Cooperativity of Negative Autoregulation Confers Increased Mutational Robustness

Abstract

Negative autoregulation is universally found across organisms. In the bacterium Escherichia coli, transcription factors often repress their own expression to form a negative feedback network motif that enables robustness to changes in biochemical parameters. Here we present a simple phenomenological model of a negative feedback transcription factor repressing both itself and another target gene. The strength of the negative feedback is characterized by three parameters: the cooperativity in self-repression, the maximal expression rate of the transcription factor, and the apparent dissociation constant of the transcription factor binding to its own promoter. Analysis of the model shows that the target gene levels are robust to mutations in the transcription factor, and that the robustness improves as the degree of cooperativity in self-repression increases. The prediction is tested in the LexA transcriptional network of E. coli by altering cooperativity in self-repression and promoter strength. Indeed, we find robustness is correlated with the former. Considering the proposed importance of gene regulation in speciation, parameters governing a transcription factor’s robustness to mutation may have significant influence on a cell or organism’s capacity to evolve.

Effect of caldesmon mutations in the development of zebrafish embryos

“…3B). This is consistent with a dysfunctional protein product in the case where a putative negative feedback loop regulates gene expression [21].…”

The Parameter-Fitness Landscape of lexA Autoregulation in Escherichia coli

“…The ranking of the strains in terms of the expected values for k is as follows: ΔlexA < lexA cons11 < lexA wt ∼ lexA cons06 < lexA 2L2R < lexA 0 . Of note, the double-operator configuration of the wt promoter is speculated to facilitate positive cooperative binding interactions between LexA dimers ( 11 , 20 , 22 , 23 , 28 ). Therefore, we selected the cons06 construct for strain construction for the additional reason that its degree of LexA repression was similar to that seen with the wt promoter and yet it contains only a single operator, leading to our reasoning that a direct comparison of lexA cons06 to lexA wt would provide insight into the importance of the double-operator configuration (see Discussion).…”

“…Although no formal biochemical analysis of interdimer cooperativity using purified components has been performed to our knowledge, our data show that the double-operator configuration has a negligible effect on transcriptional regulation compared to the single-operator configuration. Thus, the physiological role of the double-operator configuration, at the lexA promoter, remains unclear despite repeated speculation in the literature concerning cooperative binding (11,20,22,23,28). Of note, other SOS genes also contain multiple operators, such as recN (38) and the plasmid-borne colicin genes (39), but most SOS gene promoters contain a single operator.…”

“…Modeling of cooperative binding of the TF in NAR predicts not only faster shutoff ( 7 ) but also a decrease in the input dynamic range ( 8 ). It has also been suggested that cooperative binding can promote “mutational robustness” and can potentially foster TF evolution by buffering against the fitness effects of deleterious TF gene mutations ( 20 ). In our analysis of the lexA promoter, however, we observed no evidence of interdimer cooperativity in the mode of repression.…”

“…1B , “α”), was examined in the SOS system using LexA variants with a range of autoproteolysis rates. Those studies showed that higher self-cleavage rates resulted in lower steady-state LexA levels and greater amounts of SOS activation ( 19 , 20 ). The second parameter, β, or “promoter strength,” is the rate of mRNA synthesis in the unrepressed state of the promoter and dictates the maximum rate of synthesis of repressor protein ( Fig.…”