Identification of softness syndrome-associated candidate genes and DNA sequence variation in the sea squirt, Halocynthia roretzi

Marine Biotechnology

Volumn 10, Issue 4, 2008, Pages 447-456

  Cho, Hyun Kook ^a,b   Nam, Bo Hye ^b   Kong, Hee Jeong ^b   Han, Hyon Sob ^b   Hur, Young Baek ^c   Choi, Tae Jin ^b   Choi, Yung Hyun ^d   Kim, Woo Jin ^b   Cheong, Jaehun ^a  

^a Pusan National University   (South Korea)

^b National Fisheries Research and Development Institute (NFRDI)   (South Korea)

^c Research Center for Aquaculture Environment   (South Korea)

^d Dong Eui University   (South Korea)

Author keywords

Halocynthia reretzi; Metalloproteinase; Polymorphism; Sea squirt; Softness syndrome

Indexed keywords

HALOCYNTHIA RERETZI; METALLOPROTEINASE; SEA SQUIRT; SOFTNESS SYNDROME;

DNA SEQUENCES; ENZYME ACTIVITY; GENES; TISSUE;

AQUACULTURE;

METALLOPROTEINASE;

AQUACULTURE INDUSTRY; DNA; GENE EXPRESSION; GENOTYPE; IDENTIFICATION METHOD; INVERTEBRATE; MOLECULAR ANALYSIS; PATHOGEN; POLYMERASE CHAIN REACTION; SELECTIVE BREEDING;

AMINO ACID SEQUENCE; ANIMAL; ARTICLE; CHEMISTRY; GENE EXPRESSION REGULATION; GENETIC POLYMORPHISM; GENETIC VARIABILITY; GENETICS; GENOTYPE; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROMOTER REGION; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY; UROCHORDATA;

AMINO ACID SEQUENCE; ANIMALS; BASE SEQUENCE; GENE EXPRESSION REGULATION; GENOTYPE; METALLOPROTEASES; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; PROMOTER REGIONS (GENETICS); SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; UROCHORDATA; VARIATION (GENETICS);

ASIA; EURASIA;

ASCIDIACEA; HALOCYNTHIA; HALOCYNTHIA RORETZI;

EID: 44949202543     PISSN: 14362228     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10126-008-9084-y     Document Type: Article

References (35)

1. Ailenberg M, Silverman M (2000) Controlled hot start and improved specificity in carrying out PCR utilizing touch-up and loop incorporated primers (TULIPS). Biotechniques 29:1018-1020
2. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
3. Bond JS, Beynon RJ (1995) The astacin family of metalloendopeptidases. Protein Sci 4:1247-1261
4. Breathnach R, Chambon P (1981) Organization and expression of eucaryotic split genes coding for proteins. Annu Rev Biochem 50:349-383
5. Brownie J, Shawcross S, Theaker J, Whitcombe D, Ferrie R, Newton C, Little S (1997) The elimination of primer-dimer accumulation in PCR. Nucleic Acids Res 25:3235-3241
6. Chen SL, Li J, Deng SP, Tian YS, Wang QY, Zhuang ZM, Sha ZX, Xu JY (2007) Isolation of female-specific AFLP markers and molecular identification of genetic sex in half-smooth tongue sole (Cynoglossus semilaevis). Mar Biotechno l 9:273-280
7. Corden J, Wasylyk B, Buchwalder A, Sassone-Corsi P, Kedinger C, Chambon P (1980) Promoter sequences of eukaryotic protein-coding genes. Science 209:1406-1414
8. Dumermuth E, Eldering JA, Grünberg J, Jiang W, Sterchi EE (1993) Cloning of the PABA peptide hydrolase alpha subunit (PPH alpha) from human small intestine and its expression in COS-1 cells. FEBS Lett 335:367-375
9. Elaroussi MA, DeLuca HF (1994) A new member to the astacin family of metalloendopeptidases: a novel 1,25-dihydroxyvitamin D-3-stimulated mRNA from chorioallantoic membrane of quail. Biochim Biophys Acta 1217:1-8
10. Fang S, Jin X, Wang R, Li Y, Guo W, Wang N, Wang Y, Wen D, Wei L, Zhang J (2005) Polymorphisms in the MMP1 and MMP3 promoter and non-small cell lung carcinoma in North China. Carcinogenesis 26:481-486
11. Fukagawa M, Suzuki N, Hogan BL, Jones CM (1994) Embryonic expression of mouse bone morphogenetic protein-1 (BMP-1), which is related to the Drosophila dorsoventral gene tolloid and encodes a putative astacin metalloendopeptidase. Dev Biol 163:175-183
12. Gorbea CM, Marchand P, Jiang W, Copeland NG, Gilbert DJ, Jenkins NA, Bond JS (1993) Cloning, expression, and chromosomal localization of the mouse meprin beta subunit. J Biol Chem 268:21035-21043
13. He H, Linder DP, Rodgers KR, Chakraborty I, Arif AM (2004) A thiazole-containing tripodal ligand: synthesis, characterization, and interactions with metal ions and matrix metalloproteinases. Inorg Chem 43:2392-2401
14. Hultmark D, Klemenz R, Gehring WJ (1986) Translational and transcriptional control elements in the untranslated leader of the heat-shock gene hsp22. Cell 44:429-438
15. Hwang IT, Kim YJ, Kim SH, Kwak CI, Gu YY, Chun JY (2003) Annealing control primer system for improving specificity of PCR amplification. Biotechniques 35:1180-1184
16. Jansen RC, Nap JP (2004) Regulating gene expression: surprises still in store. Trends Genet 20:223-225
17. Kadonaga JT (2002) The DPE, a core promoter element for transcription by RNA polymerase II. Exp Mol Med 34:259-264
18. Katagiri C, Maeda R, Yamashika C, Mita K, Sargent TD, Yasumasu S (1997) Molecular cloning of Xenopus hatching enzyme and its specific expression in hatching gland cells. Int J Dev Biol 41:19-25
19. Lara-Pezzi E, Gómez-Gaviro MV, Gálvez BG, Mira E, Iñiguez MA, Fresno M, Martínez-A C, Arroyo AG, López-Cabrera M (2002) The hepatitis B virus X protein promotes tumor cell invasion by inducing membrane-type matrix metalloproteinase-1 and cyclooxygenase-2 expression. J Clin Invest 110:1831-1838
20. Martoglio B, Dobberstein B (1998) Signal sequences: more than just greasy peptides. Trends Cell Biol 8:410-415
21. McPherson MJ, Moller SJ (2000) PCR the basics from background to bench. BIOS Scientific Publishers, Oxford
22. Nielsen H, Engelbrecht J, Brunak S, von Heijne G (1997) Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng 10:1-6
23. Okamoto T, Akuta T, Tamura F, Der Vliet A, Akaike T (2004) Molecular mechanism for activation and regulation of matrix metalloproteinases during bacterial infections and respiratory inflammation. Biol Chem 385:997-1006
24. Park CH, Lee MJ, Ahn J, Kim S, Kim HH, Kim KH, Eun HC, Chung JH (2004) Heat shock-induced matrix metalloproteinase (MMP)-1 and MMP-3 are mediated through ERK and JNK activation and via an autocrine interleukin-6 loop. J Invest Dermatol 123:1012-1019
25. Passmore AJ, Jarman SN, Swadling KM, Kawaguchi S, McMinn A, Nicol S (2006) DNA as a dietary biomarker in Antarctic krill, Euphausia superba. Mar Biotechnol 8:686-696
26. Pearce E, Tregouet DA, Samnegard A, Morgan AR, Cox C, Hamsten A, Eriksson P, Ye S (2005) Haplotype effect of the matrix metalloproteinase-1 gene on risk of myocardial infarction. Circ Res 97:958-960
27. Saiki RK, Walsh PS, Levenson CH, Erlich HA (1989) Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc Natl Acad Sci USA 86:6230-6234
28. Shimell MJ, Ferguson EL, Childs SR, O'Connor MB (1991) The Drosophila dorsal-ventral patterning gene tolloid is related to human bone morphogenetic protein 1. Cell 67:469-481
29. Sugimoto M, Yoshida S, Kennedy S, Deguchi M, Ohara N, Maruo T (2006) Matrix metalloproteinase-1 and -9 promoter polymorphisms and endometrial carcinoma risk in a Japanese population. J Soc Gynecol Investig 13:523-529
30. Takahara K, Lyons GE, Greenspan DS (1994) Bone morphogenetic protein-1 and a mammalian tolloid homologue (mTld) are encoded by alternatively spliced transcripts which are differentially expressed in some tissues. J Biol Chem 269:32572-32578
31. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673-4680
32. Titani K, Torff HJ, Hormel S, Kumar S, Walsh KA, Rodl J, Neurath H, Zwilling R (1987) Amino acid sequence of a unique protease from the crayfish Astacus fluviatilis. Biochemistry 26:222-226
33. Woo S, Yum S, Jung JH, Shim WJ, Lee CH, Lee TK (2006) Heavy metal-induced differential gene expression of metallothionein in Javanese medaka, Oryzias javanicus. Mar Biotechnol 8:654-662
34. Wozney JM, Rosen V, Celeste AL, Mitsock LM, Whitters MJ, Kriz RW, Hewick RM, Wang EA (1988) Novel regulators of bone formation: molecular clones and activities. Science 242:1528-1534
35. Yasumasu S, Iuchi I, Yamagami K (1994) cDNA and the genes of HCE and lCE, fwo constituents of the medaka hatching enzyme. Dev Growth Differ 36:241-250