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Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes
Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) prote...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138268/ https://www.ncbi.nlm.nih.gov/pubmed/34018328 http://dx.doi.org/10.15252/msb.20209880 |
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author | Smyshlyaev, Georgy Bateman, Alex Barabas, Orsolya |
author_facet | Smyshlyaev, Georgy Bateman, Alex Barabas, Orsolya |
author_sort | Smyshlyaev, Georgy |
collection | PubMed |
description | Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination. |
format | Online Article Text |
id | pubmed-8138268 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-81382682021-06-03 Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes Smyshlyaev, Georgy Bateman, Alex Barabas, Orsolya Mol Syst Biol Articles Mobile genetic elements (MGEs) sequester and mobilize antibiotic resistance genes across bacterial genomes. Efficient and reliable identification of such elements is necessary to follow resistance spreading. However, automated tools for MGE identification are missing. Tyrosine recombinase (YR) proteins drive MGE mobilization and could provide markers for MGE detection, but they constitute a diverse family also involved in housekeeping functions. Here, we conducted a comprehensive survey of YRs from bacterial, archaeal, and phage genomes and developed a sequence‐based classification system that dissects the characteristics of MGE‐borne YRs. We revealed that MGE‐related YRs evolved from non‐mobile YRs by acquisition of a regulatory arm‐binding domain that is essential for their mobility function. Based on these results, we further identified numerous unknown MGEs. This work provides a resource for comparative analysis and functional annotation of YRs and aids the development of computational tools for MGE annotation. Additionally, we reveal how YRs adapted to drive gene transfer across species and provide a tool to better characterize antibiotic resistance dissemination. John Wiley and Sons Inc. 2021-05-20 /pmc/articles/PMC8138268/ /pubmed/34018328 http://dx.doi.org/10.15252/msb.20209880 Text en © 2021 The Authors. Published under the terms of the CC BY 4.0 license https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Articles Smyshlyaev, Georgy Bateman, Alex Barabas, Orsolya Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title | Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title_full | Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title_fullStr | Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title_full_unstemmed | Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title_short | Sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
title_sort | sequence analysis of tyrosine recombinases allows annotation of mobile genetic elements in prokaryotic genomes |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8138268/ https://www.ncbi.nlm.nih.gov/pubmed/34018328 http://dx.doi.org/10.15252/msb.20209880 |
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