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SOP033: Finding Genes that are Important in Specific Types of Pathogens

This procedure explains how to use the NMPDR SigGenes? page (Signature Genes Tool) to compare and contrast whole genomes with the goal of defining what certain types of pathogens have in common. Such genes may be critical to the survival or virulence of the pathogens, making them useful drug targets? .

• For example, what genes are common to GramNegative? respiratory pathogens?

The Signature Genes Tool requires you to specify a reference genome, an inclusion set, and an exclusion set. In this case, we will not be using an exclusion set. The tool looks for genes from the reference genome that are common in the inclusion set.

As the reference genome, select a commonly used strain of a relevant species.

• For example, choose Pseudomonas aeruginosa strain PAO1, which is a well characterized lab strain.

In the inclusion set, select any number of genomes that share a phenotype with the reference genome.

• For example, include all available strains of Chlamydophila pneumoniae, Haemophilus influenzae, Mycoplasma pneumoniae, Legionella pneumophila, and Pseudomonas aeruginosa to determine the core set of genes shared by these strains.

Leave the remainder of the settings at their default values and click the Go button. You may use the form below. The results will open in a new window or tab.

The tool searches the database to find every protein in the reference genome that has a BidirectionalBestHit? (BBH) with at least 80% of the genomes in the inclusion set. The result score will be a number from 0.8 to 1.0. A value of 1 indicates that there was a BBH to every genome in the inclusion set.

• For example, 22 proteins in Pseudomonas aeruginosa strain PA01 have BBHs of various quality with all of the other genomes selected (which are of various quality), and another 163 have BBHs in most of the Gram-negative respiratory pathogens selected. These are a starting point for finding genes that may be targets for therapeutics. Results may be saved as protein or DNA sequences, or as a icon tab-delimited file suitable for opening and resorting in a spreadsheet application such as Excel.

To refine the list of potential drug targets, examine the subsystems these candidates play roles in, and look at their closest sequence matches using the BidirectionalBestHits? or similarities on the respective FIG.GenomeViewer? protein pages.

Because we have annotated the results of a genome-wide essentiality screen for the reference genome, Pseudomonas aeruginosa strain PA01, this list may be narrowed to those genes demonstrated to be essential in the reference strain. Type essential in the Search Words field of the Signature Genes form and repeat the search. This reduces the number of candidates to 107.

Another avenue for investigating essential genes is via the Essential Genes page, which lists genes demonstrated to be essential (or potentially essential when there is severe growth attenuation or the possibility of polar effects) in genome-wide screens of 10 different pathogens.