Mann, M. 2008. The sea urchin (Strongylocentrotus purpuratus) test and spine proteomes. Proteome science 6(1): 22.  
Mann 2007                         Mann, K., Siedler, F., Treccani, L., Heinemann, F. & Fritz, M. 2007. Perlinhibin, a Cysteine-, Histidine-, and Arginine-Rich Miniprotein from Abalone (Haliotis laevigata) Nacre, Inhibits In Vitro Calcium Carbonate Crystallization. Biophys J 93(4): 1246-1254.  
Mann 2010                         Mann, K., Wilt, F. H. & Poustka, A. J. 2010. Proteomic analysis of sea urchin (Strongylocentrotus purpuratus) spicule matrix. Proteome Science 8: 33.  
Marie 2010                        Marie, B., Marie, A., Jackson, D., Dubost, L., Degnan, B., Milet, C. & Marin, F. 2010. Proteomic analysis of the organic matrix of the abalone Haliotis asinina calcified shell. Proteome science 8(1): 54.  
Marie 2011 Mar Biotechnol         Marie, B., Roy, N., Zanella-Cleon, I., Becchi, M. & Marin, F. 2011. Molecular evolution of mollusc shell proteins: Insights from proteomic analysis of the edible mussel Mytilus. J Mol Evol 72(5-6): 531-546.  
Marie 2011 J Mol Evol             Marie, B., Trinkler, N., Zanella-Cleon, I., Guichard, N., Becchi, M., Paillard, C. & Marin, F. 2011. Proteomic identification of novel proteins from the calcifying shell matrix of the Manila clam Venerupis philippinarum. Mar Biotechnol 13(5): 955-962.  
Marin 2005                        Marin, F., Amons, R., Guichard, N., Stigter, M., Hecker, A., Luquet, G., Layrolle, P., Alcaraz, G., Riondet, C. & Westbroek, P. 2005. Caspartin and Calprismin, Two Proteins of the Shell Calcitic Prisms of the Mediterranean Fan Mussel Pinna nobilis. J Biol Chem 280(40): 33895-33908.  
Marin 2000                        Marin, F., Corstjens, P., De Gaulejac, B., De Vrind-De Jong, E. & Westbroek, P. 2000. Mucins and Molluscan Calcification: Molecular characterization of mucoperlin, a novel mucin-like protein from the nacreous shell layer of the fan mussel Pinna nobilis (Bivalvia, Pteriomorphia). J Biol Chem 275(27): 20667-20675.  
Martin 2011                       Martin, S., Richier, S., Pedrotti, M.-L., Dupont, S., Castejon, C., Gerakis, Y., Kerros, M.-E., Oberhansli, F., Teyssie, J.-L., Jeffree, R., et al. 2011. Early development and molecular plasticity in the Mediterranean sea urchin Paracentrotus lividus exposed to CO2-driven acidification. The Journal of Experimental Biology 214(8): 1357-1368.  
Mass 2013                         Mass, T., Drake, Jeana l., Haramaty, L., Kim, J. D., Zelzion, E., Bhattacharya, D. & Falkowski, Paul G. 2013. Cloning and characterization of four novel coral acid-rich proteins that precipitate carbonates in vitro. Curr Biol 23(12): 1126-1131.  
Michenfelder 2003                 Michenfelder, M., Fu, G., Lawrence, C., Weaver, J. C., Wustman, B. A., Taranto, L., Evans, J. S. & Morse, D. E. 2003. Characterization of two molluscan crystal-modulating biomineralization proteins and identification of putative mineral binding domains. Biopolymers 70(4): 522-533.  
Miyamoto 1996                     Miyamoto, H., Miyashita, T., Okushima, M., Nakano, S., Morita, T. & Matsushiro, A. 1996. A carbonic anhydrase from the nacreous layer in oyster pearls. Proceedings of the National Academy of Sciences 93(18): 9657-9660.  
Miyashita 2000                    Miyashita, T., Takagi, R., Okushima, M., Nakano, S., Miyamoto, H., Nishikawa, E. & Matsushiro, A. 2000. Complementary DNA cloning and characterization of pearlin, a new class of matrix protein in the nacreous layer of oyster pearls. Mar Biotechnol 2(5): 409-418.  
Moya 2012                         Moya, A., Huisman, L., Ball, E. E., Hayward, D. C., Grasso, L. C., Chua, C. M., Woo, H. N., Gattuso, J. P., Foret, S. & Miller, D. J. 2012. Whole transcriptome analysis of the coral Acropora millepora reveals complex responses to CO2-driven acidification during the initiation of calcification. Mol Ecol 21(10): 2440-2454.  
Moya 2008                         Moya, A., Tambutte, S., Bertucci, A., Tambutte, E., Lotto, S., Vullo, D., Supuran, C. T., Allemand, D. & Zoccola, D. 2008. Carbonic anhydrase in the scleractinian coral Stylophora pistillata. J Biol Chem 283(37): 25475-25484.  
Nogawa 2012                       Nogawa, C., Baba, H., Masaoka, T., Aoki, H. & Samata, T. 2012. Genetic structure and polymorphisms of the N16 gene in Pinctada fucata. Gene 504(1): 84-91.  
Puverel 2005                      Puverel, S., Tambutte, E., Pereira-Mouries, L., Zoccola, D., Allemand, D. & Tambutte, S. 2005. Soluble organic matrix of two Scleractinian corals: partial and comparative analysis. Comparative Biochemistry and Physiology Part B 141: 480-487.  
Rahman 2011                       Rahman, A., Oomori, T. & Woerheide, G. 2011. Calcite formation in soft coral sclerites is determined by a single reactive extracellular protein. J Biol Chem.  
Rahman 2005 J Exp Mar Biol Ecol   M. Azizur Rahman, Yeishin Isa. 2005. Characterization of proteins from the matrix of spicules from the alcyonarian, Lobophytum crassum. J. Exp. Mar. Biol. Ecol. 321(1): 71-82. doi: 10.1016/j.jembe.2005.01.012  
Rahman 2005 Proteomics            Rahman, M. A., Isa, Y. & Yuehara, T. 2005. Proteins of calcified endoskeleton: II partial amino acid sequences of endoskeletal proteins and the characterization of proteinaceous organic matrix of spicules from the alcyonarian, Synularia polydactyla. Proteomics 5: 885-893.  
Rahman 2006                       Rahman, M. A., Isa, Y., Takemura, A. & Uehara, T. 2006. Analysis of proteinaceous components of the organic matrix of endoskeletal sclerites from the Alcyonarian Lobophytum crassum. Calcif Tissue Int 78: 178-185.  
Ramos-Silva 2013                  Ramos-Silva, P., Kaandorp, J., Huisman, L., Marie, B., Zanella-Cleon, I., Guichard, N., Miller, D. J. & Marin, F. 2013. The skeletal proteome of the coral Acropora millepora: The evolution of calcification by cooption and domain shuffling. Mol Biol Evol.  
Reyes-Bermudez 2009               Reyes-Bermudez, A., Lin, Z., Hayward, D. C., Miller, D. J. & Ball, E. E. 2009. Differential expression of three galaxin-related genes during settlement and metamorphosis in the scleractinian coral Acropora millepora. BMC Evol Biol 9: 178.  
Samata 1999                       Samata, T., Hayashi, N., Kono, M., Hasegawa, K., Horita, C. & Akera, S. 1999. A new matrix protein family related to the nacreous layer formation of Pinctada fucata. FEBS Lett 462(1-2): 225-229.  
Sarashina & Endo 1998             Sarashina, I. & Endo, K. 1998. Primary structure of a soluble matrix protein of scallop shell: implications for calcium carbonate biomineralization. American Mineralogist 83: 1510-1515.  
Sarashina & Endo 2001             Sarashina, I. & Endo, K. 2001. The complete primary structure of molluscan shell protein 1 (MSP-1), an acidic glycoprotein in the shell matrix of the scallop Patinopecten yessoensis. Mar Biotechnol 3(4): 362-369.  
Shen 1997                         Shen, X., Belcher, A. M., Hansma, P. K., Stucky, G. D. & Morse, D. E. 1997. Molecular Cloning and Characterization of Lustrin A, a Matrix Protein from Shell and Pearl Nacre of Haliotis rufescens. J Biol Chem 272(51): 32472-32481.  
Shiomi 2012                       Shiomi, K., Yamazaki, A., Kagawa, M., Kiyomoto, M. & Yamaguchi, M. 2012. Par6 regulates skeletogenesis and gut differentiation in sea urchin larvae. Dev Genes Evol 222(5): 269-278.  
Stumpp 2011                       Stumpp, M., Dupont, S., Thorndyke, M. C. & Melzner, F. 2011. CO2 induced seawater acidification impacts sea urchin larval development II: Gene expression patterns in pluteus larvae. Comparative Biochemistry and Physiology Part A: Molecular & Integrative Physiology 160(3): 320-330.  
Sudo 1997                         Sudo, S., Fujikawa, T., Nagakura, T., Ohkubo, T., Sakaguchi, K., Tanaka, M., Nakashima, K. & Takahashi, T. 1997. Structures of mollusc shell framework proteins. Nature 387(6633): 563-564.  
Suzuki 2004                       Suzuki, M., Murayama, E., Inoue, H., Ozaki, N., Tohse, H., Kogure, T. & Nagasawa, H. 2004. Characterization of Prismalin-14, a novel matrix protein from the prismatic layer of the Japanese pearl oyster (Pinctada fucata). Biochem J 382(1): 205-213.  
Suzuki 2009                       Suzuki, M., Saruwatari, K., Kogure, T., Yamamoto, Y., Nishimura, T., Kato, T. & Nagasawa, H. 2009. An acidic matrix protein, Pif, Is a key macromolecule for nacre formation. Science 325(5946): 1388-1390.  
Takagi & Miyashita 2010           Takagi, R. & Miyashita, T. 2010. Prismin: A New Matrix Protein Family in the Japanese Pearl Oyster (Pinctada fucata) Involved in Prismatic Layer Formation. Zool Sci 27(5): 416-426.  
Todgham & Hofmann 2009            Todgham, A. E. & Hofmann, G. E. 2009. Transcriptomic response of sea urchin larvae Strongylocentrotus purpuratus to CO2-driven seawater acidification. J Exp Biol 212(16): 2579-2594.  
Traylor-Knowles 2009              Traylor-Knowles, N., Granger, B., Lubinski, T., Parikh, J., Garamszegi, S., Xia, Y., Marto, J., Kaufman, L. & Finnerty, J. 2011. Production of a reference transcriptome and a transcriptomic database (PocilloporaBase) for the cauliflower coral, Pocillopora damicornis. BMC Genomics 12(1): 585.  
Treccani 2006                     Treccani, L., Mann, K., Heinemann, F. & Fritz, M. 2006. Perlwapin, an Abalone Nacre Protein with Three Four-Disulfide Core (Whey Acidic Protein) Domains, Inhibits the Growth of Calcium Carbonate Crystals. Biophys J 91(7): 2601-2608.  
Tsukamoto 2004                    Tsukamoto, D., Sarashina, I. & Endo, K. 2004. Structure and expression of an unusually acidic matrix protein of pearl oyster shells. Biochem Biophys Res Commun 320(4): 1175-1180.  
Weiss 2000                        Weiss, I. M., Kaufmann, S., Mann, K. & Fritz, M. 2000. Purification and Characterization of Perlucin and Perlustrin, Two New Proteins from the Shell of the Mollusc Haliotis laevigata. Biochem Biophys Res Commun 267(1): 17-21.  
Yano 2006                         Yano, M., Nagai, K., Morimoto, K. & Miyamoto, H. 2006. Shematrin: A family of glycine-rich structural proteins in the shell of the pearl oyster Pinctada fucata. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 144(2): 254-262.  
Yano 2007                         Yano, M., Nagai, K., Morimoto, K. & Miyamoto, H. 2007. A novel nacre protein N19 in the pearl oyster Pinctada fucata. Biochem Biophys Res Commun 362(1): 158-163.  
Yano et al. submitted             ?               
Yin 2005                          Yin, Y., Huang, J., Paine, M. L., Reinhold, V. N. & Chasteen, N. D. 2005. Structural Characterization of the Major Extrapallial Fluid Protein of the Mollusc Mytilus edulis: Implications for Function. Biochemistry 44(31): 10720-10731.  
Zhang 2006                        Zhang, C., Xie, L., Huang, J., Liu, X. & Zhang, R. 2006. A novel matrix protein family participating in the prismatic layer framework formation of pearl oyster, Pinctada fucata. Biochem Biophys Res Commun 344(3): 735-740.  
Zhang 2012                        Zhang, G., Fang, X., Guo, X., Li, L., Luo, R., Xu, F., Yang, P., Zhang, L., Wang, X., Qi, H., et al. 2012. The oyster genome reveals stress adaptation and complexity of shell formation. Nature 490(7418): 49-54.  
Zhang 2003                        Zhang, Y., Xie, L., Meng, Q., Jiang, T., Pu, R., Chen, L. & Zhang, R. 2003. A novel matrix protein participating in the nacre framework formation of pearl oyster, Pinctada fucata. Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology 135(3): 565-573.  
Zocolla 2009                      Zoccola, D., Moya, A., Beranger, G., Tambutte, E., Allemand, D., Carle, G. & Tambutte, S. 2009. Specific expression of BMP2/4 ortholog in biomineralizing tissues of corals and action on mouse BMP receptor. Mar Biotechnol 11(2): 260-269.