Polyphosphate acts as an architectural regulator of carbon fixation and nucleoid structure in cyanobacteria

ABSTRACT Polyphosphate (polyP) is a conserved inorganic polymer traditionally viewed as a stress-induced phosphate and energy reserve. In cyanobacteria, however, polyP granules are constitutively present and are frequently observed in close proximity to carboxysomes, the bacterial microcompartments that mediate CO 2 fixation. Here, we show that polyP functions as a spatially organized regulator of the photosynthetic cytoplasm in Synechococcus elongatus . PolyP granules localize to the nucleoid and are periodically arranged along the cell axis, independent of the McdAB carboxysome positioning system. Despite this independence, polyP and carboxysomes associate non-randomly, and this association is enhanced when active carboxysome positioning by the McdAB system is disrupted. Loss of polyP synthesis leads to nucleoid expansion, an increased number of smaller carboxysomes with high mobility, and severe defects in growth under ambient CO 2 . Perturbation of polyP turnover further reveals structural connections to both carboxysomes and thylakoid membranes. Together, these findings identify polyP as an architectural integrator that couples chromosome organization, metabolic compartmentalization, and photosynthetic fitness. IMPORTANCE Polyphosphate (polyP) is a ubiquitous storage polymer found across all three domains of life. In bacteria, polyP is involved in virulence, energy metabolism, DNA structure, and stress. Here, we investigate the physical and functional relationships between polyP and the carboxysome—a carbon-fixing organelle that encapsulates the most abundant enzyme on Earth and is responsible for a significant amount of atmospheric CO 2 sequestration. We discover that polyP is important for proper carboxysome assembly and organization in the cell and is also required for robust cell growth under ambient CO 2 conditions. As carboxysomes are one class of the broader group of bacterial microcompartments, these findings have broader implications for polyP in the function and organization of the bacterial cytoplasm.