Dataset for: Temperature sensitivity of carbon concentrating mechanisms in the diatom Phaeodactylum tricornutum

Marine diatoms are key primary producers across diverse habitats in the global ocean. Diatoms rely on a biophysical carbon concentrating mechanism (CCM) to supply high concentrations of CO2 around their carboxylating enzyme, RuBisCO. The necessity and energetic cost of the CCM are likely to be highly sensitive to temperature, as temperature impacts CO2 concentration, diffusivity, and the kinetics of CCM components. Here, we used membrane inlet mass spectrometry (MIMS) and modeling to capture temperature regulation of the CCM in the diatom Phaeodactylum tricornutum (Pt). We found that enhanced carbon fixation rates by Pt at elevated temperatures were accompanied by increased CCM activity capable of maintaining RuBisCO close to CO2 saturation but that the mechanism varied. At 10 and 18 °C, diffusion of CO2 into the cell, driven by Pt’s ‘chloroplast pump’ was the major inorganic carbon source. However, at 18 °C, upregulation of the chloroplast pump enhanced (while retaining the proportion of) both diffusive CO2 and active HCO3- uptake into the cytosol, and significantly increased chloroplast HCO3- concentrations. In contrast, at 25 °C, compared to 18 °C, the chloroplast pump had only a slight increase in activity. While diffusive uptake of CO2 into the cell remained constant, active HCO3- uptake across the cell membrane increased resulting in Pt depending equally on both CO2 and HCO3- as inorganic carbon sources. Despite changes in the CCM, the overall rate of active carbon transport remained double that of carbon fixation across all temperatures tested. The implication of the energetic cost of the Pt CCM in response to increasing temperatures was discussed.

Methods
The dataset was collected using membrane inlet mass spectrometry and processed using customized Python scripts. The data analysis tool can be found in GitHub: https://github.com/limengwsu/Fcyl_CCM

海洋硅藻是全球海洋各类生境中关键的初级生产者。硅藻依赖生物物理型碳浓缩机制（biophysical carbon concentrating mechanism, CCM）在其羧化酶RuBisCO周围维持高浓度CO₂。碳浓缩机制的必要性与能量成本极有可能对温度高度敏感，因为温度会影响CO₂浓度、扩散能力以及碳浓缩机制组分的动力学特性。本研究采用膜进样质谱（membrane inlet mass spectrometry, MIMS）结合建模方法，解析了三角褐指藻（Phaeodactylum tricornutum, Pt）的碳浓缩机制温度调控规律。研究发现，三角褐指藻在升温环境下固碳速率提升的同时，其碳浓缩机制活性也随之增强，可维持RuBisCO接近CO₂饱和状态，但调控机制存在差异：在10℃与18℃条件下，由三角褐指藻“叶绿体泵”驱动的CO₂跨膜扩散是主要的无机碳来源；而在18℃时，叶绿体泵的上调不仅增强了扩散性CO₂摄入（同时维持了两种碳源的摄取比例），还提升了胞质中活性HCO₃⁻的摄取量，并显著提高了叶绿体基质内的HCO₃⁻浓度。与之形成对比的是，在25℃条件下，相较于18℃，叶绿体泵的活性仅小幅提升。尽管细胞的CO₂扩散摄取量保持恒定，但跨细胞膜的活性HCO₃⁻摄取量有所增加，使得三角褐指藻对CO₂与HCO₃⁻这两种无机碳源的依赖程度趋于一致。尽管碳浓缩机制发生了上述变化，但在所有测试温度下，活性碳转运的总速率始终保持为固碳速率的两倍。本研究还讨论了三角褐指藻碳浓缩机制的能量成本随温度升高的响应情况。
方法
本数据集通过膜进样质谱采集所得，并通过定制化Python脚本进行处理。数据分析工具可在GitHub平台获取：https://github.com/limengwsu/Fcyl_CCM