Altering translation allows E. coli to overcome G-quadruplex stabilizers

G-quadruplex (G4) structures can form in guanine-rich DNA or RNA and have been found to modulate cellular processes including replication, transcription, and translation. Many studies on the cellular roles of G4s have focused on eukaryotic systems, with far fewer probing bacterial G4s. Using a chemical-genetic approach, we identified genes in Escherichia coli that are important for growth in G4-stabilizing conditions. Reducing levels of elongation factor Tu or slowing translation elongation with chloramphenicol suppress the effects of G4 stabilization. In contrast, reducing the expression of certain 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 are less abundant in G4-stabilizing conditions. Our results suggest that RNA G4s can present barriers to E. coli growth and reducing the rate of translatio..., Strain construction
All cells used in this study are derived from an Escherichia coli MG1655 parent strain unless otherwise specified. For CRISPR interference strains, strains were a gift from Jason Peters (46). To generate E. coli knockout strains, P1 transductions were carried out using Keio collection strains as the donor strain (63,64). P1 phage lysate was grown on Keio collection donor strains, which was used to transduce the MG1655 strains or CRISPR interference strains (to make the tolC knockout of selected CRISPRi strains) which were sensitive to kanamycin. To validate strains, transductions were grown on LB plates supplemented with 50 µg/mL kanamycin and screened using colony PCR to validate proper insertion of the kanamycin resistance cassette. To remove the kanamycin resistant cassette from MG1655 tolC::kan to enable additional P1 transductions in this strain, MG1655 tolC::kan electrocompetent cells were generated and transformed with a plasmid encoding the FLP recombinase (p..., , # Altering translation allows E. coli to overcome chemically stabilized G-quadruplexes

[https://doi.org/10.5061/dryad.zcrjdfnn9](https://doi.org/10.5061/dryad.zcrjdfnn9)

## Description of the data and file structure

The data included in this Dryad submission was collected in order to understand how the model organism* Escherichia coli* overcomes stabilized G-quadruplexes. This work involved a multi-omics approach to studying how the G-quadruplex stabilizers NMM and Braco-19 impact growth, gene importance, and mRNA/proteomic abundance in G-quadruplex stabilizing conditions. 

### Files and variables

#### File: Western\_total\_protein\_stain\_1.tif

**Description:** Total protein staining for western blots assessing EF-Tu abundance in ∆tolC, ∆tolC tufA::kan, and ∆tolC tufB::kan cells. Order of gel is ∆tolC, ∆tolC tufA::kan, and ∆tolC tufB::kan at three different dilutions added into the gel. This is the total protein stain image used in the figure of the manuscript.

#### File: Wester...