Identification of gene targets regulated by the IclR-like regulator SL1344_3500 in <i>Salmonella</i> Typhimurium

Transcriptional regulation of metabolic operons is important for optimal carbohydrate use and for mitigating the accumulation of toxic intermediates. Here, we characterize <i>SL1344_3500</i>, encoding a putative IclR-like regulator in <i>Salmonella enterica</i> Typhimurium. We present genetic and transcriptional evidence that it regulates the expression of two neighboring operons, one designated here as <i>xynABC</i>, enables utilization of xylonate as a sole carbon source. Furthermore, our findings indicate that <i>SL1344_3500</i> is important for luminal growth in several mouse models, exerting its effects through the suppression of the <i>xynABC</i> operon. Based on the observation that the Δ<i>SL1344_3500</i> deletion can be stably complemented <i>in vivo</i>, we developed a plasmid stabilization strategy. This gene complementation approach shows promise for generating stable gene reporters for long-term colonization experiments.IMPORTANCEUnderstanding transcriptional regulation in <i>Salmonella enterica</i> Typhimurium is crucial for revealing how enteric pathogens optimize metabolism to compete with commensals in the gut. SL1344_3500, an IclR-like transcriptional regulator controlling genes linked to sugar acid metabolism, is essential for luminal growth in mouse models through gene suppression and represents a potential target for antimicrobial development. Based on these observations, we developed stable reporter plasmids that use gene complementation of SL1344_3500 to prevent plasmid loss during long-term <i>in vivo</i> studies.