Data from: Freeze-quenched maize mesophyll and bundle sheath separation uncovers bias in previous tissue-specific RNA-Seq data

The high efficiency of C4 photosynthesis relies on spatial division of labor, classically with initial carbon fixation in the mesophyll and carbon reduction in the bundle sheath. By employing grinding and serial filtration over liquid nitrogen, we enriched C4 tissues along a developing leaf gradient. This method treats both C4 tissues in an integrity-preserving and consistent manner, while allowing complementary measurements of metabolite abundance and enzyme activity, thus providing a comprehensive data set. Meta-analysis of this and the previous studies highlights the strengths and weaknesses of different C4 tissue separation techniques. While the method reported here achieves the least enrichment, it is the only one that shows neither strong 3′ (degradation) bias, nor different severity of 3′ bias between samples. The meta-analysis highlighted previously unappreciated observations, such as an accumulation of evidence that aspartate aminotransferase is more mesophyll specific than expected from the current NADP-ME C4 cycle model, and a shift in enrichment of protein synthesis genes from bundle sheath to mesophyll during development.

C4光合作用（C4 photosynthesis）的高效运转依赖于空间分工，经典模式为初始碳固定发生于叶肉细胞，碳还原过程则在维管束鞘细胞中进行。我们采用液氮研磨结合连续过滤的方法，沿发育中的叶片梯度富集了C4组织。该方法可在完整保留两类C4组织完整性的同时进行标准化处理，同时兼容代谢物含量与酶活性的互补性检测，最终构建得到一套全面的数据集。对本研究数据集及既往相关研究的荟萃分析（meta-analysis），系统梳理了不同C4组织分离技术的优势与局限性。尽管本研究报道的方法富集程度最低，但它是唯一既未表现出强烈的3'端（降解）偏好性，也未在不同样本间出现3'端偏好性程度差异的技术。本次荟萃分析还揭示了多项此前未被重视的观测结果：例如越来越多的证据表明，天冬氨酸转氨酶（aspartate aminotransferase）的叶肉细胞特异性远超当前NADP-ME型C4循环模型的预期；此外，蛋白质合成基因的富集趋势在叶片发育过程中，从维管束鞘细胞向叶肉细胞发生了偏移。