Lan Yang, Hu Jiang-tao, Zhang Yu-juan
College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
Yi Chuan. 2017 Feb 20;39(2):89-97. doi: 10.16288/j.yczz.16-343.
Stoichiogenomics is a newly arisen research field, which concerns the element usage biases of biological macromolecules at genome, transcriptome, proteome, metabonome levels. Different biological macromolecules have different element compositions and contents. When the supply of some elements was constrained, natural selection might bias the usage of the monomers (amino acid or nucleotide) to reduce constrained element costs in the synthesis of biological macromolecules. This field is flourishing with the intensive applications of high throughput sequencing and assembly technologies, more and more available metagenomic and metatranscriptomic data, and the applications of new analysis strategies. As a newly emerged cross discipline field, stoichiogenomics integrates stoichiometry, ecology, evolutionary biology, genomics and bioinformatics to provide a whole new perspective for investigating the interactions of the macromolecular evolution and ecosystem, and data mining in the post genomic era. In this review, we summarize the latest research progress of stoichiogenomics from the aspect of the element usage biases in proteins and nucleic acids. Furthermore, new research directions are discussed to provide some valuable references for the research and application of stoichiogenomics.
化学计量基因组学是一个新兴的研究领域，它关注基因组、转录组、蛋白质组和代谢组水平上生物大分子的元素使用偏好。不同的生物大分子具有不同的元素组成和含量。当某些元素的供应受到限制时，自然选择可能会使单体（氨基酸或核苷酸）的使用产生偏好，以降低生物大分子合成中受限元素的成本。随着高通量测序和组装技术的广泛应用、越来越多可用的宏基因组和宏转录组数据以及新分析策略的应用，这个领域正在蓬勃发展。作为一个新兴的交叉学科领域，化学计量基因组学整合了化学计量学、生态学、进化生物学、基因组学和生物信息学，为研究大分子进化与生态系统的相互作用以及后基因组时代的数据挖掘提供了全新的视角。在这篇综述中，我们从蛋白质和核酸的元素使用偏好方面总结了化学计量基因组学的最新研究进展。此外，还讨论了新的研究方向，为化学计量基因组学的研究和应用提供一些有价值的参考。
