Diversity of Contact-Dependent Growth Inhibition Systems of Pseudomonas aeruginosa

Abstract

Contact-dependent growth inhibition (CDI) systems are used in bacterial competition to hinder the growth of neighboring microbes. These systems utilize a two-partner secretion mechanism to display the CdiA exoprotein at the bacterial cell surface. CdiA forms a long filamentous stalk that facilitates binding to a target cell and delivery of a C-terminal toxin (CT) domain. This CT domain is processed and delivered into the cytoplasm of a target cell upon contact. CDI systems also encode a cognate immunity protein (CdiI) that protects siblings and resistant targeted cells from intoxication by high-affinity binding to the CT. CdiA CT domains vary among strains within a species, and many alleles encode enzymatic functions that target nucleic acids. This variation is thought to help drive diversity and adaptation within a species. CdiA diversity is well studied in Escherichia coli and several other bacteria, but little is known about the extent of this diversity in Pseudomonas aeruginosa. The purpose of this review is to highlight the variability that exists in CDI systems of P. aeruginosa. We show that this diversity is apparent even among strains isolated from a single geographical region, suggesting that CDI systems play an important role in the ecology of P. aeruginosa.

FIG 1

Current model of CDI intoxication. (A) A cartoon diagram of CdiA in its native state at the cell surface of an attacking bacterium, as modeled by Ruhe et al. (25). The corresponding CdiA protein domains are illustrated to scale below the cartoon. See the text for details. (B) CdiA-dependent intoxication of a target bacterium. Upon binding of the CdiA-RBD to an outer membrane receptor (OMR) on a target bacterium, the periplasmic domains are released from the attacking bacterium to deliver the CT into the cytosol of the target bacterium. This is thought to occur through a stepwise process whereby the FHA2 domain delivers the TD and CT into the periplasm of a target cell and the TD binds an inner membrane receptor (IMR) that facilitates translocation of the CT into the cytosol through an unknown mechanism.

FIG 2

Organization of P. aeruginosa CDI systems. (A) The cdi1 and cdi2 loci are displayed as blue arrows in their genetic orientation within P. aeruginosa strain PAO1. Core genes outside the cdi loci are colored purple. O28 and O30, colored orange, represent orphan immunity genes located in the intergenic region downstream of the functional cdiBAI cluster. Black arrows indicate the predicted promoter sites. (B) Alignment of the P. aeruginosa strain PAO1 cdi2 locus and flanking regions to the same genetic region in strain DK2, which does not contain a cdi2 locus.

FIG 3

CdiA protein diversity. CdiA protein domain organization of E. coli CdiA^EC93 and CdiA^STEC_031 based upon the work of Ruhe et al. (24) and of CdiA1^PAO1, CdiA1^BL012, and CdiA2^PAO1 from this work. Roman numerals indicate the P. aeruginosa CdiA class type (20). Colors reflect the different predicted protein domains from sequence alignments, domain searches, and domain descriptions in E. coli. Sec, general secretory signal.

FIG 4

Distribution of CdiA domains in the PABL and NCBI strain collections. (A to C) The occurrence of each CT (A), TD (B), and RBD (C) variant was determined for the P. aeruginosa PABL and NCBI strain collections. Each bar represents the number of strains that contain the indicated domain variant, which are labeled based on designations in Fig. S3. Notations above the CT graph reflect predicted enzymatic functions determined by a conserved domain search (https://www.ncbi.nlm.nih.gov/cdd). (D) Counts represent the number of intergenic orphan cdiI genes at a cdi locus for each strain collection.

FIG 5

P. aeruginosa CdiA C-terminal diversity. Pairwise comparison of CdiA translocation domains (TD) and respective C-terminal toxin (CT) domains were performed for the NCBI and PABL strain collections. Cells colored red indicate that the TD-CT combination was observed at the CDI1 locus, and blue indicates the CDI2 locus. Numbers indicate the number of strains with that observed TD-CT combination.

FIG 6

Phylogenetic distribution of cdiA alleles. The RBDs (inner ring), TDs (middle ring), and CTs (outer ring) for CdiA1 (A) and CdiA2 (B) were mapped onto maximum likelihood core genome trees of the PABL (red) and NCBI (black) strains. Ring colors represent different variants of the respective domains as noted in Fig. S1 and S3. Branches with dots at the tips indicate a class II C terminus. A red circle means the downstream orphan class V CdiA C terminus is the same as the functional class V CdiA C terminus of the closest phylogenetic neighbor.

FIG 7

Illustration of cdiA1 C-terminal class switching. Alignments from Fig. S4 indicate that a cdiA class II C terminus can recombine with a region of conserved sequence immediately upstream of the FHA2 domain, shifting the original class V C terminus into the downstream intergenic region. The source of the class II C terminus is unknown.