Department of Physics, Tianjin University, Tianjin, China.
PLoS One. 2011;6(6):e21683. doi: 10.1371/journal.pone.0021683. Epub 2011 Jun 28.
Essential genes, those indispensable for the survival of an organism, play a key role in the emerging field, synthetic biology. Characterization of functions encoded by essential genes not only has important practical implications, such as in identifying antibiotic drug targets, but can also enhance our understanding of basic biology, such as functions needed to support cellular life. Enzymes are critical for almost all cellular activities. However, essential genes have not been systematically examined from the aspect of enzymes and the chemical reactions that they catalyze. Here, by comprehensively analyzing essential genes in 14 bacterial genomes in which large-scale gene essentiality screens have been performed, we found that enzymes are enriched in essential genes. Essential enzymes have overrepresented ligases (especially those forming carbon-oxygen bonds and carbon-nitrogen bonds), nucleotidyltransferases and phosphotransferases, while have underrepresented oxidoreductases. Furthermore, essential enzymes tend to associate with more gene ontology domains. These results, from the aspect of chemical reactions, provide further insights into the understanding of functions needed to support natural cellular life, as well as synthetic cells, and provide additional parameters that can be integrated into gene essentiality prediction algorithms.
必需基因是生物体生存所必需的基因，在新兴的合成生物学领域发挥着关键作用。对必需基因编码功能的特征描述不仅具有重要的实际意义，如确定抗生素药物靶点，还可以增强我们对基本生物学的理解，如支持细胞生命所需的功能。酶几乎参与所有细胞活动。然而，从酶及其催化的化学反应的角度来看，必需基因尚未被系统地研究。在这里，通过全面分析在 14 个已进行大规模基因必需性筛选的细菌基因组中的必需基因，我们发现酶在必需基因中富集。必需酶具有更多的连接酶（尤其是形成碳-氧键和碳-氮键的连接酶）、核苷酸转移酶和磷酸转移酶，而氧化还原酶则较少。此外，必需酶往往与更多的基因本体论领域相关联。这些结果从化学反应的角度进一步深入了解了支持自然细胞生命以及合成细胞所需的功能，并提供了可集成到基因必需性预测算法中的其他参数。
