UC San Diego

Cyanobacteria are key primary producers in the environment, models for photosynthesis and the circadian clock in the lab, and emerging biological production platforms for industry. Despite their scope of importance some of the most fundamental components of their biology are poorly understood. We know little about the functions encoded by most of their genes, and research traditionally focused on constant light has left the organisms’ physiology in day-night conditions obscure. In the studies comprising my thesis, we worked to illuminate both of these knowledge gaps in the model cyanobacterium Synechococcus elongatus PCC 7942. We employed traditional molecular biology and -omic techniques, and developed and applied a high-throughput approach for whole genome mutant screens in S. elongatus (RB-TnSeq). Chapter one introduces what is known about cyanobacterial physiology in Light-Dark Cycles (LDCs). It also describes RB-TnSeq, which is used here to elucidate gene function both generally and specifically to LDCs. Chapter two reports the characterization of cellular activities upon light transitions that facilitate survival in LDCs. Chapter three presents the development of RB-TnSeq in S. elongatus and its use for the assignment of gene importance, the development of an improved metabolic model for S. elongatus, and the implementation of screens to further our understanding of these genes'. Chapter four reports the application of RB-TnSeq to understand survival in LDCs. In it, we identified the set of genes specifically important for survival of LDCs and followed up on them. This work resulted in improved understanding for the roles of the circadian clock and nucleotide signaling in LDC survival. Chapter five concludes by synthesizing the core achievements of the dissertation and suggesting future directions. Together, these chapters explain the development of a powerful genomic approach, RB-TnSeq, and its use to illuminate the genetic unknowns in Cyanobacteria as well as the organisms’ LDC physiology. These findings will be applicable to the basic understanding of this important phylum, its industrial use, and photosynthetic organisms more generally, for which Cyanobacteria are the most tractable models.