CDI Systems Are Stably Maintained by a Cell-Contact Mediated Surveillance Mechanism

Abstract

Contact-dependent growth inhibition (CDI) systems are widespread amongst Gram-negative bacteria where they play important roles in inter-cellular competition and biofilm formation. CDI+ bacteria use cell-surface CdiA proteins to bind neighboring bacteria and deliver C-terminal toxin domains. CDI+ cells also express CdiI immunity proteins that specifically neutralize toxins delivered from adjacent siblings. Genomic analyses indicate that cdi loci are commonly found on plasmids and genomic islands, suggesting that these Type 5 secretion systems are spread through horizontal gene transfer. Here, we examine whether CDI toxin and immunity activities serve to stabilize mobile genetic elements using a minimal F plasmid that fails to partition properly during cell division. This F plasmid is lost from Escherichia coli populations within 50 cell generations, but is maintained in ~60% of the cells after 100 generations when the plasmid carries the cdi gene cluster from E. coli strain EC93. By contrast, the ccdAB "plasmid addiction" module normally found on F exerts only a modest stabilizing effect. cdi-dependent plasmid stabilization requires the BamA receptor for CdiA, suggesting that plasmid-free daughter cells are inhibited by siblings that retain the CDI+ plasmid. In support of this model, the CDI+ F plasmid is lost rapidly from cells that carry an additional cdiI immunity gene on a separate plasmid. These results indicate that plasmid stabilization occurs through elimination of non-immune cells arising in the population via plasmid loss. Thus, genetic stabilization reflects a strong selection for immunity to CDI. After long-term passage for more than 300 generations, CDI+ plasmids acquire mutations that increase copy number and result in 100% carriage in the population. Together, these results show that CDI stabilizes genetic elements through a toxin-mediated surveillance mechanism in which cells that lose the CDI system are detected and eliminated by their siblings.

Fig 1. E. coli cdiBAI gene clusters are located on genomic islands.

E. coli genomic islands harboring cdiBAI genes were aligned using the Artemis comparison tool. PAI II islands from 4 different E. coli strains are shown in panel A. Panel B displays 4 genomic islands inserted at pheV in the indicated strains. Homologous CDI DNA sequences are highlighted in blue-violet, homologous non-CDI DNA sequences are shown in light green (direct orientation) and light red (inverted orientation), and genes of interest are shown in orange. Abbreviations: yeeUV, toxin-antitoxin module; choline util, genes involved in choline metabolism; hly, hemolysin biosynthesis; F17, F17 fimbrial genes; prf, P-related fimbriae; lipid biosyn., putative lipid biosynthesis operon; HBA, genes involved in hydroxybenzoate degradation; kps, capsular assembly operon; T1SS, Type I secretion system.

Fig 2. CDI-mediated plasmid stabilization.

E. coli EPI100 populations harboring mini-F plasmid derivatives were passaged daily in broth culture for 100 generations. Randomly selected colonies were screened Amp^R after each passage to determine the percentage of cells that retain the plasmid. The average percentage of Amp^R colonies is plotted with the standard error indicated by grey shading. A) E. coli EP100 ΔbamA::cat pZS21-BamA pOri_F. B) E. coli EP100 ΔbamA::cat pZS21-BamA pCcdAB. C) E. coli EP100 ΔbamA::cat pZS21-BamA pCdiBAI. D) E. coli EP100 ΔbamA::cat pZS21-BamA^ECL pCdiBAI.

Fig 3. Ethidium bromide uptake analysis.

A) E. coli EPI100 populations carrying the indicated mini-F derivatives were stained with EtBr and visualized by fluorescence microscopy. B) The fraction of EtBr-stained cells was quantified from the populations in panel A and presented as the average ± standard error of the mean.

Fig 4. Plasmid stabilization reflects the selection for immunity to CDI.

E. coli EPI100 populations harboring mini-F plasmid derivatives were passaged daily in broth culture for 100 generations. Randomly selected colonies were screened Amp^R after each passage to determine the percentage of cells that retain the plasmid. The average percentage of Amp^R colonies is plotted with the standard error indicated by grey shading. A) E. coli EP100 pOri_F pACYC184. B) E. coli EP100 pOri_F pCdiI. C) E. coli EP100 pCdiBAI pACYC184. D) E. coli EP100 pCdiBAI pCdiI.

Fig 5. Plasmid pCdiBAI becomes fixed in populations after long-term passage.

A) Three E. coli EPI100 pCdiBAI lineages were passaged for 500 cell generations, and the percentage of cells that carry plasmid pCdiBAI determined. B) Total DNA was isolated from the lineages shown in panel A after 500 generations (g500). DNA samples were digested with PstI and analyzed by Southern blot using radiolabeled probes specific for plasmid pCdiBAI and the groL chromosomal locus. Control samples isolated from cells lacking plasmid (F-), cells carrying pOri_F and unpassaged cells carrying pCdiBAI (pCdiBAI^g0) were also analyzed. Molecular standards were generated by PCR of plasmid pCdiBAI and the genomic groL locus. C) Plasmid DNA was isolated from the lineages in panel A after 0 (g0), 100 (g100), 200 (g200) and 300 (g300) generations. The plasmids were transformed into E. coli ΔbamA::cat pZS21-BamA^ECL and the percentage of cells carrying plasmid pCdiBAI was monitored over 100 generations.

Fig 6. Colicin/immunity genes stabilize genetic elements.

E. coli populations harboring mini-F plasmid derivatives were passaged daily in broth culture for 100 generations. Randomly selected colonies were screened for Amp^R after each passage to determine the percentage of cells that retain the plasmid. The average percentage of Amp^R colonies is plotted with the standard error indicated by grey shading. A) E. coli MG1655 pOri_F. B) E. coli MG1655 pColE5. C) E. coli MG1655 pCdiBAI. D) Plasmid pColE5 provides a competitive advantage. E. coli MG1655 harboring the indicated mini-F derivatives were co-cultured at a 1:1 ratio with plasmid-free, Rif^R MG1655 cells. The competitive index was calculated as described in Methods. The average ± standard error is presented for three independent experiments.

Fig 7. The cdiBAI^EC93 genes are functional after horizontal transfer.

A). C. freundii cells harboring pDAL878-cat (CDI^–) or pDAL660Δ1-39-cat (CDI⁺) were co-cultured with E. coli MG1655 target cells that carry pTrc99A (vector, Amp^R) or pTrc99A::cdiI^EC93 (pCdiI, Amp^R). Competitive indices were calculated as the ratio of C. freundii to E. coli cells at 4 h divided by the initial ratio. The average ± standard error is presented for three independent experiments. B to D). C. freundii cells harboring pDAL660Δ1-39-cat (CDI⁺) or pDAL878-cat (CDI^–) were passaged daily in broth culture for 50 generations. The cells also contained plasmids that express bamA^Eco or bamA^ECL where indicated. Randomly selected colonies were screened for Cm-resistance after each passage to determine the percentage of cells that retain the plasmid. The average percentage of Cm^R colonies is plotted with the standard error indicated by grey shading.