Dual RNA-Seq Uncovers ESX-1- and ESX-5-Dependent Virulence Programs of Mycobacterium marinum in Human and Murine Macrophages
The secretion systems known as ESX-1 and ESX-5 are critical for the virulence of pathogenic mycobacteria, such as Mycobacterium marinum (Mmar), a close genetic relative of Mycobacterium tuberculosis. To shed light on how these secretion systems drive host-pathogen interactions, we did simultaneous RNA-seq using human THP-1 as well as murine RAW macrophages, infected with wild type Mmar E11 and its ESX-1 and ESX-5 mutants. Our study revealed distinct host specific transcriptomic responses to infection, with murine macrophages exhibiting higher expression of pro-inflammatory genes compared to human cells. However, comparative analysis of transcriptomes of wild type, ESX-1 and ESX-5 mutants identified differentially expressed virulent genes across strains and hosts, highlighting the dynamic regulation of PE/PPE proteins, stress response genes, and components of the ESX systems. Furthermore, functional enrichment analysis of the host responses demonstrated that ESX dependent activation of immune pathways, including interferon signaling, cytokine-mediated responses, and lipid metabolism. Notably, lack of functional ESX-1 or ESX-5 secretion resulted in impaired bacterial virulence gene expression together with reduced host immune activation. Protein–protein interaction analyses were also identified both conserved and host specific immune signatures, including shared antiviral markers and distinct inflammatory mediators, in human and murine macrophages. These findings highlight the pivotal role of ESX systems in mediating Mmar virulence and demonstrate how host species significantly influence transcriptional and immune responses outcomes during mycobacterial infection.