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...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2023-02-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.15252/msb.202110523 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849331253543698432 |
|---|---|
| author | Lucas Coppens Tanya Tschirhart Dagmar H Leary Sophie M Colston Jaimee R Compton William Judson Hervey Karl L Dana Gary J Vora Sergio Bordel Rodrigo Ledesma‐Amaro |
| author_facet | Lucas Coppens Tanya Tschirhart Dagmar H Leary Sophie M Colston Jaimee R Compton William Judson Hervey Karl L Dana Gary J Vora Sergio Bordel Rodrigo Ledesma‐Amaro |
| author_sort | Lucas Coppens |
| collection | DOAJ |
| description | 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. |
| format | Article |
| id | doaj-art-20fb8d7197224a56b273f4451e2099d1 |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2023-02-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-20fb8d7197224a56b273f4451e2099d12025-08-20T03:46:41ZengSpringer NatureMolecular Systems Biology1744-42922023-02-0119411610.15252/msb.202110523Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocationLucas Coppens0Tanya Tschirhart1Dagmar H Leary2Sophie M Colston3Jaimee R Compton4William Judson Hervey5Karl L Dana6Gary J Vora7Sergio Bordel8Rodrigo Ledesma‐Amaro9Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College LondonUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringNOVA Research IncUS Naval Research Laboratory, Center for Bio/Molecular Science and EngineeringDepartment of Chemical Engineering and Environmental Technology, School of Industrial Engineering, University of ValladolidDepartment of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College LondonAbstract 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.https://doi.org/10.15252/msb.202110523genome‐scale metabolic modelingmetabolic engineeringresource allocationsynthetic biologyVibrio natriegens |
| spellingShingle | Lucas Coppens Tanya Tschirhart Dagmar H Leary Sophie M Colston Jaimee R Compton William Judson Hervey Karl L Dana Gary J Vora Sergio Bordel Rodrigo Ledesma‐Amaro Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation Molecular Systems Biology genome‐scale metabolic modeling metabolic engineering resource allocation synthetic biology Vibrio natriegens |
| title | Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation |
| title_full | Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation |
| title_fullStr | Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation |
| title_full_unstemmed | Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation |
| title_short | Vibrio natriegens genome‐scale modeling reveals insights into halophilic adaptations and resource allocation |
| title_sort | vibrio natriegens genome scale modeling reveals insights into halophilic adaptations and resource allocation |
| topic | genome‐scale metabolic modeling metabolic engineering resource allocation synthetic biology Vibrio natriegens |
| url | https://doi.org/10.15252/msb.202110523 |
| work_keys_str_mv | AT lucascoppens vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT tanyatschirhart vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT dagmarhleary vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT sophiemcolston vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT jaimeercompton vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT williamjudsonhervey vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT karlldana vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT garyjvora vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT sergiobordel vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation AT rodrigoledesmaamaro vibrionatriegensgenomescalemodelingrevealsinsightsintohalophilicadaptationsandresourceallocation |