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- Title
Mslar: Microbial synthetic lethal and rescue database.
- Authors
Zhu, Sen-Bin; Jiang, Qian-Hu; Chen, Zhi-Guo; Zhou, Xiang; Jin, Yan-ting; Deng, Zixin; Guo, Feng-Biao
- Abstract
Synthetic lethality (SL) occurs when mutations in two genes together lead to cell or organism death, while a single mutation in either gene does not have a significant impact. This concept can also be extended to three or more genes for SL. Computational and experimental methods have been developed to predict and verify SL gene pairs, especially for yeast and Escherichia coli. However, there is currently a lack of a specialized platform to collect microbial SL gene pairs. Therefore, we designed a synthetic interaction database for microbial genetics that collects 13,313 SL and 2,994 Synthetic Rescue (SR) gene pairs that are reported in the literature, as well as 86,981 putative SL pairs got through homologous transfer method in 281 bacterial genomes. Our database website provides multiple functions such as search, browse, visualization, and Blast. Based on the SL interaction data in the S. cerevisiae, we review the issue of duplications' essentiality and observed that the duplicated genes and singletons have a similar ratio of being essential when we consider both individual and SL. The Microbial Synthetic Lethal and Rescue Database (Mslar) is expected to be a useful reference resource for researchers interested in the SL and SR genes of microorganisms. Mslar is open freely to everyone and available on the web at http://guolab.whu.edu.cn/Mslar/. Author summary: Research on SL interaction could provide novel drug targets and help construct a minimal genome. There have been many studies using metabolic models of different microbial systems or experimental array screen to study SL interactions. Here we developed a database to collect SL gene pairs of microorganisms, while also including SR gene pairs. Studies have transferred SL gene pairs onto other species through lineal homology, and also found that there are SL interactions. Based on this principle, we also used Escherichia coli as a reference set to calculate potential SL interactions among more than 2,700 bacteria, among which 281 have homologous SL gene pairs verified in E. coli.
- Subjects
DATABASES; GENETIC databases; MICROBIAL genetics; BACTERIAL genomes; ESCHERICHIA coli
- Publication
PLoS Computational Biology, 2023, Vol 19, Issue 6, p1
- ISSN
1553-734X
- Publication type
Article
- DOI
10.1371/journal.pcbi.1011218