Abstract
EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides – a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluation of the defensin expression profile are presented. Prevalent expression tissues were leaf roll, lateral bark, root apex, base of inflorescence, developing seed, and calli. Bioinformatics and phylogenetic analysis of the primary structure of the sugarcane defensin candidates as well as the 3D structures obtained by comparative modeling support their role as antimicrobials.
Keywords: Data mining, EST-database, comparative modeling, defense system, crop evolution, drug discovery
Current Protein & Peptide Science
Title: EST-Database Search of Plant Defensins – An Example Using Sugarcane, a Large and Complex Genome
Volume: 11 Issue: 3
Author(s): L.C. Belarmino, P.V.S.Z. Capriles, S. Crovella, L.E. Dardenne and A.M. Benko-Iseppon
Affiliation:
Keywords: Data mining, EST-database, comparative modeling, defense system, crop evolution, drug discovery
Abstract: EST (Expressed Sequence Tags) databases are increasing in number and size, especially regarding cultivated plants. Sugarcane is one of the most important tropical and subtropical crops, presenting a complex polyploid genome of hybrid origin, bearing a challenge for the understanding of genetic processes in higher plants. In the present work a general search was carried out on the largest Sugarcane EST Database (SUCEST) that includes 237,954 ESTs aiming to identify defensin antimicrobial peptides – a class of small, basic, cysteine-rich peptides distributed throughout the kingdoms. Using a computational approach 17 new defensin isoforms could be identified. Main steps for the search, characterization and evaluation of the defensin expression profile are presented. Prevalent expression tissues were leaf roll, lateral bark, root apex, base of inflorescence, developing seed, and calli. Bioinformatics and phylogenetic analysis of the primary structure of the sugarcane defensin candidates as well as the 3D structures obtained by comparative modeling support their role as antimicrobials.
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Cite this article as:
Belarmino L.C., Capriles P.V.S.Z., Crovella S., Dardenne L.E. and Benko-Iseppon A.M., EST-Database Search of Plant Defensins – An Example Using Sugarcane, a Large and Complex Genome, Current Protein & Peptide Science 2010; 11 (3) . https://dx.doi.org/10.2174/138920310791112048
DOI https://dx.doi.org/10.2174/138920310791112048 |
Print ISSN 1389-2037 |
Publisher Name Bentham Science Publisher |
Online ISSN 1875-5550 |
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