Philippine Science Letters
vol. 5 | no. 1 | 2012
published online June 15, 2012


Partial gene sequence and characterization of EDEN-1, a major water-soluble protein from the economically important alga Eucheuma denticulatum

by Paulina B. Suarez-Aspilla1,2, Mailyn M. Terrado1, Maria Cristina A. Dancel3, Giuseppe C. Zuccarello4, Nina Rosario L. Rojas1*

1 Department of Chemistry, School of Science and Engineering, Ateneo de Manila University,
Loyola Heights, Quezon City, Philippines 1108
2 Department of Chemistry, Silliman University, Dumaguete City, Philippines
3 Mass Spectrometry Facility, Department of Chemistry, University of Florida, Gainesville,
FL 32611- 7200, U. S. A.
4 School of Biological Sciences, Victoria University of Wellington, PO Box 600, Wellington,
6140 New Zealand



Eucheuma denticulatum is a major aquaculture product worldwide as a source for iota-carrageenan, but its protein chemistry is not well known. This study reports the isolation, characterization, and partial gene and amino acid sequences of a major water-soluble protein from E. denticulatum, which we called EDEN-1. The protein was purified by ion-exchange chromatography on a strong anion exchanger. It is compact and monomeric by size exclusion chromatography, and has an intact molecular mass of 27.83 kDa by mass spectrometry. Its isoelectric point is 4.7, which is consistent with its amino acid composition. It is not glycosylated, based on periodic acid-Schiff staining. Peptide sequencing by tandem mass spectrometry of tryptic fragments yielded 5 short internal peptide sequences. These peptide sequences were back-translated to design degenerate primers to obtain a partial cDNA sequence for EDEN-1. The results of de novo peptide sequencing and cDNA sequencing were combined and verified with peptide mass fingerprinting of tryptic digests to yield partial gene and amino acid sequences of EDEN-1. This sequence accounts for 13,414 Da, or 48.2% of the intact mass of the protein. The amino acid sequence of EDEN-1 was found to be homologous to lectin ESA-2 from E. serra. This is the first known report of a cDNA sequence for this family of proteins. Consistent with its homology to lectin-like proteins, EDEN-1 is mainly beta-sheet based on its circular dichroism spectrum. EDEN-1 also shows weak glucoside hydrolase activity, suggesting that it may bind to carbohydrate moieties despite a lack of appreciable hemagglutinating activity.

*Corresponding author
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Submitted: February 15, 2012
Revised: March 28, 2012
Accepted: April 1, 2012
Published: June 15, 2012
Editor-in-charge: Eduardo A. Padlan