Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae
Bacterial toxin-antitoxin (TA) systems consist of two or more adjacent genes, encoding a toxin and an antitoxin. TA systems are implicated in evolutionary and physiological functions including genome maintenance, antibiotics persistence, phage defense, and virulence. Eight classes of TA systems have...
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Frontiers Media S.A.
2022-01-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2021.815911/full |
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| author | Prem P. Kandel Marina Naumova Chad Fautt Ravikumar R. Patel Lindsay R. Triplett Kevin L. Hockett Kevin L. Hockett |
| author_facet | Prem P. Kandel Marina Naumova Chad Fautt Ravikumar R. Patel Lindsay R. Triplett Kevin L. Hockett Kevin L. Hockett |
| author_sort | Prem P. Kandel |
| collection | DOAJ |
| description | Bacterial toxin-antitoxin (TA) systems consist of two or more adjacent genes, encoding a toxin and an antitoxin. TA systems are implicated in evolutionary and physiological functions including genome maintenance, antibiotics persistence, phage defense, and virulence. Eight classes of TA systems have been described, based on the mechanism of toxin neutralization by the antitoxin. Although studied well in model species of clinical significance, little is known about the TA system abundance and diversity, and their potential roles in stress tolerance and virulence of plant pathogens. In this study, we screened the genomes of 339 strains representing the genetic and lifestyle diversity of the Pseudomonas syringae species complex for TA systems. Using bioinformatic search and prediction tools, including SLING, BLAST, HMMER, TADB2.0, and T1TAdb, we show that P. syringae strains encode 26 different families of TA systems targeting diverse cellular functions. TA systems in this species are almost exclusively type II. We predicted a median of 15 TA systems per genome, and we identified six type II TA families that are found in more than 80% of strains, while others are more sporadic. The majority of predicted TA genes are chromosomally encoded. Further functional characterization of the predicted TA systems could reveal how these widely prevalent gene modules potentially impact P. syringae ecology, virulence, and disease management practices. |
| first_indexed | 2024-12-18T05:10:18Z |
| format | Article |
| id | doaj.art-758a3b402a8f4ffc8ee75126ca3a6f2c |
| institution | Directory Open Access Journal |
| issn | 1664-302X |
| language | English |
| last_indexed | 2024-12-18T05:10:18Z |
| publishDate | 2022-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Microbiology |
| spelling | doaj.art-758a3b402a8f4ffc8ee75126ca3a6f2c2022-12-21T21:19:54ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2022-01-011210.3389/fmicb.2021.815911815911Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringaePrem P. Kandel0Marina Naumova1Chad Fautt2Ravikumar R. Patel3Lindsay R. Triplett4Kevin L. Hockett5Kevin L. Hockett6Department of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United StatesDepartment of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United StatesDepartment of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United StatesDepartment of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United StatesDepartment of Plant Pathology and Ecology, The Connecticut Agricultural Experiment Station, New Haven, CT, United StatesDepartment of Plant Pathology and Environmental Microbiology, Pennsylvania State University, University Park, PA, United StatesThe Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, United StatesBacterial toxin-antitoxin (TA) systems consist of two or more adjacent genes, encoding a toxin and an antitoxin. TA systems are implicated in evolutionary and physiological functions including genome maintenance, antibiotics persistence, phage defense, and virulence. Eight classes of TA systems have been described, based on the mechanism of toxin neutralization by the antitoxin. Although studied well in model species of clinical significance, little is known about the TA system abundance and diversity, and their potential roles in stress tolerance and virulence of plant pathogens. In this study, we screened the genomes of 339 strains representing the genetic and lifestyle diversity of the Pseudomonas syringae species complex for TA systems. Using bioinformatic search and prediction tools, including SLING, BLAST, HMMER, TADB2.0, and T1TAdb, we show that P. syringae strains encode 26 different families of TA systems targeting diverse cellular functions. TA systems in this species are almost exclusively type II. We predicted a median of 15 TA systems per genome, and we identified six type II TA families that are found in more than 80% of strains, while others are more sporadic. The majority of predicted TA genes are chromosomally encoded. Further functional characterization of the predicted TA systems could reveal how these widely prevalent gene modules potentially impact P. syringae ecology, virulence, and disease management practices.https://www.frontiersin.org/articles/10.3389/fmicb.2021.815911/fullPseudomonas syringaetoxin-antitoxin systemsphylogroupgenomicsstress |
| spellingShingle | Prem P. Kandel Marina Naumova Chad Fautt Ravikumar R. Patel Lindsay R. Triplett Kevin L. Hockett Kevin L. Hockett Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae Frontiers in Microbiology Pseudomonas syringae toxin-antitoxin systems phylogroup genomics stress |
| title | Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae |
| title_full | Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae |
| title_fullStr | Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae |
| title_full_unstemmed | Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae |
| title_short | Genome Mining Shows Ubiquitous Presence and Extensive Diversity of Toxin-Antitoxin Systems in Pseudomonas syringae |
| title_sort | genome mining shows ubiquitous presence and extensive diversity of toxin antitoxin systems in pseudomonas syringae |
| topic | Pseudomonas syringae toxin-antitoxin systems phylogroup genomics stress |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2021.815911/full |
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