Temperature Control of Fimbriation Circuit Switch in Uropathogenic Escherichia coli: Quantitative Analysis via Automated Model Abstraction

Uropathogenic Escherichia coli (UPEC) represent the predominant cause of urinary tract infections (UTIs). A key UPEC molecular virulence mechanism is type 1 fimbriae, whose expression is controlled by the orientation of an invertible chromosomal DNA element—the fim switch. Temperature has been shown to act as a major regulator of fim switching behavior and is overall an important indicator as well as functional feature of many urologic diseases, including UPEC host-pathogen interaction dynamics. Given this panoptic physiological role of temperature during UTI progression and notable empirical challenges to its direct in vivo studies, in silico modeling of corresponding biochemical and biophysical mechanisms essential to UPEC pathogenicity may significantly aid our understanding of the underlying disease processes. However, rigorous computational analysis of biological systems, such as fim switch temperature control circuit, has hereto presented a notoriously demanding problem due to both the substantial complexity of the gene regulatory networks involved as well as their often characteristically discrete and stochastic dynamics. To address these issues, we have developed an approach that enables automated multiscale abstraction of biological system descriptions based on reaction kinetics. Implemented as a computational tool, this method has allowed us to efficiently analyze the modular organization and behavior of the E. coli fimbriation switch circuit at different temperature settings, thus facilitating new insights into this mode of UPEC molecular virulence regulation. In particular, our results suggest that, with respect to its role in shutting down fimbriae expression, the primary function of FimB recombinase may be to effect a controlled down-regulation (rather than increase) of the ON-to-OFF fim switching rate via temperature-dependent suppression of competing dynamics mediated by recombinase FimE. Our computational analysis further implies that this down-regulation mechanism could be particularly significant inside the host environment, thus potentially contributing further understanding toward the development of novel therapeutic approaches to UPEC-caused UTIs.Author Summary: Urinary tract infections (UTIs) represent a major growing threat to global public health. With over 15 million cases a year in the United States alone, UTIs are characterized by very high recurrence/reinfection rates, particularly among women and minority groups [1]. The predominant cause of UTIs is uropathogenic Escherichia coli (UPEC) bacteria, whose wide-spread and increasing antibiotic-resistance has made the development of alternative anti-UPEC treatments progressively more important and urgent. UPEC's foremost virulence factor is hair-like surface structures called type 1 fimbriae. Thus, one such potentially promising therapeutic approach may be to manipulate bacteria's own cellular circuitry toward inducing UPEC to turn off their fimbriae expression—rendering individual microbes benign. This task requires detailed understanding of molecular mechanisms involved, which may be significantly aided by in silico modeling. However, for UPEC fimbriation control circuit and many other systems, low-level all-inclusive quantitative models inevitably become too computationally demanding to remain practical, while high-level qualitative representations frequently prove inadequate owing to the substantial organizational and behavioral complexity of biological processes involved.