Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i>
Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2023-01-01
|
Series: | Fermentation |
Subjects: | |
Online Access: | https://www.mdpi.com/2311-5637/9/1/74 |
_version_ | 1797442775987257344 |
---|---|
author | Abraham A. J. Kerssemakers Süleyman Øzmerih Gürkan Sin Suresh Sudarsan |
author_facet | Abraham A. J. Kerssemakers Süleyman Øzmerih Gürkan Sin Suresh Sudarsan |
author_sort | Abraham A. J. Kerssemakers |
collection | DOAJ |
description | Industrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps <i>Yarrowia lipolytica</i>-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h<sup>−1</sup>, the largest simulated volume (90 m<sup>3</sup>) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h<sup>−1</sup>. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that <i>Y. lipolytica</i> can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for <i>Y. lipolytica</i>-based strain engineering, thereby accelerating bioprocess development. |
first_indexed | 2024-03-09T12:46:59Z |
format | Article |
id | doaj.art-7a8b26ac10a74a37819e734d28fde03c |
institution | Directory Open Access Journal |
issn | 2311-5637 |
language | English |
last_indexed | 2024-03-09T12:46:59Z |
publishDate | 2023-01-01 |
publisher | MDPI AG |
record_format | Article |
series | Fermentation |
spelling | doaj.art-7a8b26ac10a74a37819e734d28fde03c2023-11-30T22:11:08ZengMDPI AGFermentation2311-56372023-01-01917410.3390/fermentation9010074Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i>Abraham A. J. Kerssemakers0Süleyman Øzmerih1Gürkan Sin2Suresh Sudarsan3The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, DenmarkThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, DenmarkProcess and Systems Engineering Research Center, Department of Chemical and Biochemical Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, DenmarkThe Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kgs. Lyngby, DenmarkIndustrial-sized fermenters differ from the laboratory environment in which bioprocess development initially took place. One of the issues that can lead to reduced productivity on a large scale or even early termination of the process is the presence of bioreactor heterogeneities. This work proposes and adopts a design–build–test–learn-type workflow that estimates the substrate, oxygen, and resulting growth heterogeneities through a compartmental modelling approach and maps <i>Yarrowia lipolytica</i>-specific behavior in this relevant range of conditions. The results indicate that at a growth rate of 0.1 h<sup>−1</sup>, the largest simulated volume (90 m<sup>3</sup>) reached partial oxygen limitation. Throughout the fed-batch, the cells experienced dissolved oxygen values from 0 to 75% and grew at rates of 0 to 0.2 h<sup>−1</sup>. These simulated large-scale conditions were tested in small-scale cultivations, which elucidated a transcriptome with a strong downregulation of various transporter and central carbon metabolism genes during oxygen limitation. The relation between oxygen availability and differential gene expression was dynamic and did not show a simple on–off behavior. This indicates that <i>Y. lipolytica</i> can differentiate between different available oxygen concentrations and adjust its transcription accordingly. The workflow presented can be used for <i>Y. lipolytica</i>-based strain engineering, thereby accelerating bioprocess development.https://www.mdpi.com/2311-5637/9/1/74compartmental modellingmetabolic regimesoxygen limitationscale-downtranscriptome response |
spellingShingle | Abraham A. J. Kerssemakers Süleyman Øzmerih Gürkan Sin Suresh Sudarsan Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> Fermentation compartmental modelling metabolic regimes oxygen limitation scale-down transcriptome response |
title | Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> |
title_full | Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> |
title_fullStr | Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> |
title_full_unstemmed | Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> |
title_short | Dynamic Interplay between O<sub>2</sub> Availability, Growth Rates, and the Transcriptome of <i>Yarrowia lipolytica</i> |
title_sort | dynamic interplay between o sub 2 sub availability growth rates and the transcriptome of i yarrowia lipolytica i |
topic | compartmental modelling metabolic regimes oxygen limitation scale-down transcriptome response |
url | https://www.mdpi.com/2311-5637/9/1/74 |
work_keys_str_mv | AT abrahamajkerssemakers dynamicinterplaybetweenosub2subavailabilitygrowthratesandthetranscriptomeofiyarrowialipolyticai AT suleymanøzmerih dynamicinterplaybetweenosub2subavailabilitygrowthratesandthetranscriptomeofiyarrowialipolyticai AT gurkansin dynamicinterplaybetweenosub2subavailabilitygrowthratesandthetranscriptomeofiyarrowialipolyticai AT sureshsudarsan dynamicinterplaybetweenosub2subavailabilitygrowthratesandthetranscriptomeofiyarrowialipolyticai |