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Identification of putative essential protein domains from high-density transposon insertion sequencing

A first clue to gene function can be obtained by examining whether a gene is required for life in certain standard conditions, that is, whether a gene is essential. In bacteria, essential genes are usually identified by high-density transposon mutagenesis followed by sequencing of insertion sites (T...

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Autores principales: Rahman, A. S. M. Zisanur, Timmerman, Lukas, Gallardo, Flyn, Cardona, Silvia T.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8770471/
https://www.ncbi.nlm.nih.gov/pubmed/35046497
http://dx.doi.org/10.1038/s41598-022-05028-x
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author Rahman, A. S. M. Zisanur
Timmerman, Lukas
Gallardo, Flyn
Cardona, Silvia T.
author_facet Rahman, A. S. M. Zisanur
Timmerman, Lukas
Gallardo, Flyn
Cardona, Silvia T.
author_sort Rahman, A. S. M. Zisanur
collection PubMed
description A first clue to gene function can be obtained by examining whether a gene is required for life in certain standard conditions, that is, whether a gene is essential. In bacteria, essential genes are usually identified by high-density transposon mutagenesis followed by sequencing of insertion sites (Tn-seq). These studies assign the term “essential” to whole genes rather than the protein domain sequences that encode the essential functions. However, genes can code for multiple protein domains that evolve their functions independently. Therefore, when essential genes code for more than one protein domain, only one of them could be essential. In this study, we defined this subset of genes as “essential domain-containing” (EDC) genes. Using a Tn-seq data set built-in Burkholderia cenocepacia K56-2, we developed an in silico pipeline to identify EDC genes and the essential protein domains they encode. We found forty candidate EDC genes and demonstrated growth defect phenotypes using CRISPR interference (CRISPRi). This analysis included two knockdowns of genes encoding the protein domains of unknown function DUF2213 and DUF4148. These putative essential domains are conserved in more than two hundred bacterial species, including human and plant pathogens. Together, our study suggests that essentiality should be assigned to individual protein domains rather than genes, contributing to a first functional characterization of protein domains of unknown function.
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spelling pubmed-87704712022-01-20 Identification of putative essential protein domains from high-density transposon insertion sequencing Rahman, A. S. M. Zisanur Timmerman, Lukas Gallardo, Flyn Cardona, Silvia T. Sci Rep Article A first clue to gene function can be obtained by examining whether a gene is required for life in certain standard conditions, that is, whether a gene is essential. In bacteria, essential genes are usually identified by high-density transposon mutagenesis followed by sequencing of insertion sites (Tn-seq). These studies assign the term “essential” to whole genes rather than the protein domain sequences that encode the essential functions. However, genes can code for multiple protein domains that evolve their functions independently. Therefore, when essential genes code for more than one protein domain, only one of them could be essential. In this study, we defined this subset of genes as “essential domain-containing” (EDC) genes. Using a Tn-seq data set built-in Burkholderia cenocepacia K56-2, we developed an in silico pipeline to identify EDC genes and the essential protein domains they encode. We found forty candidate EDC genes and demonstrated growth defect phenotypes using CRISPR interference (CRISPRi). This analysis included two knockdowns of genes encoding the protein domains of unknown function DUF2213 and DUF4148. These putative essential domains are conserved in more than two hundred bacterial species, including human and plant pathogens. Together, our study suggests that essentiality should be assigned to individual protein domains rather than genes, contributing to a first functional characterization of protein domains of unknown function. Nature Publishing Group UK 2022-01-19 /pmc/articles/PMC8770471/ /pubmed/35046497 http://dx.doi.org/10.1038/s41598-022-05028-x Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Rahman, A. S. M. Zisanur
Timmerman, Lukas
Gallardo, Flyn
Cardona, Silvia T.
Identification of putative essential protein domains from high-density transposon insertion sequencing
title Identification of putative essential protein domains from high-density transposon insertion sequencing
title_full Identification of putative essential protein domains from high-density transposon insertion sequencing
title_fullStr Identification of putative essential protein domains from high-density transposon insertion sequencing
title_full_unstemmed Identification of putative essential protein domains from high-density transposon insertion sequencing
title_short Identification of putative essential protein domains from high-density transposon insertion sequencing
title_sort identification of putative essential protein domains from high-density transposon insertion sequencing
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8770471/
https://www.ncbi.nlm.nih.gov/pubmed/35046497
http://dx.doi.org/10.1038/s41598-022-05028-x
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