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김동혁

Kim, Donghyuk
Systems Biology and Machine Learning Lab.
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dc.citation.number 1 -
dc.citation.startPage e00896-22 -
dc.citation.title MSYSTEMS -
dc.citation.volume 8 -
dc.contributor.author Choe, Donghui -
dc.contributor.author Kim, Uigi -
dc.contributor.author Hwang, Soonkyu -
dc.contributor.author Seo, Sang Woo -
dc.contributor.author Kim, Donghyuk -
dc.contributor.author Cho, Suhyung -
dc.contributor.author Palsson, Bernhard -
dc.contributor.author Cho, Byung-Kwan -
dc.date.accessioned 2023-12-21T13:07:38Z -
dc.date.available 2023-12-21T13:07:38Z -
dc.date.created 2023-01-02 -
dc.date.issued 2023-02 -
dc.description.abstract Transposon mutagenesis is an efficient way to explore gene essentiality of a bacterial genome. However, there was a discrepancy between the essential gene set determined by transposon mutagenesis and that determined using single-gene knockout strains. The massive sequencing of transposon insertion mutant libraries (Tn-Seq) represents a commonly used method to determine essential genes in bacteria. Using a hypersaturated transposon mutant library consisting of 400,096 unique Tn insertions, 523 genes were classified as essential in Escherichia coli K-12 MG1655. This provided a useful genome-wide gene essentiality landscape for rapidly identifying 233 of 301 essential genes previously validated by a knockout study. However, there was a discrepancy in essential gene sets determined by conventional gene deletion methods and Tn-Seq, although different Tn-Seq studies reported different extents of discrepancy. We have elucidated two causes of this discrepancy. First, 68 essential genes not detected by Tn-Seq contain nonessential subgenic domains that are tolerant to transposon insertion, which leads to the false assignment of an essential gene as a nonessential or dispensable gene. These genes exhibited a high level of transposon insertion in their subgenic nonessential domains. In contrast, 290 genes were additionally categorized as essential by Tn-Seq, although their knockout mutants were available. The comparative analysis of Tn-Seq and high-resolution footprinting of nucleoid-associated proteins (NAPs) revealed that a protein-DNA interaction hinders transposon insertion. We identified 213 false-positive genes caused by NAP-genome interactions. These two limitations have to be considered when addressing essential bacterial genes using Tn-Seq. Furthermore, a comparative analysis of high-resolution Tn-Seq with other data sets is required for a more accurate determination of essential genes in bacteria.IMPORTANCE Transposon mutagenesis is an efficient way to explore gene essentiality of a bacterial genome. However, there was a discrepancy between the essential gene set determined by transposon mutagenesis and that determined using single-gene knockout strains. In this study, we generated a hypersaturated Escherichia coli transposon mutant library comprising approximately 400,000 different mutants. Determination of transposon insertion sites using next-generation sequencing provided a high-resolution essentiality landscape of the E. coli genome. We identified false negatives of essential gene discovery due to the permissive insertion of transposons in the C-terminal region. Comparisons between the transposon insertion landscape with binding profiles of DNA-binding proteins revealed interference of nucleoid-associated proteins to transposon insertion, generating false positives of essential gene discovery. Consideration of these findings is required to avoid the misinterpretation of transposon mutagenesis results. -
dc.identifier.bibliographicCitation MSYSTEMS, v.8, no.1, pp.e00896-22 -
dc.identifier.doi 10.1128/msystems.00896-22 -
dc.identifier.issn 2379-5077 -
dc.identifier.scopusid 2-s2.0-85149142544 -
dc.identifier.uri https://scholarworks.unist.ac.kr/handle/201301/60688 -
dc.identifier.url https://journals.asm.org/doi/10.1128/msystems.00896-22 -
dc.identifier.wosid 000897780800001 -
dc.language 영어 -
dc.publisher AMER SOC MICROBIOLOGY -
dc.title Revealing Causes for False-Positive and False-Negative Calling of Gene Essentiality in Escherichia coli Using Transposon Insertion Sequencing -
dc.type Article -
dc.description.isOpenAccess FALSE -
dc.relation.journalWebOfScienceCategory Microbiology -
dc.relation.journalResearchArea Microbiology -
dc.type.docType Article; Early Access -
dc.description.journalRegisteredClass scie -
dc.description.journalRegisteredClass scopus -
dc.subject.keywordAuthor gene essentiality -
dc.subject.keywordAuthor subgenic-level essentiality -
dc.subject.keywordAuthor Tn-Seq -
dc.subject.keywordAuthor DNA-binding proteins -
dc.subject.keywordAuthor nucleoid-associated proteins -
dc.subject.keywordPlus SCALE -

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