CIA5 and its interacting metal-binding GTPase ZNG3 are degraded by the proteasome in Zn deficiency.

Carbon and zinc (Zn) metabolism are tightly connected in phototrophs, as carbonic anhydrases critical for CO2 assimilation are highly abundant Zn enzymes. The eukaryotic green alga Chlamydomonas (Chlamydomonas reinhardtii) maintains efficient phototrophic growth in ambient or low CO2 environments by establishing a carbon concentrating mechanism (CCM). We show that Chlamydomonas raises its cellular Zn quota to accommodate higher Zn demand under low CO2 conditions, an adjustment that is dependent on CIA5, a major regulator of the CCM. We demonstrate that CIA5 is constitutively expressed regardless of Zn supply, but its encoded protein undergoes proteasomal degradation under Zn deficiency, providing a checkpoint that prevents CCM induction when Zn cofactors are unavailable. We identified a COBW domain-containing GTPase, ZNG3, as a constitutive interacting partner of CIA5. As CIA5, ZNG3 does not accumulate in low Zn and is degraded by the proteasome. Unlike cia5 mutants, zng3 mutants grow like wild-type without CO2 supplementation but exhibit a growth defect when grown in the presence of high CO2 or acetate. Transcriptome sequencing revealed that expression of genes encoding central components of the CCM is mostly unchanged in zng3 mutants, while a subset of genes induced in Zn deficiency, including ZRT2 encoding for a Zn transporter, is increasingly expressed. Under low CO2 conditions, cia5 zng3 double mutants exhibit a more severe phenotype than cia5 single mutants. This result points to a condition-dependent genetic interaction between CIA5 and ZNG3, suggesting both proteins provide distinct but partially overlapping contributions to fitness depending on carbon availability.