Identification of putative essential protein domains from high-density transposon insertion sequencing
A S M Zisanur Rahman1, Lukas Timmerman2, Flyn Gallardo1
1Department of Microbiology, University of Manitoba, Winnipeg, MB, Canada.
Scientific Reports
|January 20, 2022
Summary
This study redefines essential genes in bacteria by identifying essential protein domains, not just whole genes. This approach helps pinpoint critical functions within essential domain-containing (EDC) genes for better understanding of bacterial biology.
Area of Science:
- Microbiology
- Genomics
- Protein Domain Analysis
Background:
- Essential genes are crucial for bacterial survival under standard conditions.
- Current methods identify essential genes, but not specific essential protein domains within them.
- Genes can contain multiple protein domains with independent functions, complicating essentiality assignment.
Purpose of the Study:
- To develop an in silico pipeline for identifying essential domain-containing (EDC) genes and their essential protein domains.
- To functionally characterize novel essential protein domains, including those of unknown function.
- To propose a shift in essentiality assignment from whole genes to individual protein domains.
Main Methods:
- Utilized transposon mutagenesis sequencing (Tn-seq) data from Burkholderia cenocepacia K56-2.
- Developed and applied an in silico pipeline to identify EDC genes and essential domains.
- Validated candidate EDC genes and essential domains using CRISPR interference (CRISPRi) for growth defect analysis.
Main Results:
- Identified forty candidate EDC genes in Burkholderia cenocepacia K56-2.
- Demonstrated growth defect phenotypes for selected EDC gene knockdowns.
- Characterized two putative essential domains of unknown function (DUF2213 and DUF4148), conserved across numerous bacterial species.
Conclusions:
- Essentiality is more accurately assigned to individual protein domains rather than entire genes.
- The identification of EDC genes and essential domains provides functional insights into bacterial survival.
- This work offers a foundation for the functional characterization of unannotated protein domains, including those in pathogens.
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