Bhetwal, A. | Search bioRxiv

bioRxiv2026

Dual Screen for Gut Metabolites Suppressing Enterobacterial Growth and Invasiveness Reveals Structure - Activity Relationships among Anti-Infective Indoles

The antibiotic resistance crisis makes characterization of new anti-infective molecules a pressing matter. Molecules that suppress bacterial growth and survival, virulence, or the combination of these traits, all warrant further exploration. Naturally occurring microbe-host ecosystems, such as the human gut, provide incompletely tapped resources in this regard. We developed a flexible platform to parallelly assess how gut metabolites affect the growth and epithelial cell invasion capacity of the enteropathogens Salmonella enterica Typhimurium (Salmonella) and Shigella flexneri. By screening a gut metabolite library, the assays identified multiple anti-infective compound classes and extended previously reported antibacterial activities for e.g. medium chain fatty acids, bile acids, purine nucleotides, and indole. Importantly, a targeted follow-up screen combined with chemical biology iterations showed how the anti-infective activity of indole is impacted by its derivatization. Specifically, a methyl group at either of the carbons of the indole scaffold potentiated the suppressive effect on type-III-secretion-system-mediated virulence, flagellar motility (for Salmonella), and growth, in a concentration-dependent manner. By contrast, N1-methylation markedly attenuated the activity of indole and its C-derivatized versions. The study, hence, offers assays for dual growth and virulence analysis of invasive enterobacteria exposed to anti-infective candidate molecules, and informs on structure-activity relationships among indole metabolites.

microbiology↗

bioRxiv2025

The pcnB gene sustains Shigella flexneri virulence

The enteropathogen Shigella flexneri employs a Type Three Secretion System (T3SS) to colonize intestinal epithelial cells. Genes encoding the T3SS are located on a large IncFII virulence plasmid, pINV. T3SS expression comes at the expense of slowed Shigella growth and is therefore strictly controlled by both transcriptional and post-transcriptional mechanisms. Following up on a recent genome-wide screen, we here show that the chromosomal gene pcnB, encoding the poly-A polymerase I (PAP-I), slows Shigella growth at 37{degrees}C, while at the same time promotes early colonization of a human epithelial enteroid model. Proteomic profiling revealed that pcnB drives global increase of the Shigella T3SS virulence program. Accordingly, pcnB sustains pINV replication to a level optimal for Shigella virulence. This is achieved through increased degradation of the antisense RNA CopA, involved in plasmid replication control. The pcnB effect on pINV replication was found to also ensure longer-term intraepithelial expansion of Shigella following human intestinal epithelium invasion. Our findings exemplify how an optimal pINV level is necessary for the execution of Shigellas infection cycle. AUTHOR SUMMARYBacterial infections represent a major global threat. Understanding the genetic determinants promoting infections is crucial to overcome this threat. Shigella is an intracellular bacterial pathogen that invades and disseminates in the intestinal epithelium, causing bacillary dysentery in humans. Shigellas ability to cause disease relies on the delivery of effector proteins into the host cells through an injection machinery, with most of the genes involved in this process located on a large virulence plasmid. Here we show that the chromosomal gene pcnB sustains an optimal virulence plasmid level. This is crucial for Shigella to maximize virulence protein expression and thereby efficiently invade, replicate and spread within the intestinal epithelium.

microbiology↗