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Generation of Expressed Sequence Tags for Immune Gene Discovery and Marker Development in the Sea Squirt, Halocynthia roretzi  

Kim, Young-Ok (Biotechnology Research Institute, National Fisheries Research and Development Institute)
Cho, Hyun-Kook (Department of Molecular Biology, Pusan National University)
Park, Eun-Mi (Biotechnology Research Institute, National Fisheries Research and Development Institute)
Nam, Bo-Hye (Biotechnology Research Institute, National Fisheries Research and Development Institute)
Hur, Young-Baek (Research Center for Aquaculture Environment)
Lee, Sang-Jun (Biotechnology Research Institute, National Fisheries Research and Development Institute)
Cheong, Jae-Hun (Department of Molecular Biology, Pusan National University)
Publication Information
Journal of Microbiology and Biotechnology / v.18, no.9, 2008 , pp. 1510-1517 More about this Journal
Abstract
Expresssed sequence tag (EST) analysis was developed from three cDNA libraries constructed from cells of the digestive tract, gonad, and liver of sea squirt. Randomly selected cDNA clones were partially sequenced to generate a total of 922 ESTs, in which 687 unique ESTs were identified respectively. Results of BLASTX search showed that 612 ESTs (89%) have homology to genes of known function whereas 75 ESTs (11%) were unidentified or novel. Based on the major function of their encoded proteins, the identified clones were classified into ten broad categories. We also identified several kinds of immune-related genes as identifying novel genes. Sequence analysis of ESTs revealed the presence of microsatellite-containing genes that may be valuable for further gene mapping studies. The accumulation of a large number of identified cDNA clones is invaluable for the study of sea squirt genetics and developmental biology. Further studies using cDNA microarrays are needed to identify the differentially expressed transcripts after disease infection.
Keywords
Sea squirt; Halocynthia roretzi; expressed sequence tags (ESTs); immune gene; marker;
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1 Delaunay, A., A. D. Isnard, and M. B. Toledano. 2000. $H_2O_2$ sensing through oxidation of the Yap1 transcription factor. EMBO J. 19: 5157-5166   DOI   ScienceOn
2 Edgar, P. F. 1995. Hucolin, a new corticosteroid-binding protein from human plasma with structural similarities to ficolins, transforming growth $factor-{\beta}1-binding$ proteins. FEBS Lett. 375: 159-161   DOI
3 Fritz, I. B., P. S. Tung, and M. Ailenberg. 1993. Proteases and antiproteases in the seminiferous tubule, pp. 217-235. In L. D. Russell and M. D. Griswold (eds.). The Sertoli Cell. Cache River Press, Clearwater, FL
4 Huang, S. S., P. O. Grady, and J. S. Huang. 1998. Human transforming growth $factor-{\beta}-{\alpha}2-macroglobulin$ complex is a latent form of transforming growth factor ${\beta}$. J. Biol. Chem. 263: 1535-1541
5 Lublin, D. M. 2005. [Review] Cromer and DAF: Role in health and disease. Immunohematology 21: 39-47
6 Miwa, T. and W. C. Song. 2001. Membrane complement regulatory proteins: Insight from animal studies and relevance to human diseases. Int. Immunopharmacol. 1: 445-459   DOI   ScienceOn
7 Sambrook, J., E. F. Frisch, and T. Maniatis. 1989. Molecular Cloning: A Laboratory Manual, 2nd Ed. Cold Spring Habor Laboratory Press, Cold Spring Habor, NY, U.S.A
8 Sottrup-Jensen, L. 1989. Alpha-macroglobulins: Structure, shape, and mechanism of proteinase complex formation. J. Biol. Chem. 264: 11539-11542
9 Chu, C. T., D. S. Rubenstein, J. J. Enghild, and S. V. Pizzo. 1991. Mechanism of insulin incorporation into ${\alpha}2-macroglobulin$: Implication for the study of peptide and growth factor binding. Biochemistry 30: 1551-1560   DOI   ScienceOn
10 Lu, J., Y. Le, L. Kon, J. Chan, and S. H. Lee. 1996. Biosynthesis of human ficolin, an Escherichia coli-binding protein, by monocytes: Comparison with the synthesis of two macrophagespecific proteins, C1q and the mannose receptor. Immunology 89: 289-294   DOI   ScienceOn
11 Serapion, J., H. Kucuktas, J. Feng, and Z. Liu. 2004. Bioinformatic mining of type I microsatellites from expressed sequence tags of channel catfish (Ictalurus punctatus). Mar. Biotechnol. 6: 364-377   DOI   ScienceOn
12 Morgan, B. P. 1999. Regulation of the complement membrane attack pathway. Crit. Rev. Immunol. 19: 173-198
13 Parsons, J. D. 1995. Improved tools for DNA comparison and clustering. Comp. Appl. Biosci. 1: 603-613
14 Blount, P. and J. P. Merlie. 1991. BIP associates with newly synthesized subunits of the mouse muscle nicotinic receptor. J. Cell Biol. 113: 1125-1132   DOI   ScienceOn
15 Liu, Z., P. Li, A. Kocabas, Z. Ju, A. Karsi, D. Cao, and A. Patterson. 2001. Microsatellite-containing genes from the channel catfish brain: Evidence of trinucleotide repeat expansion in the coding region of nucleotide excision repair gene RAD23B. Biochem. Biophys. Res. Commun. 289: 317-324   DOI   ScienceOn
16 Somerville, C. and S. Somerville. 1999. Plant functional genetics. Science 285: 380-383   DOI
17 Makabe, K. W., T. Kawashima, S. Kawashima, T. Minokawa, A. Adachi, H. Kawamura, et al. 2001. Large-scale cDNA analysis of the maternal genetic information in the egg of Halocynthia roretzi for a gene expression catalog of ascidian development. Development 128: 2555-2567
18 Carmel-Harel, O. and G. Storz. 2000. Roles of the glutathioneand thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. Annu. Rev. Microbiol. 54: 439-461   DOI   ScienceOn
19 James, K. 1990. Interactions between cytokines and ${\alpha}2-macroglobulin$. Immunol. Today 11: 163-166   DOI   ScienceOn
20 Gasque, P. 2004. Complement: A unique innate immune sensor for danger signals. Mol. Immunol. 41: 1089-1098   DOI   ScienceOn
21 Murakawa, K., K. Matsubara, A. Fukushima, J. Yoshii, and K. Okubo. 1994. Chromosomal assignments of 3'-directed partial cDNA sequences representing novel genes expressed in granulocytoid cells. Genomics 23: 379-389   DOI   ScienceOn
22 Kantety, R. V., M. La Rota, D. E. Matthews, and M. E. Sorrells. 2002. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Mol. Biol. 48: 501-510   DOI   ScienceOn
23 Hass, I. G. and M. Wabl. 1983. Immunoglobulin heavy chain binding protein. Nature 306: 387-389   DOI   ScienceOn
24 Cho, H. K., B. H. Nam, H. J. Kong, H. S. Han, Y. B. Hur, T. J. Choi, Y. H. Choi, W. J. Kim, and J. H. Cheong. 2008. Identification of softness syndrome-associated candidate genes and DNA sequence variation in the sea squirt, Halocynthia roretzi. Mar. Biotechnol. 10: 447-456   DOI   ScienceOn
25 Cordeiro, G.., M. R. Casu, C. L. McIntyre, J. M. Manners, and R. J. Henry. 2001. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. Plant Sci. 160: 1115-1123   DOI   ScienceOn
26 Le, Y., S. H. Lee, O. L. Kon, and J. Lu. 1998. Human L-ficolin: plasma levels, sugar specificity, and assignment of its lectin activity to the fibrinogen-like (FBG) domain. FEBS Lett. 425: 367-370   DOI   ScienceOn
27 He, C., L. Chen, M. Simmons, P. Li, S. Kim, and Z. J. Liu. 2003. Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis. Anim. Genet. 34: 445-448   DOI   ScienceOn
28 Hurtley, S. M., D. G. Bole, H. Hoover-Litty, A. Helenius, and C. S. Copeland. 1989. Interactions of misfolded influenza virus hemagglutinin with binding protein (Bip). J. Cell Biol. 108: 2117-2126   DOI   ScienceOn
29 Ichijo, H., L. Ronnstrand, K. Miyagawa, H. Ohashi, C. H. Heldin, and K. Miyazono. 1991. Purification of transforming growth $factor-{\beta}$ 1 binding proteins from porcine uterus membranes. J. Biol. Chem. 266: 22459-22464
30 Ichijo, H., U. Hellman, C. Wernstedt, L. J. Gonez, L. Claesson- Welsh, C. H. Helden, and K. Miyazono. 1993. Molecular cloning and characterization of ficolin, a multimeric protein with fibrinogen- and collagen-like domains. J. Biol. Chem. 268: 14505-14513
31 Kuge, S., M. Arita, A. Murayama, K. Maeta, S. Izawa, Y. Inoue, and A. Nomoto. 2001. Regulation of the yeast Yap1p nuclear export signal is mediated by redox signal-induced reversible disulfide bond formation. Mol. Cell. Biol. 21: 6139-6150   DOI   ScienceOn
32 Harumiya, S., A. Omori, T. Sugiura, Y. Fukumoto, H. Tachikawa, and D. Fujimoto. 1995. EBP-37, a new elastin-binding protein in human plasma: Structural similarity to ficolins, tranforming growth $factor-{\beta}1-binding proteins. J. Biochem. 117: 1029-1035   DOI
33 He, G., R. Meng, M. Newman, G. Gao, R. N. Pittman, and C. S. Prakash. 2003. Microsatellites as DNA markers in cultivated peanut (Arachis hypogaea L.). BMC Plant Biol. 3: 1-6   DOI   ScienceOn
34 Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang, W. Miller, and D. J. Lipman. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search program. Nucleic Acids Res. 25: 3389-3402   DOI   ScienceOn
35 Lublin, D. M., S. Kompelli, J. R. Storry, and M. E. Reid. 2000. Molecular basis of Cromer blood group antigens. Transfusion 40: 208-213   DOI   ScienceOn