Fig. 6: Mechanistic overview of in trans R-loop formation and genomic stability in P. aeruginosa biofilms.
From: Stress-induced toxic genomic R-loops support biofilm extracellular matrix formation
Amino acid starvation in biofilms activates stringent stress response (SSR) and ppGpp alarmone overproduction. ppGpp binds to RNA polymerase, slows down mRNA degradation and only activates transcription of stress response genes. ppGpp activates programmed cell death (PCD) in a subpopulation of suicidal cells using the AlpA master regulator. In suicidal cells, the RecA protein binds to single-stranded DNA (ssDNA) at sites of damage and facilitates the recruitment of excess mRNA that has accumulated within the cell to these damaged regions. In trans R-loop formation is generated by RecA across the genome, which creates widespread stalling of replication forks and subsequently genomic instability. The SOS response additionally induces explosive cell lysis through endolysin overproduction. R-loop structures are released into the biofilm matrix from suicidal cells. In contrast, RecA activates DNA repair machinery in survivor cells. Stress response genes such as lasB are released into the matrix and interact with R-loops to act as building blocks for biofilm formation. Created in BioRender. Group, S. (2025) https://BioRender.com/y95q1n6.
