Cyanobacteria are tiny photosynthetic microbial organisms responsible for producing roughly an eighth of the oxygen we breathe. Synechococcus is a model cyanobacteria, meaning the species has characteristics making it easy to study and modify. As a scientific community, we don’t know the function or purpose of many genes expressed by Synechococcus. The goal of this project is to determine the function of particular genes hypothesized to be important to the adaptive survival of Synechococcus in different environments. We are approaching this by building a start-to-finish gene characterization method, starting with computational analysis to identify genes of interest, followed by knocking out, or disabling these genes and observing the effect on the growth of the culture. On the computational side, I’m now analyzing residual gene expression, using that information to characterize gene clusters, and analyzing external data to infer genetic context. On the laboratory side, I’ve characterized the growth of the un-modified base strains and developed procedures for genetic modification. Identifying the function of Synechococcus genes allows scientists to better study the response of Synechococcus to varying environments, which is especially important in a changing climate. Increasing understanding of the molecular mechanisms of Synechococcus also opens the door to genome engineering for the production of biofuels, plastics, and other commodities, or for using Synechococcus as a tool for bioremedial carbon sequestration. Additionally, the genes of Synechococcus are similar to those in other related oceanic microbes such as Prochlorococcus, the most ubiquitous photosynthetic organism in the world. For all these reasons, Synechococcus is an important model organism, and a deeper understanding of its biology will bolster our sparse understanding of marine genomics.

Cyanobacteria are ancient single-celled photosynthetic organisms, prevalent throughout Earth's oceans. Over billions of years, cyanobacteria have evolved genes that enable them to survive across a diversity of adverse, ever-changing environmental conditions. However, researchers are faced with the problem of not understanding the role of many of these genes. This research project entails tracking down the function of some high variance genes in marine Synechococcus, an important model organism and a genus of cyanobacteria. We will test gene function by generating knockout strains in which a gene of interest is inactivated, and testing the growth of these mutant strains in various conditions. In particular, our project focuses on the importance of the flavodoxin gene, which codes for an electron transport protein that is involved in photosynthesis and is expressed in response to iron scarcity. This gene inactivation is done with a plasmid, which is a genetic structure in bacteria that can replicate itself independent of bacterial chromosomal replication, that’s enabled to knock out the flavodoxin I gene when inserted into Synechococcus cells. We insert the plasmid into our Synechococcus cells and once the DNA is taken up by the cell, we then use CRISPR technology to remove the gene. Successfully creating the flavodoxin knockout of Synechococcus establishes the procedures necessary for generating knockouts of other genes that could be expressed in similar patterns as flavodoxin. Ultimately, this research furthers our understanding of how Synechococcus’ genes allow it to adapt to various environments and contributes to ongoing research on how organisms might withstand the pressures of Earth’s ever-changing climate.