Journal Article

Transcriptome-Wide Changes in Chlamydomonas reinhardtii Gene Expression Regulated by Carbon Dioxide and the CO₂-Concentrating Mechanism Regulator CIA5/CCM1

Spalding, Martin H., Si, Yaqing, Casero, David, Fang, Wei, Douglass, Stephen, Merchant, Sabeeha S., Liu, Peng, Ladunga, Istvan, Pellegrini, Matteo

2012

Overview

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.

• Publisher: American Society of Plant Biologists
• Subject: Acclimatization / Calvin cycle / Carbon dioxide / Carbon Dioxide - pharmacology / Chlamydomonas reinhardtii / Chlamydomonas reinhardtii - drug effects / Chlamydomonas reinhardtii - genetics / Chloroplasts / Datasets / Gene expression / Gene Expression - drug effects / Gene Expression - genetics / Gene expression regulation / Gene Expression Regulation - drug effects / Gene Expression Regulation - genetics / Genes / Inorganic carbon / microalgae / Molecular Sequence Data / multigene family / Plant cells / Protein metabolism / transcription (genetics) / transcription factors / Transcriptome - drug effects / Transcriptome - genetics / Transcriptomes