Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome
Summary: Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach t...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2023-06-01
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| Series: | Cell Reports |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2211124723006307 |
| _version_ | 1827931902866096128 |
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| author | Jongoh Shin Kevin Rychel Bernhard O. Palsson |
| author_facet | Jongoh Shin Kevin Rychel Bernhard O. Palsson |
| author_sort | Jongoh Shin |
| collection | DOAJ |
| description | Summary: Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens’s transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism. |
| first_indexed | 2024-03-13T06:59:31Z |
| format | Article |
| id | doaj.art-dea8380a35754e2093da7b84133b6185 |
| institution | Directory Open Access Journal |
| issn | 2211-1247 |
| language | English |
| last_indexed | 2024-03-13T06:59:31Z |
| publishDate | 2023-06-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Cell Reports |
| spelling | doaj.art-dea8380a35754e2093da7b84133b61852023-06-07T04:47:55ZengElsevierCell Reports2211-12472023-06-01426112619Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptomeJongoh Shin0Kevin Rychel1Bernhard O. Palsson2Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USADepartment of Bioengineering, University of California San Diego, La Jolla, CA 92093, USADepartment of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Lyngby, Denmark; Department of Pediatrics, University of California, San Diego, La Jolla, CA, USA; Corresponding authorSummary: Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture and transport. However, the extensive genetic and transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose Vibrio natriegens’s transcriptome into 45 groups of independently modulated sets of genes (iModulons). Our findings show that competency is associated with the repression of two housekeeping iModulons (iron metabolism and translation) and the activation of six iModulons; including TfoX and QstR, a novel iModulon of unknown function, and three housekeeping iModulons (representing motility, polycations, and reactive oxygen species [ROS] responses). Phenotypic screening of 83 gene deletion strains demonstrates that loss of iModulon function reduces or eliminates competency. This database-iModulon-discovery cycle unveils the transcriptomic basis for competency and its relationship to housekeeping functions. These results provide the genetic basis for systems biology of competency in this organism.http://www.sciencedirect.com/science/article/pii/S2211124723006307CP: GenomicsCP: Microbiology |
| spellingShingle | Jongoh Shin Kevin Rychel Bernhard O. Palsson Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome Cell Reports CP: Genomics CP: Microbiology |
| title | Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| title_full | Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| title_fullStr | Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| title_full_unstemmed | Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| title_short | Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| title_sort | systems biology of competency in vibrio natriegens is revealed by applying novel data analytics to the transcriptome |
| topic | CP: Genomics CP: Microbiology |
| url | http://www.sciencedirect.com/science/article/pii/S2211124723006307 |
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