Research Interests

Optogenetics in near-infrared, Listeria-plant biofilms, and Listerial bactodrones

The Gomelsky Lab has several foci of interest, including Optogenetics in near-infrared, Listeria-plant biofilms and Listerial bactodrones as cancer therapy.

Optogenetics in near-infrared

Light within the near-infrared optical window (~670-900 nm) penetrates mammalian tissues much deeper than visible light; therefore, it can activate engineered cells located under the skin or skull (Fig. C). To "teach" mammalian cells how to respond to the near-infrared light, we are employing bacteriophytochromes, a class of natural photoreceptors (Fig. A&B). We have deciphered principles of engineering homodimeric bacteriophytochromes to guide construction of protein chimeras, comprising the bacteriophytochrome photosensory module and the desired output module. One example is an engineered chimeric near-infrared light-activated adenylate cyclase (Fig. B). It can increase insulin production in mammalian cells or suppress cAMP-dependent neuronal waves in mice (Fig. B&C). We intend to optimize the near-infrared light-activated adenylate cyclase for optogenetic applications in diabetes type I and in neuronal regulation. We are also engineering new homodimeric bacteriophytochrome enzymes to control activities of mammalian cells noninvasively, via externally localized sources of near-infrared light.

Collage of scientific images including molecular structures, spectral graphs, images of mice, and diagrams of cellular signaling pathways.

Listeria-plant biofilms

Fresh produce contaminated with the foodborne pathogen, Listeria monocytogenes, has caused major listeriosis outbreaks in the USA in the past decades. The 2011 cantaloupe-associated outbreak was the highest mortality food-poisoning incident in the USA history in almost a century. Despite the growing prevalence of fruits and vegetables as sources of listerial contamination, we know little about how Listeria colonizes them, which hinders our ability to prevent fresh produce contamination with Listeria.

We discovered that Listeria synthesizes a novel exopolysaccharide (EPS), {4)-β-ManpNAc-(1-4)-[α-Galp-(1-6)]-β-ManpNAc-(1-}, where ManpNAc is N-acetylmannosamine and Galp is galactose, and hypothesized that it is involved in listerial growth and survival on fresh produce. The pss operon contains the genes for EPS biosynthesis. The Pss synthetic machinery is activated by the second messenger, c-di-GMP (Fig. A). Figs B&C show that the EPS is synthesized by Listeria on plant surfaces and increases colonization. In this project we want to understand regulation of Listeria biofilm formation on plant surfaces, to characterize the role of the EPS-biofilms in listerial colonization and long-term survival on fresh produce, and to devise the means of preventing biofilm formation. For example, one natural, plant-derived compound blocks listerial colonization (Fig. C).

Schematic diagram, microorganism images, and photos of fruit and vegetable samples.

Listerial bactodrones as cancer therapy

The attenuated strains of Listeria monocytogenes injected intraperitonially are phagocytosed by myeloid-derived suppressor cells (MDSCs), which deliver them to primary tumors and metastases (Fig. A, B). In the immune suppressive tumor microenvironment, Listeria propagates and spreads into tumor cells. We are employing the tools of synthetic microbiology to turn Listeria into remotely controlled bacterial drones, bactodrones, that can deliver various therapeutic payloads to tumor and immune cells and release them upon activation (Figs. A, C, D). Our goal is to engineer a fleet of listerial bactodrones to effectively target various cancers.

Illustration describing different aspects and mechanisms of Lm-based therapy, including genetic engineering, cellular interactions, and immune system targeting.

Metabolic and cellular engineering

Most bacteria are believed to divide generating two identical daughter cells. However, a simple polar-localized signaling system (red dot) can convert bacterial cell division into asymmetric division. The ability to generate daughter cells that have different fates and functions (grey with a red pole and green without a pole) is of significant interest in microbial biotechnology, because it offers a way to separate cell growth and product synthesis.

A diagram of genetic circuits and bacterial cell changes over time, with fluorescent markers shown in micrographs.

Cyclic dimeric GMP, c-di-GMP, is a broadly distributed second messenger that controls biofilm formation, motility and virulence in diverse bacteria. We engineered optogenetic systems to manipulate bacterial behavior by increasing or lowering c-di-GMP levels with red and blue light.

Collage of petri dishes with bacterial cultures and a diagram of molecular processes involving "PAS," "GAF," and other domains affecting "c-di-GMP."

Hydrogen is a clean fuel. Anoxygenic phototrophic bacteria can utilize solar energy and organic waste products to synthesize large quantities of hydrogen. We used metabolic maps, flux balance analysis and global gene regulatory systems of a model bacterium Rhodobacter sphaeroides to engineer a high hydrogen producing strain.