Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

G-quadruplex (G4) structures can form in guanine-rich stretches of DNA or RNA and have been found to modulate a variety of cellular processes including replication, transcription, and translation. Most studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing G4s in bacteria. We utilized a chemical-genetic approach to identify genes in Escherichia coli that are important for growth in conditions that stabilize G4s. Our screens reveal translation elongation to be a key process that is impacted by G4 stabilization. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, downregulating the levels of certain essential translation termination or ribosome recycling proteins is detrimental to growth in G4-stabilizing conditions. Proteomic and transcriptomic analyses demonstrate that ribosome assembly factors and other proteins involved in translation generally are less abundantly expressed under G4-stabilizing conditions. Taken together, the results suggest that RNA G4s present barriers to E. coli growth in G4-stabilizing conditions and reducing the rate of translation can help compensate for G4-related stress. Overall design: To investigate the effects of stabilizing G-quadruplexes on Escherichia coli, cells were grown in the presence of the G-quadruplex stabilizing compound, NMM, and RNA-seq was performed. This was done for the control cell strain (MG1655 dtolC) as well as a strain with a decrease in a translation elongation factor (MG1655 dtolC tufA::kan). TPM values were used for differential gene expression analysis between each growth condition. All samples were grown and sequenced in triplicate.