Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation

Abstract

Vibrio natriegens is a Gram‐negative bacterium with an exceptional growth rate that has the potential to become a standard biotechnological host for laboratory and industrial bioproduction. Despite this burgeoning interest, the current lack of organism‐specific qualitative and quantitative computational tools has hampered the community's ability to rationally engineer this bacterium. In this study, we present the first genome‐scale metabolic model (GSMM) of V. natriegens . The GSMM (iLC858) was developed using an automated draft assembly and extensive manual curation and was validated by comparing predicted yields, central metabolic fluxes, viable carbon substrates, and essential genes with empirical data. Mass spectrometry‐based proteomics data confirmed the translation of at least 76% of the enzyme‐encoding genes predicted to be expressed by the model during aerobic growth in a minimal medium. iLC858 was subsequently used to carry out a metabolic comparison between the model organism Escherichia coli and V. natriegens , leading to an analysis of the model architecture of V. natriegens ' respiratory and ATP‐generating system and the discovery of a role for a sodium‐dependent oxaloacetate decarboxylase pump. The proteomics data were further used to investigate additional halophilic adaptations of V. natriegens . Finally, iLC858 was utilized to create a Resource Balance Analysis model to study the allocation of carbon resources. Taken together, the models presented provide useful computational tools to guide metabolic engineering efforts in V. natriegens . image iLC858 is the first constructed and validated genome‐scale metabolic model for the fast‐growing bacterium Vibrio natriegens. This new model enabled the study of V. natriegens metabolism, halophilic adaptions, and resource analysis. Construction and curation of a draft genome‐scale metabolic model reconstruction iLC858 for V. natriegens were performed. Validation of iLC858 showed a good correlation between model predictions and experimental data. A comparison to the metabolism of model organism E. coli led to the discovery of a new role for a sodium‐dependent oxaloacetate decarboxylase in V. natriegens growth under aerobic conditions. Proteomics data provided novel insights into halophilic adaptations and resource allocation of V. natriegens.