Transcriptome-wide changes in Chlamydomonas reinhardtii gene expression regulated by carbon dioxide and the CO₂-concentrating mechanism regulator CIA5/CCM1.

摘要

We used RNA sequencing to query the Chlamydomonas reinhardtii transcriptome for regulation by CO₂ and by the transcription regulator CIA5 (CCM1). Both CO₂ and CIA5 are known to play roles in acclimation to low CO₂ and in induction of an essential CO₂-concentrating mechanism (CCM), but less is known about their interaction and impact on the whole transcriptome. Our comparison of the transcriptome of a wild type versus a cia5 mutant strain under three different CO₂ conditions, high CO₂ (5%), low CO₂ (0.03 to 0.05%), and very low CO₂ (<0.02%), provided an entry into global changes in the gene expression patterns occurring in response to the interaction between CO₂ and CIA5. We observed a massive impact of CIA5 and CO₂ on the transcriptome, affecting almost 25% of all Chlamydomonas genes, and we discovered an array of gene clusters with distinctive expression patterns that provide insight into the regulatory interaction between CIA5 and CO₂. Several individual clusters respond primarily to either CIA5 or CO₂, providing access to genes regulated by one factor but decoupled from the other. Three distinct clusters clearly associated with CCM-related genes may represent a rich source of candidates for new CCM components, including a small cluster of genes encoding putative inorganic carbon transporters.