Prediction of molecular mimicry candidates in human pathogenic bacteria

Abstract

Molecular mimicry of host proteins is a common strategy adopted by bacterial pathogens to interfere with and exploit host processes. Despite the availability of pathogen genomes, few studies have attempted to predict virulence-associated mimicry relationships directly from genomic sequences. Here, we analyzed the proteomes of 62 pathogenic and 66 non-pathogenic bacterial species, and screened for the top pathogen-specific or pathogen-enriched sequence similarities to human proteins. The screen identified approximately 100 potential mimicry relationships including well-characterized examples among the top-scoring hits (e.g., RalF, internalin, yopH, and others), with about 1/3 of predicted relationships supported by existing literature. Examination of homology to virulence factors, statistically enriched functions, and comparison with literature indicated that the detected mimics target key host structures (e.g., extracellular matrix, ECM) and pathways (e.g., cell adhesion, lipid metabolism, and immune signaling). The top-scoring and most widespread mimicry pattern detected among pathogens consisted of elevated sequence similarities to ECM proteins including collagens and leucine-rich repeat proteins. Unexpectedly, analysis of the pathogen counterparts of these proteins revealed that they have evolved independently in different species of bacterial pathogens from separate repeat amplifications. Thus, our analysis provides evidence for two classes of mimics: complex proteins such as enzymes that have been acquired by eukaryote-to-pathogen horizontal transfer, and simpler repeat proteins that have independently evolved to mimic the host ECM. Ultimately, computational detection of pathogen-specific and pathogen-enriched similarities to host proteins provides insights into potentially novel mimicry-mediated virulence mechanisms of pathogenic bacteria.

Keywords: bacteria; collagen; extracellular matrix; leucine-rich repeats; mimicry; pathogenomics; pathogens; proteins; proteomes; virulence factors.

Figure 1. Computational pipeline for detection of molecular mimicry candidates in human pathogenic bacteria.

Figure 2. Top BLAST matches for human proteins in pathogen vs. non-pathogen proteomes. Left: −log₁₀E-values for top BLAST matches to human proteins in 62 human pathogens vs. 66 non-pathogens. Right: −log₁₀E-values for top BLAST matches to human proteins with different host/pathogen definitions (6 plant pathogens vs. 16 non-pathogens). Values above ~60 are not shown. Collagens (top detected mimicry relationship) and ADP-ribosylating factors (positive control mimicry relationship) have pathogen-elevated E-value distributions.

Figure 3. Top pathogen vs. non-pathogen protein similarities to a selected set of predicted human mimicry targets. Predicted human mimicry targets were selected from the top 25 detected relationships (Table 1), and the top BLAST matches by bitscore (x-axis) in pathogen vs. non-pathogen proteomes (frequency on y-axis) have been plotted. In each case, it can be seen that a subset of pathogen proteomes encode putative mimics that exhibit much greater similarities to human proteins than similarities found in non-pathogen proteins. A selected portion of the alignment is shown for the top-scoring pathogen mimic in each case. See Data File S1 for additional details regarding pairwise alignments.

Figure 4. Independent evolution of ECM mimics from separate repeat amplifications. High-scoring collagen-like (A) and leucine-rich repeat (B) protein mimics were selected and divided into their constituent protein repeats, which were aligned and used to generate sequence logos. Differences between the sequence logos of each repetitive protein suggest evolution from separate progenitor peptides and repeat amplifications. (C) An example demonstrating similarity of leucine-rich repeat sequence conservation patterns between a human NOD-like receptor (NLRC3) and a predicted mimicry candidate (lpl1579) from Legionella pneumophila. The detected level of sequence similarity between these two proteins is far above that observed in non-pathogens (blue) and other pathogens (red) as indicated by the BLAST bitscore distribution (left panel).

Figure 5. Phylogenetic trees of bacterial pathogen encoded collagen-like repeats (left) and leucine-rich repeats (right) from Figure 4. The repeats are colored in the tree according to their parent protein. Top-aligning repeats from human proteins have also been included and are colored light green. Repeats cluster predominantly by protein of origin, suggesting that different pathogen repeat proteins have evolved by independent repeat amplifications. Interestingly, the pathogen repeat classes generally cluster with a specific human repeat, suggesting that ancestral progenitor repeats may be host-derived.