Toxinome—the bacterial protein toxin database
ABSTRACTProtein toxins are key molecular weapons in biology that are used to attack neighboring cells. Bacteria use protein toxins to kill or inhibit the growth of prokaryotic and eukaryotic cells using various modes of action that target essential cellular components. The toxins are responsible for...
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| Format: | Article |
| Language: | English |
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American Society for Microbiology
2024-01-01
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| Series: | mBio |
| Subjects: | |
| Online Access: | https://journals.asm.org/doi/10.1128/mbio.01911-23 |
| _version_ | 1797353861497749504 |
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| author | Aleks Danov Ofir Segev Avi Bograd Yedidya Ben Eliyahu Noam Dotan Tommy Kaplan Asaf Levy |
| author_facet | Aleks Danov Ofir Segev Avi Bograd Yedidya Ben Eliyahu Noam Dotan Tommy Kaplan Asaf Levy |
| author_sort | Aleks Danov |
| collection | DOAJ |
| description | ABSTRACTProtein toxins are key molecular weapons in biology that are used to attack neighboring cells. Bacteria use protein toxins to kill or inhibit the growth of prokaryotic and eukaryotic cells using various modes of action that target essential cellular components. The toxins are responsible for shaping microbiomes in different habitats, for abortive phage infection, and for severe infectious diseases in animals and plants. Although several toxin databases have been developed, each one is devoted to a specific toxin family, and they encompass a relatively small number of toxins. Antimicrobial toxins are often accompanied by antitoxins (or immunity proteins) that neutralize the cognate toxins. Here, we combined toxins and antitoxins from many resources and created Toxinome, a comprehensive and updated bacterial protein toxin database. The Toxinome includes a total of 1,483,028 toxins and 491,345 antitoxins encoded in 59,475 bacterial genomes across the tree of life. We identified a depletion of toxin and antitoxin genes in bacteria that dwell in extreme temperatures. We defined 5,161 unique Toxin Islands within phylogenetically diverse bacterial genomes, which are loci dense in toxin and antitoxin genes. By focusing on the unannotated genes within these islands, we characterized a number of these genes as toxins or antitoxins. Finally, we developed an interactive Toxinome website (http://toxinome.pythonanywhere.com) that allows searching and downloading of our database. The Toxinome resource will be useful to the large research community interested in bacterial toxins and can guide toxin discovery and function elucidation, and infectious disease diagnosis and treatment.IMPORTANCEMicrobes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas “Toxin Islands.” The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins. |
| first_indexed | 2024-03-08T13:37:06Z |
| format | Article |
| id | doaj.art-2ba82e8d5f534597b7eb686f724296d1 |
| institution | Directory Open Access Journal |
| issn | 2150-7511 |
| language | English |
| last_indexed | 2024-03-08T13:37:06Z |
| publishDate | 2024-01-01 |
| publisher | American Society for Microbiology |
| record_format | Article |
| series | mBio |
| spelling | doaj.art-2ba82e8d5f534597b7eb686f724296d12024-01-16T15:40:00ZengAmerican Society for MicrobiologymBio2150-75112024-01-0115110.1128/mbio.01911-23Toxinome—the bacterial protein toxin databaseAleks Danov0Ofir Segev1Avi Bograd2Yedidya Ben Eliyahu3Noam Dotan4Tommy Kaplan5Asaf Levy6Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, IsraelDepartment of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, IsraelDepartment of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, IsraelDepartment of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, IsraelDepartment of Brain Sciences, Weizmann Institute of Science, Rehovot, IsraelSchool of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, IsraelDepartment of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, IsraelABSTRACTProtein toxins are key molecular weapons in biology that are used to attack neighboring cells. Bacteria use protein toxins to kill or inhibit the growth of prokaryotic and eukaryotic cells using various modes of action that target essential cellular components. The toxins are responsible for shaping microbiomes in different habitats, for abortive phage infection, and for severe infectious diseases in animals and plants. Although several toxin databases have been developed, each one is devoted to a specific toxin family, and they encompass a relatively small number of toxins. Antimicrobial toxins are often accompanied by antitoxins (or immunity proteins) that neutralize the cognate toxins. Here, we combined toxins and antitoxins from many resources and created Toxinome, a comprehensive and updated bacterial protein toxin database. The Toxinome includes a total of 1,483,028 toxins and 491,345 antitoxins encoded in 59,475 bacterial genomes across the tree of life. We identified a depletion of toxin and antitoxin genes in bacteria that dwell in extreme temperatures. We defined 5,161 unique Toxin Islands within phylogenetically diverse bacterial genomes, which are loci dense in toxin and antitoxin genes. By focusing on the unannotated genes within these islands, we characterized a number of these genes as toxins or antitoxins. Finally, we developed an interactive Toxinome website (http://toxinome.pythonanywhere.com) that allows searching and downloading of our database. The Toxinome resource will be useful to the large research community interested in bacterial toxins and can guide toxin discovery and function elucidation, and infectious disease diagnosis and treatment.IMPORTANCEMicrobes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas “Toxin Islands.” The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.https://journals.asm.org/doi/10.1128/mbio.01911-23bacterial toxinsmicrobial toxinstoxinseffectorsdatabaseprotein toxins |
| spellingShingle | Aleks Danov Ofir Segev Avi Bograd Yedidya Ben Eliyahu Noam Dotan Tommy Kaplan Asaf Levy Toxinome—the bacterial protein toxin database mBio bacterial toxins microbial toxins toxins effectors database protein toxins |
| title | Toxinome—the bacterial protein toxin database |
| title_full | Toxinome—the bacterial protein toxin database |
| title_fullStr | Toxinome—the bacterial protein toxin database |
| title_full_unstemmed | Toxinome—the bacterial protein toxin database |
| title_short | Toxinome—the bacterial protein toxin database |
| title_sort | toxinome the bacterial protein toxin database |
| topic | bacterial toxins microbial toxins toxins effectors database protein toxins |
| url | https://journals.asm.org/doi/10.1128/mbio.01911-23 |
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