Microbial communities and the interactions that comprise them have impacts that reach far beyond the microscopic. From agriculture to biogeochemical cycling, microbial communities play a key role in processes that sustain life on Earth. A microbe may interact with a neighboring organism in a number of ways that range from the mutualistic to the antagonistic. While the complexity of these interactions makes untangling them a challenge, homing in on one piece of the puzzle allows us to begin to understand microbial communities as a whole. A key process that sustains communities is the sharing of nutrients. The study of corrinoids, the vitamin B12 family of cofactors, has been proposed as a model for studying nutrient sharing interactions in microbial communities. Corrinoids provide a lens with which to view nutrient sharing interactions at many scales. In this dissertation, I use corrinoid biology to study a mechanism for sensing and responding to corrinoids at the molecular scale and to probe the trade-off between two methionine synthases at the organismal scale. In the first chapter I position the study of corrinoids as a model shared nutrient by reviewing corrinoid biology at the molecular, organismal, and community scales. I review both what is known and describe outstanding questions at each scale. This provides a comprehensive look at the state of the field of corrinoid biology.
In the second chapter I dissect the regulatory mechanisms of several corrinoid riboswitches and present the first corrinoid riboswitch known to activate gene expression. Riboswitches are the dominant method of corrinoid-based gene regulation used by bacteria. They rely on two functional domains, the aptamer domain responsible for ligand binding and the expression platform which contains structures responsible for regulating gene expression. Corrinoid riboswitches were known to rely on a kissing loop interaction for communication between these two domains, but the structural changes in the expression platform conferred by ligand binding by the aptamer domain were unknown. I used a fluorescent reporter to uncover the alternative structures responsible for gene regulation in a repressing and novel activating corrinoid riboswitch. Finally, I demonstrated our understanding of the regulatory mechanisms by engineering several synthetic activating corrinoid riboswitches.
In the third chapter I examine the effects on fitness of bacterial strains expressing either the corrinoid-independent or corrinoid-dependent methionine synthase. Of the two enzymes, the corrinoid-dependent methionine synthase, MetH, is the more efficient with a 50-fold higher turnover rate. However, the corrinoid-independent methionine synthase, MetE, does not rely on corrinoids which relatively few bacteria are predicted to produce. It is unknown whether expressing the more efficient enzyme, MetH, would confer a fitness advantage over relying on MetE for methionine synthesis in the presence of corrinoids. I competed Escherichia coli strains expressing either MetE or MetH in a variety of conditions and found that in most conditions, the MetE-expressing strain comprised the majority of the coculture. These results are in contrast to what is found in the literature about the susceptibility of MetE to certain stress conditions.
Together, this work demonstrates the breadth of study facilitated by corrinoids as a model nutrient. At the molecular scale, I presented novel insights about the mechanisms of regulation by corrinoid riboswitches, one of the most widespread riboswitches among bacteria. At the organismal scale, I explored the trade-off between a highly efficient methionine synthase and a methionine synthase that is unrestricted by a reliance on cofactor that is costly to produce. Through our increased understanding of corrinoid biology we increase our understanding of microbial interactions and their effects on important global processes.