ORCID IDs: 0000-0002-7224-9134 (I.O.); 0000-0002-2517-4440 (M.F.); 0000-0001-9675-4883 (J.K.).Cyanobacteria have efficient carbon concentration mechanisms and suppress photorespiration in response to inorganic carbon (Ci) limitation. We studied intracellular Ci limitation in the slow-growing CO 2 /HCO 3 2 -uptake mutant DndhD3 (for NADH dehydrogenase subunit D3)/ndhD4 (for NADH dehydrogenase subunit D4)/cmpA (for bicarbonate transport system substratebinding protein A)/sbtA (for sodium-dependent bicarbonate transporter A): D4 mutant of Synechocystis sp. PCC 6803. When cultivated under high-CO 2 conditions, Δ4 phenocopies wild-type metabolic and transcriptomic acclimation responses after the shift from high to low CO 2 supply. The Δ4 phenocopy reveals multiple compensation mechanisms and differs from the preacclimation of the transcriptional Ci regulator mutant ΔndhR (for ndhF3 operon transcriptional regulator). Contrary to the carboxysomeless ΔccmM (for carbon dioxide concentrating mechanism protein M) mutant, the metabolic photorespiratory burst triggered by shifting to low CO 2 is not enhanced in Δ4. However, levels of the photorespiratory intermediates 2-phosphoglycolate and glycine are increased under high CO 2 . The number of carboxysomes is increased in Δ4 under high-CO 2 conditions and appears to be the major contributing factor for the avoidance of photorespiration under intracellular Ci limitation. The Δ4 phenocopy is associated with the deregulation of Ci control, an overreduced cellular state, and limited photooxidative stress. Our data suggest multiple layers of Ci regulation, including inversely regulated modules of antisense RNAs and cognate target messenger RNAs and specific trans-acting small RNAs, such as the posttranscriptional PHOTOSYNTHESIS REGULATORY RNA1 (PsrR1), which shows increased expression in Δ4 and is involved in repressing many photosynthesis genes at the posttranscriptional level. In conclusion, our insights extend the knowledge on the range of compensatory responses of Synechocystis sp. PCC 6803 to intracellular Ci limitation and may become a valuable reference for improving biofuel production in cyanobacteria, in which Ci is channeled off from central metabolism and may thus become a limiting factor.Cyanobacteria evolved more than 2.5 billion years ago and shaped the atmosphere by decreasing the CO 2 concentration while increasing the proportion of molecular oxygen. In marine environments, cyanobacteria are still important CO 2 sinks and contribute significantly to the global carbon cycle (Stuart, 2011) via net fixation of inorganic carbon (Ci). Cyanobacteria are the evolutionary ancestors of all eukaryotic plastids (Mereschkowski, 1905;Deusch et al., 2008;Ochoa de Alda et al., 2014) and serve as prokaryotic models in which to study photosynthesis and plant Ci fixation.Rubisco catalyzes the central reaction of photosynthetic Ci fixation, in which ribulose-1,5-bisphosphate reacts with CO 2 to produce two molecules of 3-phosphoglycerate (3PGA). High levels of atmospheric CO 2 in Ea...