A genome-wide analysis of biomineralization-related proteins in the sea urchin Strongylocentrotus purpuratus

Developmental Biology - Tập 300 Số 1 - Trang 335-348 - 2006
Brian T. Livingston1, Christopher E. Killian2, Fred H. Wilt2, R. Andrew Cameron3, Melissa Landrum4, Olga Ermolaeva4, Victor Sapojnikov4, Donna Maglott4, Alex Buchanan5, Charles A. Ettensohn5
1Department of Biology, University of South Florida, Tampa, FL 33620, USA
2Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
3Division of Biology, California Institute of Technology, Pasadena, CA 91125 USA
4National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20892, USA
5Department of Biological Sciences, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA 15213, USA

Tóm tắt

Từ khóa


Tài liệu tham khảo

Akasaka, 1994, Genomic organization of a gene encoding the spicule matrix protein SM30 in the sea urchin Strongylocentrotus purpuratus, J. Biol. Chem., 269, 20592, 10.1016/S0021-9258(17)32034-3

Altschul, 1997, Gapped BLAST and PSI-BLAST: a new generation of protein database search programs, Nucleic Acids Res., 25, 3389, 10.1093/nar/25.17.3389

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

Amore, 2003, Spdeadringer, a sea urchin embryo gene required separately in skeletogenic and oral ectoderm gene regulatory networks, Dev. Biol., 261, 55, 10.1016/S0012-1606(03)00278-1

Angerer, 1988, Expression of a collagen gene in mesenchyme lineages of the Strongylocentrotus purpuratus embryo, Genes Dev., 2, 239, 10.1101/gad.2.2.239

Angerer, L., Hussain, S., Wei, Z., Livingston, B.T., this issue. Sea urchin metalloproteases in development: a genomic survey of the tolloid-like, MMP and ADAM families. Dev. Biol. (doi:10.1016/j.ydbio.2006.07.046).

Aspberg, 1999, Fibulin-1 is a ligand for the C-type lectin domains of aggrecan and versican, J. Biol. Chem., 274, 20444, 10.1074/jbc.274.29.20444

Bateman, 2004, The Pfam protein families database, Nucleic Acids Res., 32, D138, 10.1093/nar/gkh121

Bengtson, 1994, The advent of animal skeletons, 412

Benson, 1987, A lineage-specific gene encoding a major matrix protein of the sea urchin embryo spicule. I. Authentication of the cloned gene and its developmental expression, Dev. Biol., 120, 499, 10.1016/0012-1606(87)90253-3

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

Beverdam, 2001, Severe nasal clefting and abnormal embryonic apoptosis in Alx3/Alx4 double mutant mice, Development, 128, 3975, 10.1242/dev.128.20.3975

Blankenship, 1984, Collagen metabolism and spicule formation in sea urchin micromeres, Exp. Cell Res., 152, 98, 10.1016/0014-4827(84)90233-7

Brown, 1995, Spiculogenesis in the sea urchin embryo: studies on the SM30 spicule matrix protein, Dev. Growth Differ., 37, 69, 10.1046/j.1440-169X.1995.00008.x

Carson, 1985, A monoclonal antibody inhibits calcium accumulation and skeleton formation in cultured embryonic cells of the sea urchin, Cell, 41, 639, 10.1016/S0092-8674(85)80036-2

Chang, 1999, Expression and signal transduction of calcium-sensing receptors in cartilage and bone, Endocrinology, 140, 5883, 10.1210/endo.140.12.7190

Cheers, 2005, P16 is an essential regulator of skeletogenesis in the sea urchin embryo, Dev. Biol., 283, 384, 10.1016/j.ydbio.2005.02.037

Chow, 1979, Carbonic anhydrase activity in developing sea urchin embryos, Exp. Cell Res., 124, 451, 10.1016/0014-4827(79)90223-4

Clements, 2004, The tissue kallikrein family of serine proteases: functional roles in human disease and potential as clinical biomarkers, Crit. Rev. Clin. Lab. Sci., 41, 265, 10.1080/10408360490471931

Coffman, 2004, Evaluation of developmental phenotypes produced by morpholino antisense targeting of a sea urchin Runx gene, BMC Biol., 2, 6, 10.1186/1741-7007-2-6

Dominguez, 2002, Paired gill slits in a fossil with a calcite skeleton, Nature, 417, 841, 10.1038/nature00805

Donoghue, 2002, Origin and early evolution of vertebrate skeletonization, Microsc. Res. Tech., 59, 352, 10.1002/jemt.10217

Drager, 1989, The expression of embryonic primary mesenchyme genes of the sea urchin, Strongylocentrotus purpuratus, in the adult skeletogenic tissues of this and other species of echinoderms, Dev. Biol., 133, 14, 10.1016/0012-1606(89)90292-3

Delsuc, 2006, Tunicates and not cephalochordates are the closest living relatives of vertebrates, Nature, 439, 965, 10.1038/nature04336

Eddy, 1998, Profile hidden Markov models, Bioinformatics, 14, 755, 10.1093/bioinformatics/14.9.755

Emlet, 1985, Crystal axes in recent and fossil adult echinoids indicate trophic mode of larval development, Science, 230, 937, 10.1126/science.230.4728.937

Ettensohn, 1997, The morphogenesis of the skeletal system of the sea urchin embryo, vol. VII, 225

Ettensohn, 2003, Alx1, a member of the Cart1/Alx3/Alx4 subfamily of Paired-class homeodomain proteins, is an essential component of the gene network controlling skeletogenic fate specification in the sea urchin embryo, Development, 130, 2917, 10.1242/dev.00511

Exposito, 1994, Identification of a cell lineage-specific gene coding for a sea urchin alpha 2(IV)-like collagen chain, J. Biol. Chem., 269, 13167, 10.1016/S0021-9258(17)36814-X

Farach-Carson, 1989, A calcium-binding, asparagine-linked oligosaccharide is involved in skeleton formation in the sea urchin embryo, J. Cell Biol., 109, 1289, 10.1083/jcb.109.3.1289

Fisher, 2001, Flexible structures of SIBLING proteins, bone sialoprotein, and osteopontin, Biochem. Biophys. Res. Commun., 280, 460, 10.1006/bbrc.2000.4146

Fuchikami, 2002, T-brain homologue (HpTb) is involved in the archenteron induction signals of micromere descendant cells in the sea urchin embryo, Development, 129, 5205, 10.1242/dev.129.22.5205

Gee, 1996

George, 1991, Characterization and expression of a gene encoding a 30.6-kDa Strongylocentrotus purpuratus spicule matrix protein, Dev. Biol., 147, 334, 10.1016/0012-1606(91)90291-A

Hanalych, 2004, The new view of animal phylogeny, Annu. Rev. Ecol. Evol. Syst., 35, 229, 10.1146/annurev.ecolsys.35.112202.130124

Harkey, 1995, Structure, expression, and extracellular targeting of PM27, a skeletal protein associated specifically with growth of the sea urchin larval spicule, Dev. Biol., 168, 549, 10.1006/dbio.1995.1101

Heatfield, 1975, Ultrastructural studies of regenerating spines of the sea urchin Strongylocentrotus purpuratus, J. Morphol., 145, 13, 10.1002/jmor.1051450103

Holland, 2001, Origin and early evolution of the vertebrates: new insights from advances in molecular biology, anatomy, and palaeontology, BioEssays, 23, 142, 10.1002/1521-1878(200102)23:2<142::AID-BIES1021>3.0.CO;2-5

Illies, 2002, Identification and developmental expression of new biomineralization proteins in the sea urchin Strongylocentrotus purpuratus, Dev. Genes Evol., 212, 419, 10.1007/s00427-002-0261-0

InterPro Consortium (R. Apweiler, T.K. Attwood, A. Bairoch, A. Bateman, E. Birney, M. Biswas, P. Bucher, L. Cerutti, F. Corpet, M.D.R. Croning, R. Durbin, L. Falquet, W. Fleischmann, J. Gouzy, H. Hermjakob, N. Hulo, I. Jonassen, D. Kahn, A. Kanapin, Y. Karavidopoulou, R. Lopez, B. Marx, N.J. Mulder, T.M. Oinn, M. Pagni, F. Servant, C.J.A. Sigrist, E.M. Zdobnov), 2001. The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucl. Acid. Res. 29, 37–40.

Jefferies, 1986, The Ancestry of the Vertebrates, British Museum (Natural History), London

Kabakoff, 1992, Characterization of post-translational modifications common to three primary mesenchyme cell-specific glycoproteins involved in sea urchin embryonic skeleton formation, Dev. Biol., 150, 294, 10.1016/0012-1606(92)90243-A

Katoh-Fukui, 1991, The corrected structure of the SM50 spicule matrix protein of Strongylocentrotus purpuratus, Dev. Biol., 145, 201, 10.1016/0012-1606(91)90226-S

Kawasaki, 2006, Evolutionary genetics of vertebrate tissue mineralization: the origin and evolution of the secretory calcium-binding phosphoprotein family, J. Exp. Zool., 306B, 1, 10.1002/jez.b.21088

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

Kawasaki, 2005, Phenogenetic drift in evolution: the changing genetic basis of vertebrate teeth, Proc. Natl. Acad. Sci. U. S. A., 102, 18063, 10.1073/pnas.0509263102

Killian, 1996, Characterization of the proteins comprising the integral matrix of Strongylocentrotus purpuratus embryonic spicules, J. Biol. Chem., 271, 9150, 10.1074/jbc.271.15.9150

Kitajima, 2000, Differential distribution of spicule matrix proteins in the sea urchin embryo skeleton, Dev. Growth Differ., 42, 295, 10.1046/j.1440-169x.2000.00513.x

Kurokawa, 1999, HpEts, an ets-related transcription factor implicated in primary mesenchyme cell differentiation in the sea urchin embryo, Mech. Dev., 80, 41, 10.1016/S0925-4773(98)00192-0

Lambert, 1990, Protochordate biomineralization, 461

Leaf, 1987, Antibodies to a fusion protein identify a cDNA clone encoding msp130, a primary mesenchyme-specific cell surface protein of the sea urchin embryo, Dev. Biol., 121, 29, 10.1016/0012-1606(87)90135-7

Lee, 1999, SM37, a skeletogenic gene of the sea urchin embryo linked to the SM50 gene, Dev. Growth Differ., 41, 303, 10.1046/j.1440-169X.1999.413429.x

Letunic, 2006, SMART 5: domains in the context of genomes and networks, Nucleic Acids Res., 34, D257, 10.1093/nar/gkj079

Lindskog, 1997, Structure and mechanism of carbonic anhydrase, Pharmacol. Ther., 74, 1, 10.1016/S0163-7258(96)00198-2

Logan, 1999, Nuclear beta-catenin is required to specify vegetal cell fates in the sea urchin embryo, Development, 126, 345, 10.1242/dev.126.2.345

Markel, 1986, Ultrastructural investigation of matrix mediated biomineralization in echinoids, Zoomorphology, 105, 197

Mavrogiannis, 2001, Haploinsufficiency of the human homeobox gene ALX4 causes skull ossification defects, Nat. Genet., 27, 17, 10.1038/83703

Mitsunga, 1986, Carbonic anhydrase activity in developing sea urchin embryos with special reference to calcification of spicules, Cell Differ., 18, 257, 10.1016/0045-6039(86)90057-6

Oliveri, 2002, A gene regulatory network that directs micromere specification in the sea urchin embryo, Dev. Biol., 246, 209, 10.1006/dbio.2002.0627

Ortega, 2003, How proteases regulate bone morphogenesis, Ann. N. Y. Acad Sci., 995, 109, 10.1111/j.1749-6632.2003.tb03214.x

Panopoulou, 2003, New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes, Genome Res., 13, 1056, 10.1101/gr.874803

Peled-Kamar, 2002, Spicule matrix protein LSM34 is essential for biomineralization of the sea urchin spicule, Exp. Cell Res., 272, 56, 10.1006/excr.2001.5398

Pennington, 1990, Consequences of the calcite skeleton of planktonic echinoderm larvae for orientation, swimming, and shape, Biol. Bull., 179, 121, 10.2307/1541746

Peterson, 2001, Animal phylogeny and the ancestry of bilaterians: inferences from morphology and 18S rDNA gene sequences, Evol. Dev., 3, 170, 10.1046/j.1525-142x.2001.003003170.x

Porter, 2005, The ADAMTS metalloproteinases, Biochem. J., 386, 15, 10.1042/BJ20040424

Poustka, 2003, Generation, annotation, evolutionary analysis, and database integration of 20,000 unique sea urchin EST clusters, Genome Res., 13, 2736, 10.1101/gr.1674103

Qin, 2004, Post-translational modifications of sibling proteins and their roles in osteogenesis and dentinogenesis, Crit. Rev. Oral Biol. Med., 15, 126, 10.1177/154411130401500302

Raouf, 2000, Ets transcription factors and targets in osteogenesis, Oncogene, 19, 6455, 10.1038/sj.onc.1204037

Richardson, 1989, Expression of an embryonic spicule matrix gene in calcified tissues of adult sea urchins, Dev. Biol., 132, 266, 10.1016/0012-1606(89)90222-4

Robertson, 2002, The expression of SpRunt during sea urchin embryogenesis, Mech. Dev., 117, 327, 10.1016/S0925-4773(02)00201-0

Samanta, M.P., Tongprasit, W., Istrail, S., Cameron, A., Tu, Q., Davidson, E.H., Stolc, V., 2006. A high-resolution transcriptome map of the sea urchin embryo.

Seto, 2004, The localization of occluded matrix proteins in calcareous spicules of sea urchin larvae, J. Struct. Biol., 148, 123, 10.1016/j.jsb.2004.04.001

Shu, 2003, A new species of yunnanozoan with implications for deuterostome evolution, Science, 299, 1380, 10.1126/science.1079846

Shu, 2004, Ancestral echinoderms from the Chengjiang deposits of China, Nature, 430, 422, 10.1038/nature02648

Sly, 1995, Human carbonic anhydrases and carbonic anhydrase deficiencies, Annu. Rev. Biochem., 64, 375, 10.1146/annurev.bi.64.070195.002111

Smith, 2004, Echinoderm roots, Nature, 430, 411, 10.1038/430411a

Steck, 2001, Chondrocyte expressed protein-68 (CEP-68), a novel human marker gene for cultured chondrocytes, Biochem. J., 353, 169, 10.1042/0264-6021:3530169

Sucov, 1987, A lineage-specific gene encoding a major matrix protein of the sea urchin embryo spicule. II. Structure of the gene and derived sequence of the protein, Dev. Biol., 120, 507, 10.1016/0012-1606(87)90254-5

Suzuki, 1997, Comparative analysis of fibrillar and basement membrane collagen expression in embryos of the sea urchin, Strongylocentrotus purpuratus, Zool. Sci., 14, 449, 10.2108/zsj.14.449

Urry, 2000, Expression of spicule matrix proteins in the sea urchin embryo during normal and experimentally altered spiculogenesis, Dev. Biol., 225, 201, 10.1006/dbio.2000.9828

Veis, 2002, Mineral-related proteins of sea urchin teeth: Lytechinus variegatus, Microsc. Res. Tech., 59, 342, 10.1002/jemt.10216

Weitzel, 2004, Differential stability of beta-catenin along the animal–vegetal axis of the sea urchin embryo mediated by dishevelled, Development, 131, 2947, 10.1242/dev.01152

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

Wilt, 2002, Biomineralization of the spicules of sea urchin embryos, Zool. Sci., 19, 253, 10.2108/zsj.19.253

Wilt, 2005, Developmental biology meets materials science: morphogenesis of biomineralized structures, Dev. Biol., 280, 15, 10.1016/j.ydbio.2005.01.019

Wilt, 2003, Development of calcareous skeletal elements in invertebrates, Differentiation, 71, 237, 10.1046/j.1432-0436.2003.7104501.x

Yamauchi, 2005, Involvement of calcium-sensing receptor in osteoblastic differentiation of mouse MC3T3-E1 cells, Am. J. Physiol.: Endocrinol. Metab., 288, 608

Zhu, 2001, A large-scale analysis of mRNAs expressed by primary mesenchyme cells of the sea urchin embryo, Development, 128, 2615, 10.1242/dev.128.13.2615