Analysis of cytoskeletal and motility proteins in the sea urchin genome assembly

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2 Asai, 2004, The dynein heavy chain family, J. Eukaryot. Microbiol., 51, 23, 10.1111/j.1550-7408.2004.tb00157.x Begg, 1979, pH regulates the polymerization of actin in the sea urchin egg cortex, J. Cell Biol., 83, 241, 10.1083/jcb.83.1.241 Bi, 1997, Kinesin- and myosin-driven steps of vesicle recruitment for Ca2+-regulated exocytosis, J. Cell Biol., 138, 999, 10.1083/jcb.138.5.999 Blair, 2005, Evolutionary sequence analysis of complete eukaryote genomes, BMC Bioinformatics, 6, 53, 10.1186/1471-2105-6-53 Bloom, 1985, Use of multiple monoclonal antibodies to characterize the major microtubule-associated protein in sea urchin eggs, Cell Motil., 5, 431, 10.1002/cm.970050602 Brokaw, 1973, Localized activation of bending in proximal, medial and distal regions of sea-urchin sperm flagella, J. Cell Sci., 13, 1, 10.1242/jcs.13.1.1 Bryan, 1993, Fascin, an echinoid actin-bundling protein, is a homolog of the Drosophila singed gene product, Proc. Natl. Acad. Sci. U. S. A., 90, 9115, 10.1073/pnas.90.19.9115 Carlini, 2000, Actin gene family evolution and the phylogeny of coleoid cephalopods mollusca, cephalopoda, Mol. Biol. Evol., 17, 1353, 10.1093/oxfordjournals.molbev.a026419 Chui, 2000, Roles of two homotetrameric kinesins in sea urchin embryonic cell division, J. Biol. Chem., 275, 38005, 10.1074/jbc.M005948200 Cohen, 1970, An estimate of the amount of microtubule protein in the isolated mitotic apparatus, J. Cell Sci., 6, 159, 10.1242/jcs.6.1.159 Cole, 1995, Purification of kinesin-related protein complexes from eggs and embryos, Biophys. J., 68, 158s Cole, 1992, Isolation of a sea urchin egg kinesin-related protein using peptide antibodies, J.Cell Sci., 101, 291, 10.1242/jcs.101.2.291 Cole, 1993, Novel heterotrimeric kinesin-related protein purified from sea urchin eggs, Nature, 366, 268, 10.1038/366268a0 Collins, 1986, A microtubule-activated ATPase from sea urchin eggs, distinct from cytoplasmic dynein and kinesin, Proc. Natl. Acad. Sci. U. S. A., 83, 4799, 10.1073/pnas.83.13.4799 D'Andrea, 1994, Identification of coelomocyte unconventional myosin and its association with in vivo particle/vesicle motility, J. Cell. Sci., 107, 2081, 10.1242/jcs.107.8.2081 Dutcher, 2003, Long-lost relatives reappear, identification of new members of the tubulin superfamily, Curr. Opin. Microbiol., 6, 634, 10.1016/j.mib.2003.10.016 Edds, 1980, The formation and elongation of filopodia during transformation of sea urchin coelomocytes, Cell Motil., 1, 131, 10.1002/cm.970010110 Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res., 32, 1792, 10.1093/nar/gkh340 Fang, 1996, Expression of the actin gene family in embryos of the sea urchin Lytechinus pictus, Dev. Biol., 173, 306, 10.1006/dbio.1996.0025 Felsenstein, 1985, Confidence limits on phylogenies, an approach using the bootstrap, Evolution, 39, 783, 10.2307/2408678 Felsenstein, J., 2005. PHYLIP (Phylogeny Inference Package) version 3.6. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle. Fishkind, 1987, Isolation and characterization of sea urchin egg spectrin, calcium modulation of the spectrin-actin interaction, Cell Motil. Cytoskeleton, 7, 304, 10.1002/cm.970070403 Folker, 2005, Interactions between CLIP-170, tubulin, and microtubules: implications for the mechanism of Clip-170 plus-end tracking behavior, Mol. Biol. Cell, 16, 5373, 10.1091/mbc.E04-12-1106 Gianguzza, 1989, DNA sequence and pattern of expression of the sea urchin (Paracentrotus lividus) alpha-tubulin genes, Mol. Reprod. Dev., 1, 170, 10.1002/mrd.1080010305 Gibbons, 1991, Multiple nucleotide-binding sites in the sequence of dynein beta heavy chain, Nature, 352, 640, 10.1038/352640a0 Gibbons, 1994, Phylogeny and expression of axonemal and cytoplasmic dynein genes in sea urchins, Mol. Biol. Cell, 5, 57, 10.1091/mbc.5.1.57 Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520 Hammarback, 1991, MAP1B is encoded as a polyprotein that is processed to form a complex N-terminal microtubule-binding domain, Neuron, 7, 129, 10.1016/0896-6273(91)90081-A Harvey, 1956 Hiramoto, 1968, The mechanics and mechanism of cleavage in the sea-urchin egg, Symp. Soc. Exp. Biol., 22, 311 Hodge, 2000, A myosin family tree, J. Cell Sci., 113, 3353, 10.1242/jcs.113.19.3353 Holleran, 1998, Speculating about spectrin: new insights into the Golgi-associated cytoskeleton, Trends Cell Biol., 8, 26, 10.1016/S0962-8924(97)01195-1 Jones, 1992, The rapid generation of mutation data matrices from protein sequences, Comp. Appl. Biosci. (CABIOS), 8, 275 Kagami, 1998, A dynein light chain of sea urchin sperm flagella is a homolog of mouse Tctex 1, which is encoded by a gene of the t complex sterility locus, Gene, 211, 383, 10.1016/S0378-1119(98)00128-0 Kane, 1967, The mitotic apparatus: identification of the major soluble component of the glycerol-isolated mitotic apparatus, J. Cell Biol., 32, 243, 10.1083/jcb.32.2.243 Kane, 1983, Interconversion of structural and contractile actin gels by insertion of myosin during assembly, J. Cell Biol., 97, 1745, 10.1083/jcb.97.6.1745 Kane, 1986, Components of the actin-based cytoskeleton, Methods Cell Biol., 27, 229, 10.1016/S0091-679X(08)60351-9 Katoh, 2005, MAFFT version 5: improvement in accuracy of multiple sequence alignment, Nucleic Acids Res., 33, 511, 10.1093/nar/gki198 Kelleher, 1995, Sequences, structural models, and cellular localization of the actin-related proteins Arp2 and Arp3 from Acanthamoeba, J. Cell Biol., 131, 385, 10.1083/jcb.131.2.385 Kent, 2002, BLAT—The BLAST-like alignment tool, Genome Res., 12, 656, 10.1101/gr.229202. Article published online before March 2002 Krause, 2003, Ena/VASP proteins, regulators of the actin cytoskeleton and cell migration, Annu. Rev. Cell Dev. Biol., 19, 541, 10.1146/annurev.cellbio.19.050103.103356 Langkopf, 1992, Microtubule-associated proteins 1A and LC2. Two proteins encoded in one messenger RNA, J. Biol. Chem., 267, 16561, 10.1016/S0021-9258(18)42039-X Lawrence, 2004, A standardized kinesin nomenclature, J. Cell Biol., 167, 19, 10.1083/jcb.200408113 Lee, 1984, Sea urchin actin gene subtypes. Gene number, linkage and evolution, J. Mol. Biol., 172, 149, 10.1016/S0022-2836(84)80035-2 Li, 1994, Molecular characterization of the 77-kDa echinoderm microtubule-associated protein. Homology to the beta-transducin family, J. Biol. Chem., 269, 31777, 10.1016/S0021-9258(18)31763-0 Mabuchi, 1973, A myosin-like protein in the cortical layer of the sea urchin egg, J. Cell. Biol., 59, 542, 10.1083/jcb.59.2.542 Mabuchi, 1986, Biochemical aspects of cytokinesis, Int. Rev. Cytol., 101, 175, 10.1016/S0074-7696(08)60249-1 Mabuchi, 1977, The effect of myosin antibody on the division of starfish blastomeres, J. Cell Biol., 74, 251, 10.1083/jcb.74.1.251 Mabuchi, 1980, Purification and properties of soluble actin from sea urchin eggs, J. Biochem. (Tokyo), 87, 785, 10.1093/oxfordjournals.jbchem.a132808 Maekawa, 1992, A novel 24-kDa microtubule-associated protein purified from sea urchin eggs, Eur. J. Biochem., 205, 1195, 10.1111/j.1432-1033.1992.tb16890.x Maekawa, 1994, Purification of a low molecular weight microtubule binding protein from sea urchin eggs, Biochim. Biophys. Acta, 1207, 194, 10.1016/0167-4838(94)00075-1 Masuda, 1979, Species specific pattern of ciliogenesis in developing sea urchin embryos, Dev. Growth Differ., 21, 545, 10.1111/j.1440-169X.1979.00545.x McKean, 2001, The extended tubulin superfamily, J. Cell Sci., 114, 2723, 10.1242/jcs.114.15.2723 Miki, 2005, Analysis of the kinesin superfamily: insights into structure and function, Trends Cell Biol., 15, 467, 10.1016/j.tcb.2005.07.006 Morris, 1997, Heterotrimeric kinesin-II is required for the assembly of motile 9+2 ciliary axonemes on sea urchin embryos, J. Cell Biol., 138, 1009, 10.1083/jcb.138.5.1009 Nei, 2001, Estimation of divergence times from multiprotein sequences for a few mammalian species and several distantly related organisms, Proc. Natl. Acad. Sci., 98, 2497, 10.1073/pnas.051611498 Ogawa, 1991, Four ATP-binding sites in the midregion of the beta heavy chain of dynein, Nature, 352, 643, 10.1038/352643a0 Ogawa, 1996, Is outer arm dynein intermediate chain 1 multifunctional?, Mol. Biol. Cell, 7, 1895, 10.1091/mbc.7.12.1895 Patel, 2001, Myr 8, a novel unconventional myosin expressed during brain development associates with the protein phosphatase catalytic subunits 1alpha and 1gamma1, J. Neurosci., 21, 7954, 10.1523/JNEUROSCI.21-20-07954.2001 Pazour, 2005, Proteomic analysis of a eukaryotic cilium, J. Cell Biol., 170, 103, 10.1083/jcb.200504008 Pazour, 2006, Identification of predicted human outer dynein arm genes: candidates for primary ciliary dyskinesia genes, J. Med. Genet., 43, 62, 10.1136/jmg.2005.033001 Perumal, 2005, Intron position conservation across eukaryotic lineages in tubulin genes, Front. Biosci., 10, 2412, 10.2741/1706 Pfister, 2005, Cytoplasmic dynein nomenclature, J. Cell Biol., 171, 411, 10.1083/jcb.200508078 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 Rappaport, 1996 Rashid, 1995, Heterodimerization of the two motor subunits of the heterotrimeric kinesin, KRP85/95, J. Mol. Biol., 252, 157, 10.1006/jmbi.1995.0484 Rasmusson, 1994, A family of dynein genes in Drosophila melanogaster, Mol. Biol. Cell, 5, 45, 10.1091/mbc.5.1.45 Rogers, 1999, Identification of kinesin-C, a calmodulin-binding carboxy-terminal kinesin in animal (Strongylocentrotus purpuratus) cells, J. Mol. Biol., 294, 1, 10.1006/jmbi.1999.3249 Rogers, 2000, A kinesin-related protein, KRP(180), positions prometaphase spindle poles during early sea urchin embryonic cell division, J. Cell Biol., 150, 499, 10.1083/jcb.150.3.499 Ronquist, 2003, MrBayes 3: Bayesian phylogenetic inference under mixed models, Bioinformatics, 19, 1572, 10.1093/bioinformatics/btg180 Saitou, 1987, The neighbor joining method: a new method for reconstructing phylogenetic trees, Mol. Biol. Evol., 4, 406 Salmon, 1975, Spindle microtubules: thermodynamics of in vivo assembly and role in chromosome movement, Ann. N. Y. Acad. Sci., 253, 383, 10.1111/j.1749-6632.1975.tb19216.x Scholey, 1984, Isolation of microtubules and a dynein-like MgATPase from unfertilized sea urchin eggs, J. Biol. Chem., 259, 6516, 10.1016/S0021-9258(20)82172-3 Scholey, 1985, Identification of kinesin in sea urchin eggs, and evidence for its localization in the mitotic spindle, Nature, 318, 483, 10.1038/318483a0 Schroeder, 1968, Cytokinesis: filaments in the cleavage furrow, Exp. Cell Res., 53, 272, 10.1016/0014-4827(68)90373-X Sharp, 2000, Microtubule motors in mitosis, Nature, 407, 41, 10.1038/35024000 Shen, 2003, Involvement of actin-related proteins in ATP-dependent chromatin remodeling, Mol. Cell., 12, 147, 10.1016/S1097-2765(03)00264-8 Sirotkin, 2000, Characterization of sea urchin unconventional myosins and analysis of their patterns of expression during early embryogenesis, Mol. Reprod. Dev., 57, 111, 10.1002/1098-2795(200010)57:2<111::AID-MRD2>3.0.CO;2-T Sjöblom, T., Jones, S., Wood, L.D., Parsons, D.W., Lin, J., Barber, T., Mandelker, D., Leary, R.J., Ptak, J., Silliman, N., Szabo, S., Buckhaults, P., Farrell, C., Meeh, P., Markowitz, S.D., Willis, J., Dawson, D., Willson, J.K., Gazdar, A.F., Hartigan, J., Wu, L., Liu, C., Parmigiani, G., Park, B.H., Bachman, K.E., Papadopoulos, N., Vogelstein, B., Kinzler, K.W., Velculescu, V.E., in press. The consensus coding sequences of human breast and colorectal cancers. Science. Sluder, 1979, Role of spindle microtubules in the control of cell cycle timing, J. Cell Biol., 80, 674, 10.1083/jcb.80.3.674 Smith, 1992, SpCoel1: a sea urchin profilin gene expressed specifically in coelomocytes in response to injury, Mol. Biol. Cell, 3, 403, 10.1091/mbc.3.4.403 Stephens, 1995, Ciliogenesis in sea urchin embryos—A subroutine in the program of development, BioEssays, 17, 331, 10.1002/bies.950170409 Strickland, 2005, Interaction between EB1 and p150glued is required for anaphase astral microtubule elongation and stimulation of cytokinesis, Curr. Biol., 15, 2249, 10.1016/j.cub.2005.10.073 Suprenant, 2000, Conservation of the WD-repeat, microtubule-binding protein, EMAP, in sea urchins, humans, and the nematode C. elegans, Dev. Genes Evol., 210, 2, 10.1007/PL00008183 Terasaki, 1997, Identification of actin-binding proteins from sea urchin eggs by F-actin affinity column chromatography, J. Biochem. (Tokyo), 122, 226, 10.1093/oxfordjournals.jbchem.a021733 Thompson, 1997, The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools, Nucleic Acids Res., 25, 4876, 10.1093/nar/25.24.4876 Tilney, 1969, Microtubules and filaments in the filopodia of the secondary mesenchyme cells of Arbacia punctulata and Echinarachnius parma, J. Cell Sci., 5, 195, 10.1242/jcs.5.1.195 Tilney, 1973, The polymerization of actin, its role in the generation of the acrosomal process of certain echinoderm sperm, J. Cell Biol., 59, 109, 10.1083/jcb.59.1.109 Togel, 1999, A 45 amino acid residue domain necessary and sufficient for proteolytic cleavage of the MAP1B polyprotein precursor, FEBS Lett., 451, 15, 10.1016/S0014-5793(99)00523-2 Vale, 2003, The molecular motor toolbox for intracellular transport, Cell, 112, 467, 10.1016/S0092-8674(03)00111-9 Vallee, 1983, Isolation of sea urchin egg microtubules with taxol and identification of mitotic spindle microtubule-associated proteins with monoclonal antibodies, Proc. Natl. Acad. Sci. U. S. A., 80, 6259, 10.1073/pnas.80.20.6259 Vaughan, 1996, Multiple mouse chromosomal loci for dynein-based motility, Genomics, 36, 29, 10.1006/geno.1996.0422 Wain, 2004, Genew: the Human Gene Nomenclature Database, 2004 updates, Nucleic Acids Res., 32, D255, 10.1093/nar/gkh072 Wang, 1997, The mouse formin (Fmn) gene: genomic structure, novel exons, and genetic mapping, Genomics, 39, 303, 10.1006/geno.1996.4519 Wedaman, 1993, Sequences of sea urchin kinesin light chain isoforms, J. Mol. Biol., 231, 155, 10.1006/jmbi.1993.1267 Wedaman, 1996, Sequence and submolecular localization of the 115-kD accessory subunit of the heterotrimeric kinesin-II (KRP85/95) complex, J. Cell Biol., 132, 371, 10.1083/jcb.132.3.371 Whittaker, 2006, The echinoderm adhesome, Dev. Biol., 300, 252, 10.1016/j.ydbio.2006.07.044 Wickstead, 2006, A “holistic” kinesin phylogeny reveals new kinesin families and predicts protein functions, Mol. Biol. Cell, 17, 1734, 10.1091/mbc.E05-11-1090 Wright, 1991, Subcellular localization and sequence of sea urchin kinesin heavy chain: evidence for its association with membranes in the mitotic apparatus and interphase cytoplasm, J. Cell Biol., 113, 817, 10.1083/jcb.113.4.817 Wright, 1993, Roles of kinesin and kinesin-like proteins in sea urchin embryonic cell division: evaluation using antibody microinjection, J. Cell Biol., 123, 681, 10.1083/jcb.123.3.681 Yokota, 1987, Activation of sea urchin sperm flagellar dynein ATPase activity by salt-extracted axonemes, J. Biochem. (Tokyo), 102, 31, 10.1093/oxfordjournals.jbchem.a122038 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