1
|
Wang Z, Li M, Xu S, Sun L, Li L. High-throughput relative quantification of fatty acids by 12-plex isobaric labeling and microchip capillary electrophoresis - Mass spectrometry. Anal Chim Acta 2024; 1318:342905. [PMID: 39067909 PMCID: PMC11299455 DOI: 10.1016/j.aca.2024.342905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Accepted: 06/23/2024] [Indexed: 07/30/2024]
Abstract
BACKGROUND Fatty acids (FAs) are essential cellular components and play important roles in various biological processes. Importantly, FAs produced by microorganisms from renewable sugars are considered sustainable substrates for biodiesels and oleochemicals. Their complex structures and diverse functional roles in biochemical processes necessitate the development of efficient and accurate methods for their quantitative analysis. RESULTS Here, we developed a novel method for relative quantification of FAs by combining 12-plex isobaric N,N-dimethyl leucine-derivatized ethylenediamine (DiLeuEN) labeling and microchip capillary electrophoresis-mass spectrometry (CE-MS). This method enables simultaneous quantification of 12 samples in a single MS analysis. DiLeuEN labeling introduced tertiary amine center structure into FAs, which makes them compatible with the positive mode separation of commercial microchip CE systems and further improves the sensitivity. The CE separation parameters were optimized, and the quantification accuracy was assessed using FA standards. Microchip CE-MS detection exhibited high sensitivity with a femtomole level detection limit and a total analysis time within 8 min. Finally, the applicability of our method to complex biological samples was demonstrated by analyzing FAs produced by four industrially relevant yeast strains (Saccharomyces cerevisiae, Yarrowia lipolytica YB-432, Yarrowia lipolytica Po1f and Rhodotorula glutinis). The analysis time for each sample is less than 1 min. SIGNIFICANCE This work addresses the current challenges in the field by introducing a method that combines microchip-based capillary electrophoresis separation with multiplex isobaric labeling. Our method not only offers remarkable sensitivity and rapid analysis speed but also the capability to quantify fatty acids across multiple samples simultaneously, which holds significant potential for extensive application in FA quantitative studies in diverse research areas, promising an enhanced understanding of FA functions and mechanisms.
Collapse
Affiliation(s)
- Zicong Wang
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Miyang Li
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Shuling Xu
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Liang Sun
- Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, 53726, USA
| | - Lingjun Li
- School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA; Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA; Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI, 53705, USA.
| |
Collapse
|
2
|
Trivellin C, Torello Pianale L, Olsson L. Robustness quantification of a mutant library screen revealed key genetic markers in yeast. Microb Cell Fact 2024; 23:218. [PMID: 39098937 PMCID: PMC11298085 DOI: 10.1186/s12934-024-02490-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 07/24/2024] [Indexed: 08/06/2024] Open
Abstract
BACKGROUND Microbial robustness is crucial for developing cell factories that maintain consistent performance in a challenging environment such as large-scale bioreactors. Although tools exist to assess and understand robustness at a phenotypic level, the underlying metabolic and genetic mechanisms are not well defined, which limits our ability to engineer more strains with robust functions. RESULTS This study encompassed four steps. (I) Fitness and robustness were analyzed from a published dataset of yeast mutants grown in multiple environments. (II) Genes and metabolic processes affecting robustness or fitness were identified, and 14 of these genes were deleted in Saccharomyces cerevisiae CEN.PK113-7D. (III) The mutants bearing gene deletions were cultivated in three perturbation spaces mimicking typical industrial processes. (IV) Fitness and robustness were determined for each mutant in each perturbation space. We report that robustness varied according to the perturbation space. We identified genes associated with increased robustness such as MET28, linked to sulfur metabolism; as well as genes associated with decreased robustness, including TIR3 and WWM1, both involved in stress response and apoptosis. CONCLUSION The present study demonstrates how phenomics datasets can be analyzed to reveal the relationship between phenotypic response and associated genes. Specifically, robustness analysis makes it possible to study the influence of single genes and metabolic processes on stable microbial performance in different perturbation spaces. Ultimately, this information can be used to enhance robustness in targeted strains.
Collapse
Affiliation(s)
- Cecilia Trivellin
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Luca Torello Pianale
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Lisbeth Olsson
- Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, 412 96, Gothenburg, Sweden.
| |
Collapse
|
3
|
Koster CC, Kleefeldt AA, van den Broek M, Luttik M, Daran JM, Daran-Lapujade P. Long-read direct RNA sequencing of the mitochondrial transcriptome of Saccharomyces cerevisiae reveals condition-dependent intron abundance. Yeast 2024; 41:256-278. [PMID: 37642136 DOI: 10.1002/yea.3893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
Mitochondria fulfil many essential roles and have their own genome, which is expressed as polycistronic transcripts that undergo co- or posttranscriptional processing and splicing. Due to the inherent complexity and limited technical accessibility of the mitochondrial transcriptome, fundamental questions regarding mitochondrial gene expression and splicing remain unresolved, even in the model eukaryote Saccharomyces cerevisiae. Long-read sequencing could address these fundamental questions. Therefore, a method for the enrichment of mitochondrial RNA and sequencing using Nanopore technology was developed, enabling the resolution of splicing of polycistronic genes and the quantification of spliced RNA. This method successfully captured the full mitochondrial transcriptome and resolved RNA splicing patterns with single-base resolution and was applied to explore the transcriptome of S. cerevisiae grown with glucose or ethanol as the sole carbon source, revealing the impact of growth conditions on mitochondrial RNA expression and splicing. This study uncovered a remarkable difference in the turnover of Group II introns between yeast grown in either mostly fermentative or fully respiratory conditions. Whether this accumulation of introns in glucose medium has an impact on mitochondrial functions remains to be explored. Combined with the high tractability of the model yeast S. cerevisiae, the developed method enables to monitor mitochondrial transcriptome responses in a broad range of relevant contexts, including oxidative stress, apoptosis and mitochondrial diseases.
Collapse
Affiliation(s)
- Charlotte C Koster
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Askar A Kleefeldt
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Marijke Luttik
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | |
Collapse
|
4
|
Ehrmann AK, Wronska AK, Perli T, de Hulster EAF, Luttik MAH, van den Broek M, Carqueija Cardoso C, Pronk JT, Daran JM. Engineering Saccharomyces cerevisiae for fast vitamin-independent aerobic growth. Metab Eng 2024; 82:201-215. [PMID: 38364997 DOI: 10.1016/j.ymben.2024.01.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 01/08/2024] [Accepted: 01/26/2024] [Indexed: 02/18/2024]
Abstract
Chemically defined media for cultivation of Saccharomyces cerevisiae strains are commonly supplemented with a mixture of multiple Class-B vitamins, whose omission leads to strongly reduced growth rates. Fast growth without vitamin supplementation is interesting for industrial applications, as it reduces costs and complexity of medium preparation and may decrease susceptibility to contamination by auxotrophic microbes. In this study, suboptimal growth rates of S. cerevisiae CEN.PK113-7D in the absence of pantothenic acid, para-aminobenzoic acid (pABA), pyridoxine, inositol and/or biotin were corrected by single or combined overexpression of ScFMS1, ScABZ1/ScABZ2, ScSNZ1/ScSNO1, ScINO1 and Cyberlindnera fabianii BIO1, respectively. Several strategies were explored to improve growth of S. cerevisiae CEN.PK113-7D in thiamine-free medium. Overexpression of ScTHI4 and/or ScTHI5 enabled thiamine-independent growth at 83% of the maximum specific growth rate of the reference strain in vitamin-supplemented medium. Combined overexpression of seven native S. cerevisiae genes and CfBIO1 enabled a maximum specific growth rate of 0.33 ± 0.01 h-1 in vitamin-free synthetic medium. This growth rate was only 17 % lower than that of a congenic reference strain in vitamin-supplemented medium. Physiological parameters of the engineered vitamin-independent strain in aerobic glucose-limited chemostat cultures (dilution rate 0.10 h-1) grown on vitamin-free synthetic medium were similar to those of similar cultures of the parental strain grown on vitamin-supplemented medium. Transcriptome analysis revealed only few differences in gene expression between these cultures, which primarily involved genes with roles in Class-B vitamin metabolism. These results pave the way for development of fast-growing vitamin-independent industrial strains of S. cerevisiae.
Collapse
Affiliation(s)
- Anja K Ehrmann
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800 Kgs, Lyngby, Denmark
| | - Anna K Wronska
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Thomas Perli
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Erik A F de Hulster
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marijke A H Luttik
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Marcel van den Broek
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Clara Carqueija Cardoso
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, the Netherlands.
| |
Collapse
|
5
|
Kerruish DWM, Cormican P, Kenny EM, Kearns J, Colgan E, Boulton CA, Stelma SNE. The origins of the Guinness stout yeast. Commun Biol 2024; 7:68. [PMID: 38216745 PMCID: PMC10786833 DOI: 10.1038/s42003-023-05587-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/14/2023] [Indexed: 01/14/2024] Open
Abstract
Beer is made via the fermentation of an aqueous extract predominantly composed of malted barley flavoured with hops. The transforming microorganism is typically a single strain of Saccharomyces cerevisiae, and for the majority of major beer brands the yeast strain is a unique component. The present yeast used to make Guinness stout brewed in Dublin, Ireland, can be traced back to 1903, but its origins are unknown. To that end, we used Illumina and Nanopore sequencing to generate whole-genome sequencing data for a total of 22 S. cerevisiae yeast strains: 16 from the Guinness collection and 6 other historical Irish brewing. The origins of the Guinness yeast were determined with a SNP-based analysis, demonstrating that the Guinness strains occupy a distinct group separate from other historical Irish brewing yeasts. Assessment of chromosome number, copy number variation and phenotypic evaluation of key brewing attributes established Guinness yeast-specific SNPs but no specific chromosomal amplifications. Our analysis also demonstrated the effects of yeast storage on phylogeny. Altogether, our results suggest that the Guinness yeast used today is related to the first deposited Guinness yeast; the 1903 Watling Laboratory Guinness yeast.
Collapse
Affiliation(s)
| | | | | | - Jessica Kearns
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
| | - Eibhlin Colgan
- Diageo Ireland, St James's Gate, The Liberties, Dublin, Ireland
| | | | | |
Collapse
|
6
|
Zhang X, Nijland JG, Driessen AJM. Maltose accumulation-induced cell death in Saccharomyces cerevisiae. FEMS Yeast Res 2024; 24:foae012. [PMID: 38565313 PMCID: PMC11037483 DOI: 10.1093/femsyr/foae012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/12/2024] [Accepted: 04/01/2024] [Indexed: 04/04/2024] Open
Abstract
Pretreatment of lignocellulose yields a complex sugar mixture that potentially can be converted into bioethanol and other chemicals by engineered yeast. One approach to overcome competition between sugars for uptake and metabolism is the use of a consortium of specialist strains capable of efficient conversion of single sugars. Here, we show that maltose inhibits cell growth of a xylose-fermenting specialist strain IMX730.1 that is unable to utilize glucose because of the deletion of all hexokinase genes. The growth inhibition cannot be attributed to a competition between maltose and xylose for uptake. The inhibition is enhanced in a strain lacking maltase enzymes (dMalX2) and completely eliminated when all maltose transporters are deleted. High-level accumulation of maltose in the dMalX2 strain is accompanied by a hypotonic-like transcriptional response, while cells are rescued from maltose-induced cell death by the inclusion of an extracellular osmolyte such as sorbitol. These data suggest that maltose-induced cell death is due to high levels of maltose uptake causing hypotonic-like stress conditions and can be prevented through engineering of the maltose transporters. Transporter engineering should be included in the development of stable microbial consortia for the efficient conversion of lignocellulosic feedstocks.
Collapse
Affiliation(s)
- Xiaohuan Zhang
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Nijenborgh 7, 9747AG Groningen, the Netherlands
| |
Collapse
|
7
|
Yao L, Jia Y, Zhang Q, Zheng X, Yang H, Dai J, Chen X. Adaptive laboratory evolution to obtain furfural tolerant Saccharomyces cerevisiae for bioethanol production and the underlying mechanism. Front Microbiol 2024; 14:1333777. [PMID: 38239732 PMCID: PMC10794740 DOI: 10.3389/fmicb.2023.1333777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/05/2023] [Indexed: 01/22/2024] Open
Abstract
Introduction Furfural, a main inhibitor produced during pretreatment of lignocellulose, has shown inhibitory effects on S. cerevisiae. Method In the present study, new strains named 12-1 with enhanced resistance to furfural were obtained through adaptive laboratory evolution, which exhibited a shortened lag phase by 36 h, and an increased ethanol conversion rate by 6.67% under 4 g/L furfural. Results and Discussion To further explore the mechanism of enhanced furfural tolerance, ADR1_1802 mutant was constructed by CRISPR/Cas9 technology, based on whole genome re-sequencing data. The results indicated that the time when ADR1_1802 begin to grow was shortened by 20 h compared with reference strain (S. cerevisiae CEN.PK113-5D) when furfural was 4 g/L. Additionally, the transcription levels of GRE2 and ADH6 in ADR1_ 1802 mutant were increased by 53.69 and 44.95%, respectively, according to real-time fluorescence quantitative PCR analysis. These findings suggest that the enhanced furfural tolerance of mutant is due to accelerated furfural degradation. Importance: Renewable carbon worldwide is vital to achieve "zero carbon" target. Bioethanol obtained from biomass is one of them. To make bioethanol price competitive to fossil fuel, higher ethanol yield is necessary, therefore, monosaccharide produced during biomass pretreatment should be effectively converted to ethanol by Saccharomyces cerevisiae. However, inhibitors formed by glucose or xylose oxidation could make ethanol yield lower. Thus, inhibitor tolerant Saccharomyces cerevisiae is important to this process. As one of the main component of pretreatment hydrolysate, furfural shows obvious impact on growth and ethanol production of Saccharomyces cerevisiae. To get furfural tolerant Saccharomyces cerevisiae and find the underlying mechanism, adaptive laboratory evolution and CRISPR/Cas9 technology were applied in the present study.
Collapse
Affiliation(s)
- Lan Yao
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Youpiao Jia
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Qingyan Zhang
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Xueyun Zheng
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Haitao Yang
- Hubei Provincial Key Laboratory of Green Materials for Light Industry, Hubei University of Technology, Wuhan, China
| | - Jun Dai
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| | - Xiong Chen
- Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education and Hubei Province), College of Bioengineering, Hubei University of Technology, Wuhan, China
| |
Collapse
|
8
|
Torello Pianale L, Caputo F, Olsson L. Four ways of implementing robustness quantification in strain characterisation. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:195. [PMID: 38115067 PMCID: PMC10729505 DOI: 10.1186/s13068-023-02445-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 12/05/2023] [Indexed: 12/21/2023]
Abstract
BACKGROUND In industrial bioprocesses, microorganisms are generally selected based on performance, whereas robustness, i.e., the ability of a system to maintain a stable performance, has been overlooked due to the challenges in its quantification and implementation into routine experimental procedures. This work presents four ways of implementing robustness quantification during strain characterisation. One Saccharomyces cerevisiae laboratory strain (CEN.PK113-7D) and two industrial strains (Ethanol Red and PE2) grown in seven different lignocellulosic hydrolysates were assessed for growth-related functions (specific growth rate, product yields, etc.) and eight intracellular parameters (using fluorescent biosensors). RESULTS Using flasks and high-throughput experimental setups, robustness was quantified in relation to: (i) stability of growth functions in response to the seven hydrolysates; (ii) stability of growth functions across different strains to establish the impact of perturbations on yeast metabolism; (iii) stability of intracellular parameters over time; (iv) stability of intracellular parameters within a cell population to indirectly quantify population heterogeneity. Ethanol Red was the best-performing strain under all tested conditions, achieving the highest growth function robustness. PE2 displayed the highest population heterogeneity. Moreover, the intracellular environment varied in response to non-woody or woody lignocellulosic hydrolysates, manifesting increased oxidative stress and unfolded protein response, respectively. CONCLUSIONS Robustness quantification is a powerful tool for strain characterisation as it offers novel information on physiological and biochemical parameters. Owing to the flexibility of the robustness quantification method, its implementation was successfully validated at single-cell as well as high-throughput levels, showcasing its versatility and potential for several applications.
Collapse
Affiliation(s)
- Luca Torello Pianale
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Fabio Caputo
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Lisbeth Olsson
- Industrial Biotechnology Division, Department of Life Sciences, Chalmers University of Technology, Gothenburg, Sweden.
| |
Collapse
|
9
|
van Aalst ACA, van der Meulen IS, Jansen MLA, Mans R, Pronk JT. Co-cultivation of Saccharomyces cerevisiae strains combines advantages of different metabolic engineering strategies for improved ethanol yield. Metab Eng 2023; 80:151-162. [PMID: 37751790 DOI: 10.1016/j.ymben.2023.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 09/14/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023]
Abstract
Glycerol is the major organic byproduct of industrial ethanol production with the yeast Saccharomyces cerevisiae. Improved ethanol yields have been achieved with engineered S. cerevisiae strains in which heterologous pathways replace glycerol formation as the predominant mechanism for anaerobic re-oxidation of surplus NADH generated in biosynthetic reactions. Functional expression of heterologous phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) genes enables yeast cells to couple a net oxidation of NADH to the conversion of glucose to ethanol. In another strategy, NADH-dependent reduction of exogenous acetate to ethanol is enabled by introduction of a heterologous acetylating acetaldehyde dehydrogenase (A-ALD). This study explores potential advantages of co-cultivating engineered PRK-RuBisCO-based and A-ALD-based strains in anaerobic bioreactor batch cultures. Co-cultivation of these strains, which in monocultures showed reduced glycerol yields and improved ethanol yields, strongly reduced the formation of acetaldehyde and acetate, two byproducts that were formed in anaerobic monocultures of a PRK-RuBisCO-based strain. In addition, co-cultures on medium with low acetate-to-glucose ratios that mimicked those in industrial feedstocks completely removed acetate from the medium. Kinetics of co-cultivation processes and glycerol production could be optimized by tuning the relative inoculum sizes of the two strains. Co-cultivation of a PRK-RuBisCO strain with a Δgpd1 Δgpd2 A-ALD strain, which was unable to grow in the absence of acetate and evolved for faster anaerobic growth in acetate-supplemented batch cultures, further reduced glycerol formation but led to extended fermentation times. These results demonstrate the potential of using defined consortia of engineered S. cerevisiae strains for high-yield, minimal-waste ethanol production.
Collapse
Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Igor S van der Meulen
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613, AX, Delft, the Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
| |
Collapse
|
10
|
Wang H, Li Q, Zhang Z, Ayepa E, Xiang Q, Yu X, Zhao K, Zou L, Gu Y, Li X, Chen Q, Zhang X, Yang Y, Jin X, Yin H, Liu ZL, Tang T, Liu B, Ma M. Discovery of new strains for furfural degradation using adaptive laboratory evolution in Saccharomyces cerevisiae. JOURNAL OF HAZARDOUS MATERIALS 2023; 459:132090. [PMID: 37480608 DOI: 10.1016/j.jhazmat.2023.132090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/15/2023] [Accepted: 07/17/2023] [Indexed: 07/24/2023]
Abstract
In industrial production, the excessive discharge of furfural can pose harm to soil microorganisms, aquatic animals and plants, as well as humans. Therefore, it is crucial to develop efficient and cost-effective methods for degrading furfural in the environment. Currently, the use of Saccharomyces cerevisiae for furfural degradation in water has shown effectiveness, but there is a need to explore improved efficiency and tolerance in S. cerevisiae for this purpose. In this study, we isolated and evolved highly efficient furfural degradation strains, namely YBA_08 and F60C. These strains exhibited remarkable capabilities, degrading 59% and 99% furfural in the YPD medium after 72 h of incubation, significantly higher than the 31% achieved by the model strain S288C. Through analysis of the efficient degradation mechanism in the evolutionary strain F60C, we discovered a 326% increase in the total amount of NADH and NADPH. This increase likely promotes faster furfural degradation through intracellular aldehyde reductases. Moreover, the decrease in NADPH content led to a 406% increase in glutathione content at the background level, which protects cells from damage caused by reactive oxygen species. Mutations and differential expression related to cell cycle and cell wall synthesis were observed, enabling cell survival in the presence of furfural and facilitating rapid furfural degradation and growth recovery. Based on these findings, it is speculated that strains YBA_08 and F60C have the potential to contribute to furfural degradation in water and the production of furfuryl alcohol, ethanol, and FDCA in biorefinery processes.
Collapse
Affiliation(s)
- Hanyu Wang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China; College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China; Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China
| | - Qian Li
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Zhengyue Zhang
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Ellen Ayepa
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Quanju Xiang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiumei Yu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Ke Zhao
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Likou Zou
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Yunfu Gu
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xi Li
- College of Landscape Architecture, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Qiang Chen
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Xiaoping Zhang
- Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Yaojun Yang
- College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China; Bamboo Diseases and Pests Control and Resources Development Key Laboratory of Sichuan Province, College of Life Science, Leshan Normal University, Leshan, Sichuan 614000, China
| | - Xuejiao Jin
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, Zhejiang 311300, China
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China
| | - Z Lewis Liu
- The US Department of Agriculture, Agricultural Research Service, National Center for Agricultural Utilization Research, Bioenergy Research Unit, 1815 N University Street, Peoria, IL 61604, USA
| | - Tianle Tang
- Key Laboratory of Tropical Transitional Medicine of Ministry of Education, Hainan Medical University, No.3 Xueyuan Road, Haikou, Hainan 571199, China.
| | - Beidong Liu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Lin'an, Hangzhou, Zhejiang 311300, China; Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9C, 413 90 Göteburg, Sweden.
| | - Menggen Ma
- Institute of Resources and Geographic Information Technology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China; Department of Applied Microbiology, College of Resources, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan 611130, China.
| |
Collapse
|
11
|
van Aalst ACA, Jansen MLA, Mans R, Pronk JT. Quantification and mitigation of byproduct formation by low-glycerol-producing Saccharomyces cerevisiae strains containing Calvin-cycle enzymes. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:81. [PMID: 37173767 PMCID: PMC10176687 DOI: 10.1186/s13068-023-02329-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 04/24/2023] [Indexed: 05/15/2023]
Abstract
BACKGROUND Anaerobic Saccharomyces cerevisiae cultures require glycerol formation to re-oxidize NADH formed in biosynthetic processes. Introduction of the Calvin-cycle enzymes phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) has been shown to couple re-oxidation of biosynthetic NADH to ethanol production and improve ethanol yield on sugar in fast-growing batch cultures. Since growth rates in industrial ethanol production processes are not constant, performance of engineered strains was studied in slow-growing cultures. RESULTS In slow-growing anaerobic chemostat cultures (D = 0.05 h-1), an engineered PRK/RuBisCO strain produced 80-fold more acetaldehyde and 30-fold more acetate than a reference strain. This observation suggested an imbalance between in vivo activities of PRK/RuBisCO and formation of NADH in biosynthesis. Lowering the copy number of the RuBisCO-encoding cbbm expression cassette from 15 to 2 reduced acetaldehyde and acetate production by 67% and 29%, respectively. Additional C-terminal fusion of a 19-amino-acid tag to PRK reduced its protein level by 13-fold while acetaldehyde and acetate production decreased by 94% and 61%, respectively, relative to the 15 × cbbm strain. These modifications did not affect glycerol production at 0.05 h-1 but caused a 4.6 fold higher glycerol production per amount of biomass in fast-growing (0.29 h-1) anaerobic batch cultures than observed for the 15 × cbbm strain. In another strategy, the promoter of ANB1, whose transcript level positively correlated with growth rate, was used to control PRK synthesis in a 2 × cbbm strain. At 0.05 h-1, this strategy reduced acetaldehyde and acetate production by 79% and 40%, respectively, relative to the 15 × cbbm strain, without affecting glycerol production. The maximum growth rate of the resulting strain equalled that of the reference strain, while its glycerol production was 72% lower. CONCLUSIONS Acetaldehyde and acetate formation by slow-growing cultures of engineered S. cerevisiae strains carrying a PRK/RuBisCO bypass of yeast glycolysis was attributed to an in vivo overcapacity of PRK and RuBisCO. Reducing the capacity of PRK and/or RuBisCO was shown to mitigate this undesirable byproduct formation. Use of a growth rate-dependent promoter for PRK expression highlighted the potential of modulating gene expression in engineered strains to respond to growth-rate dynamics in industrial batch processes.
Collapse
Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands.
| |
Collapse
|
12
|
Minden S, Aniolek M, Noorman H, Takors R. Mimicked Mixing-Induced Heterogeneities of Industrial Bioreactors Stimulate Long-Lasting Adaption Programs in Ethanol-Producing Yeasts. Genes (Basel) 2023; 14:genes14050997. [PMID: 37239357 DOI: 10.3390/genes14050997] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 04/24/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
Commercial-scale bioreactors create an unnatural environment for microbes from an evolutionary point of view. Mixing insufficiencies expose individual cells to fluctuating nutrient concentrations on a second-to-minute scale while transcriptional and translational capacities limit the microbial adaptation time from minutes to hours. This mismatch carries the risk of inadequate adaptation effects, especially considering that nutrients are available at optimal concentrations on average. Consequently, industrial bioprocesses that strive to maintain microbes in a phenotypic sweet spot, during lab-scale development, might suffer performance losses when said adaptive misconfigurations arise during scale-up. Here, we investigated the influence of fluctuating glucose availability on the gene-expression profile in the industrial yeast Ethanol Red™. The stimulus-response experiment introduced 2 min glucose depletion phases to cells growing under glucose limitation in a chemostat. Even though Ethanol Red™ displayed robust growth and productivity, a single 2 min depletion of glucose transiently triggered the environmental stress response. Furthermore, a new growth phenotype with an increased ribosome portfolio emerged after complete adaptation to recurring glucose shortages. The results of this study serve a twofold purpose. First, it highlights the necessity to consider the large-scale environment already at the experimental development stage, even when process-related stressors are moderate. Second, it allowed the deduction of strain engineering guidelines to optimize the genetic background of large-scale production hosts.
Collapse
Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany
| |
Collapse
|
13
|
Soares Rodrigues CI, den Ridder M, Pabst M, Gombert AK, Wahl SA. Comparative proteome analysis of different Saccharomyces cerevisiae strains during growth on sucrose and glucose. Sci Rep 2023; 13:2126. [PMID: 36746999 PMCID: PMC9902475 DOI: 10.1038/s41598-023-29172-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 01/30/2023] [Indexed: 02/08/2023] Open
Abstract
Both the identity and the amount of a carbon source present in laboratory or industrial cultivation media have major impacts on the growth and physiology of a microbial species. In the case of the yeast Saccharomyces cerevisiae, sucrose is arguably the most important sugar used in industrial biotechnology, whereas glucose is the most common carbon and energy source used in research, with many well-known and described regulatory effects, e.g. glucose repression. Here we compared the label-free proteomes of exponentially growing S. cerevisiae cells in a defined medium containing either sucrose or glucose as the sole carbon source. For this purpose, bioreactor cultivations were employed, and three different strains were investigated, namely: CEN.PK113-7D (a common laboratory strain), UFMG-CM-Y259 (a wild isolate), and JP1 (an industrial bioethanol strain). These strains present different physiologies during growth on sucrose; some of them reach higher specific growth rates on this carbon source, when compared to growth on glucose, whereas others display the opposite behavior. It was not possible to identify proteins that commonly presented either higher or lower levels during growth on sucrose, when compared to growth on glucose, considering the three strains investigated here, except for one protein, named Mnp1-a mitochondrial ribosomal protein of the large subunit, which had higher levels on sucrose than on glucose, for all three strains. Interestingly, following a Gene Ontology overrepresentation and KEGG pathway enrichment analyses, an inverse pattern of enriched biological functions and pathways was observed for the strains CEN.PK113-7D and UFMG-CM-Y259, which is in line with the fact that whereas the CEN.PK113-7D strain grows faster on glucose than on sucrose, the opposite is observed for the UFMG-CM-Y259 strain.
Collapse
Affiliation(s)
- Carla Inês Soares Rodrigues
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands.,School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil.,Cargill R&D Centre Europe, Havenstraat 84, 1800, Vilvoorde, Belgium.,DAB.bio, Alexander Fleminglaan 1, 2613 AX, Delft, The Netherlands
| | - Maxime den Ridder
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Martin Pabst
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - Sebastian Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629 HZ, Delft, The Netherlands. .,Lehrstuhl für Bioverfahrenstechnik, Friedrich-Alexander Universität Erlangen-Nürnberg, Paul-Gordan-Str. 3-5, 91052, Erlangen, Germany.
| |
Collapse
|
14
|
van Aalst ACA, Geraats EH, Jansen MLA, Mans R, Pronk JT. Optimizing the balance between heterologous acetate- and CO2-reduction pathways in anaerobic cultures of Saccharomyces cerevisiae strains engineered for low-glycerol production. FEMS Yeast Res 2023; 23:foad048. [PMID: 37942589 PMCID: PMC10647013 DOI: 10.1093/femsyr/foad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 10/24/2023] [Accepted: 11/03/2023] [Indexed: 11/10/2023] Open
Abstract
In anaerobic Saccharomyces cerevisiae cultures, NADH (reduced form of nicotinamide adenine dinucleotide)-cofactor balancing by glycerol formation constrains ethanol yields. Introduction of an acetate-to-ethanol reduction pathway based on heterologous acetylating acetaldehyde dehydrogenase (A-ALD) can replace glycerol formation as 'redox-sink' and improve ethanol yields in acetate-containing media. Acetate concentrations in feedstock for first-generation bioethanol production are, however, insufficient to completely replace glycerol formation. An alternative glycerol-reduction strategy bypasses the oxidative reaction in glycolysis by introducing phosphoribulokinase (PRK) and ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). For optimal performance in industrial settings, yeast strains should ideally first fully convert acetate and, subsequently, continue low-glycerol fermentation via the PRK-RuBisCO pathway. However, anaerobic batch cultures of a strain carrying both pathways showed inferior acetate reduction relative to a strain expressing only the A-ALD pathway. Complete A-ALD-mediated acetate reduction by a dual-pathway strain, grown anaerobically on 50 g L-1 glucose and 5 mmol L-1 acetate, was achieved upon reducing PRK abundance by a C-terminal extension of its amino acid sequence. Yields of glycerol and ethanol on glucose were 55% lower and 6% higher, respectively, than those of a nonengineered reference strain. The negative impact of the PRK-RuBisCO pathway on acetate reduction was attributed to sensitivity of the reversible A-ALD reaction to intracellular acetaldehyde concentrations.
Collapse
Affiliation(s)
- Aafke C A van Aalst
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Ellen H Geraats
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Mickel L A Jansen
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
15
|
Holyavkin C, Turanlı-Yıldız B, Yılmaz Ü, Alkım C, Arslan M, Topaloğlu A, Kısakesen Hİ, de Billerbeck G, François JM, Çakar ZP. Genomic, transcriptomic, and metabolic characterization of 2-Phenylethanol-resistant Saccharomyces cerevisiae obtained by evolutionary engineering. Front Microbiol 2023; 14:1148065. [PMID: 37113225 PMCID: PMC10127108 DOI: 10.3389/fmicb.2023.1148065] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/13/2023] [Indexed: 04/29/2023] Open
Abstract
2-Phenylethanol is an aromatic compound commonly used in the food, cosmetic, and pharmaceutical industries. Due to increasing demand for natural products by consumers, the production of this flavor by microbial fermentation is gaining interest, as a sustainable alternative to chemical synthesis or expensive plant extraction, both processes relying on the use of fossil resources. However, the drawback of the fermentation process is the high toxicity of 2-phenylethanol to the producing microorganism. The aim of this study was to obtain a 2-phenylethanol-resistant Saccharomyces cerevisiae strain by in vivo evolutionary engineering and characterize the adapted yeast at the genomic, transcriptomic and metabolic levels. For this purpose, the tolerance to 2-phenylethanol was developed by gradually increasing the concentration of this flavor compound through successive batch cultivations, leading to an adapted strain that could tolerate 3.4 g/L of 2-phenylethanol, which was about 3-times better than the reference strain. Genome sequencing of the adapted strain identified point mutations in several genes, notably in HOG1 that encodes the Mitogen-Activated Kinase of the high-osmolarity signaling pathway. As this mutation is localized in the phosphorylation lip of this protein, it likely resulted in a hyperactive protein kinase. Transcriptomic analysis of the adapted strain supported this suggestion by revealing a large set of upregulated stress-responsive genes that could be explained in great part by HOG1-dependent activation of the Msn2/Msn4 transcription factor. Another relevant mutation was found in PDE2 encoding the low affinity cAMP phosphodiesterase, the missense mutation of which may lead to hyperactivation of this enzyme and thereby enhance the stressful state of the 2-phenylethanol adapted strain. In addition, the mutation in CRH1 that encodes a chitin transglycosylase implicated in cell wall remodeling could account for the increased resistance of the adapted strain to the cell wall-degrading enzyme lyticase. Finally, the potent upregulation of ALD3 and ALD4 encoding NAD+ -dependent aldehyde dehydrogenase together with the observed phenylacetate resistance of the evolved strain suggest a resistance mechanism involving conversion of 2-phenylethanol into phenylacetaldehyde and phenylacetate implicating these dehydrogenases.
Collapse
Affiliation(s)
- Can Holyavkin
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Burcu Turanlı-Yıldız
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ülkü Yılmaz
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Ceren Alkım
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Mevlüt Arslan
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Alican Topaloğlu
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | - Halil İbrahim Kısakesen
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
| | | | - Jean Marie François
- Toulouse Biotechnology Institute (TBI), CNRS, INRA, INSA, Université de Toulouse, Toulouse, France
- *Correspondence: Jean Marie François,
| | - Z. Petek Çakar
- Department of Molecular Biology & Genetics, Faculty of Science & Letters, Istanbul Technical University, Istanbul, Turkey
- Dr. Orhan Öcalgiray Molecular Biology, Biotechnology and Genetics Research Center (ITU-MOBGAM), Istanbul Technical University, Istanbul, Turkey
- Z. Petek Çakar,
| |
Collapse
|
16
|
Žun G, Doberšek K, Petrovič U. Construction and evaluation of gRNA arrays for multiplex CRISPR-Cas9. Yeast 2023; 40:32-41. [PMID: 36536407 PMCID: PMC10107897 DOI: 10.1002/yea.3833] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Revised: 11/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Endonuclease system CRISPR-Cas9 represents a powerful toolbox for the budding yeast's Saccharomyces cerevisiae genome perturbation. The resulting double-strand breaks are preferentially repaired via highly efficient homologous recombination, which subsequently leads to marker-free genome editing. The goal of this study was to evaluate precise targeting of multiple loci simultaneously. To construct an array of independently expressing guide RNAs (gRNAs), the genes encoding them were assembled through a BioBrick construction procedure. We designed a multiplex CRISPR-Cas9 system for targeting 6 marker genes, whereby the gRNA array was expressed from a single plasmid. To evaluate the performance of the gRNA array, the activity of the designed system was assessed by the success rate of the introduction of perturbations within the target loci: successful gRNA expression, followed by target DNA double-strand breaks formation and their repair by homologous recombination led to premature termination of the coding sequence of the marker genes, resulting in the prevention of growth of the transformants on the corresponding selection media. In conclusion, we successfully introduced up to five simultaneous perturbations within single cells of yeast S. cerevisiae using the multiplex CRISPR-Cas9 system. While this has been done before, we here present an alternative sequential BioBrick assembly with the capability to accommodate many highly similar gRNA-expression cassettes, and an exhaustive evaluation of their performance.
Collapse
Affiliation(s)
- Gašper Žun
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| | - Katja Doberšek
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Chemistry and Biochemistry, Faculty of Chemistry and Chemical TechnologyUniversity of LjubljanaLjubljanaSlovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical SciencesJožef Stefan InstituteLjubljanaSlovenia
- Department of Biology, Biotechnical FacultyUniversity of LjubljanaLjubljanaSlovenia
| |
Collapse
|
17
|
Coral-Medina A, Morrissey JP, Camarasa C. The growth and metabolome of Saccharomyces uvarum in wine fermentations are strongly influenced by the route of nitrogen assimilation. J Ind Microbiol Biotechnol 2022; 49:6825455. [PMID: 36370452 PMCID: PMC9923386 DOI: 10.1093/jimb/kuac025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 11/01/2022] [Indexed: 11/13/2022]
Abstract
Nitrogen is a critical nutrient in beverage fermentations, influencing fermentation performance and formation of compounds that affect organoleptic properties of the product. Traditionally, most commercial wine fermentations rely on Saccharomyces cerevisiae but the potential of alternative yeasts is increasingly recognised because of the possibility to deliver innovative products and process improvements. In this regard, Saccharomyces uvarum is an attractive non-traditional yeast that, while quite closely related to S. cerevisiae, displays a different fermentative and aromatic profile. Although S. uvarum is used in cider-making and in some winemaking, better knowledge of its physiology and metabolism is required if its full potential is to be realised. To address this gap, we performed a comparative analysis of the response of S. uvarum and S. cerevisiae to 13 different sources of nitrogen, assessing key parameters such as growth, fermentation performance, the production of central carbon metabolites and aroma volatile compounds. We observed that the two species differ in the production of acetate, succinate, medium-chain fatty acids, phenylethanol, phenylethyl acetate, and fusel/branched acids in ways that reflect different distribution of fluxes in the metabolic network. The integrated analysis revealed different patterns of yeast performance and activity linked to whether growth was on amino acids metabolised via the Ehrlich pathway or on amino acids and compounds assimilated through the central nitrogen core. This study highlights differences between the two yeasts and the importance that nitrogen metabolism can play in modulating the sensory profile of wine when using S. uvarum as the fermentative yeast.
Collapse
Affiliation(s)
- Angela Coral-Medina
- SPO, Univ Montpellier, INRAE, Institut Agro, Montpellier, France,School of Microbiology, University College Cork, T12 K8AF, Cork, Ireland
| | - John P Morrissey
- School of Microbiology, University College Cork, T12 K8AF, Cork, Ireland,Environmental Research Institute and SUSFERM Fermentation Science Centre, University College Cork, T12 K8AF, Cork, Ireland
| | | |
Collapse
|
18
|
An engineered non-oxidative glycolytic bypass based on Calvin-cycle enzymes enables anaerobic co-fermentation of glucose and sorbitol by Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:112. [PMID: 36253796 PMCID: PMC9578259 DOI: 10.1186/s13068-022-02200-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 09/17/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Saccharomyces cerevisiae is intensively used for industrial ethanol production. Its native fermentation pathway enables a maximum product yield of 2 mol of ethanol per mole of glucose. Based on conservation laws, supply of additional electrons could support even higher ethanol yields. However, this option is disallowed by the configuration of the native yeast metabolic network. To explore metabolic engineering strategies for eliminating this constraint, we studied alcoholic fermentation of sorbitol. Sorbitol cannot be fermented anaerobically by S. cerevisiae because its oxidation to pyruvate via glycolysis yields one more NADH than conversion of glucose. To enable re-oxidation of this additional NADH by alcoholic fermentation, sorbitol metabolism was studied in S. cerevisiae strains that functionally express heterologous genes for ribulose-1,5-bisphosphate carboxylase (RuBisCO) and phosphoribulokinase (PRK). Together with the yeast non-oxidative pentose-phosphate pathway, these Calvin-cycle enzymes enable a bypass of the oxidative reaction in yeast glycolysis. RESULTS Consistent with earlier reports, overproduction of the native sorbitol transporter Hxt15 and the NAD+-dependent sorbitol dehydrogenase Sor2 enabled aerobic, but not anaerobic growth of S. cerevisiae on sorbitol. In anaerobic, slow-growing chemostat cultures on glucose-sorbitol mixtures, functional expression of PRK-RuBisCO pathway genes enabled a 12-fold higher rate of sorbitol co-consumption than observed in a sorbitol-consuming reference strain. Consistent with the high Km for CO2 of the bacterial RuBisCO that was introduced in the engineered yeast strains, sorbitol consumption and increased ethanol formation depended on enrichment of the inlet gas with CO2. Prolonged chemostat cultivation on glucose-sorbitol mixtures led to loss of sorbitol co-fermentation. Whole-genome resequencing after prolonged cultivation suggested a trade-off between glucose-utilization and efficient fermentation of sorbitol via the PRK-RuBisCO pathway. CONCLUSIONS Combination of the native sorbitol assimilation pathway of S. cerevisiae and an engineered PRK-RuBisCO pathway enabled RuBisCO-dependent, anaerobic co-fermentation of sorbitol and glucose. This study demonstrates the potential for increasing the flexibility of redox-cofactor metabolism in anaerobic S. cerevisiae cultures and, thereby, to extend substrate range and improve product yields in anaerobic yeast-based processes by enabling entry of additional electrons.
Collapse
|
19
|
de Mello FDSB, Coradini ALV, Carazzolle MF, Maneira C, Furlan M, Pereira GAG, Teixeira GS. Genetic mapping of a bioethanol yeast strain reveals new targets for hydroxymethylfurfural- and thermotolerance. Microbiol Res 2022; 263:127138. [DOI: 10.1016/j.micres.2022.127138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/14/2022] [Accepted: 07/14/2022] [Indexed: 10/16/2022]
|
20
|
Pfister B, Shields JM, Kockmann T, Grossmann J, Abt MR, Stadler M, Zeeman SC. Tuning heterologous glucan biosynthesis in yeast to understand and exploit plant starch diversity. BMC Biol 2022; 20:207. [PMID: 36153520 PMCID: PMC9509603 DOI: 10.1186/s12915-022-01408-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/13/2022] [Indexed: 11/30/2022] Open
Abstract
Background Starch, a vital plant-derived polysaccharide comprised of branched glucans, is essential in nutrition and many industrial applications. Starch is often modified post-extraction to alter its structure and enhance its functionality. Targeted metabolic engineering of crops to produce valuable and versatile starches requires knowledge of the relationships between starch biosynthesis, structure, and properties, but systematic studies to obtain this knowledge are difficult to conduct in plants. Here we used Saccharomyces cerevisiae as a testbed to dissect the functions of plant starch biosynthetic enzymes and create diverse starch-like polymers. Results We explored yeast promoters and terminators to tune the expression levels of the starch-biosynthesis machinery from Arabidopsis thaliana. We systematically modulated the expression of each starch synthase (SS) together with a branching enzyme (BE) in yeast. Protein quantification by parallel reaction monitoring (targeted proteomics) revealed unexpected effects of glucan biosynthesis on protein abundances but showed that the anticipated broad range of SS/BE enzyme ratios was maintained during the biosynthetic process. The different SS/BE ratios clearly influenced glucan structure and solubility: The higher the SS/BE ratio, the longer the glucan chains and the more glucans were partitioned into the insoluble fraction. This effect was irrespective of the SS isoform, demonstrating that the elongation/branching ratio controls glucan properties separate from enzyme specificity. Conclusions Our results provide a quantitative framework for the in silico design of improved starch biosynthetic processes in plants. Our study also exemplifies a workflow for the rational tuning of a complex pathway in yeast, starting from the selection and evaluation of expression modules to multi-gene assembly and targeted protein monitoring during the biosynthetic process. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01408-x.
Collapse
|
21
|
Abstract
Saccharomyces cerevisiae, whose evolutionary past includes a whole-genome duplication event, is characterized by a mosaic genome configuration with substantial apparent genetic redundancy. This apparent redundancy raises questions about the evolutionary driving force for genomic fixation of “minor” paralogs and complicates modular and combinatorial metabolic engineering strategies. While isoenzymes might be important in specific environments, they could be dispensable in controlled laboratory or industrial contexts. The present study explores the extent to which the genetic complexity of the central carbon metabolism (CCM) in S. cerevisiae, here defined as the combination of glycolysis, the pentose phosphate pathway, the tricarboxylic acid cycle, and a limited number of related pathways and reactions, can be reduced by elimination of (iso)enzymes without major negative impacts on strain physiology. Cas9-mediated, groupwise deletion of 35 of the 111 genes yielded a “minimal CCM” strain which, despite the elimination of 32% of CCM-related proteins, showed only a minimal change in phenotype on glucose-containing synthetic medium in controlled bioreactor cultures relative to a congenic reference strain. Analysis under a wide range of other growth and stress conditions revealed remarkably few phenotypic changes from the reduction of genetic complexity. Still, a well-documented context-dependent role of GPD1 in osmotolerance was confirmed. The minimal CCM strain provides a model system for further research into genetic redundancy of yeast genes and a platform for strategies aimed at large-scale, combinatorial remodeling of yeast CCM.
Collapse
|
22
|
Booth TJ, Bozhüyük KAJ, Liston JD, Batey SFD, Lacey E, Wilkinson B. Bifurcation drives the evolution of assembly-line biosynthesis. Nat Commun 2022; 13:3498. [PMID: 35715397 PMCID: PMC9205934 DOI: 10.1038/s41467-022-30950-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2021] [Accepted: 05/18/2022] [Indexed: 11/09/2022] Open
Abstract
Reprogramming biosynthetic assembly-lines is a topic of intense interest. This is unsurprising as the scaffolds of most antibiotics in current clinical use are produced by such pathways. The modular nature of assembly-lines provides a direct relationship between the sequence of enzymatic domains and the chemical structure of the product, but rational reprogramming efforts have been met with limited success. To gain greater insight into the design process, we wanted to examine how Nature creates assembly-lines and searched for biosynthetic pathways that might represent evolutionary transitions. By examining the biosynthesis of the anti-tubercular wollamides, we uncover how whole gene duplication and neofunctionalization can result in pathway bifurcation. We show that, in the case of the wollamide biosynthesis, neofunctionalization is initiated by intragenomic recombination. This pathway bifurcation leads to redundancy, providing the genetic robustness required to enable large structural changes during the evolution of antibiotic structures. Should the new product be non-functional, gene loss can restore the original genotype. However, if the new product confers an advantage, depreciation and eventual loss of the original gene creates a new linear pathway. This provides the blind watchmaker equivalent to the design, build, test cycle of synthetic biology.
Collapse
Affiliation(s)
- Thomas J Booth
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.,School of Molecular Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Kenan A J Bozhüyük
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.,Molecular Biotechnology, Department of Biosciences, Goethe University Frankfurt, 60438, Frankfurt am Main, Germany.,Max-Planck-Institute for Terrestrial Microbiology, Department of Natural Products in Organismic Interactions, 35043, Marburg, Germany
| | - Jonathon D Liston
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Sibyl F D Batey
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK
| | - Ernest Lacey
- Microbial Screening Technologies, Smithfield, NSW, 2164, Australia
| | - Barrie Wilkinson
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| |
Collapse
|
23
|
de Mello FDSB, Maneira C, Suarez FUL, Nagamatsu S, Vargas B, Vieira C, Secches T, Coradini ALV, Silvello MADC, Goldbeck R, Pereira GAG, Teixeira GS. Rational engineering of industrial S. cerevisiae: towards xylitol production from sugarcane straw. J Genet Eng Biotechnol 2022; 20:80. [PMID: 35612634 PMCID: PMC9133290 DOI: 10.1186/s43141-022-00359-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 05/02/2022] [Indexed: 12/15/2022]
Abstract
Background Sugarcane hemicellulosic material is a compelling source of usually neglected xylose that could figure as feedstock to produce chemical building blocks of high economic value, such as xylitol. In this context, Saccharomyces cerevisiae strains typically used in the Brazilian bioethanol industry are a robust chassis for genetic engineering, given their robustness towards harsh operational conditions and outstanding fermentation performance. Nevertheless, there are no reports on the use of these strains for xylitol production using sugarcane hydrolysate. Results Potential single-guided RNA off-targets were analyzed in two preeminent industrial strains (PE-2 and SA-1), providing a database of 5′-NGG 20 nucleotide sequences and guidelines for the fast and cost-effective CRISPR editing of such strains. After genomic integration of a NADPH-preferring xylose reductase (XR), FMYX (SA-1 hoΔ::xyl1) and CENPKX (CEN.PK-122 hoΔ::xyl1) were tested in varying cultivation conditions for xylitol productivity to infer influence of the genetic background. Near-theoretical yields were achieved for all strains; however, the industrial consistently outperformed the laboratory strain. Batch fermentation of raw sugarcane straw hydrolysate with remaining solid particles represented a challenge for xylose metabolization, and 3.65 ± 0.16 g/L xylitol titer was achieved by FMYX. Finally, quantification of NADPH — cofactor implied in XR activity — revealed that FMYX has 33% more available cofactors than CENPKX. Conclusions Although widely used in several S. cerevisiae strains, this is the first report of CRISPR-Cas9 editing major yeast of the Brazilian bioethanol industry. Fermentative assays of xylose consumption revealed that NADPH availability is closely related to mutant strains’ performance. We also pioneer the use of sugarcane straw as a substrate for xylitol production. Finally, we demonstrate how industrial background SA-1 is a compelling chassis for the second-generation industry, given its inhibitor tolerance and better redox environment that may favor production of reduced sugars. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00359-8.
Collapse
Affiliation(s)
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Frank Uriel Lizarazo Suarez
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Basic Sciences, University of Pamplona, Pamplona, Colombia
| | - Sheila Nagamatsu
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Beatriz Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Carla Vieira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Thais Secches
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | - Alessando L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil
| | | | - Rosana Goldbeck
- School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Campinas, São Paulo, Brazil.,School of Food Engineering, University of Campinas, Campinas, São Paulo, Brazil
| |
Collapse
|
24
|
de Valk SC, Mans R. Novel Evolutionary Engineering Approach to Alter Substrate Specificity of Disaccharide Transporter Mal11 in Saccharomyces cerevisiae. J Fungi (Basel) 2022; 8:jof8040358. [PMID: 35448589 PMCID: PMC9024999 DOI: 10.3390/jof8040358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/28/2022] [Accepted: 03/29/2022] [Indexed: 11/17/2022] Open
Abstract
A major challenge in the research of transport proteins is to understand how single amino acid residues contribute to their structure and biological function. Amino acid substitutions that result in a selective advantage in adaptive laboratory evolution experiments can provide valuable hints at their role in transport proteins. In this study, we applied an evolutionary engineering strategy to alter the substrate specificity of the proton-coupled disaccharide transporter Mal11 in Saccharomyces cerevisiae, which has affinity for sucrose, maltose and glucose. The introduction of MAL11 in a strain devoid of all other sugar transporters and disaccharide hydrolases restored growth on glucose but rendered the strain highly sensitive to the presence of sucrose or maltose. Evolution in glucose-limited continuous cultures with pulse-wise addition of a concentrated sucrose solution at increasing frequency resulted in the enrichment of spontaneous mutant cells that were less sensitive to the presence of sucrose and maltose. Sequence analysis showed that in each of the two independent experiments, three mutations occurred in MAL11, which were found responsible for the disaccharide-insensitive phenotype via reverse engineering. Our work demonstrates how laboratory evolution with proton-motive force-driven uptake of a non-metabolizable substrate can be a powerful tool to provide novel insights into the role of specific amino acid residues in the transport function of Mal11.
Collapse
|
25
|
Minden S, Aniolek M, Sarkizi Shams Hajian C, Teleki A, Zerrer T, Delvigne F, van Gulik W, Deshmukh A, Noorman H, Takors R. Monitoring Intracellular Metabolite Dynamics in Saccharomyces cerevisiae during Industrially Relevant Famine Stimuli. Metabolites 2022; 12:metabo12030263. [PMID: 35323706 PMCID: PMC8953226 DOI: 10.3390/metabo12030263] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/08/2022] [Accepted: 03/16/2022] [Indexed: 11/16/2022] Open
Abstract
Carbon limitation is a common feeding strategy in bioprocesses to enable an efficient microbiological conversion of a substrate to a product. However, industrial settings inherently promote mixing insufficiencies, creating zones of famine conditions. Cells frequently traveling through such regions repeatedly experience substrate shortages and respond individually but often with a deteriorated production performance. A priori knowledge of the expected strain performance would enable targeted strain, process, and bioreactor engineering for minimizing performance loss. Today, computational fluid dynamics (CFD) coupled to data-driven kinetic models are a promising route for the in silico investigation of the impact of the dynamic environment in the large-scale bioreactor on microbial performance. However, profound wet-lab datasets are needed to cover relevant perturbations on realistic time scales. As a pioneering study, we quantified intracellular metabolome dynamics of Saccharomyces cerevisiae following an industrially relevant famine perturbation. Stimulus-response experiments were operated as chemostats with an intermittent feed and high-frequency sampling. Our results reveal that even mild glucose gradients in the range of 100 µmol·L−1 impose significant perturbations in adapted and non-adapted yeast cells, altering energy and redox homeostasis. Apparently, yeast sacrifices catabolic reduction charges for the sake of anabolic persistence under acute carbon starvation conditions. After repeated exposure to famine conditions, adapted cells show 2.7% increased maintenance demands.
Collapse
Affiliation(s)
- Steven Minden
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Maria Aniolek
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Christopher Sarkizi Shams Hajian
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Tobias Zerrer
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
| | - Frank Delvigne
- Microbial Processes and Interactions (MiPI), TERRA Research and Teaching Centre, Gembloux Agro Bio Tech, University of Liege, 5030 Gembloux, Belgium;
| | - Walter van Gulik
- Department of Biotechnology, Delft University of Technology, van der Maasweg 6, 2629 HZ Delft, The Netherlands;
| | - Amit Deshmukh
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
| | - Henk Noorman
- Royal DSM, 2613 AX Delft, The Netherlands; (A.D.); (H.N.)
- Department of Biotechnology, Delft University of Technology, 2628 CD Delft, The Netherlands
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, 70569 Stuttgart, Germany; (S.M.); (M.A.); (C.S.S.H.); (A.T.); (T.Z.)
- Correspondence:
| |
Collapse
|
26
|
Elsemman IE, Rodriguez Prado A, Grigaitis P, Garcia Albornoz M, Harman V, Holman SW, van Heerden J, Bruggeman FJ, Bisschops MMM, Sonnenschein N, Hubbard S, Beynon R, Daran-Lapujade P, Nielsen J, Teusink B. Whole-cell modeling in yeast predicts compartment-specific proteome constraints that drive metabolic strategies. Nat Commun 2022; 13:801. [PMID: 35145105 PMCID: PMC8831649 DOI: 10.1038/s41467-022-28467-6] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 01/27/2022] [Indexed: 01/20/2023] Open
Abstract
When conditions change, unicellular organisms rewire their metabolism to sustain cell maintenance and cellular growth. Such rewiring may be understood as resource re-allocation under cellular constraints. Eukaryal cells contain metabolically active organelles such as mitochondria, competing for cytosolic space and resources, and the nature of the relevant cellular constraints remain to be determined for such cells. Here, we present a comprehensive metabolic model of the yeast cell, based on its full metabolic reaction network extended with protein synthesis and degradation reactions. The model predicts metabolic fluxes and corresponding protein expression by constraining compartment-specific protein pools and maximising growth rate. Comparing model predictions with quantitative experimental data suggests that under glucose limitation, a mitochondrial constraint limits growth at the onset of ethanol formation—known as the Crabtree effect. Under sugar excess, however, a constraint on total cytosolic volume dictates overflow metabolism. Our comprehensive model thus identifies condition-dependent and compartment-specific constraints that can explain metabolic strategies and protein expression profiles from growth rate optimisation, providing a framework to understand metabolic adaptation in eukaryal cells. Metabolically active organelles compete for cytosolic space and resources during metabolism rewiring. Here, the authors develop a computational model of yeast metabolism and resource allocation to predict condition- and compartment-specific proteome constraints that govern metabolic strategies.
Collapse
Affiliation(s)
- Ibrahim E Elsemman
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark.,Department of Information Systems, Faculty of Computers and Information, Assiut University, Assiut, Egypt
| | - Angelica Rodriguez Prado
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.,Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Pranas Grigaitis
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | | | - Victoria Harman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Stephen W Holman
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Johan van Heerden
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Frank J Bruggeman
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Mark M M Bisschops
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Nikolaus Sonnenschein
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark
| | - Simon Hubbard
- Division of Evolution & Genomic Sciences, University of Manchester, Manchester, UK
| | - Rob Beynon
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, UK
| | - Pascale Daran-Lapujade
- Department of Industrial Microbiology, Technical University Delft, Delft, The Netherlands
| | - Jens Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK2800, Lyngby, Denmark. .,Department of Biology and Biological Engineering, Chalmers University of Technology, SE41296, Gothenburg, Sweden.
| | - Bas Teusink
- Systems Biology Lab, Amsterdam Institute of Molecular and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands.
| |
Collapse
|
27
|
Liu T, Gou Y, Zhang B, Gao R, Dong C, Qi M, Jiang L, Ding X, Li C, Lian J. Construction of Ajmalicine and Sanguinarine
de novo
Biosynthetic Pathways using Stable Integration Sites in Yeast. Biotechnol Bioeng 2022; 119:1314-1326. [DOI: 10.1002/bit.28040] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/22/2021] [Accepted: 01/02/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Tengfei Liu
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Yuanwei Gou
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Bei Zhang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Rui Gao
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Chang Dong
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| | - Mingming Qi
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Lihong Jiang
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
| | - Xuanwei Ding
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Chun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology Beijing 100081 China
| | - Jiazhang Lian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education, College of Chemical and Biological Engineering, Zhejiang University Hangzhou 310027 China
- Hangzhou Global Scientific and Technological Innovation Center, Zhejiang University Hangzhou 310027 China
| |
Collapse
|
28
|
Engineering precursor supply for the high-level production of ergothioneine in Saccharomyces cerevisiae. Metab Eng 2022; 70:129-142. [DOI: 10.1016/j.ymben.2022.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/10/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022]
|
29
|
Coradini ALV, da Silveira Bezerra de Mello F, Furlan M, Maneira C, Carazzolle MF, Pereira GAG, Teixeira GS. QTL mapping of a Brazilian bioethanol strain links the cell wall protein-encoding gene GAS1 to low pH tolerance in S. cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:239. [PMID: 34915919 PMCID: PMC8675505 DOI: 10.1186/s13068-021-02079-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/17/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Saccharomyces cerevisiae is largely applied in many biotechnological processes, from traditional food and beverage industries to modern biofuel and biochemicals factories. During the fermentation process, yeast cells are usually challenged in different harsh conditions, which often impact productivity. Regarding bioethanol production, cell exposure to acidic environments is related to productivity loss on both first- and second-generation ethanol. In this scenario, indigenous strains traditionally used in fermentation stand out as a source of complex genetic architecture, mainly due to their highly robust background-including low pH tolerance. RESULTS In this work, we pioneer the use of QTL mapping to uncover the genetic basis that confers to the industrial strain Pedra-2 (PE-2) acidic tolerance during growth at low pH. First, we developed a fluorescence-based high-throughput approach to collect a large number of haploid cells using flow cytometry. Then, we were able to apply a bulk segregant analysis to solve the genetic basis of low pH resistance in PE-2, which uncovered a region in chromosome X as the major QTL associated with the evaluated phenotype. A reciprocal hemizygosity analysis revealed the allele GAS1, encoding a β-1,3-glucanosyltransferase, as the casual variant in this region. The GAS1 sequence alignment of distinct S. cerevisiae strains pointed out a non-synonymous mutation (A631G) prevalence in wild-type isolates, which is absent in laboratory strains. We further showcase that GAS1 allele swap between PE-2 and a low pH-susceptible strain can improve cell viability on the latter of up to 12% after a sulfuric acid wash process. CONCLUSION This work revealed GAS1 as one of the main causative genes associated with tolerance to growth at low pH in PE-2. We also showcase how GAS1PE-2 can improve acid resistance of a susceptible strain, suggesting that these findings can be a powerful foundation for the development of more robust and acid-tolerant strains. Our results collectively show the importance of tailored industrial isolated strains in discovering the genetic architecture of relevant traits and its implications over productivity.
Collapse
Affiliation(s)
- Alessandro L V Coradini
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
- Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, 90089-2910, USA
| | - Fellipe da Silveira Bezerra de Mello
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Monique Furlan
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Carla Maneira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Marcelo F Carazzolle
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| | - Gonçalo Amarante Guimaraes Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil.
| | - Gleidson Silva Teixeira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, University of Campinas, Rua Monteiro Lobato 255, Campinas, 13083-862, Brazil
| |
Collapse
|
30
|
Brink DP, Borgström C, Persson VC, Ofuji Osiro K, Gorwa-Grauslund MF. D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers. Int J Mol Sci 2021; 22:12410. [PMID: 34830296 PMCID: PMC8625115 DOI: 10.3390/ijms222212410] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.
Collapse
Affiliation(s)
- Daniel P. Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
| | - Viktor C. Persson
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Karen Ofuji Osiro
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil
| | - Marie F. Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| |
Collapse
|
31
|
Bouwknegt J, Wiersma SJ, Ortiz-Merino RA, Doornenbal ESR, Buitenhuis P, Giera M, Müller C, Pronk JT. A squalene-hopene cyclase in Schizosaccharomyces japonicus represents a eukaryotic adaptation to sterol-limited anaerobic environments. Proc Natl Acad Sci U S A 2021; 118:e2105225118. [PMID: 34353908 PMCID: PMC8364164 DOI: 10.1073/pnas.2105225118] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Biosynthesis of sterols, which are key constituents of canonical eukaryotic membranes, requires molecular oxygen. Anaerobic protists and deep-branching anaerobic fungi are the only eukaryotes in which a mechanism for sterol-independent growth has been elucidated. In these organisms, tetrahymanol, formed through oxygen-independent cyclization of squalene by a squalene-tetrahymanol cyclase, acts as a sterol surrogate. This study confirms an early report [C. J. E. A. Bulder, Antonie Van Leeuwenhoek, 37, 353-358 (1971)] that Schizosaccharomyces japonicus is exceptional among yeasts in growing anaerobically on synthetic media lacking sterols and unsaturated fatty acids. Mass spectrometry of lipid fractions of anaerobically grown Sch. japonicus showed the presence of hopanoids, a class of cyclic triterpenoids not previously detected in yeasts, including hop-22(29)-ene, hop-17(21)-ene, hop-21(22)-ene, and hopan-22-ol. A putative gene in Sch. japonicus showed high similarity to bacterial squalene-hopene cyclase (SHC) genes and in particular to those of Acetobacter species. No orthologs of the putative Sch. japonicus SHC were found in other yeast species. Expression of the Sch. japonicus SHC gene (Sjshc1) in Saccharomyces cerevisiae enabled hopanoid synthesis and stimulated anaerobic growth in sterol-free media, thus indicating that one or more of the hopanoids produced by SjShc1 could at least partially replace sterols. Use of hopanoids as sterol surrogates represents a previously unknown adaptation of eukaryotic cells to anaerobic growth. The fast anaerobic growth of Sch. japonicus in sterol-free media is an interesting trait for developing robust fungal cell factories for application in anaerobic industrial processes.
Collapse
Affiliation(s)
- Jonna Bouwknegt
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Sanne J Wiersma
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Eline S R Doornenbal
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Petrik Buitenhuis
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Christoph Müller
- Department of Pharmacy, Center for Drug Research, Ludwig-Maximillians University Munich, 81377 Munich, Germany
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, 2629 HZ Delft, The Netherlands;
| |
Collapse
|
32
|
Rienzo M, Lin KC, Mobilia KC, Sackmann EK, Kurz V, Navidi AH, King J, Onorato RM, Chao LK, Wu T, Jiang H, Valley JK, Lionberger TA, Leavell MD. High-throughput optofluidic screening for improved microbial cell factories via real-time micron-scale productivity monitoring. LAB ON A CHIP 2021; 21:2901-2912. [PMID: 34160512 DOI: 10.1039/d1lc00389e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The industrial synthetic biology sector has made huge investments to achieve relevant miniaturized screening systems for scalable fermentation. Here we present the first example of a high-throughput (>103 genotypes per week) perfusion-based screening system to improve small-molecule secretion from microbial strains. Using the Berkeley Lights Beacon® system, the productivity of each strain could be directly monitored in real time during continuous culture, yielding phenotypes that correlated strongly (r2 > 0.8, p < 0.0005) with behavior in industrially relevant bioreactor processes. This method allows a much closer approximation of a typical fed-batch fermentation than conventional batch-like droplet or microplate culture models, in addition to rich time-dependent data on growth and productivity. We demonstrate these advantages by application to the improvement of high-productivity strains using whole-genome random mutagenesis, yielding mutants with substantially improved (by up to 85%) peak specific productivities in bioreactors. Each screen of ∼5 × 103 mutants could be completed in under 8 days (including 5 days involving user intervention), saving ∼50-75% of the time required for conventional microplate-based screening methods.
Collapse
Affiliation(s)
- Matthew Rienzo
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Ke-Chih Lin
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Kellen C Mobilia
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Eric K Sackmann
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Volker Kurz
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Adam H Navidi
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Jarett King
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Robert M Onorato
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Lawrence K Chao
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Tony Wu
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Hanxiao Jiang
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Justin K Valley
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| | - Troy A Lionberger
- Technology and Business Development, Berkeley Lights, Inc., 5858 Horton St., Unit 320, Emeryville, CA 94608, USA.
| | - Michael D Leavell
- Research and Development, Amyris, Inc., 5885 Hollis St., Suite 100, Emeryville, CA 94608, USA.
| |
Collapse
|
33
|
Arhar S, Gogg-Fassolter G, Ogrizović M, Pačnik K, Schwaiger K, Žganjar M, Petrovič U, Natter K. Engineering of Saccharomyces cerevisiae for the accumulation of high amounts of triacylglycerol. Microb Cell Fact 2021; 20:147. [PMID: 34315498 PMCID: PMC8314538 DOI: 10.1186/s12934-021-01640-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/19/2021] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND Fatty acid-based substances play an important role in many products, from food supplements to pharmaceutical products and biofuels. The production of fatty acids, mainly in their esterified form as triacylglycerol (TAG), has been intensively studied in oleaginous yeasts, whereas much less effort has been invested into non-oleaginous species. In the present work, we engineered the model yeast Saccharomyces cerevisiae, which is commonly regarded as non-oleaginous, for the storage of high amounts of TAG, comparable to the contents achieved in oleaginous yeasts. RESULTS We investigated the effects of several mutations with regard to increased TAG accumulation and identified six of them as important for this phenotype: a point mutation in the acetyl-CoA carboxylase Acc1p, overexpression of the diacylglycerol acyltransferase Dga1p, deletions of genes coding for enzymes involved in the competing pathways glycogen and steryl ester synthesis and TAG hydrolysis, and a deletion of CKB1, the gene coding for one of the regulatory subunits of casein kinase 2. With the combination of these mutations in a S. cerevisiae strain with a relatively high neutral lipid level already in the non-engineered state, we achieved a TAG content of 65% in the dry biomass. High TAG levels were not only obtained under conditions that favor lipid accumulation, but also in defined standard carbon-limited media. CONCLUSIONS Baker's yeast, which is usually regarded as inefficient in the storage of TAG, can be converted into a highly oleaginous strain that could be useful in processes aiming at the synthesis of fatty acid-based products. This work emphasizes the importance of strain selection in combination with metabolic engineering to obtain high product levels.
Collapse
Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Gabriela Gogg-Fassolter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mojca Ogrizović
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Klavdija Pačnik
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Katharina Schwaiger
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria
| | - Mia Žganjar
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
| | - Uroš Petrovič
- Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Ljubljana, Slovenia
- Department of Biology, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010, Graz, Austria.
| |
Collapse
|
34
|
Cao W, Zhao W, Yang B, Wang X, Shen Y, Wei T, Qin W, Li Z, Bao X. Proteomic analysis revealed the roles of YRR1 deletion in enhancing the vanillin resistance of Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:142. [PMID: 34301255 PMCID: PMC8305865 DOI: 10.1186/s12934-021-01633-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 07/15/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Vanillin is one of the important phenolic inhibitors in Saccharomyces cerevisiae for bioconversion of lignocellulosic materials and has been reported to inhibit the translation process in cells. In our previous studies, it was confirmed that the deletion of the transcription factor gene YRR1 enhanced vanillin resistance by promoting some translation-related processes at the transcription level. In this work, we investigated the effects of proteomic changes upon induction of vanillin stress and deletion of YRR1 to provide unique perspectives from a transcriptome analysis for comprehending the mechanisms of YRR1 deletion in the protective response of yeast to vanillin. RESULTS In wild-type cells, vanillin reduced two dozens of ribosomal proteins contents while upregulated proteins involved in glycolysis, oxidative phosphorylation, and the pentose phosphate pathway in cells. The ratios of NADPH/NADP+ and NADH/NAD+ were increased when cells responded to vanillin stress. The differentially expressed proteins perturbed by YRR1 deletion were much more abundant than and showed no overlaps with transcriptome changes, indicating that Yrr1 affects the synthesis of certain proteins. Forty-eight of 112 upregulated proteins were involved in the stress response, translational and transcriptional regulation. YRR1 deletion increased the expression of HAA1-encoding transcriptional activator, TMA17-encoding proteasome assembly chaperone and MBF1-encoding coactivator at the protein level, as confirmed by ELISA. Cultivation data showed that the overexpression of HAA1 and TMA17 enhanced resistance to vanillin in S. cerevisiae. CONCLUSIONS Cells conserve energy by decreasing the content of ribosomal proteins, producing more energy and NAD(P)H for survival in response to vanillin stress. Yrr1 improved vanillin resistance by increasing the protein quantities of Haa1, Tma17 and Mbf1. These results showed the response of S. cerevisiae to vanillin and how YRR1 deletion increases vanillin resistance at the protein level. These findings may advance our knowledge of how YRR1 deletion protects yeast from vanillin stress and offer novel targets for genetic engineering of designing inhibitor-resistant ethanologenic yeast strains.
Collapse
Affiliation(s)
- Wenyan Cao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Weiquan Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Bolun Yang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xinning Wang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China.
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Tiandi Wei
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Binhai Road 72, Qingdao, 266237, China
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Rd, Thunder Bay, ON, P7B 5E1, Canada
| | - Zailu Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| | - Xiaoming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Key Laboratory of Shandong Microbial Engineering, Qilu University of Technology (Shandong Academy of Sciences), 3501 Daxue Road, Jinan, 250353, China
| |
Collapse
|
35
|
Dekker WJC, Ortiz-Merino RA, Kaljouw A, Battjes J, Wiering FW, Mooiman C, Torre PDL, Pronk JT. Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth. Metab Eng 2021; 67:347-364. [PMID: 34303845 DOI: 10.1016/j.ymben.2021.07.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 07/06/2021] [Accepted: 07/13/2021] [Indexed: 10/20/2022]
Abstract
Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.
Collapse
Affiliation(s)
- Wijbrand J C Dekker
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Raúl A Ortiz-Merino
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Astrid Kaljouw
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Julius Battjes
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Frank W Wiering
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Pilar de la Torre
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ Delft, the Netherlands.
| |
Collapse
|
36
|
Potassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides. Appl Environ Microbiol 2021; 87:e0310020. [PMID: 33893111 DOI: 10.1128/aem.03100-20] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K+ to CEN.PK cultures reduced Na+ toxicity and increased the specific growth rate 4-fold. The higher K+ and Na+ concentrations impaired ethanol and acetate metabolism in CEN.PK and acetate metabolism in W303. In R. toruloides cultures, these salt supplementations induced a trade-off between glucose utilization and cellular aggregate formation. Their combined use increased the beta-carotene yield by 60% compared with that of the reference. Neural network-based image analysis of exponential-phase cultures showed that the vacuole-to-cell volume ratio increased with increased cell volume for W303 and K. marxianus but not for CEN.PK and R. toruloides in response to salt stress. Our results provide insights into common salt stress responses in yeasts and will help design efficient bioprocesses. IMPORTANCE Characterization of microbial cell factories under industrially relevant conditions is crucial for designing efficient bioprocesses. Salt stress, typical in industrial bioprocesses, impinges upon cell volume and affects productivity. This study presents an open-source neural network-based analysis method to evaluate volumetric changes using yeast optical microscopy images. It allows quantification of cell and vacuole volumes relevant to cellular physiology. On applying salt stress in yeasts, we found that the combined use of K+ and Na+ improves the cellular fitness of Saccharomyces cerevisiae strain CEN.PK and increases the beta-carotene productivity in Rhodotorula toruloides, a commercially important antioxidant and a valuable additive in foods.
Collapse
|
37
|
Donzella L, Varela JA, Sousa MJ, Morrissey JP. Identification of novel pentose transporters in Kluyveromyces marxianus using a new screening platform. FEMS Yeast Res 2021; 21:6247623. [PMID: 33890624 PMCID: PMC8110514 DOI: 10.1093/femsyr/foab026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 04/21/2021] [Indexed: 11/29/2022] Open
Abstract
The capacity of yeasts to assimilate xylose or arabinose is strongly dependent on plasma membrane transport proteins. Because pentoses comprise a substantial proportion of available sugars in lignocellulosic hydrolysates, their utilisation is centrally important for the development of second generation biorefineries. Relatively few native pentose transporters have been studied and there is intense interest in expanding the repertoire. To aid the identification of novel transporters, we developed a screening platform in the native pentose-utilising yeast Kluyveromyces marxianus. This involved the targeted deletion of twelve transporters of the major facilitator superfamily (MFS) and application of a synthetic biology pipeline for rapid testing of candidate pentose transporters. Using this K. marxianus ΔPT platform, we identified several K. marxianus putative xylose or arabinose transporter proteins that recovered a null strain's ability to growth on these pentoses. Four proteins of the HGT-family were able to support growth in media with high or low concentrations of either xylose or arabinose, while six HXT-like proteins displayed growth only at high xylose concentrations, indicating solely low affinity transport activity. The study offers new insights into the evolution of sugar transporters in yeast and expands the set of native pentose transporters for future functional and biotechnological studies.
Collapse
Affiliation(s)
- Lorena Donzella
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland.,Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, R. da Universidade, Braga 4710-057, Portugal
| | - Javier A Varela
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland
| | - Maria João Sousa
- Centre of Environmental and Molecular Biology, Department of Biology, University of Minho, Campus of Gualtar, R. da Universidade, Braga 4710-057, Portugal
| | - John P Morrissey
- School of Microbiology, Environmental Research Institute, APC Microbiome Institute, University College Cork, Cork T12 K8AF, Ireland
| |
Collapse
|
38
|
Pendón MD, Madeira JV, Romanin DE, Rumbo M, Gombert AK, Garrote GL. A biorefinery concept for the production of fuel ethanol, probiotic yeast, and whey protein from a by-product of the cheese industry. Appl Microbiol Biotechnol 2021; 105:3859-3871. [PMID: 33860834 DOI: 10.1007/s00253-021-11278-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 03/24/2021] [Accepted: 04/06/2021] [Indexed: 11/29/2022]
Abstract
Agroindustrial by-products and residues can be transformed into valuable compounds in biorefineries. Here, we present a new concept: production of fuel ethanol, whey protein, and probiotic yeast from cheese whey. An initial screening under industrially relevant conditions, involving thirty Kluyveromyces marxianus strains, was carried out using spot assays to evaluate their capacity to grow on cheese whey or on whey permeate (100 g lactose/L), under aerobic or anaerobic conditions, in the absence or presence of 5% ethanol, at pH 5.8 or pH 2.5. The four best growing K. marxianus strains were selected and further evaluated in a miniaturized industrial fermentation process using reconstituted whey permeate (100 g lactose/L) with cell recycling (involving sulfuric acid treatment). After five consecutive fermentation cycles, the ethanol yield on sugar reached 90% of the theoretical maximum in the best cases, with 90% cell viability. Cells harvested at this point displayed probiotic properties such as the capacity to survive the passage through the gastrointestinal tract and capacity to modulate the innate immune response of intestinal epithelium, both in vitro. Furthermore, the CIDCA 9121 strain was able to protect against histopathological damage in an animal model of acute colitis. Our findings demonstrate that K. marxianus CIDCA 9121 is capable of efficiently fermenting the lactose present in whey permeate to ethanol and that the remaining yeast biomass has probiotic properties, enabling an integrated process for the obtainment of whey protein (WP), fuel ethanol, and probiotics from cheese whey.Key points• K. marxianus-selected strains ferment whey permeate with 90% ethanol yield.• Industrial fermentation conditions do not affect selected yeast probiotic capacity.• Whey permeate, fuel ethanol, and probiotic biomass can be obtained in a biorefinery.
Collapse
Affiliation(s)
- María Dolores Pendón
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CIDCA (UNLP-CONICET-CIC.PBA), La Plata, Argentina
| | - José V Madeira
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - David E Romanin
- Instituto de Estudios Inmunológicos y Fisiopatológicos, IIFP (UNLP-CONICET-CIC.PBA), La Plata, Argentina
| | - Martín Rumbo
- Instituto de Estudios Inmunológicos y Fisiopatológicos, IIFP (UNLP-CONICET-CIC.PBA), La Plata, Argentina
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, Campinas, SP, 13083-862, Brazil
| | - Graciela L Garrote
- Centro de Investigación y Desarrollo en Criotecnología de Alimentos, CIDCA (UNLP-CONICET-CIC.PBA), La Plata, Argentina.
| |
Collapse
|
39
|
Rodrigues CIS, Wahl A, Gombert AK. Aerobic growth physiology of Saccharomyces cerevisiae on sucrose is strain-dependent. FEMS Yeast Res 2021; 21:6214418. [PMID: 33826723 DOI: 10.1093/femsyr/foab021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 04/01/2021] [Indexed: 12/22/2022] Open
Abstract
Present knowledge on the quantitative aerobic physiology of the yeast Saccharomyces cerevisiae during growth on sucrose as sole carbon and energy source is limited to either adapted cells or to the model laboratory strain CEN.PK113-7D. To broaden our understanding of this matter and open novel opportunities for sucrose-based biotechnological processes, we characterized three strains, with distinct backgrounds, during aerobic batch bioreactor cultivations. Our results reveal that sucrose metabolism in S. cerevisiae is a strain-specific trait. Each strain displayed distinct extracellular hexose concentrations and invertase activity profiles. Especially, the inferior maximum specific growth rate (0.21 h-1) of the CEN.PK113-7D strain, with respect to that of strains UFMG-CM-Y259 (0.37 h-1) and JP1 (0.32 h-1), could be associated to its low invertase activity (0.04-0.09 U/mgDM). Moreover, comparative experiments with glucose or fructose alone, or in combination, suggest mixed mechanisms of sucrose utilization by the industrial strain JP1, and points out the remarkable ability of the wild isolate UFMG-CM-259 to grow faster on sucrose than on glucose in a well-controlled cultivation system. This work hints to a series of metabolic traits that can be exploited to increase sucrose catabolic rates and bioprocess efficiency.
Collapse
Affiliation(s)
- Carla Inês Soares Rodrigues
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, 13083-862, Campinas, SP, Brazil.,Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629HZ Delft, The Netherlands
| | - Andreas K Gombert
- School of Food Engineering, University of Campinas, Rua Monteiro Lobato 80, 13083-862, Campinas, SP, Brazil
| |
Collapse
|
40
|
Peroxiredoxins couple metabolism and cell division in an ultradian cycle. Nat Chem Biol 2021; 17:477-484. [PMID: 33574615 DOI: 10.1038/s41589-020-00728-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/22/2020] [Indexed: 01/30/2023]
Abstract
Redox cycles have been reported in ultradian, circadian and cell cycle-synchronized systems. Redox cycles persist in the absence of transcription and cyclin-CDK activity, indicating that cells harbor multiple coupled oscillators. Nonetheless, the causal relationships and molecular mechanisms by which redox cycles are embedded within ultradian, circadian or cell division cycles remain largely elusive. Yeast harbor an ultradian oscillator, the yeast metabolic cycle (YMC), which comprises metabolic/redox cycles, transcriptional cycles and synchronized cell division. Here, we reveal the existence of robust cycling of H2O2 and peroxiredoxin oxidation during the YMC and show that peroxiredoxin inactivation disrupts metabolic cycling and abolishes coupling with cell division. We find that thiol-disulfide oxidants and reductants predictably modulate the switching between different YMC metabolic states, which in turn predictably perturbs cell cycle entry and exit. We propose that oscillatory H2O2-dependent protein thiol oxidation is a key regulator of metabolic cycling and its coordination with cell division.
Collapse
|
41
|
Ong JY, Pence JT, Molik DC, Shepherd HAM, Goodson HV. Yeast grown in continuous culture systems can detect mutagens with improved sensitivity relative to the Ames test. PLoS One 2021; 16:e0235303. [PMID: 33730086 PMCID: PMC7968628 DOI: 10.1371/journal.pone.0235303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 02/18/2021] [Indexed: 11/20/2022] Open
Abstract
Continuous culture systems allow for the controlled growth of microorganisms over a long period of time. Here, we develop a novel test for mutagenicity that involves growing yeast in continuous culture systems exposed to low levels of mutagen for a period of approximately 20 days. In contrast, most microorganism-based tests for mutagenicity expose the potential mutagen to the biological reporter at a high concentration of mutagen for a short period of time. Our test improves upon the sensitivity of the well-established Ames test by at least 20-fold for each of two mutagens that act by different mechanisms (the intercalator ethidium bromide and alkylating agent methyl methanesulfonate). To conduct the tests, cultures were grown in small, inexpensive continuous culture systems in media containing (potential) mutagen, and the resulting mutagenicity of the added compound was assessed via two methods: a canavanine-based plate assay and whole genome sequencing. In the canavanine-based plate assay, we were able to detect a clear relationship between the amount of mutagen and the number of canavanine-resistant mutant colonies over a period of one to three weeks of exposure. Whole genome sequencing of yeast grown in continuous culture systems exposed to methyl methanesulfonate demonstrated that quantification of mutations is possible by identifying the number of unique variants across each strain. However, this method had lower sensitivity than the plate-based assay and failed to distinguish the different concentrations of mutagen. In conclusion, we propose that yeast grown in continuous culture systems can provide an improved and more sensitive test for mutagenicity.
Collapse
Affiliation(s)
- Joseph Y. Ong
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Julia T. Pence
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - David C. Molik
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Heather A. M. Shepherd
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
| | - Holly V. Goodson
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, United States of America
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, United States of America
| |
Collapse
|
42
|
Kumar K, Venkatraman V, Bruheim P. Adaptation of central metabolite pools to variations in growth rate and cultivation conditions in Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:64. [PMID: 33750414 PMCID: PMC7941957 DOI: 10.1186/s12934-021-01557-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 03/01/2021] [Indexed: 11/19/2022] Open
Abstract
Background Saccharomyces cerevisiae is a well-known popular model system for basic biological studies and serves as a host organism for the heterologous production of commercially interesting small molecules and proteins. The central metabolism is at the core to provide building blocks and energy to support growth and survival in normal situations as well as during exogenous stresses and forced heterologous protein production. Here, we present a comprehensive study of intracellular central metabolite pool profiling when growing S. cerevisiae on different carbon sources in batch cultivations and at different growth rates in nutrient-limited glucose chemostats. The latest versions of absolute quantitative mass spectrometry-based metabolite profiling methodology were applied to cover glycolytic and pentose phosphate pathway metabolites, tricarboxylic acid cycle (TCA), complete amino acid, and deoxy-/nucleoside phosphate pools. Results Glutamate, glutamine, alanine, and citrate were the four most abundant metabolites for most conditions tested. The amino acid is the dominant metabolite class even though a marked relative reduction compared to the other metabolite classes was observed for nitrogen and phosphate limited chemostats. Interestingly, glycolytic and pentose phosphate pathway (PPP) metabolites display the largest variation among the cultivation conditions while the nucleoside phosphate pools are more stable and vary within a closer concentration window. The overall trends for glucose and nitrogen-limited chemostats were increased metabolite pools with the increasing growth rate. Next, comparing the chosen chemostat reference growth rate (0.12 h−1, approximate one-fourth of maximal unlimited growth rate) illuminates an interesting pattern: almost all pools are lower in nitrogen and phosphate limited conditions compared to glucose limitation, except for the TCA metabolites citrate, isocitrate and α-ketoglutarate. Conclusions This study provides new knowledge-how the central metabolism is adapting to various cultivations conditions and growth rates which is essential for expanding our understanding of cellular metabolism and the development of improved phenotypes in metabolic engineering. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01557-8.
Collapse
Affiliation(s)
- Kanhaiya Kumar
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Vishwesh Venkatraman
- Department of Chemistry, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway
| | - Per Bruheim
- Department of Biotechnology and Food Science, Norwegian University of Science and Technology (NTNU), 7491, Trondheim, Norway.
| |
Collapse
|
43
|
Collins JH, Keating KW, Jones TR, Balaji S, Marsan CB, Çomo M, Newlon ZJ, Mitchell T, Bartley B, Adler A, Roehner N, Young EM. Engineered yeast genomes accurately assembled from pure and mixed samples. Nat Commun 2021; 12:1485. [PMID: 33674578 PMCID: PMC7935868 DOI: 10.1038/s41467-021-21656-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 02/04/2021] [Indexed: 01/31/2023] Open
Abstract
Yeast whole genome sequencing (WGS) lacks end-to-end workflows that identify genetic engineering. Here we present Prymetime, a tool that assembles yeast plasmids and chromosomes and annotates genetic engineering sequences. It is a hybrid workflow-it uses short and long reads as inputs to perform separate linear and circular assembly steps. This structure is necessary to accurately resolve genetic engineering sequences in plasmids and the genome. We show this by assembling diverse engineered yeasts, in some cases revealing unintended deletions and integrations. Furthermore, the resulting whole genomes are high quality, although the underlying assembly software does not consistently resolve highly repetitive genome features. Finally, we assemble plasmids and genome integrations from metagenomic sequencing, even with 1 engineered cell in 1000. This work is a blueprint for building WGS workflows and establishes WGS-based identification of yeast genetic engineering.
Collapse
Affiliation(s)
- Joseph H Collins
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Kevin W Keating
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Trent R Jones
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Shravani Balaji
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Celeste B Marsan
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Marina Çomo
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Zachary J Newlon
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA
| | - Tom Mitchell
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Bryan Bartley
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Aaron Adler
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Nicholas Roehner
- Synthetic Biology, Raytheon BBN Technologies, Cambridge, MA, USA
| | - Eric M Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, MA, USA.
| |
Collapse
|
44
|
Garcia-Albornoz M, Holman SW, Antonisse T, Daran-Lapujade P, Teusink B, Beynon RJ, Hubbard SJ. A proteome-integrated, carbon source dependent genetic regulatory network in Saccharomyces cerevisiae. Mol Omics 2021; 16:59-72. [PMID: 31868867 DOI: 10.1039/c9mo00136k] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Integrated regulatory networks can be powerful tools to examine and test properties of cellular systems, such as modelling environmental effects on the molecular bioeconomy, where protein levels are altered in response to changes in growth conditions. Although extensive regulatory pathways and protein interaction data sets exist which represent such networks, few have formally considered quantitative proteomics data to validate and extend them. We generate and consider such data here using a label-free proteomics strategy to quantify alterations in protein abundance for S. cerevisiae when grown on minimal media using glucose, galactose, maltose and trehalose as sole carbon sources. Using a high quality-controlled subset of proteins observed to be differentially abundant, we constructed a proteome-informed network, comprising 1850 transcription factor interactions and 37 chaperone interactions, which defines the major changes in the cellular proteome when growing under different carbon sources. Analysis of the differentially abundant proteins involved in the regulatory network pointed to their significant roles in specific metabolic pathways and function, including glucose homeostasis, amino acid biosynthesis, and carbohydrate metabolic process. We noted strong statistical enrichment in the differentially abundant proteome of targets of known transcription factors associated with stress responses and altered carbon metabolism. This shows how such integrated analysis can lend further experimental support to annotated regulatory interactions, since the proteomic changes capture both magnitude and direction of gene expression change at the level of the affected proteins. Overall this study highlights the power of quantitative proteomics to help define regulatory systems pertinent to environmental conditions.
Collapse
Affiliation(s)
- M Garcia-Albornoz
- School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Oxford Road, Manchester M13 9PT, UK.
| | | | | | | | | | | | | |
Collapse
|
45
|
Nagamatsu ST, Coutouné N, José J, Fiamenghi MB, Pereira GAG, Oliveira JVDC, Carazzolle MF. Ethanol production process driving changes on industrial strains. FEMS Yeast Res 2021; 21:6070656. [PMID: 33417685 DOI: 10.1093/femsyr/foaa071] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022] Open
Abstract
Ethanol production has key differences between the two largest producing countries of this biofuel, Brazil and the USA, such as feedstock source, sugar concentration and ethanol titers in industrial fermentation. Therefore, it is highly probable that these specificities have led to genome adaptation of the Saccharomyces cerevisiae strains employed in each process to tolerate different environments. In order to identify particular adaptations, in this work, we have compared the genomes of industrial yeast strains widely used to produce ethanol from sugarcane, corn and sweet sorghum, and also two laboratory strains as reference. The genes were predicted and then 4524 single-copy orthologous were selected to build the phylogenetic tree. We found that the geographic location and industrial process were shown as the main evolutionary drivers: for sugarcane fermentation, positive selection was identified for metal homeostasis and stress response genes, whereas genes involved in membrane modeling have been connected with corn fermentation. In addition, the corn specialized strain Ethanol Red showed an increased number of copies of MAL31, a gene encoding a maltose transporter. In summary, our work can help to guide new strain chassis selection for engineering strategies, to produce more robust strains for biofuel production and other industrial applications.
Collapse
Affiliation(s)
- Sheila Tiemi Nagamatsu
- Division of Human Genetics, Department of Psychiatry, Yale School of Medicine, 333 Cedar St, New Haven, CT, 06510, USA.,Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Natalia Coutouné
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Juliana José
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Mateus Bernabe Fiamenghi
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| | - Juliana Velasco de Castro Oliveira
- Laboratório Nacional de Biorrenováveis (LNBR), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), CEP 13083-970, Campinas, São Paulo, Brazil
| | - Marcelo Falsarella Carazzolle
- Laboratório de Genômica e BioEnergia, Departamento de Genética, Evolução, Microbiologia e Imunologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Campinas, São Paulo, 13083-970, Brazil
| |
Collapse
|
46
|
Abstract
Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction. Microbial cells experience physiological changes due to environmental change, such as pH and temperature, the release of bactericidal agents, or nutrient limitation. This has been shown to affect community assembly and physiological processes (e.g., stress tolerance, virulence, or cellular metabolic activity). Metabolic stress is typically quantified by measuring community phenotypic properties such as biomass growth, reactive oxygen species, or cell permeability. However, bulk community measurements do not take into account single-cell phenotypic diversity, which is important for a better understanding and the subsequent management of microbial populations. Raman spectroscopy is a nondestructive alternative that provides detailed information on the biochemical makeup of each individual cell. Here, we introduce a method for describing single-cell phenotypic diversity using the Hill diversity framework of Raman spectra. Using the biomolecular profile of individual cells, we obtained a metric to compare cellular states and used it to study stress-induced changes. First, in two Escherichia coli populations either treated with ethanol or nontreated and then in two Saccharomyces cerevisiae subpopulations with either high or low expression of a stress reporter. In both cases, we were able to quantify single-cell phenotypic diversity and to discriminate metabolically stressed cells using a clustering algorithm. We also described how the lipid, protein, and nucleic acid compositions changed after the exposure to the stressor using information from the Raman spectra. Our results show that Raman spectroscopy delivers the necessary resolution to quantify phenotypic diversity within individual cells and that this information can be used to study stress-driven metabolic diversity in microbial populations. IMPORTANCE Microbial cells that live in the same community can exist in different physiological and morphological states that change as a function of spatiotemporal variations in environmental conditions. This phenomenon is commonly known as phenotypic heterogeneity and/or diversity. Measuring this plethora of cellular expressions is needed to better understand and manage microbial processes. However, most tools to study phenotypic diversity only average the behavior of the sampled community. In this work, we present a way to quantify the phenotypic diversity of microbial samples by inferring the (bio)molecular profile of its constituent cells using Raman spectroscopy. We demonstrate how this tool can be used to quantify the phenotypic diversity that arises after the exposure of microbes to stress. Raman spectroscopy holds potential for the detection of stressed cells in bioproduction.
Collapse
|
47
|
Naranjo‐Ortiz MA, Gabaldón T. Fungal evolution: cellular, genomic and metabolic complexity. Biol Rev Camb Philos Soc 2020; 95:1198-1232. [PMID: 32301582 PMCID: PMC7539958 DOI: 10.1111/brv.12605] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Revised: 03/31/2020] [Accepted: 04/02/2020] [Indexed: 12/13/2022]
Abstract
The question of how phenotypic and genomic complexity are inter-related and how they are shaped through evolution is a central question in biology that historically has been approached from the perspective of animals and plants. In recent years, however, fungi have emerged as a promising alternative system to address such questions. Key to their ecological success, fungi present a broad and diverse range of phenotypic traits. Fungal cells can adopt many different shapes, often within a single species, providing them with great adaptive potential. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout the evolutionary history of fungi. Similarly, fungal genomes are very diverse in their architecture. Deep changes in genome organization can occur very quickly, and these phenomena are known to mediate rapid adaptations to environmental changes. Finally, the biochemical complexity of fungi is huge, particularly with regard to their secondary metabolites, chemical products that mediate many aspects of fungal biology, including ecological interactions. Herein, we explore how the interplay of these cellular, genomic and metabolic traits mediates the emergence of complex phenotypes, and how this complexity is shaped throughout the evolutionary history of Fungi.
Collapse
Affiliation(s)
- Miguel A. Naranjo‐Ortiz
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG)The Barcelona Institute of Science and TechnologyDr. Aiguader 88, Barcelona08003Spain
- Department of Experimental Sciences, Universitat Pompeu Fabra (UPF)Dr. Aiguader 88, 08003BarcelonaSpain
- ICREAPg. Lluís Companys 23, 08010BarcelonaSpain
| |
Collapse
|
48
|
Marques WL, Anderson LA, Sandoval L, Hicks MA, Prather KLJ. Sequence-based bioprospecting of myo-inositol oxygenase (Miox) reveals new homologues that increase glucaric acid production in Saccharomyces cerevisiae. Enzyme Microb Technol 2020; 140:109623. [PMID: 32912683 DOI: 10.1016/j.enzmictec.2020.109623] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 05/27/2020] [Accepted: 06/11/2020] [Indexed: 12/20/2022]
Abstract
myo-Inositol oxygenase (Miox) is a rate-limiting enzyme for glucaric acid production via microbial fermentation. The enzyme converts myo-inositol to glucuronate, which is further converted to glucaric acid, a natural compound with industrial uses that range from detergents to pharmaceutical synthesis to polymeric materials. More than 2,000 Miox sequences are available in the Uniprot database but only thirteen are classified as reviewed in Swiss-Prot (August 2019). In this study, sequence similarity networks were used to identify new homologues to be expressed in Saccharomyces cerevisiae for glucaric acid production. The expression of four homologues did not lead to product formation. Some of these enzymes may have a defective "dynamic lid" - a structural feature important to close the reaction site - which might explain the lack of activity. Thirty-one selected Miox sequences did allow for product formation, of which twenty-five were characterized for the first time. Expression of Talaromyces marneffei Miox led to the accumulation of 1.76 ± 0.33 g glucaric acid/L from 20 g glucose/L and 10 g/L myo-inositol. Specific glucaric acid titer with TmMiox increased 44 % compared to the often-used Arabidopsis thaliana variant AtMiox4 (0.258 vs. 0.179 g glucaric acid/g biomass). AtMiox4 activity decreased from 12.47 to 0.40 nmol/min/mg protein when cells exited exponential phase during growth on glucose, highlighting the importance of future research on Miox stability in order to further improve microbial production of glucaric acid.
Collapse
Affiliation(s)
- Wesley Leoricy Marques
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Lisa A Anderson
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Luis Sandoval
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Michael A Hicks
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kristala L J Prather
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| |
Collapse
|
49
|
Squalene-Tetrahymanol Cyclase Expression Enables Sterol-Independent Growth of Saccharomyces cerevisiae. Appl Environ Microbiol 2020; 86:AEM.00672-20. [PMID: 32561581 PMCID: PMC7440791 DOI: 10.1128/aem.00672-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/14/2020] [Indexed: 02/08/2023] Open
Abstract
The laboratory experiments described in this report simulate a proposed horizontal gene transfer event during the evolution of strictly anaerobic fungi. The demonstration that expression of a single heterologous gene sufficed to eliminate anaerobic sterol requirements in the model eukaryote Saccharomyces cerevisiae therefore contributes to our understanding of how sterol-independent eukaryotes evolved in anoxic environments. This report provides a proof of principle for a metabolic engineering strategy to eliminate sterol requirements in yeast strains that are applied in large-scale anaerobic industrial processes. The sterol-independent yeast strains described in this report provide a valuable platform for further studies on the physiological roles and impacts of sterols and sterol surrogates in eukaryotic cells. Biosynthesis of sterols, which are considered essential components of virtually all eukaryotic membranes, requires molecular oxygen. Anaerobic growth of the yeast Saccharomyces cerevisiae therefore strictly depends on sterol supplementation of synthetic growth media. Neocallimastigomycota are a group of strictly anaerobic fungi which, instead of containing sterols, contain the pentacyclic triterpenoid “sterol surrogate” tetrahymanol, which is formed by cyclization of squalene. Here, we demonstrate that expression of the squalene-tetrahymanol cyclase gene TtTHC1 from the ciliate Tetrahymena thermophila enables synthesis of tetrahymanol by S. cerevisiae. Moreover, expression of TtTHC1 enabled exponential growth of anaerobic S. cerevisiae cultures in sterol-free synthetic media. After deletion of the ERG1 gene from a TtTHC1-expressing S. cerevisiae strain, native sterol synthesis was abolished and sustained sterol-free growth was demonstrated under anaerobic as well as aerobic conditions. Anaerobic cultures of TtTHC1-expressing S. cerevisiae on sterol-free medium showed lower specific growth rates and biomass yields than ergosterol-supplemented cultures, while their ethanol yield was higher. This study demonstrated that acquisition of a functional squalene-tetrahymanol cyclase gene offers an immediate growth advantage to S. cerevisiae under anaerobic, sterol-limited conditions and provides the basis for a metabolic engineering strategy to eliminate the oxygen requirements associated with sterol synthesis in yeasts. IMPORTANCE The laboratory experiments described in this report simulate a proposed horizontal gene transfer event during the evolution of strictly anaerobic fungi. The demonstration that expression of a single heterologous gene sufficed to eliminate anaerobic sterol requirements in the model eukaryote Saccharomyces cerevisiae therefore contributes to our understanding of how sterol-independent eukaryotes evolved in anoxic environments. This report provides a proof of principle for a metabolic engineering strategy to eliminate sterol requirements in yeast strains that are applied in large-scale anaerobic industrial processes. The sterol-independent yeast strains described in this report provide a valuable platform for further studies on the physiological roles and impacts of sterols and sterol surrogates in eukaryotic cells.
Collapse
|
50
|
Gao S, Zhou H, Zhou J, Chen J. Promoter-Library-Based Pathway Optimization for Efficient (2 S)-Naringenin Production from p-Coumaric Acid in Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:6884-6891. [PMID: 32458684 DOI: 10.1021/acs.jafc.0c01130] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Pathway optimization plays an important role in fine-tuning metabolic pathways. In most conditions, more than three genes are involved in the biosynthesis pathway of a specific target product. To improve the titer of products, rational regulation of a group of genes by a series of promoters with different strengths is essential. On the basis of a series of RNA-Seq data, a set of 66 native promoters was chosen to fine-tune gene expression in Saccharomyces cerevisiae. Promoter strength was characterized by measuring the fluorescence strength of the enhanced green fluorescent protein through fluorescence-activated cell sorting. The expressions of PTDH1, PPGK1, PINO1, PSED1, and PCCW12 were stronger than that of PTDH3, whereas those of another 15 promoters were stronger than that of PTEF1. Then, 30 promoters were chosen to optimize the biosynthesis pathway of (2S)-naringenin from p-coumaric acid. With a high-throughput screening method, the highest titer of (2S)-naringenin in a 5 L bioreactor reached 1.21 g/L from p-coumaric acid, which is the highest titer according to the currently available reports.
Collapse
Affiliation(s)
- Song Gao
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Hengrui Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jian Chen
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Key Laboratory of Industrial Biotechnology, Ministry of Education and School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| |
Collapse
|