Contextualization of the E. Coli Lsr System: Relative Orthology, Relative Qs Activity, and Emergent Behavior

Title of Document: CONTEXTUALIZATION OF THE E. COLI LSR SYSTEM: RELATIVE ORTHOLOGY, RELATIVE QS ACTIVITY, AND EMERGENT BEHAVIOR David Nathan Quan, Doctor of Philosophy, 2014 Directed By: Professor William E. Bentley Fischell Department of Bioengineering Within bacterial consortia there exist innumerable combinatorial circumstances, some of which may tip the scale toward pathogenicity, some of which may favor asymptomatic phenotypes. Indeed, the lines and intersections between commensal, pathogenic, and opportunistic bacteria are not always clean. As a foothold to mediate pathogenicity arising from consortia, many have puzzled at communication between bacteria. Primary among such considerations is quorum sensing (QS). Analogous to autocrine signaling in multicellular organisms, QS is a self-signaling process involving small molecules. Generally, QS activation is believed to have pleiotropic effects, and has been associated with numerous pathogenic phenotypes. The research herein focuses on autoinducer-2 (AI-2) based QS signaling transduced through the Lsr system. Produced by over 80 species of bacteria, AI-2 is believed to be an interspecies signaling molecule. Outside of the marine bacteria genera Vibrio and Marinomonas, the only known AI-2 based QS transduction pathway is the Lsr system. We sought to deepen the characterization of the Lsr system in contexts outside of the batch cultures in which it was originally defined. First, we interrogated E. coli K-12 W3110 Lsr system orthologs relative to the same strain’s lac system. Both systems are induced by the molecule which they import and catabolize. We searched for homologs by focusing on the gene order along a genome, as gene arrangement can bear signaling consequences for autoregulatory circuits. We found that the Lsr system signal was phylogenetically dispersed if not particularly deep, especially outside of Enterobacteriales and Pasteurellaceaes, indicating that the system has generally been conferred horizontally. This contrasts with the lac system, whose signal is strong but limited to a select group of highly related enterobacteria. We then modeled the Lsr system with ODEs, revealing bimodality in silico, bolstering preliminary experimental evidence. This bifurcated expression was seen to depend upon nongenetic heterogeneity, which we modeled as a variation of a single compound parameter, basal, representing the basal rate of AI-2 flux into the cell through a low flux pathway. Moreover, in our finite difference-agent based models, bimodal expression could not arise from spatial stochasticity alone. This lies in contrast with the canonical LuxIR QS system, which employs an intercellular positive feedback loop to activate the entire population. We examined the consequences of this contrast, by modeling both systems under conditions of colony growth using finite difference-agent based methods. We additionally investigated the confluence of Lsr signaling with chemotactic sensitivity to AI-2, which has been demonstrated in E. coli. Finally, the consequences of bimodality in interspecies interactions were assessed by posing two populations containing different Lsr systems against each other. While few natural consortia consist of only two interacting bacteria, these studies indicate that AI-2 based Lsr signaling may mediate a multitude of transitional intraspecies and interspecies bacterial dynamics, the specifics of which will vary with the context and the homologs involved. CONTEXTUALIZATION OF THE E. COLI LSR SYSTEM: RELATIVE ORTHOLOGY, RELATIVE QS ACTIVITY, AND EMERGENT BEHAVIOR By David Nathan Quan Dissertation submitted to the Faculty of the Graduate School of the University of Maryland, College Park, in partial fulfillment of the requirements for the degree of Doctor of Philosophy 2014 Advisory Committee: Professor William E. Bentley, Chair Associate Professor Michael P. Cummings Associate Professor Nam Sun Wang Associate Professor Adam Hsieh Assistant Professor Ganesh Sriram © Copyright by David Nathan Quan 2015