Sample-derived cDNA guides broad host RNA depletion for in vivo pathogen transcriptomics www.biorxiv.org/content/10.64898/2026.03...

Bacterial Stress Responses Lower mRNA-Protein Level Correlations Diverse bacterial pathogens have evolved complex regulatory mechanisms to adapt to various environmental stresses during infection. The uncertainty in mRNA-protein levels in response to environmental stressors complicates our understanding of bacterial physiology and their adaptation to stressful environments. To examine this issue, we have integrated transcriptomics and proteomics data on three human bacterial pathogens Salmonella enterica Typhimurium\[CE4.1\]\[KA4.2\], Yersinia pseudotuberculosis, and Staphylococcus aureus under ten infection-relevant stress conditions. We observed positive correlations between mRNA and protein levels, which were decreased under different stress conditions. Essential genes exhibited higher expression levels with lower variation across the conditions and stronger mRNA-protein correlations compared to non-essential genes, highlighting their [JA5.1]critical role in bacterial adaptability and survival. Moreover, we identified a substantial number of genes with stress-induced non-correlating mRNA-protein levels, particularly under conditions triggering strong stress responses. Particularly this level was dramatically lowered for osmotic stress specific genes affected by impaired translational activity under osmotic stress. Our findings highlight the prevalence of non-correlating mRNA-protein levels and the potential role of post-translational modifications in modulating protein levels in response to environmental stressors during infection. This study provides a comprehensive framework for integrating transcriptomics and proteomics data and identifies potential gene products that might significantly impact the ability of diverse bacterial pathogens to adapt to hostile infection environments. ### Competing Interest Statement The authors have declared no competing interest. Swedish Research Council, https://ror.org/03zttf063, 2021-02466 Kempe Foundation, https://ror.org/05cszw148, JCK22-0017 Medical Faculty umeå, FS 2.1.6-281-22 Swedish Research Council Excellence Center, 2022-06543 Knut and Alice Wallenberg Foundation, https://ror.org/004hzzk67, KAW 2020.0239

Bacterial Stress Responses Lower mRNA-Protein Level Correlations | bioRxiv www.biorxiv.org/content/10.64898/2026.03...

Using in vivo single-cell transcriptomics, we show how bacterial cells, just millimetres apart, use 6S RNA to coordinate virulence and stress adaptation during epithelial barrier crossing
#microbiology #6SRNA #spatialomics #hostpathogen #preprint