Bioinformation 15(9): 678-688

Analysis of glycoside hydrolases from oat (Avena sativa) seedling extract

^{Faculty of Medicine of Sfax, University of Sfax, Sfax-Tunisia}

^{Nihed Ben Halima}moc.liamg@amilahnebdehin

Received 2019 Apr 12; Revised 2019 Oct 7; Accepted 2019 Oct 12.

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.

Abstract

The abundance and the diversity of oligo- and polysaccharides provide a wide range of biological roles attributed either to these carbohydrates or to their relevant enzymes, i.e., the glycoside hydrolases (GHs). The biocatalysis by these families of enzymes is highly attractive for the generation of products used in potential applications, e.g., pharmaceuticals and food industries. It is thus very important to extract and characterize such enzymes, particularly from plant tissues. In this study, we characterized novel sequences of class I chitinases from seedlings extract of the common oat (Avena sativa L.) using proteomics and sequence-structure-function analysis. These enzymes, which belong to the GH19 family of protein, were extracted from oat and identified using SDS-PAGE, trypsin digestion, LC-MS-MS, and sequence-structure-function analysis. The amino acid sequences of the oat tryptic peptides were used to identify cDNAs from the Avena sativa databases of the expressed sequence tags (ESTs) and transcriptome shotgun assembly (TSA). Based upon the Avena sativa sequences of ESTs and TSA, at least 4 predicted genes that encoded oat class I chitinases were identified and reported. The structural characterization of the oat sequences of chitinases provided valuable insights to the context.

Keywords: Avena sativa, Glycoside hydrolases, GH19, Functional proteomics, Mass spectrometry, Bioinformatics analysis

Abstract

Acknowledgments

The author thanks the Tunisian Ministry of Higher Education and Scientific Research for facilities. The author is very grateful to Pr. Slim Abdelkafi and Pr. Chantal Pichon for their previous supervisions. The author would like also to express gratitude to Dr. Guillaume Gabant from the “Plateforme de Spectrométrie de Masse et Protéomique du Centre de Biophysique Moléculaire” (Orleans, France) for mass spectrometry analysis as well as for his precious discussion. The open access charge for this article is sponsored by Biomedical Informatics (P) Ltd, India.

Acknowledgments

The corresponding author states that there is no conflict of interest

Edited by P Kangueane

Citation: Ben Halima et al. Bioinformation 15(9):678-688 (2019)

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