Employing synthetic biology to expand antibiotic discovery

Antimicrobial-resistant (AMR) bacterial pathogens are a continually growing threat as our methods for combating these infections continue to be overcome by the evolution of resistance mechanisms. Recent therapeutic methods have not staved off the concern of AMR infections, so continued research focuses on new ways of identifying small molecules to treat AMR pathogens. While chemical modification of existing antibiotics is possible, there has been rapid development of resistance by pathogens that were initially susceptible to these compounds. Synthetic biology is becoming a key strategy in trying to predict and induce novel, natural antibiotics. Advances in cloning and mutagenesis techniques applied through a synthetic biology lens can help characterize the native regulation of antibiotic biosynthetic gene clusters (BGCs) to identify potential modifications leading to more potent antibiotic activity. Additionally, many cryptic antibiotic BGCs are derived from non-ribosomal peptide synthase (NRPS) and polyketide synthase (PKS) biosynthetic pathways; complex, clustered genetic sequences that give rise to amino acid-derived natural products. Synthetic biology can be applied to modify and metabolically engineer these enzyme-based systems to promote rapid and sustainable production of natural products and their variants. This review will focus on recent advances related to synthetic biology as applied to genetic pathway characterization and identification of antibiotics from naturally occurring BGCs. Specifically, we will summarize recent efforts to characterize BGCs via general genomic mutagenesis, endogenous gene expression, and heterologous gene expression.

Profiling the metabolic signals involved in chemical communication between microbes using imaging mass spectrometry

The ability of microbes to secrete bioactive chemical signals into their environment has been known for over a century. However, it is only in the last decade that imaging mass spectrometry has provided us with the ability to directly visualize the spatial distributions of these microbial metabolites. This technology involves collecting mass spectra from multiple discrete locations across a biological sample, yielding chemical ‘maps’ that simultaneously reveal the distributions of hundreds of metabolites in two dimensions. Advances in microbial imaging mass spectrometry summarized here have included the identification of novel strain- or coculture-specific compounds, the visualization of biotransformation events (where one metabolite is converted into another by a neighboring microbe), and the implementation of a method to reconstruct the 3D subsurface distributions of metabolites, among others. Here we review the recent literature and discuss how imaging mass spectrometry has spurred novel insights regarding the chemical consequences of microbial interactions.

Yersinia pestis activates both IL-1β and IL-1 receptor antagonist to modulate lung inflammation during pneumonic plague

Pneumonic plague is the most rapid and lethal form of Yersinia pestis infection. Increasing evidence suggests that Y. pestis employs multiple levels of innate immune evasion and/or suppression to produce an early “pre-inflammatory” phase of pulmonary infection, after which the disease is highly inflammatory in the lung and 100% fatal. In this study, we show that IL-1β/IL-18 cytokine activation occurs early after bacteria enter the lung, and this activation eventually contributes to pulmonary inflammation and pathology during the later stages of infection. However, the inflammatory effects of IL-1β/IL-1-receptor ligation are not observed during this first stage of pneumonic plague. We show that Y. pestis also activates the induction of IL-1 receptor antagonist (IL-1RA), and this activation likely contributes to the ability of Y. pestis to establish the initial pre-inflammatory phase of disease.

Inhalation of respiratory droplets containing Yersinia pestis results in a rapidly developing and lethal pneumonia. Interestingly, early interactions between Y. pestis and host cells in the lung contribute to significant immune evasion, but also ultimately result in severe innate immune activation. Our results demonstrate that Y. pestis activates pro-inflammatory cytokines IL-1β and IL-18 in the lung early during infection. However, there is very little early pulmonary inflammation while Y. pestis continues to multiply in the lung compartment. We show that the host protein IL-1RA is activated concurrently with IL-1β, attenuating early immune activation by this cytokine. We propose that this allows the organism to replicate to high titers, eventually triggering a vigorous inflammatory response and facilitating aerosol transmission. Therefore, evaluating early host activation of IL-1RA by Y. pestis may provide therapeutic targets against pneumonic plague.

Early host cell targets of Yersinia pestis during primary pneumonic plague

Inhalation of Yersinia pestis causes primary pneumonic plague, a highly lethal syndrome with mortality rates approaching 100%. Pneumonic plague progression is biphasic, with an initial pre-inflammatory phase facilitating bacterial growth in the absence of host inflammation, followed by a pro-inflammatory phase marked by extensive neutrophil influx, an inflammatory cytokine storm, and severe tissue destruction. Using a FRET-based probe to quantitate injection of effector proteins by the Y. pestis type III secretion system, we show that these bacteria target alveolar macrophages early during infection of mice, followed by a switch in host cell preference to neutrophils. We also demonstrate that neutrophil influx is unable to limit bacterial growth in the lung and is ultimately responsible for the severe inflammation during the lethal pro-inflammatory phase.

Inhalation of the bacterium Yersinia pestis results in primary pneumonic plague, a severe necrotizing pneumonia with mortality rates approaching 100% in the absence of timely antibiotic administration. Despite the notoriety of Y. pestis as a potential biological weapon and its well-established pandemic potential, very little is known regarding early host-pathogen interactions that lead to the progression of pulmonary infection. Y. pestis harbors a type III secretion system (T3SS) for delivery of Yersinia outer protein (Yop) effectors into host cells, an early and essential step in pathogenesis. In the work presented here, we identify the host cell targets of Y. pestis Yop secretion in the lung. We show that Y. pestis initially targets alveolar macrophages, followed by a shift in host cell preference to neutrophils. Through cellular depletion studies, we demonstrate that Y. pestis is highly resistant to macrophage- and neutrophil-mediated clearance, and that the accumulation of neutrophils in the lung is responsible for the severe necrotizing pneumonia that develops during the pro-inflammatory phase of pneumonic plague.