A Matter of Location: Influence of G-Quadruplexes on Escherichia coli Gene Expression

Abstract

We provide important insights into secondary-structure-mediated regulation of gene expression in Escherichia coli. In a comprehensive survey, we show that the strand orientation and the exact position of a G-quadruplex sequence strongly influence its effect on transcription and translation. We generated a series of reporter gene constructs that contained systematically varied positions of quadruplexes and respective control sequences inserted into several positions within the promoter, 50-UTR, and 30-UTR regions. G-rich sequences at specific locations in the promoter and also in proximity to the ribosome-binding site (RBS) showed pronounced inhibitory effects. Additionally, we rationally designed a system where quadruplex formation showed a gene-activating behavior. Moreover, we characterized quadruplexes in proximity to the RBS that occur naturally in E. coli genes, demonstrating that some of these quadruplexes exert significant modulation of gene expression. Taken together, our data show strong position-dependent effects of quadruplex secondary structures on bacterial gene expression.

G-quadruplex prediction inE. coligenome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

“…Computational interrogation of 140 different bacterial genomes revealed that potential GQ-forming sequences are highly enriched in regulatory regions (−200 to −1 bp upstream from the transcription start site) of many prokaryotic genes (3). Indeed, similar to eukaryotes, where the effects of GQs on gene expression were already known, a recently published elegant work provided evidence that GQ sequences are critical for gene expressions in bacteria, strongly indicating that regulatory roles of GQ sequences are highly conserved between eukaryotes and bacteria (21). Additionally, it was also reported that, similar to specific binding of human MSH2/MSH6 (bacterial homolog of MutSα) to GQs located in the immunoglobulin switch regions, bacterial E. coli MutSα was found to bind to GQ-forming sequences (19,21).…”

“…Though many features of prokaryotic DNA organizations differ from eukaryotes (circular versus linear, absence of a chromatin-like nucleosome structure, etc. ), it was not until recently that GQ DNA structures were found to be enriched in the genomes of lower organisms including bacteria (3,17–21). Computational interrogation of 140 different bacterial genomes revealed that potential GQ-forming sequences are highly enriched in regulatory regions (−200 to −1 bp upstream from the transcription start site) of many prokaryotic genes (3).…”

G-quadruplex prediction in E.coli genome reveals a conserved putative G-quadruplex-Hairpin-Duplex switch

“…Computational interrogation of 140 different bacterial genomes revealed that potential GQ-forming sequences are highly enriched in regulatory regions (−200 to −1 bp upstream from the transcription start site) of many prokaryotic genes (3). Indeed, similar to eukaryotes, where the effects of GQs on gene expression were already known, a recently published elegant work provided evidence that GQ sequences are critical for gene expressions in bacteria, strongly indicating that regulatory roles of GQ sequences are highly conserved between eukaryotes and bacteria (21). Additionally, it was also reported that, similar to specific binding of human MSH2/MSH6 (bacterial homolog of MutS␣) to GQs located in the immunoglobulin switch regions, bacterial E. coli MutS␣ was found to bind to GQ-forming sequences (19,21).…”

“…Indeed, similar to eukaryotes, where the effects of GQs on gene expression were already known, a recently published elegant work provided evidence that GQ sequences are critical for gene expressions in bacteria, strongly indicating that regulatory roles of GQ sequences are highly conserved between eukaryotes and bacteria (21). Additionally, it was also reported that, similar to specific binding of human MSH2/MSH6 (bacterial homolog of MutS␣) to GQs located in the immunoglobulin switch regions, bacterial E. coli MutS␣ was found to bind to GQ-forming sequences (19,21). In addition to MutS, Henderson et al identified many non-telomeric GQ DNA binding proteins in human, yeast, Escherichia coli and Arabidopsis.…”

“…Though many features of prokaryotic DNA organizations differ from eukaryotes (circular versus linear, absence of a chromatin-like nucleosome structure, etc. ), it was not until recently that GQ DNA structures were found to be enriched in the genomes of lower organisms including bacteria (3,(17)(18)(19)(20)(21). Computational interrogation of 140 different bacterial genomes revealed that potential GQ-forming sequences are highly enriched in regulatory regions (−200 to −1 bp upstream from the transcription start site) of many prokaryotic genes (3).…”