PathFams: statistical detection of pathogen-associated protein domains

Abstract

Background: A substantial fraction of genes identified within bacterial genomes encode proteins of unknown function. Identifying which of these proteins represent potential virulence factors, and mapping their key virulence determinants, is a challenging but important goal.

Results: To facilitate virulence factor discovery, we performed a comprehensive analysis of 17,929 protein domain families within the Pfam database, and scored them based on their overrepresentation in pathogenic versus non-pathogenic species, taxonomic distribution, relative abundance in metagenomic datasets, and other factors.

Conclusions: We identify pathogen-associated domain families, candidate virulence factors in the human gut, and eukaryotic-like mimicry domains with likely roles in virulence. Furthermore, we provide an interactive database called PathFams to allow users to explore pathogen-associated domains as well as identify pathogen-associated domains and domain architectures in user-uploaded sequences of interest. PathFams is freely available at https://pathfams.uwaterloo.ca .

Keywords: Environmental association; Hypothetical proteins; Lineage specificity; Pathogens; Proteins of unknown function; Virulence factors.

Fig. 1

Scatterplots of Pfam domain pathogen-association. a Pfam domain presence in pathogen versus non-pathogen proteomes, with significant pathogen-associated patterns shown. Only domains present in > = 5 pathogens were included. b Trends in pathogenesis GO term annotation shown with respect to enrichment in pathogen proteomes and a measure of lineage specificity, the F1 score. The horizontal dotted line is at log₁₀(0.05), showing the pathogen-association threshold. The vertical dotted line is at an F1 score of 30

Fig. 2

Detected Pfam families with strong environmental associations. a Abundance heatmap of Pfam families with significant environmental-specificity scores (p_adj < 1 × 10^− 15). The adjusted family size was calculated as the logarithm of the normalized adjusted family size (base 10), scaled across the domain values. The red lines on the right-side of the plot denote DUF rows. b Selected DUF families with strong environment-specificity scores. Plotted are the per-sample distributions of normalized adjusted family size in three environments: human gut, marine, and soil

Fig. 3

Screenshot of the domain info page from PathFams for the LcrG Pfam family (PF07216)

Fig. 4

Detection of pathogen-associated domains and domain architectures for four example proteins by the online PathFams resource. Accession IDs are OTO22244.1 (Enterococcus faecium BoNT/En toxin), WP_034687872.1 (Chryseobacterium piperi Cp1 toxin), BAB87738.1 (Clostridium haemolyticum flagellinolysin), and OKB66574.1 (Serratia marascens hypothetical protein). Sensitive mode with an E-value cut-off of 1 × 10^− 7 was used for all sequences except the C. piperi Cp1 toxin. For the C. piperi sequence, an E-value cut-off of 1 × 10^− 3 was required to visualize the more divergent ricin domains