Deciphering the interplay between the genotoxic and probiotic activities of Escherichia coli Nissle 1917

Abstract

Although Escherichia coli Nissle 1917 (EcN) has been used therapeutically for over a century, the determinants of its probiotic properties remain elusive. EcN produces two siderophore-microcins (Mcc) responsible for an antagonistic activity against other Enterobacteriaceae. EcN also synthesizes the genotoxin colibactin encoded by the pks island. Colibactin is a virulence factor and a putative pro-carcinogenic compound. Therefore, we aimed to decouple the antagonistic activity of EcN from its genotoxic activity. We demonstrated that the pks-encoded ClbP, the peptidase that activates colibactin, is required for the antagonistic activity of EcN. The analysis of a series of ClbP mutants revealed that this activity is linked to the transmembrane helices of ClbP and not the periplasmic peptidase domain, indicating the transmembrane domain is involved in some aspect of Mcc biosynthesis or secretion. A single amino acid substitution in ClbP inactivates the genotoxic activity but maintains the antagonistic activity. In an in vivo salmonellosis model, this point mutant reduced the clinical signs and the fecal shedding of Salmonella similarly to the wild type strain, whereas the clbP deletion mutant could neither protect nor outcompete the pathogen. The ClbP-dependent antibacterial effect was also observed in vitro with other E. coli strains that carry both a truncated form of the Mcc gene cluster and the pks island. In such strains, siderophore-Mcc synthesis also required the glucosyltransferase IroB involved in salmochelin production. This interplay between colibactin, salmochelin, and siderophore-Mcc biosynthetic pathways suggests that these genomic islands were co-selected and played a role in the evolution of E. coli from phylogroup B2. This co-evolution observed in EcN illustrates the fine margin between pathogenicity and probiotic activity, and the need to address both the effectiveness and safety of probiotics. Decoupling the antagonistic from the genotoxic activity by specifically inactivating ClbP peptidase domain opens the way to the safe use of EcN.

The manifold roles of microbial ribosomal peptide–based natural products in physiology and ecology

“…enterica serovar Typhimurium or adherent invasive E. coli. Moreover, in a recent study, evidence that the posttranslational modification of EcN microcins with a siderophore is required for antibacterial activity in vivo has been obtained (111). This study also shows that the biosynthesis pathway of siderophore microcins tightly depends on that of the genotoxin colibactin (112), which is also produced by EcN and is correlated with the frequency and severity of colorectal cancer in humans (113), making the use of this commercialized probiotic problematic.…”

The Genotoxin Colibactin Shapes Gut Microbiota in Mice

“…We studied the effects on both gut microbiota and microbiome on pups at day 15 and 35 after birth. Beyond colibactin, pks island genes are involved in the synthesis of multiple factors such as bacterial analgesic lipopeptide [14] and antibiotic molecules such as siderophore-microcins [15]. Given the strong importance of the mother as an E. coli transmissing factor [16], to get mice pups colonized by E. coli the most natural way, we decided to colonize the mother with the E. coli of interest.…”

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling

“…Thirteen of them encode enzymes of metabolic pathways (aes, icd, pabB, trpA, trpB, fumC, mdh, purA, aspC, fadD, uidA, aroE, mtlD); ten belong to replication, repair, or transcription systems (polB, gyrA, recA, dinB, dnaG, mutS, arcA, cyaA, grpE, rpoS), and the remaining four control the production of two symporters (putP, lysP), kinase (adk) and protease (clpX). The sequences of these genes were obtained from 124 E. coli genomes (listed in Supplementary Table S1), including 59 complete genomes, whose phylogroups were previously identified in original papers [45,52,[55][56][57][58][59][60][61][62][63][64][65][66][67][68][69] (shown in bold in Supplementary Table S1). The remaining 65 genomes unassigned to phylogroups and containing orthologs of discriminatory genes were added to increase the resolution of phylogenetic trees.…”

“…Another example is the phylogroup C. Previously, it was represented by only three strains with complete genomes (ACN002, APEC O78 and str. 789) [52,57,60]. It is also worth noting the apparent divergence of the groups D and F. Although the transfer of some strains from group D into a separate phylogroup F was proposed in 2008 [51], the feasibility of this was finally accepted only in 2013 [45], when six strains with either complete genomes or contigs were ascribed to it.…”