Gene essentiality analysis based on DEG 10, an updated database of essential genes

Methods Mol Biol. 2015;1279:219-33. doi: 10.1007/978-1-4939-2398-4_14.

Abstract

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacteria / genetics
  • Databases, Genetic*
  • Fungi / genetics
  • Gene Ontology
  • Genes, Bacterial
  • Genes, Essential*
  • Genes, Fungal
  • Genome Size
  • Open Reading Frames / genetics
  • Phylogeny