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Studies on genetic and character differences of Japanese scallop (Patinopecten yessoensis) with different shell colors
Abstracts / Journal of Biotechnology 136S (2008) S22–S71
average expected heterozygosity was 0.77465, 0.7678, 0.7778, 0.6539 and 0.7274, respectively. (3) Population differentiation testing showed that genetic distances of the five populations were great. UPGMA tree constructed according to the genetic distance of the five populations and phylogenic analysis indicates relatively distant relationships among the populations. The results support the conclusion that geographic isolation plays an important role in shaping genetic structure of the populations and little gene flow occurs among them. Keywords: Sea cucumber; Apostichopus japonicus; Microsatellite; Genetic variation; Geographic isolation; Population genetics
S67
References Guao, Y.M., Li, G.X., Zhao, Y.L., 2004. Genetic structure of Japanese scallop Patinopecten yessoensis hatched population in Dalian sea areas. J. Dalian Fish. Univ. 19 (2), 142–145. Kijas, J.M.H., Fowler, J.C.S., Garbett, C.A., et al., 1994. Enrichment of microsatellites from the citrus genome using bi-otinylated oligonucleotide sequences bound to streptavid in-coated magnetic particles[J]. Biotechniques 16, 657–662.
doi:10.1016/j.jbiotec.2008.07.147 I1-YP-072 A systematic proteome-based approach for high-level extracellular production of recombinant proteins in Escherichia coli Zhi-Gang Qian 1,∗ , Xiao-Xia Xia 1 , Jong Hyun Choi 1 , Sang Yup Lee 1,2
References Kanno, M., Suyama, Y., Li, Q., Kijima, A., 2006. Microsatellite analysis of Japanese sea Cucumber, Stichopus (Apostichopus) japonicus, supports reproductive isolation in color variants. Mar. Biotechnol. 8 (6), 672–685. Liang, J., Li, D.J., Lu, L.Q., 2005. Microsatellite variation between Japanese eel (Anguilla japonica) and European eel (Anguilla). Chin. J. Oceanol. Limnol. 23, 448–454. Nelson, J., Cooper, G., Garner, T., Schnupf, P., 2002. Polymorphic markers for the sea cucumber Parastichopus californicus. Mol. Ecol. Notes 2, 33–235.
doi:10.1016/j.jbiotec.2008.07.146 I1-YP-054 Studies on genetic and character differences of Japanese scallop (Patinopecten yessoensis) with different shell colors Chunyan Li ∗ , Jun Ding, Shiwei Zhu, Yaqing Chang Dalian Fisheries University, Key Laboratory of Mariculture and Biotechnology, Dalian 116023, China E-mail address: [email protected] (C. Li). Japanese scallop (Patinopecten yessoensis) was introduced from Japan to Dalian in 1980s and has been cultured in this area in large scale now. Some scallops with white left shell appeared in some cultured groups after over 20 years’ cultivation in China (Guao et al., 2004). Compared with normal scallops, these white scallops presented better growth quality. To explain this phenomenon, three parts of work has been developed as follows: (1) a genomic DNA library of Japanese scallops was built by magnetic bead-hybridization selection protocol (Kijas et al., 1994). 160 microsatellites were obtained from 171 positive clones (from 175 clones). 42.39% of those positive clones were perfect, 46.24% were imperfect, and the rest ones were of compound type (11.11%). 56 pairs of microsatellite primers were screened out and 15 loci showed polymorphism. (2) Analyzed morphological characters for differences between the normal and the white shells Japanese scallops by one-way analysis of variance (ANOVA). The results showed that white shells scallops were significantly superior to normal Japanese scallops in shell length, height, width, soft weight, gonad weight, adductor muscle weight and wet weight. (3) Genetic differences of the populations of scallops with different shell colors were analyzed. The observed (H0 ) and expected (He ) heterozygosity values, the polymorphic information content (PIC) and the number of effective alleles (Ne ) were all obtained. The analysis showed that the genetic differences were not significant. The significance in the differences of morphological characters cannot be sustained by genetic differences according to this study and further ecological and genetic research is needed to reveal those mechanisms. Keywords: Scallop; Genetic difference; Shell color; Microsatellite
1
Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program) and BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea 2 Department of Bio and Brain Engineering, and Bioinformatics Research Center, KAIST, Daejeon, Republic of Korea E-mail address: [email protected] (Z.-G. Qian). Extracellular production of recombinant proteins in Escherichia coli has received considerable attention due to its significant advantages over cytoplasmic or periplasmic production (Choi and Lee, 2004). However, efficient secretion of recombinant proteins into the culture medium of E. coli remains a challenge due to the intrinsic limitations of the secretion machinery (Zhang et al., 2006). Here we report a systematic proteome-based approach for high-level extracellular production of recombinant proteins. First, the extracellular proteome of an E. coli B strain was analyzed to identify motifs as potential fusion partners. Next, we expressed each open reading frame of the selected motifs and determined the protein profiles of the culture medium. The highest secreting motif was used as the carrier protein to produce several “passenger proteins” in the culture medium. Those model passenger proteins show a wide versatility with respect to the proteins’ length and origin. In addition, the polypeptides accumulated in the medium at high concentrations ranging from 15 to 500 mg/L. These findings demonstrate a proteome-based approach for high-level production of recombinant proteins in the culture medium of E. coli. Acknowledgements This work was supported by the Korean Systems Biology Project of the Ministry of Education, Science and Technology. Further supports by the LG Chem Chair Professorship and KOSEF through the CUPS are appreciated. References Choi, J.H., Lee, S.Y., 2004. Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl. Microbiol. Biotechnol. 64, 625–635. Zhang, G., Brokx, S., Weiner, J.H., 2006. Extracellular accumulation of recombinant proteins fused to the carrier protein YebF in Escherichia coli. Nat. Biotechnol. 24, 100–104.
doi:10.1016/j.jbiotec.2008.07.148
average expected heterozygosity was 0.77465, 0.7678, 0.7778, 0.6539 and 0.7274, respectively. (3) Population differentiation testing showed that genetic distances of the five populations were great. UPGMA tree constructed according to the genetic distance of the five populations and phylogenic analysis indicates relatively distant relationships among the populations. The results support the conclusion that geographic isolation plays an important role in shaping genetic structure of the populations and little gene flow occurs among them. Keywords: Sea cucumber; Apostichopus japonicus; Microsatellite; Genetic variation; Geographic isolation; Population genetics
S67
References Guao, Y.M., Li, G.X., Zhao, Y.L., 2004. Genetic structure of Japanese scallop Patinopecten yessoensis hatched population in Dalian sea areas. J. Dalian Fish. Univ. 19 (2), 142–145. Kijas, J.M.H., Fowler, J.C.S., Garbett, C.A., et al., 1994. Enrichment of microsatellites from the citrus genome using bi-otinylated oligonucleotide sequences bound to streptavid in-coated magnetic particles[J]. Biotechniques 16, 657–662.
doi:10.1016/j.jbiotec.2008.07.147 I1-YP-072 A systematic proteome-based approach for high-level extracellular production of recombinant proteins in Escherichia coli Zhi-Gang Qian 1,∗ , Xiao-Xia Xia 1 , Jong Hyun Choi 1 , Sang Yup Lee 1,2
References Kanno, M., Suyama, Y., Li, Q., Kijima, A., 2006. Microsatellite analysis of Japanese sea Cucumber, Stichopus (Apostichopus) japonicus, supports reproductive isolation in color variants. Mar. Biotechnol. 8 (6), 672–685. Liang, J., Li, D.J., Lu, L.Q., 2005. Microsatellite variation between Japanese eel (Anguilla japonica) and European eel (Anguilla). Chin. J. Oceanol. Limnol. 23, 448–454. Nelson, J., Cooper, G., Garner, T., Schnupf, P., 2002. Polymorphic markers for the sea cucumber Parastichopus californicus. Mol. Ecol. Notes 2, 33–235.
doi:10.1016/j.jbiotec.2008.07.146 I1-YP-054 Studies on genetic and character differences of Japanese scallop (Patinopecten yessoensis) with different shell colors Chunyan Li ∗ , Jun Ding, Shiwei Zhu, Yaqing Chang Dalian Fisheries University, Key Laboratory of Mariculture and Biotechnology, Dalian 116023, China E-mail address: [email protected] (C. Li). Japanese scallop (Patinopecten yessoensis) was introduced from Japan to Dalian in 1980s and has been cultured in this area in large scale now. Some scallops with white left shell appeared in some cultured groups after over 20 years’ cultivation in China (Guao et al., 2004). Compared with normal scallops, these white scallops presented better growth quality. To explain this phenomenon, three parts of work has been developed as follows: (1) a genomic DNA library of Japanese scallops was built by magnetic bead-hybridization selection protocol (Kijas et al., 1994). 160 microsatellites were obtained from 171 positive clones (from 175 clones). 42.39% of those positive clones were perfect, 46.24% were imperfect, and the rest ones were of compound type (11.11%). 56 pairs of microsatellite primers were screened out and 15 loci showed polymorphism. (2) Analyzed morphological characters for differences between the normal and the white shells Japanese scallops by one-way analysis of variance (ANOVA). The results showed that white shells scallops were significantly superior to normal Japanese scallops in shell length, height, width, soft weight, gonad weight, adductor muscle weight and wet weight. (3) Genetic differences of the populations of scallops with different shell colors were analyzed. The observed (H0 ) and expected (He ) heterozygosity values, the polymorphic information content (PIC) and the number of effective alleles (Ne ) were all obtained. The analysis showed that the genetic differences were not significant. The significance in the differences of morphological characters cannot be sustained by genetic differences according to this study and further ecological and genetic research is needed to reveal those mechanisms. Keywords: Scallop; Genetic difference; Shell color; Microsatellite
1
Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 Program) and BioProcess Engineering Research Center, Center for Systems and Synthetic Biotechnology, and Institute for the BioCentury, KAIST, 335 Gwahangno, Yuseong-gu, Daejeon 305-701, Republic of Korea 2 Department of Bio and Brain Engineering, and Bioinformatics Research Center, KAIST, Daejeon, Republic of Korea E-mail address: [email protected] (Z.-G. Qian). Extracellular production of recombinant proteins in Escherichia coli has received considerable attention due to its significant advantages over cytoplasmic or periplasmic production (Choi and Lee, 2004). However, efficient secretion of recombinant proteins into the culture medium of E. coli remains a challenge due to the intrinsic limitations of the secretion machinery (Zhang et al., 2006). Here we report a systematic proteome-based approach for high-level extracellular production of recombinant proteins. First, the extracellular proteome of an E. coli B strain was analyzed to identify motifs as potential fusion partners. Next, we expressed each open reading frame of the selected motifs and determined the protein profiles of the culture medium. The highest secreting motif was used as the carrier protein to produce several “passenger proteins” in the culture medium. Those model passenger proteins show a wide versatility with respect to the proteins’ length and origin. In addition, the polypeptides accumulated in the medium at high concentrations ranging from 15 to 500 mg/L. These findings demonstrate a proteome-based approach for high-level production of recombinant proteins in the culture medium of E. coli. Acknowledgements This work was supported by the Korean Systems Biology Project of the Ministry of Education, Science and Technology. Further supports by the LG Chem Chair Professorship and KOSEF through the CUPS are appreciated. References Choi, J.H., Lee, S.Y., 2004. Secretory and extracellular production of recombinant proteins using Escherichia coli. Appl. Microbiol. Biotechnol. 64, 625–635. Zhang, G., Brokx, S., Weiner, J.H., 2006. Extracellular accumulation of recombinant proteins fused to the carrier protein YebF in Escherichia coli. Nat. Biotechnol. 24, 100–104.
doi:10.1016/j.jbiotec.2008.07.148