Global Changes in Chlamydomonas Gene Expression Regulated by Carbon Dioxide and CIA5/CCM1

We used RNA-Seq to query the Chlamydomonas reinhardtii transcriptome for regulation by CO2 concentration and by the transcription regulator CIA5(CCM1). Both CO2 concentration and CIA5 are known to play roles in induction of an essential CO2-concentrating mechanism (CCM), but the degree of interaction and the extent of global regulation beyond the CCM were not previously understood. We compared the transcriptome of a wild type strain vs. a cia5 strain under 3 CO2 supply conditions: high CO2 (H-CO2; 5%); low CO2 (L-CO2; 0.03 to 0.05%); and very-low CO2 (VL-CO2; <0.02%). Our goals were to: 1) reveal candidate genes that, through changes in their expression, distinguish multiple acclimation states induced by H-CO2, L-CO2, and VL-CO2; 2) reveal genes regulated directly or indirectly by CIA5; and 3) reveal genes responding to the interaction between CIA5 and changes in CO2 concentration. Our results revealed a small group of genes as encoding putative Ci transporters based on their expression patterns. The results also showed a massive and much broader impact on global gene regulation by CIA5/CCM1, which directly or indirectly affected 15% of the Chlamydomonas genome. The transcriptomes under L-CO2 and VL-CO2 conditions were not significantly different, suggesting that these two acclimation states must be controlled by mechanisms operating beyond transcript abundance. Overall design: Both 137c wild type (cc125) and cia5 mutant were induced for 4 hours induction under H-CO2 (5%), L-CO2 (300~500 ppm), and VL-CO2 (100~200 ppm) conditions. 2 biological replicates were done for each strain -CO2 combination.

本研究采用RNA测序（RNA-Seq）技术，检测莱茵衣藻（Chlamydomonas reinhardtii）的转录组，以探究CO2浓度与转录调控因子CIA5(CCM1)对其的调控作用。已知CO2浓度与CIA5均可诱导核心CO2浓缩机制（CCM）的激活，但二者的互作强度以及CCM之外的全局调控范围此前尚未明确。
本研究在3种CO2供应条件下，对比了野生型菌株与cia5突变体菌株的转录组：高CO2（H-CO2；5%）、低CO2（L-CO2；0.03%~0.05%）以及极低CO2（VL-CO2；<0.02%）。
本研究的目标如下：1）筛选可通过表达量变化区分高CO2、低CO2与极低CO2诱导的多种适应状态的候选基因；2）鉴定受CIA5直接或间接调控的基因；3）解析响应CIA5与CO2浓度变化互作的基因。
研究结果显示，存在一小簇基因的表达模式符合潜在无机碳转运蛋白的特征。同时，CIA5/CCM1对全局基因调控具有广泛且显著的影响，其直接或间接调控了莱茵衣藻基因组中15%的基因。低CO2与极低CO2条件下的转录组无显著差异，提示这两种适应状态的调控机制并非通过转录本丰度变化实现。
实验设计：将137c野生型（cc125）与cia5突变体分别在高CO2（5%）、低CO2（300~500 ppm）以及极低CO2（100~200 ppm）条件下诱导培养4小时。每个菌株-CO2组合设置2次生物学重复。