Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae
Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that l...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2014-05-01
|
| Series: | Metabolites |
| Subjects: | |
| Online Access: | http://www.mdpi.com/2218-1989/4/2/347 |
| _version_ | 1811221835655675904 |
|---|---|
| author | Camilo A. Suarez-Mendez Andre Sousa Joseph J. Heijnen Aljoscha Wahl |
| author_facet | Camilo A. Suarez-Mendez Andre Sousa Joseph J. Heijnen Aljoscha Wahl |
| author_sort | Camilo A. Suarez-Mendez |
| collection | DOAJ |
| description | Microorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism’s physiology under dynamic conditions. We found that the biomass yield was slightly reduced (−5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments). |
| first_indexed | 2024-04-12T08:06:59Z |
| format | Article |
| id | doaj.art-b58fe519be49418eab993fb800f96b61 |
| institution | Directory Open Access Journal |
| issn | 2218-1989 |
| language | English |
| last_indexed | 2024-04-12T08:06:59Z |
| publishDate | 2014-05-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Metabolites |
| spelling | doaj.art-b58fe519be49418eab993fb800f96b612022-12-22T03:41:09ZengMDPI AGMetabolites2218-19892014-05-014234737210.3390/metabo4020347metabo4020347Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiaeCamilo A. Suarez-Mendez0Andre Sousa1Joseph J. Heijnen2Aljoscha Wahl3Department of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The NetherlandsDepartment of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The NetherlandsDepartment of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The NetherlandsDepartment of Biotechnology, Delft University of Technology, Julianalaan 67, 2628 BC Delft, The NetherlandsMicroorganisms are constantly exposed to rapidly changing conditions, under natural as well as industrial production scale environments, especially due to large-scale substrate mixing limitations. In this work, we present an experimental approach based on a dynamic feast/famine regime (400 s) that leads to repetitive cycles with moderate changes in substrate availability in an aerobic glucose cultivation of Saccharomyces cerevisiae. After a few cycles, the feast/famine produced a stable and repetitive pattern with a reproducible metabolic response in time, thus providing a robust platform for studying the microorganism’s physiology under dynamic conditions. We found that the biomass yield was slightly reduced (−5%) under the feast/famine regime, while the averaged substrate and oxygen consumption as well as the carbon dioxide production rates were comparable. The dynamic response of the intracellular metabolites showed specific differences in comparison to other dynamic experiments (especially stimulus-response experiments, SRE). Remarkably, the frequently reported ATP paradox observed in single pulse experiments was not present during the repetitive perturbations applied here. We found that intracellular dynamic accumulations led to an uncoupling of the substrate uptake rate (up to 9-fold change at 20 s.) Moreover, the dynamic profiles of the intracellular metabolites obtained with the feast/famine suggest the presence of regulatory mechanisms that resulted in a delayed response. With the feast famine setup many cellular states can be measured at high frequency given the feature of reproducible cycles. The feast/famine regime is thus a versatile platform for systems biology approaches, which can help us to identify and investigate metabolite regulations under realistic conditions (e.g., large-scale bioreactors or natural environments).http://www.mdpi.com/2218-1989/4/2/347feast/famine perturbationyeast cultivationdynamic metabolic responseATP paradox in vivo kinetics |
| spellingShingle | Camilo A. Suarez-Mendez Andre Sousa Joseph J. Heijnen Aljoscha Wahl Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae Metabolites feast/famine perturbation yeast cultivation dynamic metabolic response ATP paradox in vivo kinetics |
| title | Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae |
| title_full | Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae |
| title_fullStr | Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae |
| title_full_unstemmed | Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae |
| title_short | Fast “Feast/Famine” Cycles for Studying Microbial Physiology Under Dynamic Conditions: A Case Study with Saccharomyces cerevisiae |
| title_sort | fast feast famine cycles for studying microbial physiology under dynamic conditions a case study with saccharomyces cerevisiae |
| topic | feast/famine perturbation yeast cultivation dynamic metabolic response ATP paradox in vivo kinetics |
| url | http://www.mdpi.com/2218-1989/4/2/347 |
| work_keys_str_mv | AT camiloasuarezmendez fastfeastfaminecyclesforstudyingmicrobialphysiologyunderdynamicconditionsacasestudywithsaccharomycescerevisiae AT andresousa fastfeastfaminecyclesforstudyingmicrobialphysiologyunderdynamicconditionsacasestudywithsaccharomycescerevisiae AT josephjheijnen fastfeastfaminecyclesforstudyingmicrobialphysiologyunderdynamicconditionsacasestudywithsaccharomycescerevisiae AT aljoschawahl fastfeastfaminecyclesforstudyingmicrobialphysiologyunderdynamicconditionsacasestudywithsaccharomycescerevisiae |