Transcriptional response of the extremophile red alga Cyanidioschyzon merolae to changes in CO concentrations.

Cyanidioschyzon merolae (C. merolae) is an acidophilic red alga growing in a naturally low carbon dioxide (CO) environment. Although it uses a ribulose 1,5-bisphosphate carboxylase/oxygenase with high affinity for CO, the survival of C. merolae relies on functional photorespiratory metabolism. In this study, we quantified the transcriptomic response of C. merolae to changes in CO conditions. We found distinct changes upon shifts between CO conditions, such as a concerted up-regulation of photorespiratory genes and responses to carbon starvation. We used the transcriptome data set to explore a hypothetical CO concentrating mechanism in C. merolae, based on the assumption that photorespiratory genes and possible candidate genes involved in a CO concentrating mechanism are co-expressed. A putative bicarbonate transport protein and two α-carbonic anhydrases were identified, which showed enhanced transcript levels under reduced CO conditions. Genes encoding enzymes of a PEPCK-type C pathway were co-regulated with the photorespiratory gene cluster. We propose a model of a hypothetical low CO compensation mechanism in C. merolae integrating these low CO-inducible components.