Gao Feng, Luo Hao, Zhang Chun-Ting, Zhang Ren
Department of Physics, Tianjin University, Tianjin, 300072, China.
Methods Mol Biol. 2015;1279:219-33. doi: 10.1007/978-1-4939-2398-4_14.
The database of essential genes (DEG, available at http://www.essentialgene.org), constructed in 2003, has been timely updated to harbor essential-gene records of bacteria, archaea, and eukaryotes. DEG 10, the current release, includes not only essential protein-coding genes determined by genome-wide gene essentiality screens but also essential noncoding RNAs, promoters, regulatory sequences, and replication origins. Therefore, DEG 10 includes essential genomic elements under different conditions in three domains of life, with customizable BLAST tools. Based on the analysis of DEG 10, we show that the percentage of essential genes in bacterial genomes exhibits an exponential decay with increasing genome sizes. The functions, ATP binding (GO:0005524), GTP binding (GO:0005525), and DNA-directed RNA polymerase activity (GO:0003899), are likely required for organisms across life domains.
必需基因数据库（DEG，可在http://www.essentialgene.org获取）于2003年构建，已及时更新，包含细菌、古细菌和真核生物的必需基因记录。当前版本的DEG 10不仅包括通过全基因组基因必需性筛选确定的必需蛋白质编码基因，还包括必需非编码RNA、启动子、调控序列和复制起点。因此，DEG 10包括生命三个域中不同条件下的必需基因组元件，并配有可定制的BLAST工具。基于对DEG 10的分析，我们发现细菌基因组中必需基因的百分比随基因组大小增加呈指数衰减。ATP结合（GO:0005524）、GTP结合（GO:0005525）和DNA指导的RNA聚合酶活性（GO:0003899）这些功能可能是生命各域中的生物体所必需的。
