A nuclear CobW/WW-domain factor represses the CO ₂ -concentrating mechanism in the green alga <i>Chlamydomonas reinhardtii</i>

Microalgae induce a CO₂-concentrating mechanism (CCM) to maintain photosynthesis when CO₂ is limited. Because this system consumes a substantial portion of photosynthetically generated ATP, its suppression when CO₂ levels rise is critical for energy balance, yet the underlying mechanism remains unclear. Here, we identify a nuclear repressor of the CCM in the green alga <i>Chlamydomonas reinhardtii</i>. A pull-down screen for interacting partners of the master activator CCM1/CIA5 revealed an uncharacterized protein that tightly associates with CCM1. This protein, CCM1-binding protein 1 (CBP1), combines a CobW/CobW_C GTP-binding metallochaperone module with a WW-domain characteristic of protein-protein interactions. CBP1 colocalizes and interacts with CCM1 in the nucleus regardless of CO₂ conditions. Disruption of CBP1 does not affect growth or CCM induction under CO₂ limitation but derepresses 27 of 41 CCM1-dependent low-CO₂ inducible genes under high-CO₂ conditions. These include the periplasmic and intracellular carbonic anhydrases (CAH1 and LCIB) and inorganic carbon transporters/channels (LCIA, LCI1, BST1, and BST3). Consistently, <i>cbp1</i> mutants accumulate CAH1 and LCIB proteins and exhibit 40% higher inorganic carbon affinity under high-CO₂ conditions; this phenotype is rescued by CBP1 complementation or by acetazolamide treatment. Crucially, <i>cbp1</i> mutants exhibit significant growth delays under high-CO₂ conditions, especially when light is limiting, providing direct evidence that CBP1-mediated repression is essential for energy conservation. Thus, CBP1 prevents unnecessary CCM activity when CO₂ is abundant, acting upstream of both transporter/channel and carbonic anhydrase modules. Our findings suggest a regulatory mechanism potentially linking zinc-dependent protein chemistry to CCM gene repression, providing insights into energy-efficient CO₂ sensing in aquatic photosynthetic organisms.