Institute of Entomology and Molecular Biology, College of Life Sciences, Chongqing Normal University, Shapingba, Chongqing, 401331, People's Republic of China.
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan Province, 650223, People's Republic of China.
BMC Genomics. 2018 Jun 18;19(1):469. doi: 10.1186/s12864-018-4845-0.
Eukaryotic cells contain a huge variety of internally specialized subcellular compartments. Stoichiogenomics aims to reveal patterns of elements usage in biological macromolecules. However, the stoichiogenomic characteristics and how they adapt to various subcellular microenvironments are still unknown.
Here we first updated the definition of stoichiogenomics. Then we applied it to subcellular research, and detected distinctive nitrogen content of nuclear and hydrogen, sulfur content of extracellular proteomes. Specially, we found that acidic amino acids (AAs) content of cytoskeletal proteins is the highest. The increased charged AAs are mainly caused by the eukaryotic originated cytoskeletal proteins. Functional subdivision of the cytoskeleton showed that activation, binding/association, and complexes are the three largest functional categories. Electrostatic interaction analysis showed an increased electrostatic interaction between both primary sequences and PPI interfaces of 3D structures, in the cytoskeleton.
This study creates a blueprint of subcellular stoichiogenomic characteristics, and explains that charged AAs of the cytoskeleton increased greatly in evolution, which offer material basis for the eukaryotic cytoskeletal proteins to act in two ways of electrostatic interactions, and further perform their activation, binding/association and complex formation.
真核细胞内含有大量内部特化的亚细胞区室。计量基因组学旨在揭示生物大分子中元素使用的模式。然而，计量基因组学的特征以及它们如何适应各种亚细胞微环境仍然未知。
我们首先更新了计量基因组学的定义。然后我们将其应用于亚细胞研究，检测到核内氮含量和氢、硫含量的不同，细胞外蛋白质组的含量。特别地，我们发现细胞骨架蛋白的酸性氨基酸（AA）含量最高。带电荷的 AA 的增加主要是由真核起源的细胞骨架蛋白引起的。细胞骨架的功能细分表明，激活、结合/关联和复合物是三个最大的功能类别。静电相互作用分析表明，细胞骨架中 3D 结构的一级序列和 PPI 界面之间的静电相互作用增加。
本研究为亚细胞计量基因组学特征创建了一个蓝图，并解释了细胞骨架的带电荷 AA 在进化中大大增加，这为真核细胞骨架蛋白以静电相互作用的两种方式发挥作用提供了物质基础，从而进一步进行其激活、结合/关联和复合物形成。
