Journal of Microbiology

The Microbiological Society of Korea (한국미생물학회)
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Analysis of Expressed Sequence Tags from the Red Alga Griffithsia okiensis

  • Lee, Hyoung-Seok (Polar BioCenter, Korea Polar Research Institute (KOPRI), KORDI) ;
  • Lee, Hong-Kum (Polar BioCenter, Korea Polar Research Institute (KOPRI), KORDI) ;
  • An, Gyn-Heung (Department of Life Science, Pohang University of Science and Technology) ;
  • Lee, Yoo-Kyung (Polar BioCenter, Korea Polar Research Institute (KOPRI), KORDI)
  • Published : 2007.12.31
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Abstract

Red algae are distributed globally, and the group contains several commercially important species. Griffithsia okiensis is one of the most extensively studied red algal species. In this study, we conducted expressed sequence tag (ESTs) analysis and synonymous codon usage analysis using cultured G. okiensis samples. A total of 1,104 cDNA clones were sequenced using a cDNA library made from samples collected from Dolsan Island, on the southern coast of Korea. The clustering analysis of these sequences allowed for the identification of 1,048 unigene clusters consisting of 36 consensus and 1,012 singleton sequences. BLASTX searches generated 532 significant hits (E-value <$10^{-4}$) and via further Gene Ontology analysis, we constructed a functional classification of 434 unigenes. Our codon usage analysis showed that unigene clusters with more than three ESTs had higher GC contents (76.5%) at the third position of the codons than the singletons. Also, the majority of the optimal codons of G. okiensis and Chondrus crispus belonging to Bangiophycidae were G-ending, whereas those of Porphyra yezoensis belonging to Florideophycidae were G-ending. An orthologous gene search for the P. yezoensis EST database resulted in the identification of 39 unigenes commonly expressed in two rhodophytes, which have putative functions for structural proteins, protein degradation, signal transduction, stress response, and physiological processes. Although experiments have been conducted on a limited scale, this study provides a material basis for the development of microarrays useful for gene expression studies, as well as useful information for the comparative genomic analysis of red algae.

Keywords

References

  1. Altschul, S.F., W. Gish, W. Miller, E.W. Meyers, and D. Lipman. 1990. Basic local alignment search tool. J. Mol. Biol. 215, 403-410 https://doi.org/10.1016/S0022-2836(05)80360-2
  2. Asamizu, E., M. Nakajima, Y. Kitade, N. Saga, Y. Nakamura, S. Tabata. 2003. Comparison of RNA expression profiles between the two generations of Porphyra yezoensis (Rhodophyta), based on expressed sequence tag frequency analysis. J. Phycol. 39, 923-930 https://doi.org/10.1046/j.1529-8817.2003.03003.x
  3. Ashburner, M., C.A. Ball, J.A. Blake, D. Botstein, H. Butler, J.M. Cherry, A.P. Davis, K. Dolinski, S.S. Dwight, J.T. Eppig, M.A. Harris, D.P. Hill, L. Issel-Tarver, A. Kasarskis, S. Lewis, J.C. Matese, J.E. Richardson, M. Ringwald, G.M. Rubin, and G. Sherlock. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 1, 25-29 https://doi.org/10.1038/nm0195-25
  4. Bauman, Jr., R.W. and B.R. Jones. 1986. Electrophysiological investigations of the red alga Griffithsia pacifica KYL. J. Phycol. 22, 49-56 https://doi.org/10.1111/j.1529-8817.1986.tb02514.x
  5. Cho, E.K., Y.K. Lee, and C.B. Hong. 2005. A cyclophilin from Griffithsia japonica has thermoprotective activity and is affected by CsA. Mol. Cells 20, 142-150
  6. Collen, J., V. Roeder, S. Rousvoal, O. Collin, B. Kloareg, and C. Boyen. 2006. An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae) J. Phycol. 42, 104-112 https://doi.org/10.1111/j.1529-8817.2006.00171.x
  7. Da Silva, F.G., A. Iandolino, F. Al-Kayal, M.C. Bohlmann, M.A. Cushman, H. Lim, A. Ergul, R. Figueroa, E.K. Kabuloglu, C. Osborne, J. Rowe, E. Tattersall, A. Leslie, J. Xu, J. Baek, G.R. Cramer, J.C. Cushman, and D.R. Cook. 2005. Characterizing the grape transcriptome. Analysis of expressed sequence tags from multiple Vitis species and development of a compendium of gene expression during berry development. Plant Physiol. 139, 574-597 https://doi.org/10.1104/pp.105.065748
  8. Fernandez, P., N. Paniego, S. Lew, H.E. Hopp, and R.A. Heinz. 2003. Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project. BMC Genomics 4, 40
  9. Goff, L.J. and A.W. Coleman. 1987. The solution to the cytological paradox of isomorphy. J. Cell Biol. 104, 739-748 https://doi.org/10.1083/jcb.104.3.739
  10. Hofler, K. 1934. Regenerationsvorgänge bei Griffithsia schousboei. Flora 27, 331-344
  11. Hwang, M.S., H.S. Kim, and I.K. Lee. 1991. Regeneration and sexual differentiation of Griffithsia japonica (Ceramiaceae, Rhodophyta) through somatic cell fusion. J. Phycol. 27, 441-447 https://doi.org/10.1111/j.0022-3646.1991.00441.x
  12. Johnson, E.S., B. Bartel, W. Seufert, and A. Varshavsky. 1992. Ubiquitin as a degradation signal. EMBO J. 11, 497-505
  13. Kakinuma, M., I. Kaneko, D. Coury, T. Suzuki, and H. Amano. 2006. Isolation and identification of gametogenesis-related genes in Porphyra yezoensis (Rhodophyta) were identified using subtracted cDNA libraries. J. Appl. Phycol. 18, 489-496 https://doi.org/10.1007/s10811-006-9052-8
  14. Kim, H.S., E.C. Yang, and S.M. Boo. 2006. The occurrence of Griffithsia okiensis (Ceramiaceae, Rhodophyta) from Korea on the basis of morphology and molecular data. Algae 21, 91-101 https://doi.org/10.4490/ALGAE.2006.21.1.091
  15. Lee, H., C.G. Hur, C.J. Oh, H.B. Kim, S.Y. Park, and C.S. An. 2004. Analysis of the root nodule-enhanced transcriptome in soybean. Mol. Cells 18, 53-62
  16. Lee, Y.K., H.-G. Choi, C.B. Hong, and I.K. Lee. 1995. Sexual differentiation of Griffithsia (Ceramiales, Rhodophyta): nuclear ploidy level of mixed-phase plants in G. japonica. J. Phycol. 31, 668-673 https://doi.org/10.1111/j.1529-8817.1995.tb02564.x
  17. Lee, Y.K., C.B. Hong, N.-K. Lim, J.-S. So, and I.K. Lee. 1998a. Isolation & characterization of a cDNA encoding 40S ribosomal protein S8 from a red alga, Griffithsia japonica (Ceramiales, Rhodophyta). Algae 13, 157-163
  18. Lee, Y.K., C.B. Hong, Y. Soh, and I.K. Lee. 2002. A cDNA clone for cyclophilin from Griffithsia japonica (Ceramiales, Rhodophyta) and phylogenetic analysis of cyclophilins. Mol. Cells 13, 12-20
  19. Lee, Y.K., M.S. Hwang, and I.K. Lee. 2001. Sexual differentiation of Griffithsia monilis (Ceramiales, Rhodophyta) in hybrids between female & male thalli. Botanica Marina 44, 547-557 https://doi.org/10.1515/BOT.2001.061
  20. Lee, Y.K., S.H. Kim, C.B. Hong, O.-K. Chah, G.H. Kim and I.K. Lee. 1998b. Heat-shock protein 90 may be involved in differentiation of the female gametophytes in Griffithsia japonica (Ceramiales, Rhodophyta). J. Phycol. 34, 1017-1023 https://doi.org/10.1046/j.1529-8817.1998.341017.x
  21. Lee, Y.K. and H.K. Lee. 2003. Putative histone H2A genes from a red alga, Griffithsia japonica. Algae 18, 191-197 https://doi.org/10.4490/ALGAE.2003.18.3.191
  22. Lluisma, A.O. and M. Ragan. 1997. Expressed sequence tags (ESTs) from the marine red alga Gracilaria gracilis. J. Appl. Phycol. 9, 287-293 https://doi.org/10.1023/A:1007920607900
  23. Myers, A., R.D. Preston, and G.W. Ripley. 1956. Fine structure in the red algae. I. X-ray & electron microscope investigation of Griffithsia flosculosa. Proc. Roy. Soc. B. 144, 450-459
  24. Nikaido, I., E. Asamizu, M. Nakajima, Y. Nakamura, N. Saga, and S. Tabata. 2000. Generation of 10,154 expressed sequence tags from a leafy gametophyte of a marine red alga, Porphyra yezoensis. DNA Res. 7, 223-227 https://doi.org/10.1093/dnares/7.3.223
  25. Nollen, E.A. and R.I. Morimoto. 2002. Chaperoning signaling pathways: molecular chaperones as stress-sensing 'heat shock' proteins. J. Cell Sci. 115, 2809-2816
  26. PeyrieRe, M. 1970. Evolution de l'appareil de Golgi de la tetrasporogenese de Griffithsia flosculosa (Rhodophycee). C. R. Acad. Sci. Paris, Ser. D. 270, 2071-2074
  27. Russell, C.A., M.D. Guiry, A.R. Mcdonald, and D.J. Garbary. 1996. Actin-mediated chloroplast movement in Griffithsia pacifica (Ceramiales, Rhodophyta). Phycol. Res. 44, 57-61 https://doi.org/10.1111/j.1440-1835.1996.tb00038.x
  28. Schechter, V. 1934. Electrical control of rhizoid formation in the red alga, Griffithsia borretiana. J. Gen. Physiol. 18, 1-22 https://doi.org/10.1085/jgp.18.1.1
  29. Semon, M., D. Mouchiroud, and L. Duret. 2005. Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum. Mol. Genet. 14, 421-427 https://doi.org/10.1093/hmg/ddi038
  30. Sharp, P.M. and W.H. Li. 1987. The codon Adaptation Index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15, 1281-1295 https://doi.org/10.1093/nar/15.3.1281
  31. Sheffield, W.P., G.C. Shore, and S.K. Randall. 1990. Mitochondrial precursor protein. Effects of 70-kilodalton heat shock protein on polypeptide folding, aggregation, and import competence. J. Biol. Chem. 265, 11069-11076
  32. Stekel, D.J., Y. Git, and F. Falciani. 2000. The comparison of gene expression from multiple cDNA libraries. Genome Res. 10, 2055-2061 https://doi.org/10.1101/gr.GR-1325RR
  33. Sun, J., T. Liu, B. Guo, D. Jin, M. Weng, Y. Feng, P. Xu, D. Duan, and B. Wang. 2006. Development of SSR primers from EST sequences and their application in germplasm identification of Porphyra lines (Rhodophyta). Eur. J. Phycol. 41, 329-336 https://doi.org/10.1080/09670260600740906
  34. Susko, E. and A.J. Roger. 2004. Estimating and comparing the rates of gene discovery and expressed sequence tag (EST) frequencies in EST surveys. Bioinformatics 20, 2279-2287 https://doi.org/10.1093/bioinformatics/bth239
  35. Teo, S.-S., C.-L. Ho, S. Teoh, W.-W. Lee, J.-M. Tee, R.A. Rahim, and S.-M. Phang. 2007. Analyses of expressed sequence tags from an agarophyte, Gracilaria changii (Gracilariales, Rhodophyta). Eur. J. Phycol. 42, 41-46 https://doi.org/10.1080/09670260601012461
  36. Waaland, S.D. 1978. Parasexually produces hybrids between male and female plants of Griffithsia tenuis C. Agardh, a red alga. Planta (Berl) 138, 65-68 https://doi.org/10.1007/BF00392917
  37. Zhou, Y.H. and M.A. Ragan. 1995. Characterization of the polyubiquitin gene in the marine red alga Gracilaria verrucosa. Biochim. Biophys. Acta. 1261, 215-222 https://doi.org/10.1016/0167-4781(95)00006-3