Physiological Robustness of Model Gram-Negative Bacteria in Response to Genome Rewiring

Abstract

DNA supercoiling and nucleoid-associated proteins (NAPs) are two of the factors that govern the architecture of the bacterial genome, influencing the expression of the genetic information that it contains. Alterations to DNA topology, and to the numbers and types of NAPs, have pleiotropic effects on gene expression, suggesting that modifications to the production patterns of DNA topoisomerases and/or NAPs are likely to result in marked impacts on bacterial physiology. Knockout mutations in the genes encoding these proteins (where the mutants remain viable) result in clear physiological effects. However, genetic modifications that involve rewiring, or repositioning, of topoisomerase or NAP genes produce much more subtle outcomes. These findings demonstrate that the high-level regulatory circuitry of bacteria is robust in the face of genomic rearrangements that, a priori, might be expected to produce significant changes in bacterial lifestyle. Examples from genomic rewiring experiments, performed chiefly with the Gram-negative model bacteria Escherichia coli K-12 and Salmonella enterica serovar Typhimurium, will be used to illustrate these features. The results show not only the ability of naturally occurring bacteria to tolerate regulatory rewiring but also indicate the limits within which experiments in synthetic biology may be designed.

VariableDNAtopology is an epigenetic generator of physiological heterogeneity in bacterial populations

“…Increasing, or decreasing, the unpredictability of expression of a given gene may, in turn, have unpredictable consequences for the competitive fitness of the individual bacterium and for the wider population of its siblings. The base composition of a gene, especially one that has been acquired by horizontal gene transfer, seems to influence its sensitivity to DNA supercoiling changes (Dorman & Dorman, 2022 ), and this is likely to influence the stochasticity of its transcription.…”