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A Network Biology Approach to Antibiotic Action and Bacterial Defense Mechanisms

Research Summary

James J. Collins works in synthetic biology and systems biology, with a particular focus on using network biology approaches to study antibiotic action, bacterial defense mechanisms, and the emergence of resistance. His lab is directed toward enhancing our existing antibiotic arsenal and developing more effective means to treat resistant bacterial infections.

Our lab works in synthetic biology and systems biology, with a particular focus on using network biology approaches to study antibiotic action, bacterial defense mechanisms, and the emergence of resistance. Our goal is to enhance our existing antibiotic arsenal and to develop more effective means to treat resistant bacterial infections.

With the alarming spread of antibiotic-resistant bacterial strains, a better understanding of the specific sequences of events leading to cell death from the wide range of bactericidal antibiotics is needed for future antibacterial drug development. To further our understanding of how bacteria respond and defend themselves against antibiotics, we have developed reverse-engineering methods that enable the construction of quantitative models of gene regulatory networks, and we have shown that these models can be used to identify targets and mediators of drug treatments.

Figure 1: Antibiotic-induced bacterial cell death...

Using these network biology approaches, we discovered that major classes of bactericidal antibiotics (e.g., quinolones, β-lactams, aminoglycosides), regardless of drug-target interaction, induce a common oxidative damage cellular death pathway. Specifically, we showed that there is a common mechanism of cellular death in Gram-negative and Gram-positive bacteria underlying major classes of bactericidal antibiotics, whereby harmful reactive oxygen species (ROS) are formed as a function of drug-induced disruptions to cellular metabolism and respiration. ROS can be extremely toxic and will readily damage membrane lipids, proteins, and DNA, and we demonstrated that antibiotic-induced oxidative stress contributes to the killing efficacy of these lethal drugs.

Antibacterial drug design has focused on blocking essential cellular functions. This has yielded significant advances in antibacterial therapy; however, the ever-increasing prevalence of antibiotic-resistant strains has made it critical that we develop novel, more effective means of killing bacteria. We showed that bactericidal antibiotics could be potentiated by targeting bacterial systems that elevate endogenous ROS levels or remediate oxidative damage, including the DNA damage response, opening up new means to enhance current antimicrobial therapies. We are building on these efforts and using our systems biology approaches, in conjunction with transcriptional, metabolomic, and proteomic profiling, to gain additional insights into pathways and networks involved in the common oxidative damage cell death mechanism, and to identify triggers for different classes of bactericidal antibiotics.

We are also exploring the mechanistic implications of the common oxidative stress cellular pathway on the emergence of antibiotic resistance. As is well known, antibiotic resistance arises through mechanisms such as selection of naturally occurring resistant mutants and horizontal gene transfer. We recently showed that sublethal levels of bactericidal antibiotics induce mutagenesis, resulting in heterogeneous increases in the minimum inhibitory concentration of a range of antibiotics. This increase in mutagenesis correlates with an increase in ROS and can lead to mutant strains that are sensitive to the applied antibiotic but resistant to other antibiotics. This work establishes a radical-based molecular mechanism, whereby sublethal levels of antibiotics can lead to multidrug resistance, which has implications for the widespread use and misuse of antibiotics.

Additionally, we are using systems approaches to study bacterial population dynamics and communal interactions underlying the development of antibiotic resistance. In a recent study, we discovered that under antibiotic stress, a few spontaneous drug-resistant mutants will endure a fitness cost to produce and share among the population the metabolite indole, thus shielding the less resistant isolates from antibiotic insult. This altruism allows weaker constituents to survive and concurrently explore the space of beneficial mutations. This work establishes a population-based resistance mechanism and indicates that deeper explorations into the cooperative strategies utilized by bacteria may prove critical for the rational design of effective antibacterial therapies for treating resistant infections.

Our lab is also particularly interested in developing and implementing clinically viable means for eradicating bacterial persisters, a subpopulation of quasi-dormant cells that are resistant to antibiotic treatment. Bacterial persisters are implicated in chronic and recurrent infections and play a critical role in biofilm-related infections. We showed, using network biology approaches, that specific metabolic stimuli (e.g., sugars) enable the killing of Gram-negative and Gram-positive persisters with aminoglycosides. We demonstrated that this approach could be used to treat bacterial biofilms (which are highly resistant to antimicrobial treatments and hinder medical implants), as well as improve the treatment of chronic urinary tract infections. These developments have the potential to enhance the treatment of persistent infections in industrialized countries as well as the developing world. We are currently using systems approaches to develop additional means for eradicating persistent infections, as well as to gain insight into the mechanisms underlying persister formation.

We are also actively engaged in synthetic biology, which is an emerging field bringing together engineers and biologists to design and construct biological circuits out of proteins, genes, and other bits of DNA, and to use these circuits to rewire and reprogram organisms. In the context of synthetic biology, we have created genetic toggle switches, RNA switches, genetic counters, genetic timers, kill switches for microbes, genetic switchboards for metabolic engineering, engineered bacteriophage to combat bacterial infections, programmable cells, and tunable mammalian genetic switches. We have also developed integrated computational-experimental platforms to expand the synthetic biology toolbox and "fast-track" design efforts in the field. Our work in synthetic biology has enabled a number of biomedical applications, including in vivo biosensing, antibiotic potentiation, biofilm eradication, drug delivery and production, microbiome reengineering, and efficient stem cell reprogramming and differentiation.

In one of our current synthetic biology projects, we are engineering the probiotic strain Lactobacillus gasseri to detect Vibrio cholerae in the human intestine and respond by producing multiple antimicrobial peptides that will kill V. cholerae and prevent progression to diarrheal disease. We are generating and optimizing a synthetic circuit in L. gasseri that consists of four modules: two sensory modules that detect V. cholerae, a genetic logic gate that monitors the sensory modules for simultaneous activation, and an output module that synthesizes and secretes bacteriocins with anti–V. cholerae activity. If proven to be safe and effective, engineered probiotic strains could eventually be provided to populations in cholera endemic regions as an inexpensive lyophilized powder that could be mixed with food or water and periodically ingested to provide protection against cholera.

Grants from the National Institutes of Health, the Defense Advanced Research Projects Agency (DARPA), the Office of Naval Research (ONR), and the Bill and Melinda Gates Foundation provided partial support for these projects.

As of November 05, 2012

Scientist Profile

Massachusetts Institute of Technology
Bioengineering, Microbiology