Recent advances in the characterization of essential genes and development of a database of essential genes

Abstract

Over the past few decades, there has been a significant interest in the study of essential genes, which are crucial for the survival of an organism under specific environmental conditions and thus have practical applications in the fields of synthetic biology and medicine. An increasing amount of experimental data on essential genes has been obtained with the continuous development of technological methods. Meanwhile, various computational prediction methods, related databases and web servers have emerged accordingly. To facilitate the study of essential genes, we have established a database of essential genes (DEG), which has become popular with continuous updates to facilitate essential gene feature analysis and prediction, drug and vaccine development, as well as artificial genome design and construction. In this article, we summarized the studies of essential genes, overviewed the relevant databases, and discussed their practical applications. Furthermore, we provided an overview of the main applications of DEG and conducted comprehensive analyses based on its latest version. However, it should be noted that the essential gene is a dynamic concept instead of a binary one, which presents both opportunities and challenges for their future development.

Keywords: database of essential genes; drug and vaccine design; essential gene; gene essentiality prediction; genome design.

Figure 1

Milestones of technological breakthroughs in gene essentiality. It illustrates some of the important technological advancements and their initial applications in essential gene research. The update of different versions of the database of essential genes (DEG) and the data volume obtained through different methods in each version of DEG is also indicated.

Figure 2

Screenshots and examples of user cases in the database of essential genes (DEG). (A) Homepage of the DEG database. Interfaces to other modules are supplied and the links to experimental results information for multiple essential genes in different species. (B) The summary page of all data within DEG. (C) A screenshot of the relevant information for an experimental result of a specific strain, including strain information, cultivation conditions, and reference citations. (D) The BLAST search interface for the corresponding strain. (E) The distribution of essential genes on the leading strand/lagging strand in the corresponding strain. (F) The Kyoto Encyclopedia of Genes and Genomes analysis results for essential genes in the corresponding strain. (G) The Gene Ontology analysis results for essential genes in the corresponding strain.

Figure 3

Main applications of the database of essential genes (DEG). The applications of DEG primarily focus on the following four areas: artificial genome design and construction, drug and vaccine design, essential gene feature analysis, and the prediction of essential genes.

Figure 4

Relevant analysis results based on essential genes in the database of essential genes (DEG). (A) Numbers of essential and nonessential genes against genome length. (B) The percentage of essential genes against the total gene number. (C) The relationship between the number of core‐essential genes and total essential genes. (D) Distribution of essential genes under the pan‐genomic framework. The x‐axis represents different species. The essential genes existing in the unique, accessory, and core gene sets are highlighted in pink, green, and blue, respectively. The y‐axis represents the proportion of different types of essential genes. Those with multiple experimental results are labeled with a sequential number appended to the strain name, which was generated by ImageGP [192].