Barrick Lab :: Research

Engineering Insect Symbionts

BTK

We explore engineering endosymbionts in insects, including bees, aphids, and leafhoppers. We have created the bee microbiome toolkit (BTK) that can be used to engineer bacteria found in various insects and their gut microbiomes, as demonstrated in honey bees (Apis mellifera) and bumble bees (Bombus species). Specifically, we have engineered an induced RNAi response in a native gut bacterium, Snodgrassella alvi. Colony collapse in bees is often contributed to two factors: Varroa mites and deformed wing virus. Engineered S. alvi has been shown to kill the mites and improve bee health. This symbiont-mediated approach is helpful to protect insects that are beneficial to human health, but can this approach can also be applied to pest species to improve food security.

In aphids, we are engineering the endosymbiont Serratia symbiotica to improve protection of food crops. Aphids are known to be agricultural pests, but by engineering native bacteria, such as S. symbtiotica, we can create a natural pest control option that is insect-specific, compared to insecticides that kill both beneficial and pest insects. We are also exploring another way to use engineered symbionts in another pest insect: leafhoppers. Leafhoppers produce unique nanostructures, called brochosomes, that are super hydrophobic and have novel optical properties. Instead of changing them to be less harmful to our food crops, we want to engineer their symbionts to use them to benefit humans. We hope to create a similar toolkit as the BTK for brochosomes via proteomics to create a new way of synthesizing useful biomaterials.

Decreased survival shown in mites

Representative Publications

• Leonard et al. (2020) Science PMID: 32001655
• Leonard et al. (2018) ACS Synthetic Biol. PMID: 29608282

Funding: DARPA BRICS, DARPA AEPHID, MURI ARO

Preventing Evolutionary Failure in Synthetic Biology

Evolutionary half-lives of biological devices

Synthetic biology applies engineering principles to create living systems with predictable and useful behaviors from collections of standardized genetic parts. However, living systems – unlike mechanical devices – inevitably evolve when their DNA sequences accumulate copying errors, often resulting in "broken" cells that no longer function as they were programmed. We are addressing this challenge by better characterizing how engineered cells evolve and using this information to design DNA sequences and host cells that are more robust against unwanted evolution. This work includes: (1) the development of the Evolutionary Failure Mode (EFM) Calculator software for identifying mutational hotspots in a designed DNA sequence; (2) using experimental evolution to identify "antimutator" variants of host organisms that lead to lower-than-natural mutation rates; and (3) designing genetic circuits that kill those cells within a population that are most likely to accumulate mutations.

Resources

• Evolutionary Failure Mode (EFM) Calculator website

Representative Publications

• Jack et al. (2015) ACS Synthetic Biol. PMID:26096262
• Renda et al. (2014) Mol. Biosyst. PMID:24556867

Funding: DARPA BRICS

Dynamics of Microbial Genome Evolution

Accumulation of mutations in population Ara-1 of the LTEE over 20,000 generations of evolution

We develop the breseq computational pipeline for identifying mutations in laboratory-evolved microbial genomes from next-generation sequencing data. We have used this tool to extensively study rates of genome evolution in the 30-year Lenski long-term evolution experiment (LTEE) with E. coli. We continue to develop breseq so that it can be used for more additional applications related to strain engineering and medicine. For example, we are interested in how tracking rare variants within populations of microorganisms (such as oncoviruses) can anticipate further evolutionary trajectories and how this information might be used to better diagnose disease outcomes.

Resources

• breseq project page
• breseq code and downloads (GitHub)
• LTEE genome resources (GitHub)

• Deatherage et al. (2017) Proc. Natl. Acad. Sci. PMID: 28202733
• Tenaillon et al. (2016) Nature PMID: 27479321
• Deatherage and Barrick (2014) Methods Mol. Biol PMID:24838886
• Barrick and Lenski (2014) Nat. Rev. Genet. PMID:24166031

Funding: NIH K99/R00, NSF, NSF BEACON Center, CPRIT

Evolving and Engineering Naturally Transformable Bacteria

Naturally competent bacteria may have increased evolutionary potential because they can directly acquire new genes from their environments and incorporate them into their genomes. In addition to this possibility of a new mutational move in genotype-phenotype space (by horizontal gene transfer), these microbes provide an improved platform for studying microbial genome engineering and evolution due to the ease of reconstructing mutations and introducing new genes. We are investigating sources of genetic instability in the naturally competent bacterium Acinetobacter baylyi ADP1 and engineering a clean genome version of this strain to have reduced rates of mutations that lead to inactivation of introduced genes for synthetic biology applications. We are also using experimental evolution to test for the utility of providing foreign DNA sequences and to understand how horizontally acquired genes become domesticated after they are incorporated into a new genome. Finally, we are using ADP1 as a platform for understanding the limits of simplifying a bacterial genome by evolutionary streamlining approaches.

Representative Publication

• Suárez et al. (2020) Nucleic Acids Res. preprint
• Suárez et al. (2017) Appl. Env. Microbiol. PMID:28667117
• Renda et al. (2015) J. Bacteriol. PMID:25512307

Funding: Welch Foundation

Previous Research Projects