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Hydrobiologia

, Volume 571, Issue 1, pp 109–122 | Cite as

Comparative analysis of genes expressed in regenerating intestine and non-eviscerated intestine of Apostichopus japonicus Selenka (Aspidochirotida: Stichopodidae) and cloning of ependymin gene

  • Fa-Xin Zheng
  • Xiu-Qin Sun
  • Bao-Hai Fang
  • Xu-Guang Hong
  • Jin-Xing Zhang
Primary Research Paper

Abstract

The regeneration of the intestine of sea cucumber (Apostichopus japonicus) was studied by describing historically the changes that occurred during intestine regeneration on the fifth day after chemically-induced evisceration. An expressed sequence tag (EST) analysis was undertaken to identify major genes, which might be involved in intestine regeneration of A. japonicus. Two cDNA libraries were constructed with directional cloning method, one for regenerating intestine collected on the third, fourth and fifth day after evisceration (post-evisceration, PE), and the other for the non-eviscerated (NE). A total of 730 ESTs were generated by sequencing cDNA clones from the two libraries (372 from PE and 358 from NE). The results showed that the number of genes that were involved in primary metabolism of PE library was less than that of NE library, while the number of genes involved in cell defense/immunity, cell division, cell signal transduction/communication of PE library was more than that of NE library. The results also revealed that the expression of the genes which might be involved in regeneration was enhanced to some extent after evisceration. Only about 11.54% of the sequenced clones were shared by two libraries, which provided some clues for the existence of differential gene expression between PE and NE intestines. A gene named epenAj was also characterized in this study.

Keywords

Apostichopus japonicus ependymin encoding gene expressed sequence tag regenerating intestine regeneration associated gene 

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References

  1. Adams D. S., Hasson B., Boyer-Boiteau A., El-Khishin A. and Shashoua V. E. (2003). A peptide fragment of ependymin neurotrophic factor uses protein kinase C and the mitogen-activated protein kinase pathway to activate c-Jun N-terminal kinase and a functional AP-1 containing c-Jun and c-fos proteins in mouse NB2a cells. Journal of Neuroscience Research 72(3): 405–416PubMedCrossRefGoogle Scholar
  2. Altschul S. F., Gish W., Miller W., Myers E. W. and Lipman E. W. (1990). Basic local alignment search tool. Journal of Molecular Biology 215: 403–410PubMedCrossRefGoogle Scholar
  3. Barrinaga M. (1994). Looking to development’s future. Science 266: 561–564Google Scholar
  4. Beaudoing E., Freier S., Wyatt J. R. and Claverie J. M. (2000). Patterns of variant polyadenylation signal usage in human genes. Genome Research 10(7): 1001–1010PubMedCrossRefGoogle Scholar
  5. Chia F. and Xing J. (1996). Echinoderm Coelomocytes. Zoological Studies 35(4): 231–254Google Scholar
  6. Chou H. H. and Holmes M. H. (2001). DNA sequence quality trimming and vector removal. Bioinformatics 17: 1093–1104PubMedCrossRefGoogle Scholar
  7. Dolmatov I. Y., Eliseikina M. G., Bulgakov A. A., Ginanova T. T., Lamash N. E. and Korchagin V. P. (1996). Muscle regeneration in the holothurian Stichopus japonicus. Roux’s Archives of Developmental Biology 205: 486–493CrossRefGoogle Scholar
  8. Eliseikina M. G. and Magarlamov T. Y. (2002). Coelomocyte morphology in the Holothurians Apostichopus japonicus (Aspidochirota: Stichopodidae) and Cucumaria japonica (Dendrochirota: Cucumariidae). Russian Journal of Marine Biology 28(3): 197–202CrossRefGoogle Scholar
  9. Ewing B. and Green P. (1998). Base-calling of automated sequencer traces using Phred. II. Error probabilities. Genome Research 8: 186–194PubMedGoogle Scholar
  10. Ewing B., Hillier L., Wendl M. C. and Green P. (1998). Base-calling of automated sequencer traces using Phred: I. Accuracy assessment. Genome Research 8: 175–185PubMedGoogle Scholar
  11. Ganss B. and Hoffmann W. (1993). Calcium binding to sialic acids and its effect on the conformation of ependymins. European Journal of Biochemistry 217: 275–280PubMedCrossRefGoogle Scholar
  12. García-Arrarás J. E., Díaz-Miranda L., Torres-Vázquez I., Torres I. I., Torres-Avilán I., File S., Jiménez L., Rivera-Bermudez K., Arroyo E. and Cruz W. (1999). Regeneration of the enteric nervous system in the sea cucumber Holothuria glaberrima. The Journal of Comparative Neurology 406: 461–475PubMedCrossRefGoogle Scholar
  13. García-Arrarás J. E., Estrada-Rodgers L., Santiago R., Torres I. I., Díaz-Miranda L. and Torres-Avilán I. (1998). Cellular mechanisms of intestine regeneration in the sea cucumber, Holothuria glaberrima Selenka (Holothuroidea:Echinodermata). Journal of Experimental Zoology 281: 288–304PubMedCrossRefGoogle Scholar
  14. García-Arrarás J. E., Rojas-Soto M., Jiménez L. B. and Diaz-Miranda L. (2001). The enteric nervous system of echinoderms: unexpected complexity revealed by neurochemical analysis. The Journal of Experimental Biology 204: 865–873PubMedGoogle Scholar
  15. Gong Z., Yan T., Liao J., Lee S. E., He J. and Hew C. (1997). Rapid identification and isolation of zebrafish cDNA clones. Gene 201: 87–98PubMedCrossRefGoogle Scholar
  16. He C., Chen L., Simmons M., Li P., Kim S. and Liu Z. J. (2003). Putative SNP discovery in interspecific hybrids of catfish by comparative EST analysis. Journal of Animal Breeding and Genetics 34: 445–448Google Scholar
  17. Hoffmann W. and Schwarz H. (1996). Ependymins: meningeal-derived extracellular matrix proteins at the blood–brain barrier. International Review of Cytology 165: 121–158PubMedCrossRefGoogle Scholar
  18. Huang X. and Madan A. (1999). CAP3: a DNA sequence assembly program. Genome Research 9: 868–877PubMedCrossRefGoogle Scholar
  19. Humason G. L. (1972). Animal Tissue Techniques. W. H. Freeman and Co, San FranciscoGoogle Scholar
  20. Liu Z. J., Karsi A. and Dunham R. A. (1999). Development of polymorphic EST markers suitable for genetic linkage mapping of catfish. Journal of Marine Biotechnology 1: 437–447CrossRefGoogle Scholar
  21. Liu Z. J., Li P., Kocabas A., Ju Z., Karsi A. and Cao D. (2001). Microsatellite-containing genes from the channel catfish brain: evidence of trinucleatide repeat expansion in the coding region of nucleotide excision repair gene RAD23B. Biochemical and Biophysical Research Communications 289: 317–324PubMedCrossRefGoogle Scholar
  22. Murakawa K., Matsubara K., Fukushima A. and Yoshii J. (1994). Chromosomal assignments of 3′-directed partial cDNA sequences representing novel genes expressed in granulocytoid cells. Genomics 23: 379–389PubMedCrossRefGoogle Scholar
  23. Nimmrich I., Erdmann S., Melchers U., Chtarbova S., Finke U., Hentsch S., Hoffmann I., Oertel M., Hoffmann W. and Muller O. (2001). The novel ependymin related gene UCC1 is highly expressed in colorectal tumor cells. Cancer Letter 165(1): 71–79CrossRefGoogle Scholar
  24. Okubo K. and Matsubara K. (1997). Complementary DNA sequence (EST) collections and the expression information of the human genome. Federation of European Biochemical Societies Letter 403: 225–229Google Scholar
  25. Pradel G., Schachner M. and Schmidt R. (1999). Inhibition of memory consolidation by antibodies against cell adhesion molecules after active avoidance conditioning in zebrafish. Journal of Neurobiology 39(2): 197–206PubMedCrossRefGoogle Scholar
  26. Rother S., Schmidt R., Brysch W. and Schlingensiepen K. H. (1995). Learning-induced expression of meningeal ependymin mRNA and demonstration of ependymin in neurons and glial cells. Journal of Neurochemistry 65(4): 1456–1464PubMedCrossRefGoogle Scholar
  27. Sambrook, J., E. F. Fritsch & T. Maniatis, 1989. Molecular Cloning: A Laboratory Manual, (2nd edn.), pp. 359–361Google Scholar
  28. Schmidt J. T. and Shashoua V. E. (1988). Antibodies to ependymin block the sharpening of the regenerating retinotectal projection in goldfish. Brain Research 446(2): 269–284PubMedCrossRefGoogle Scholar
  29. Shashoua V. E. (1977). Brain protein metabolism and the acquisition of new patterns of behavior. The Proceedings of the National Academy of Sciences (USA) 74(4): 1743–1747CrossRefGoogle Scholar
  30. Shashoua V. E. (1991). Ependymin, a brain extracellular glycoprotein and CNS plasticity. Annals of the New York Academy of Sciences 627: 94–114PubMedGoogle Scholar
  31. Shashoua V. E., Adams D. and Boyer-Boiteau A. (2001). CMX-8933, a peptide fragment of the glycoprotein ependymin, promotes activation of AP-1 transcription factor in mouse neuroblastoma and rat cortical cell cultures. Neuroscience Letter 312(2): 103–107CrossRefGoogle Scholar
  32. Suárez-Castillo, E. C., W. E. Medina-Ortíz1, J. L. Roig-López2 & J. E. García-Arrarás, 2004. Ependymin, a gene involved in regeneration and neuroplasticity in vertebrates, is overexpressed during regeneration in the echinoderm Holothuria glaberrima. Gene 334: 133–143Google Scholar
  33. Tang S. J., Sun K. H., Sun G. H., Lin G., Lin W. W. and Chuang M. J. (1999). Cold-induced ependymin expression in zebrafish and carp brain: implications for cold acclimation. Federation of European Biochemical Societies Letter 459(1): 95–99Google Scholar
  34. Tomoya K. and Masahiro S. (2001). The analysis of expressed genes in the kidney of Japanese flounder, Paralichthys olivaceus, injected with the immunostimulant peptidoglycan. Fish Shellfish. The Journal of Immunology 11: 357–366Google Scholar
  35. Wu C., Huang H., Arminski L., Castro-Alvear J., Chen Y., Hu Z., Ledley R. S., Lewis K. C., Mewes H.-W., Orcutt B. C., Suzek B. E., Tsugita A., Vinayaka C. R., Yeh L.-s., Zhang J. and Barker W. C. (2002). The protein information resource: an integrated public resource of functional annotation of poteins. Nucleic Acids Research 30: 35–37PubMedCrossRefGoogle Scholar

Copyright information

© Springer 2006

Authors and Affiliations

  • Fa-Xin Zheng
    • 1
  • Xiu-Qin Sun
    • 2
  • Bao-Hai Fang
    • 1
  • Xu-Guang Hong
    • 2
  • Jin-Xing Zhang
    • 2
  1. 1.Ocean University of ChinaQingdao, ShandongP.R. China
  2. 2.The First Institute of Oceanography, SOAQingdao, ShandongP.R. China

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