Subcellular stoichiogenomics reveal cell evolution and electrostatic interaction mechanisms in cytoskeleton

• Published in: BMC genomics Vol. 19; no. 1; p. 469
• Main Authors: Zhang, Yu-Juan, Zhu, Chengxu, Ding, Yiran, Yan, Zheng-Wen, Li, Gong-Hua, Lan, Yang, Wen, Jian-Fan, Chen, Bin
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 18.06.2018; BioMed Central; BMC
• Subjects: Activation; Amino acids; Amino Acids - analysis; Analysis; Animals; Binding; Bioinformatics; Biological Evolution; Cell Nucleus - metabolism; Charge amino acid; Complex formation; Computational Biology; Cytology; Cytoskeletal proteins; Cytoskeletal Proteins - metabolism; Cytoskeleton; Cytoskeleton - physiology; Electrostatic properties; Element; Endoplasmic reticulum; Eukaryotic Cells - metabolism; Evolution; Genomics; Genomics - methods; Humans; Hydrogen - analysis; Interfaces; Macromolecules; Microenvironments; Nitrogen; Nitrogen - analysis; Prokaryotes; Prokaryotic Cells - metabolism; Protein Interaction Maps; Proteins; Proteome - analysis; Selection, Genetic; Static Electricity; Stoichiogenomics; Subcellular Fractions; Sulfur; Sulfur - analysis; Sulfur content; Stoichiogenomics; Bioinformatics; Genomics; Charge amino acid; Element
• ISSN: 1471-2164; 1471-2164
• 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.