Comparative Analysis of Gene Expression in RNA-Seq Studies of Salmonella enterica: Focus on the Type VI Secretion System

Abstract

The Type VI Secretion System (T6SS) is a complex multiprotein apparatus present in many Gram-negative bacteria, involved in injecting effectors into both microbial competitors and host cells. Encoded by Salmonella Pathogenicity Island-6 (SPI-6) in Salmonella enterica subsp. enterica serovar Typhimurium strain 14028S, its transcriptional regulation remains poorly defined under diverse conditions. To fill this gap, publicly available RNA-seq data from 23 distinct experimental settings were retrieved from the NCBI Sequence Read Archive (SRA) and reanalysed using a robust, reproducible pipeline on the Galaxy platform. The results were organized in a relational database to facilitate subsequent queries. Condition-specific expression profiles revealed a mosaic of T6SS gene activation, often confined to subsets of the cluster rather than the entire system. For instance, co-culturing with Acanthamoeba castellanii, L-arabinose supplementation, and HeLa cell infection triggered selective upregulation of structural genes, demonstrating a nuanced transcriptional responsiveness to microbial interactions and environmental signals. Downstream functional enrichment analysis further emphasised the role of secretion and virulence-associated pathways under these stimuli. This study highlights the value of leveraging public transcriptomic datasets to uncover condition-dependent regulatory dynamics in bacterial systems. It also illustrates how integrate large-scale data with curated analysis pipelines can inform future experimental hypotheses, while pointing to the importance of consistent data annotation to fully exploit the potential of open-access biological resources.