Biology subjects

Engl, C.

Publications and source records attributed to Engl, C..

3 recordsLinked to original sources

bioRxiv2025

Single-cell Analysis of Attenuation-Driven Transcription Reveals New Principles of Bacterial Gene Regulation

Transcription attenuation fine-tunes biosynthetic gene expression in bacteria via premature termination upon metabolic signals. In transcription initiation-controlled bacterial systems, promoter architecture and transcription factor binding sets the size of transcriptional bursts at {sigma}70 promoters, while distal enhancer elements and associated transcriptional activators modulate burst frequency at {sigma}54 promoters. Using the tryptophan biosynthesis operon as a model, we show that transcription attenuation, acting post-initiation and alongside transcriptional repression, simultaneously modulates both burst size and frequency from a {sigma}70 promoter. This challenges the view that frequency modulation requires distal enhancer input and reveals that post-initiation mechanisms can shape divergent transcriptional bursting. We also uncover that bacteria use cross-feeding as a previously unrecognised strategy for controlling cell-to-cell variation in gene expression, with implications for metabolic coordination among cells. These findings redefine transcription dynamics within cell populations and suggest new principles by which bacteria regulate gene expression to adapt to environmental change.

microbiology↗

bioRxiv2024

A mechanistic model of Rtc-regulated RNA repair suggests molecular targets to potentiate antibiotic effects

RNA is susceptible to damage from various internal and external factors. Given the integral role of RNA, its repair is essential for maintaining proper cell function. A highly conserved RNA repair system, the Rtc system, maintains core RNA components of the translational apparatus. In E. coli, Rtc expression is induced upon various stresses, including exposure to ribosome-targeting antibiotics. Its expression enables cells to rescue growth and survive treatment by conferring transient resistance to these antibiotics. The mechanisms by which Rtc-induced resistance arises are largely unknown. Here, we develop and analyse a computational model of Rtc-regulated maintenance of long-lived RNAs that form part of the translational apparatus. Our model analysis and experimental validation provide evidence of cell-to-cell heterogeneity in rtc expression and effects on the translational capacity of cells, indicating that individual cell fates determine antibiotic efficacy and thus rtc may induce a form of heteroresistance. Through further analysis and quantification of single-cell ribosome levels, we then identify targets within the Rtc system that can reduce translational capacity of cells, rendering cells more susceptible and so potentiating antibiotic effects. Our results provide novel tools for the systems analysis of Rtc-regulated RNA repair, they reveal a complex response underpinning resistance conferred by the innate repair system, and they suggest novel avenues to address resistance in E. coli and related clinical pathogens.

systems biology↗

bioRxiv2020

Molecular origins of transcriptional heterogeneity in diazotrophic K. oxytoca

Phenotypic heterogeneity in clonal bacterial batch cultures is an important adaptive strategy to changing environments, including in diazotrophs with the unique capacity to convert di-nitrogen into bio-available ammonium. In diazotrophic Klebsiella oxytoca we simultaneously measured mRNA levels of key regulatory (glnK-amtB, nifLA) and structural (nifHDK) operons required for establishing nitrogen fixation, using dual molecule, single cell RNA-FISH. Through stochastic transcription models and mutual information analysis we revealed likely molecular origins for heterogeneity in nitrogenase expression. In wildtype and regulatory variant strains we inferred contributions from intrinsic and extrinsic noise, finding that nifHDK transcription is inherently bursty, but that noise propagation through signalling is also significant. The regulatory gene glnK had the highest discernible effect on nifHDK variance, while noise from factors outside of the regulatory pathway were negligible. Results provide evidence that heterogeneity is a fundamental property of this regulatory system, indicating potential constraints for engineering homogeneous nitrogenase expression.

microbiology↗