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Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa
The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas ae...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9424990/ https://www.ncbi.nlm.nih.gov/pubmed/36051757 http://dx.doi.org/10.3389/fmicb.2022.951774 |
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author | Dai, Zehan Wu, Tianzhi Xu, Shuangbin Zhou, Lang Tang, Wenli Hu, Erqian Zhan, Li Chen, Meijun Yu, Guangchuang |
author_facet | Dai, Zehan Wu, Tianzhi Xu, Shuangbin Zhou, Lang Tang, Wenli Hu, Erqian Zhan, Li Chen, Meijun Yu, Guangchuang |
author_sort | Dai, Zehan |
collection | PubMed |
description | The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination. |
format | Online Article Text |
id | pubmed-9424990 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-94249902022-08-31 Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa Dai, Zehan Wu, Tianzhi Xu, Shuangbin Zhou, Lang Tang, Wenli Hu, Erqian Zhan, Li Chen, Meijun Yu, Guangchuang Front Microbiol Microbiology The toxin-antitoxin (TA) system is a widely distributed group of genetic modules that play important roles in the life of prokaryotes, with mobile genetic elements (MGEs) contributing to the dissemination of antibiotic resistance gene (ARG). The diversity and richness of TA systems in Pseudomonas aeruginosa, as one of the bacterial species with ARGs, have not yet been completely demonstrated. In this study, we explored the TA systems from the public genomic sequencing data and genome sequences. A small scale of genomic sequencing data in 281 isolates was selected from the NCBI SRA database, reassembling the genomes of these isolates led to the findings of abundant TA homologs. Furthermore, remapping these identified TA modules on 5,437 genome/draft genomes uncovers a great diversity of TA modules in P. aeruginosa. Moreover, manual inspection revealed several TA systems that were not yet reported in P. aeruginosa including the hok-sok, cptA-cptB, cbeA-cbtA, tomB-hha, and ryeA-sdsR. Additional annotation revealed that a large number of MGEs were closely distributed with TA. Also, 16% of ARGs are located relatively close to TA. Our work confirmed a wealth of TA genes in the unexplored P. aeruginosa pan-genomes, expanded the knowledge on P. aeruginosa, and provided methodological tips on large-scale data mining for future studies. The co-occurrence of MGE, ARG, and TA may indicate a potential interaction in their dissemination. Frontiers Media S.A. 2022-08-16 /pmc/articles/PMC9424990/ /pubmed/36051757 http://dx.doi.org/10.3389/fmicb.2022.951774 Text en Copyright © 2022 Dai, Wu, Xu, Zhou, Tang, Hu, Zhan, Chen and Yu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Microbiology Dai, Zehan Wu, Tianzhi Xu, Shuangbin Zhou, Lang Tang, Wenli Hu, Erqian Zhan, Li Chen, Meijun Yu, Guangchuang Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title | Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title_full | Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title_fullStr | Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title_full_unstemmed | Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title_short | Characterization of toxin-antitoxin systems from public sequencing data: A case study in Pseudomonas aeruginosa |
title_sort | characterization of toxin-antitoxin systems from public sequencing data: a case study in pseudomonas aeruginosa |
topic | Microbiology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9424990/ https://www.ncbi.nlm.nih.gov/pubmed/36051757 http://dx.doi.org/10.3389/fmicb.2022.951774 |
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