UC San Diego

Fixed nitrogen is a limited resource for growth in the environment and the fixation of atmospheric nitrogen is vital to nutrient cycling and growth. Cyanobacteria are a group of photosynthetic bacteria that evolved 4.5 billion years ago to harvest sunlight as energy. Cyanobacteria have since evolved a wide array of metabolic capabilities over time, including the ability to fix atmospheric nitrogen. Anabaena sp. strain PCC 7120, hereafter Anabaena, is a species of cyanobacteria that fixes atmospheric N₂ into ammonia by forming specialized nitrogen-fixing cells called heterocysts. Heterocysts form only in the absence of a source of fixed nitrogen and are evenly spaced along a filament of Anabaena cells. We studied the gene expression networks that regulate heterocyst development through deep sequencing, employing both RNA-seq on a nitrogen-deprived culture as well as ChIP-seq on key transcription factors involved in heterocyst development. Deep sequencing gave us a global view of gene expression in response to nitrogen deprivation in Anabaena. Our RNA- seq work identified new genes involved in heterocyst development, mapped operon structure and transcript length, and discovered abundant antisense transcription in the genome. In particular, we identified antisense transcription in the coding region of the gene nblA, which codes for a small peptide that triggers the proteolysis of the photosynthetic machinery in response to nutrient stress. Furthermore, we used ChIP-seq to identify the regulon of two transcription factors, HetR and DevH, in response to nitrogen deprivation. Our work on HetR, a transcription factor with known roles in regulating heterocyst development, identified many new HetR targets, including genes involved in HetR's role during nitrogen deprivation and during vegetative cell growth. Our work on DevH, a transcription factor required for forming the heterocyst-specific cell wall, also identified new DevH targets, including many genes involved in cell wall formation and transcriptional regulators. This work adds to our understanding of transcriptional networks that regulate heterocyst development in Anabaena. Furthermore, our study provides insight into gene structure and transcriptional regulation in cyanobacteria as a whole