Pathogenic bacteria experience pervasive RNA polymerase backtracking during infection.

Area of Science:

• Microbiology
• Molecular Biology
• Genetics

Background:

• Pathogenic bacteria and hosts engage in an evolutionary arms race, with host defenses impacting bacterial molecular processes.
• Understanding how host cells affect bacterial protein-chromosome associations during infection is crucial but challenging.
• Existing methods lack the ability to detect these events within host cells.

Approach:

• Developed and optimized PIC-seq (Protein-Chromosome Association sequencing) to map and quantify bacterial protein-chromosome associations during host cell infection.
• Utilized *Salmonella enterica* as a model pathogen to study RNA polymerase (RNAP) dynamics.
• Analyzed genome-wide RNAP association patterns and movement during infection.

Key Points:

• Host infection alters RNAP association patterns across the *Salmonella* genome, including virulence gene regions.
• Infection significantly increases RNAP backtracking, a major impediment to transcriptional progression.
• Resolution of backtracked RNAPs by GreA and GreB is essential for pathogenesis, identifying them as novel virulence factors.

Conclusions:

• Host environments profoundly impact bacterial transcription by disrupting RNAP movement.
• Increased RNAP backtracking during infection has implications for both transcriptional efficiency and bacterial mutagenesis.
• PIC-seq provides a novel tool for studying bacterial molecular dynamics within host cells.