Overview: Our lab uses evolution as an inspiration for designing synthetic, biological systems. Particularly, we are fascinated by synergistic interactions in evolution: at a cell-cell level (symbiosis), at protein-RNA level (RNA modifications), at a protein-protein level (antibodies/epitopes) and at a protein-small molecule level (coenzyme containing enzymes). We use these observations to design synthetic approaches for answering fundamental biological questions or for developing novel translational platforms for human health. Key areas in the lab include: (i) novel synthetic methods to combat emerging zoonotic pathogens, (ii) directed endosymbiosis (an engineered, symbiotic cell within a host cell) to develop platforms for evolutionary studies and photosynthetic biosynthesis, and (iii) engineering selectivity in targeting cancers.
1. Platforms to combat emerging pathogens:
(A) Targeting RNA capping enzymes from emerging pathogenic RNA viruses: It has become imperative to develop novel therapeutics to tackle emerging zoonotic RNA and DNA viruses. In order to develop novel strategies to combat these viruses, we are targeting an essential but relatively less explored targets in viral replication, translation and propagation, i.e., viral genome encoded RNA capping enzymes. During the course of evolution, viruses evolved to have an RNA cap structure that is chemically identical to the host mRNAs; essentially viruses mimic their genomes or transcripts as host mRNAs. These viral RNA cap structures are necessary for viral replication, translation and immune evasion. We are developing synthetic biology approaches to understand the molecular details of these essential viral enzymes. Further we are using a directed evolution to target these enzymes to systematically engineer attenuated variants and study the implication of these attenuated variants on viral pathogenesis. We are also using medicinal chemistry approaches to develop novel antivirals selectively targeting viral RNA capping enzymes over human RNA capping enzymes. We are expanding these approaches to combat human and animal viruses from a point of view of being better prepared for the next viral pandemic.
(B) Antibody engineering and evolution to target emerging zoonotic pathogens: Our adaptive immune system evolves antibodies in real time to combat threats associated with invading pathogens. Inspired by how our adaptive immune system evolves antibodies, we are developing novel laboratory evolution platforms for evolving antibodies targeting emerging zoonotic pathogens. Such antibody evolution approaches are expected to provide a platform for evolving human antibodies targeting epitopes on viruses, drug resistant bacteria and cancer. Our observations could also inform vaccine design and diagnostics.
2. Directed endosymbiosis for evolutionary studies and synthetic biology:
Chloroplasts are the key photosynthetic organelles in plants and green algal cells, and thereby an integral part of the global ecosystem. Endosymbiotic theory suggests that mitochondria and chloroplasts evolved from free-living prokaryotes which entered the host cell and were retained as endosymbionts; however, there is a minimal understanding of how a free living bacteria evolved and transformed in to cell entrapped organelle. Inspired by these remarkable evolutionary observations, we engineered artificial endosymbiosis between cyanobacteria and yeast cells to generate photosynthetic yeast/cyanobacteria life-forms. Our studies focus on recapitulating various stages of chloroplast evolution including but not limited to (i) cyanobacterial endosymbiont genome minimization, (ii) engineer cyanobacterial endosymbionts to secrete photosynthetic end-products, (iii) cell cycle synchronization of the host and the endosymbiont (iv) develop strategies to facilitate protein exchange between the endosymbiont and host and (v) mutation-based evolution and selection. These studies are expected to provide molecular level insights into the transformation of free-living bacteria into entrapped organelles. Further, we plan on expanding this platform for various synthetic biology applications involving photosynthetic metabolic engineering and carbon dioxide sequestration.
Biosynthesis and Metabolic engineering using “photosynthetic yeasts”: There is a huge need to develop sustainable platforms for production of high value molecules like Taxol, Artemisinin amongst others. Several semi-synthesis platforms are being developed for this purpose. We will investigate if we can utilize our genetically tractable yeast/cyanobacteria endosymbiotic platform to synthesize these molecules using photosynthesis. Our platform couples the biosynthetic and biocatalytic potential of yeast to the photosynthetic ability of cyanobacteria; essentially the cyanobacterial endosymbionts will act as artificial chloroplasts for yeast cells. This platform will allow us harnessing light and photosynthesis to biosynthesize high value molecules like natural products, biofuels among others.
3. Engineering selectivity in targeting cancer:
We are combining our expertise in synthetic biology and synthetic chemistry to develop fundamentally novel, modular platforms to engineer selectivity in targeting cancers. We are using principles of directed evolution and biomolecule delivery platforms to engineer novel biologics that specifically target cancers where the biomarkers are well characterized.