Our lab works on two main areas:
- Highly-conserved yet unexplored genes in bacteria (as a resource for improving bacterial engineering and vaccine design)
- Cloning and transfer of large gene systems in bacteria (to study their evolution and application in synthetic biology and cellular engineering across species)
Unexplored genes
The genomics revolution has allowed us to sequence and decode virtually all known bacterial genomes. This has allowed us to identify a certain category of genes that are highly-conserved across bacterial species yet are unexplored and remain totally unstudied. Nothing is known about the role of these genes in bacterial biology. We believe these genes represent an untapped resource of gene function that would be beneficial to bacterial engineering and help us learn about conserved gene mechanisms in different bacteria. We target these unexplored regions of the bacterial genome for study. We have found a variety of conserved phenotypes associated with these genes in Gram negative bacteria (mostly starting off in Salmonella but branching out to other species as well). These discoveries establish new tools for bacterial engineering, synthetic biology, and vaccine design.
Cloning and transfer of large gene systems
Using techniques termed VEX-Capture and FRT-Capture, we are able to conveniently clone large genomic segments in bacteria (40-100+ Kb) and easily transfer these segments to new bacterial recipients. We have targeted large contiguous gene systems for analysis using this approach. We cloned the entire SPI-1 and SPI-2 type three secretion systems from Salmonella enterica and have studied their expression and function in other Gram negative recipients. We have also cloned the entire pdu/cob/cbi gene system from Salmonella enterica (which functions to form a protein-based organelle called a microcompartment or MCP), and we have shown that this system is functional across different bacteria. These studies open new doors to functional applications in bacteria and to new avenues of synthetic biology.