Bioinformatics tools for marine biotechnology: a practical tutorial with a metagenomic approach

Ludovica Liguori,Mariateresa Allocca,Maria Monticelli,Maria Vittoria Cubellis,Bruno Hay Mele

doi:10.1186/s12859-020-03560-z

Abstract

BackgroundBioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. Although teaching bioinformatics has been incorporated in all traditional life science curricula, practical hands-on experiences in tight combination with wet-lab experiments are needed to motivate students.ResultsWe present a tutorial that starts from a practical problem: finding novel enzymes from marine environments. First, we introduce the idea of metagenomics, a recent approach that extends biotechnology to non-culturable microbes. We presuppose that a probe for the screening of metagenomic cosmid library is needed. The students start from the chemical structure of the substrate that should be acted on by the novel enzyme and end with the sequence of the probe. To attain their goal, they discover databases such as BRENDA and programs such as BLAST and Clustal Omega.Students’ answers to a satisfaction questionnaire show that a multistep tutorial integrated into a research wet-lab project is preferable to conventional lectures illustrating bioinformatics tools.ConclusionExperimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.

Highlights

Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects
We provide a tutorial that was administered to students of the courses of marine and environmental biology
We propose to use the enzyme found in BRENDA [24] as a query sequence to look for homologous proteins among uncharacterized open reading frames (ORF) from marine metagenomes

Summary

Introduction

Bioinformatics has pervaded all fields of biology and has become an indispensable tool for almost all research projects. At present any biologists should capitalize on the resources, data and programs, that are available online to make their experimental plans more efficient and cost-effective [1, 2] For this reason, it is desirable to train students using a problem-solving approach that integrates in silico work into a multidisciplinary experimental project(a. The experimental project proposed to the students, aims at finding an enzyme that is active on a scaffold commonly found among pollutants and synthetic compounds, a so-called “privileged scaffold” [14]. In this exercise, the scaffold taken into consideration is indole, an N-heterocyclic aromatic pollutant released in the aquatic environment through the industrial wastewater [15]

Methods

Results

Conclusion