Genome analysis of dark-adapted variants identifies the phosphatase gene <i>phsP</i> involved in the regulation of photosynthetic and dark-heterotrophic growth in the cyanobacterium <i>Leptolyngbya boryana</i>

The prevalence of parasitic plants suggests frequent evolution of photosynthetic capacity loss in the natural environments. However, no studies have observed such evolutionary events as the loss of photosynthetic capacity. Herein, we report mutations that lead to loss or decrease in the photosynthetic growth capacity of dark-adapted variants of the cyanobacterium Leptolyngbya boryana, which can grow heterotrophically even in the dark. We isolated 28 dark-adapted variants by culturing L. boryana on agar plates containing glucose and maintained them under dark-heterotrophic conditions for 7-49 months by inoculating every 10-14 days. All variants showed significantly faster dark-heterotrophic growth than the parental strains, accompanied by the loss of photosynthetic growth capacity in 15 variants. Genome resequencing revealed that 19 of the 28 variants carried various mutations in a common single gene (LBWT_21500) encoding PP2C-type serine phosphatase. Characterization of an LBWT_21500 knockout mutant revealed that the deletion of LBWT_21500 caused a trade-off between faster dark-heterotrophic growth and slower photosynthetic growth, suggesting that the mutations in LBWT_21500 are responsible for the phenotype of 8 of the 19 variants, while other additional mutations caused the loss of photosynthetic growth capacity in the other 11 variants. Transcriptomic analysis suggested that the phosphatase is involved in the global transcriptional regulatory system that optimizes photosynthetic and dark-heterotrophic metabolism using modules of the partner switching system. We proposed the name LBWT_21500 as phototrophic-heterotrophic switching phosphatase. Mutations in global transcriptional regulatory systems may serve as one of the evolutionary steps leading to the loss of photosynthetic capacity.