Systems biology of competency in Vibrio natriegens is revealed by applying novel data analytics to the transcriptome

• DOI: 10.1016/j.celrep.2023.112619
• Publication Date: 2023-06-06T16:49:18Z
• Authors: Jongoh Shin; Kevin Rychel; Bernhard O. Palsson
• Keywords: Housekeeping gene; Housekeeping

Vibrio natriegens regulates natural competence through the TfoX and QstR transcription factors, which are involved in external DNA capture transport. However, extensive genetic transcriptional regulatory basis for competency remains unknown. We used a machine-learning approach to decompose natriegens's transcriptome into 45 groups of independently modulated sets genes (iModulons). Our findings show that is associated with repression two housekeeping iModulons (iron metabolism translation) activation six iModulons; including QstR, novel iModulon unknown function, three (representing motility, polycations, reactive oxygen species [ROS] responses). Phenotypic screening 83 gene deletion strains demonstrates loss function reduces or eliminates competency. This database-iModulon-discovery cycle unveils transcriptomic its relationship functions. These results provide systems biology this organism.