Transposon insertion sequencing methods such as Tn-seq revolutionized microbiology by allowing the identification of genomic loci that are critical for viability in a specific environment on a genome-wide scale. While powerful, transposon insertion sequencing suffers from limited reproducibility when different analysis methods are compared. From the perspective of population biology, this may be explained by changes in mutant frequency due to chance (drift) rather than differential fitness (selection). Here, we develop a mathematical model of the population biology of transposon insertion sequencing experiments, i.e. the changes in size and composition of the transposon-mutagenized population during the experiment. We use this model to investigate mutagenesis, the growth of the mutant library, and its passage through bottlenecks. Specifically, we study how these processes can lead to extinction of individual mutants depending on their fitness and the distribution of fitness effects (DFE) of the entire mutant population. We find that in typical in vitro experiments few mutants with high fitness go extinct. However, bottlenecks of a size that is common in animal infection models lead to so much random extinction that a large number of viable mutants would be misclassified. While mutants with low fitness are more likely to be lost during the experiment, mutants with intermediate fitness are expected to be much more abundant and can constitute a large proportion of detected hits, i.e. false positives. Thus, incorporating the DFEs of randomly generated mutations in the analysis may improve the reproducibility of transposon insertion experiments, especially when strong bottlenecks are encountered.
Many bacteria mediate important life-style decisions by varying levels of the second messenger c-di-GMP. Behavioral transitions result from the coordination of complex cellular processes such as motility, surface adherence or the production of virulence factors and toxins. While the regulatory mechanisms responsible for these processes have been elucidated in some cases, the global pleiotropic effects of c-di-GMP are poorly understood, primarily because c-di-GMP networks are inherently complex in most bacteria. Moreover, the quantitative relationships between cellular c-di-GMP levels and c-di-GMP dependent phenotypes are largely unknown. Here, we dissect the c-di-GMP network of Caulobacter crescentus to establish a global and quantitative view of c-di-GMP dependent processes in this organism. A genetic approach that gradually reduced the number of diguanylate cyclases identified novel c-di-GMP dependent cellular processes and unraveled c-di-GMP as an essential component of C. crescentus cell polarity and its bimodal life cycle. By varying cellular c-di-GMP concentrations, we determined dose response curves for individual c-di-GMP-dependent processes. Relating these values to c-di-GMP levels modeled for single cells progressing through the cell cycle sets a quantitative frame for the successive activation of c-di-GMP dependent processes during the C. crescentus life cycle. By reconstructing a simplified c-di-GMP network in a strain devoid of c-di-GMP we defined the minimal requirements for the oscillation of c-di-GMP levels during the C. crescentus cell cycle. Finally, we show that although all c-di-GMP dependent cellular processes were qualitatively restored by artificially adjusting c-di-GMP levels with a heterologous diguanylate cyclase, much higher levels of the second messenger are required under these conditions as compared to the contribution of homologous c-di-GMP metabolizing enzymes. These experiments suggest that a common c-di-GMP pool cannot fully explain spatiotemporal regulation by c-di-GMP in C. crescentus and that individual enzymes preferentially regulate specific phenotypes during the cell cycle.
This chapter summarizes the current knowledge of cyclic di-GMP (c-di-GMP)-mediated control in Caulobacter crescentus. Several members of this family dynamically position to distinct polar sites during the C. crescentus cell cycle, where they contribute to the temporal and spatial regulation of pole morphogenesis and cell cycle progression. The finding that C. crescentus pole development is regulated by c-di-GMP raised several important questions. Recent in vitro and in vivo studies provided convincing evidence that DivK acts as an allosteric regulator of PleC kinase activity. The primary function of the complex regulatory mechanism responsible for cell cycle-dependent PleD phosphorylation is to limit PleD diguanylate cyclase (DGC) activity to the sessile stalked (ST) cell and exclude it from the motile swarmer (SW) cell. The wide range of different cellular processes and molecular targets that are regulated by c-di-GMP reflects its remarkable versatility as a signaling device. Recently, cell cycle control and regulated proteolysis have been added to this growing list of cellular functions controlled by c-di-GMP. The C. crescentus cell cycle is controlled by a cascade of four master regulators that are activated sequentially and in a hierarchical manner. The molecular and cellular mechanisms that underlie the characteristic behavior of Caulobacter cells and its regulation by c-di-GMP might thus be of general relevance for the understanding of processes involved in the motile-sessile transition in many other bacteria.
Abstract Improved predictions of antibiotic efficacy can inform the development of new antibiotics and extend the effectiveness of existing drugs and thereby help combatting the global antibiotic resistance crisis. We describe a computational model (COMBAT-COmputational Model of Bacterial Antibiotic Target-binding) that leverages accessible biochemical parameters to quantitatively predict the antimicrobial effects of antibiotics based on their drug-target affinity. We validate our model with MICs of a range of quinolone antibiotics in clinical isolates demonstrating that antibiotic efficacy can be predicted from drug-target binding (R2>0.9). Conversely, we experimentally demonstrate that changes in drug-target binding can be predicted from antibiotic efficacy with 92-94% accuracy by exposing bacteria overexpressing target molecules to ciprofloxacin. To test the generality of COMBAT, we predict target molecule occupancy at MIC from antimicrobial action with 90% accuracy for a different antibiotic class, the beta-lactam ampicillin. Finally, we predict antibiotic concentrations that can select for resistance due to novel resistance mutations. COMBAT provides a framework to inform optimal antibiotic dose levels that maximize efficacy and minimize the rise of resistant mutants.
Abstract Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and commensal E. coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC’s but not to K-12’s growth in vitro, suggesting that gene acquisition during EHEC evolution has heightened the pathogen’s reliance on certain metabolic processes that are dispensable for K-12. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Numerous mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, including tatABC, oxyR, envC, acrAB , and cvpA , promote EHEC resistance to host-derived stresses encountered in vivo. cvpA , which is also required for intestinal growth of several other enteric pathogens, proved to be required for EHEC, Vibrio cholerae and Vibrio parahaemolyticus resistance to the bile salt deoxycholate. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine. Author Summary Enterohemorrhagic E. coli (EHEC) are important food-borne pathogens that infect the colon. We created a highly saturated EHEC transposon library and used transposon insertion sequencing to identify the genes required for EHEC growth in vitro and in vivo in the infant rabbit colon. We found that there is a large infection bottleneck in the rabbit model of intestinal colonization, and refined two analytic approaches to facilitate rigorous identification of new EHEC genes that promote fitness in vivo. Besides the known type III secretion system, more than 200 additional genes were found to contribute to EHEC survival and/or growth within the intestine. The requirement for some of these new in vivo fitness factors was confirmed, and their contributions to infection were investigated. This set of genes should be of considerable value for future studies elucidating the processes that enable the pathogen to proliferate in vivo and for design of new therapeutics.
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