Methane-oxidizing bacterial communities: A novel source of bioactive chemical diversity

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 DESCRIPTION (provided by applicant): Candidate and Environment During graduate school in Dr. Matthew Bogyo's lab at Stanford University, I synthesized and applied chemical probes to both examine the activation mechanism of a toxin secreted by Clostridium difficile, a major hospital-acquired pathogen, and to understand how host cell death is triggered by Salmonella infection. I subsequently joined Dr. Mary Lidstrom's lab at the University of Washington for postdoctoral training in bacterial genetics and physiology, where I recently developed genetic tools for methane-oxidizing bacteria that have enabled both metabolic engineering and new physiological studies in these organisms. My long-term career goal is to establish a successful research program focused on leveraging biological context to understand the regulation and function of bacterially-produced secondary metabolites. My objective using this approach is to discover novel bioactive compounds with therapeutic potential, such as antibiotics, that will be used in the clinic. My scientific background at the interface of chemistry and bacterial genetics places me in a good position to accomplish this goal. However, I have not yet specifically worked on determining the function and structure of microbial secondary metabolites. Therefore, my immediate career goal is to obtain training enabled by the K99/R00 award in secondary metabolite discovery and characterization using a model methane-oxidizing bacterial community as a novel source of bioactive chemical diversity in order to transition to an independent faculty position. I have an excellent mentoring team to help me achieve these goals. At the UW I will be co-mentored by Dr. Mary Lidstrom, a distinguished bacterial physiologist and geneticist with expertise in bacteria that grow on one-carbon compounds, and Dr. Peter Greenberg, an expert and pioneer in the fields of quorum sensing and related forms of bacterial chemical communication. I will also receive guidance on secondary metabolite isolation and structural elucidation from renowned natural product chemist Dr. Jon Clardy of Harvard Medical School, and will learn to detect these compounds directly on agar surfaces using microbial imaging mass spectrometry at the University of California, San Diego in the lab of Pieter Dorrestein, the pioneer of the technique. I will also supplement this training by attending a course on microbial secondary metabolites. Furthermore, I will take advantage of the excellent academic environment at the UW to help me achieve my research and career goals. This will include using state-of-the-art core facilities for mass spectrometry and genomics, as well attending seminars, workshops, and courses on professional and career development offered by various organizations on campus. I will also receive one-on-one guidance on academic careers from mentors on my advisory committee. Together, these experiences will ensure that I will obtain the scientific experience and professional training necessary to successfully establish an independent research group studying the regulation and biological function of bacterially-produced secondary metabolites. Research Most therapeutics used today are derived from natural products, including microbially-produced secondary metabolites. However, the pipeline of these compounds has been diminishing over time, particularly in the case of novel antibiotic scaffolds. New sources of biosynthetic chemical diversity are therefore needed. Modern sequencing efforts have revealed large numbers of biosynthetic gene clusters (BGCs) in the genomes of bacteria not traditionally used for secondary metabolite discovery. However, in many cases these BGCs are not expressed at high levels in the laboratory, and the function of their products is unknown. Many diffusible secondary metabolites have evolved to mediate interactions between co-evolved species in the environment. Therefore, in order to activate and characterize the biological function of novel BGCs it is important to add biological context. The research proposed here will use a model methane-oxidizing bacterial community as a novel source of bioactive secondary metabolites. In this community methane-oxidizing bacteria support bacteria that cannot oxidize methane themselves, and the genome sequences of community isolates contain hundreds of predicted novel BGCs. Preliminary screening of community isolates alone and in pairwise interaction assays has already revealed multiple sources of antibacterial activity. The results of this work will: (1) use intra- and interspecies interactions in a metabolically-linked bacterial community to activate and characterize novel bioactive secondary metabolites, (2) determine the structure and function of a novel class of antibiotic, and (3) provide chemical probes for future studies examining how natural product-mediated interactions influence bacterial community composition, structure, and metabolic function.