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

Abstract

Background: Bioinformatics 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.

Results: We 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.

Conclusion: Experimental biologists can better operate basic bioinformatics if a problem-solving approach is chosen.

Keywords: Computer-based learning; Graduate education; Marine biotechnology.

Fig. 1

Flowchart of the training. The bioinformatics analysis (purple rectangles) and the wet-lab cosmid library synthesis (light blue rectangles) merge when the probe for the screening is designed (white rectangle) and the colony hybridization is carried out (yellow rectangle)

Fig. 2

BRENDA’s graphical interface 1. Ligand search can be selected from the Homepage

Fig. 3

BRENDA’s graphical interface 2. The structure search tool can be chosen to draw chemical scaffolds

Fig. 4

BRENDA’s graphical interface 3. Advanced search can be selected from the Homepage

Fig. 5

Performing an Advanced Search in BRENDA. The selection of specific terms is shown

Fig. 6

Classes of enzymes acting on indole in BRENDA (inset). Naphthalene 1,2-dioxygenase can be selected among the enzyme classes acting on indole

Fig. 7

Specific bacterial enzyme in BRENDA. The link to UniProt can be selected for Naphthalene 1,2-dioxygenases from specific proteins

Fig. 8

The amino acid sequence of Naphthalene 1,2-dioxygenase in the UniProt database

Fig. 9

Protein BLAST sheet

Fig. 10

BLASTp output

Fig. 11

CLUSTAL Omega sheet. Settings for multiple alignment are shown

Fig. 12

cons interface

Fig. 13

The output file of cons. The figure shows a consensus sequence for Naphthalene 1,2-dioxygenase from marine prokaryotes

Fig. 14

Reverse Translate tool web page

Fig. 15

Reverse Translate results. The figure shows the sequence to be used for the screening of the cosmid library

Fig. 16

Satisfaction test. The students were posed 7 questions concerning the tutorial and answered with a 0 for “not at all”, 1 for “slightly”, 2 for “moderately”, 3 for “very” and with a 4 for “extremely”. The weighted scores are reported for each score