Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants
Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic n...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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The American Phytopathological Society
2014-07-01
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| Series: | Molecular Plant-Microbe Interactions |
| Online Access: | https://apsjournals.apsnet.org/doi/10.1094/MPMI-12-13-0368-R |
| _version_ | 1830212828929196032 |
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| author | Tatiana V. Karpinets Byung H. Park Mustafa H. Syed Martin G. Klotz Edward C. Uberbacher |
| author_facet | Tatiana V. Karpinets Byung H. Park Mustafa H. Syed Martin G. Klotz Edward C. Uberbacher |
| author_sort | Tatiana V. Karpinets |
| collection | DOAJ |
| description | Genomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic network models, we predict external environments associated with free-living and symbiotic lifestyles and quantify dependences of symbionts on the host in terms of the consumed metabolites. We show that specific differences between the phenotypes are pronounced at the levels of metabolic enzymes, especially carbohydrate active, and protein functions. Overall, biosynthetic functions are enriched and more diverse in plant mutualists whereas processes and functions involved in degradation and host invasion are enriched and more diverse in pathogens. A distinctive characteristic of plant pathogens is a putative novel secretion system with a circadian rhythm regulator. A specific marker of plant mutualists is the co-residence of genes encoding nitrogenase and ribulose bisphosphate carboxylase/oxygenase (RuBisCO). We predict that RuBisCO is likely used in a putative metabolic pathway to supplement carbon obtained heterotrophically with low-cost assimilation of carbon from CO2. We validate results of the comparative analysis by predicting correct phenotype, pathogenic or mutualistic, for 20 symbionts in an independent set of 30 pathogens, mutualists, and commensals. |
| first_indexed | 2024-12-18T06:10:21Z |
| format | Article |
| id | doaj.art-7ab60dc0bfde4ad692e685e76bab2866 |
| institution | Directory Open Access Journal |
| issn | 0894-0282 1943-7706 |
| language | English |
| last_indexed | 2024-12-18T06:10:21Z |
| publishDate | 2014-07-01 |
| publisher | The American Phytopathological Society |
| record_format | Article |
| series | Molecular Plant-Microbe Interactions |
| spelling | doaj.art-7ab60dc0bfde4ad692e685e76bab28662022-12-21T21:18:25ZengThe American Phytopathological SocietyMolecular Plant-Microbe Interactions0894-02821943-77062014-07-0127766467710.1094/MPMI-12-13-0368-RMetabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and PlantsTatiana V. KarpinetsByung H. ParkMustafa H. SyedMartin G. KlotzEdward C. UberbacherGenomic characteristics discriminating parasitic and mutualistic relationship of bacterial symbionts with plants are poorly understood. This study comparatively analyzed the genomes of 54 mutualists and pathogens to discover genomic markers associated with the different phenotypes. Using metabolic network models, we predict external environments associated with free-living and symbiotic lifestyles and quantify dependences of symbionts on the host in terms of the consumed metabolites. We show that specific differences between the phenotypes are pronounced at the levels of metabolic enzymes, especially carbohydrate active, and protein functions. Overall, biosynthetic functions are enriched and more diverse in plant mutualists whereas processes and functions involved in degradation and host invasion are enriched and more diverse in pathogens. A distinctive characteristic of plant pathogens is a putative novel secretion system with a circadian rhythm regulator. A specific marker of plant mutualists is the co-residence of genes encoding nitrogenase and ribulose bisphosphate carboxylase/oxygenase (RuBisCO). We predict that RuBisCO is likely used in a putative metabolic pathway to supplement carbon obtained heterotrophically with low-cost assimilation of carbon from CO2. We validate results of the comparative analysis by predicting correct phenotype, pathogenic or mutualistic, for 20 symbionts in an independent set of 30 pathogens, mutualists, and commensals.https://apsjournals.apsnet.org/doi/10.1094/MPMI-12-13-0368-R |
| spellingShingle | Tatiana V. Karpinets Byung H. Park Mustafa H. Syed Martin G. Klotz Edward C. Uberbacher Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants Molecular Plant-Microbe Interactions |
| title | Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants |
| title_full | Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants |
| title_fullStr | Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants |
| title_full_unstemmed | Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants |
| title_short | Metabolic Environments and Genomic Features Associated with Pathogenic and Mutualistic Interactions Between Bacteria and Plants |
| title_sort | metabolic environments and genomic features associated with pathogenic and mutualistic interactions between bacteria and plants |
| url | https://apsjournals.apsnet.org/doi/10.1094/MPMI-12-13-0368-R |
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