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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.
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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.
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Liang Y, Gao S, Qi X, Valentovich LN, An Y. Progress in Gene Editing and Metabolic Regulation of Saccharomyces cerevisiae with CRISPR/Cas9 Tools. ACS Synth Biol 2024; 13:428-448. [PMID: 38326929 DOI: 10.1021/acssynbio.3c00685] [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] [Indexed: 02/09/2024]
Abstract
The CRISPR/Cas9 systems have been developed as tools for genetic engineering and metabolic engineering in various organisms. In this review, various aspects of CRISPR/Cas9 in Saccharomyces cerevisiae, from basic principles to practical applications, have been summarized. First, a comprehensive review has been conducted on the history of CRISPR/Cas9, successful cases of gene disruptions, and efficiencies of multiple DNA fragment insertions. Such advanced systems have accelerated the development of microbial engineering by reducing time and labor, and have enhanced the understanding of molecular genetics. Furthermore, the research progress of the CRISPR/Cas9-based systems in the production of high-value-added chemicals and the improvement of stress tolerance in S. cerevisiae have been summarized, which should have an important reference value for genetic and synthetic biology studies based on S. cerevisiae.
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Affiliation(s)
- Yaokun Liang
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Song Gao
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
| | - Xianghui Qi
- School of Life Sciences, Guangzhou University, Guangdong 511370, China
| | - Leonid N Valentovich
- Institute of Microbiology, National Academy of Sciences of Belarus, Minsk 220072, Belarus
| | - Yingfeng An
- College of Biosciences and Biotechnology, Shenyang Agricultural University, Shenyang 110065, China
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Trivellin C, Rugbjerg P, Olsson L. Performance and robustness analysis reveals phenotypic trade-offs in yeast. Life Sci Alliance 2024; 7:e202302215. [PMID: 37903627 PMCID: PMC10618107 DOI: 10.26508/lsa.202302215] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 10/20/2023] [Accepted: 10/20/2023] [Indexed: 11/01/2023] Open
Abstract
To design strains that can function efficiently in complex industrial settings, it is crucial to consider their robustness, that is, the stability of their performance when faced with perturbations. In the present study, we cultivated 24 Saccharomyces cerevisiae strains under conditions that simulated perturbations encountered during lignocellulosic bioethanol production, and assessed the performance and robustness of multiple phenotypes simultaneously. The observed negative correlations confirmed a trade-off between performance and robustness of ethanol yield, biomass yield, and cell dry weight. Conversely, the specific growth rate performance positively correlated with the robustness, presumably because of evolutionary selection for robust, fast-growing cells. The Ethanol Red strain exhibited both high performance and robustness, making it a good candidate for bioproduction in the tested perturbation space. Our results experimentally map the robustness-performance trade-offs, previously demonstrated mainly by single-phenotype and computational studies.
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Affiliation(s)
- Cecilia Trivellin
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
| | - Peter Rugbjerg
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
- Enduro Genetics ApS, Copenhagen, Denmark
| | - Lisbeth Olsson
- https://ror.org/040wg7k59 Department of Life Sciences, Division of Industrial Biotechnology, Chalmers University of Technology, Gothenburg, Sweden
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Cripwell RA, My R, Treu L, Campanaro S, Favaro L, van Zyl WH, Viljoen-Bloom M. Additional glucoamylase genes increase ethanol productivity on rice and potato waste streams by a recombinant amylolytic yeast. BIORESOURCE TECHNOLOGY 2023; 388:129787. [PMID: 37741578 DOI: 10.1016/j.biortech.2023.129787] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 09/12/2023] [Accepted: 09/13/2023] [Indexed: 09/25/2023]
Abstract
The implementation of consolidated bioprocessing for converting starch to ethanol relies on a robust yeast that produces enough amylases for rapid starch hydrolysis. Furthermore, using low-cost substrates will assist with competitive ethanol prices and support a bioeconomy, especially in developing countries. This paper addresses both challenges with the expression of additional glucoamylase gene copies in an efficient amylolytic strain (Saccharomyces cerevisiae ER T12) derived from the industrial yeast, Ethanol Red™. Recombinant ER T12 was used as a host to increase ethanol productivity during raw starch fermentation; the ER T12.7 variant, selected from various transformants, displayed enhanced raw starch conversion and a 36% higher ethanol concentration than the parental strain after 120 h. Unripe rice, rice bran, potato waste and potato peels were evaluated as alternative starchy substrates to test ER T12.7's fermenting ability. ER T12.7 produced high ethanol yields at significantly improved ethanol productivity, key criteria for its industrial application.
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Affiliation(s)
- Rosemary A Cripwell
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Rebecca My
- Waste to Bioproducts-Lab, Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020 Legnaro, Padova, Italy
| | - Laura Treu
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Stefano Campanaro
- Department of Biology, University of Padova, Via U. Bassi 58/b, 35121, Padova, Italy
| | - Lorenzo Favaro
- Waste to Bioproducts-Lab, Department of Agronomy Food Natural resources Animals and Environment (DAFNAE), Università di Padova, Agripolis, Viale dell'Università 16, 35020 Legnaro, Padova, Italy.
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Private Bag X1, Matieland 7602, South Africa
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Caballero-Sanchez L, Lázaro-Mixteco PE, Vargas-Tah A, Castro-Montoya AJ. Pilot-scale bioethanol production from the starch of avocado seeds using a combination of dilute acid-based hydrolysis and alcoholic fermentation by Saccharomyces cerevisiae. Microb Cell Fact 2023; 22:119. [PMID: 37386435 DOI: 10.1186/s12934-023-02110-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 05/01/2023] [Indexed: 07/01/2023] Open
Abstract
BACKGROUND A processing methodology of raw starch extraction from avocado seeds (ASs) and a sequential hydrolysis and fermentation bioprocess in just a few steps was successfully obtained for the bioethanol production by a single yeast Saccharomyces cerevisiae strain and this research was also to investigate the optimum conditions for the pretreatment of biomass and technical procedures for the production of bioethanol. It successfully resulted in high yields and productivity of all the experiments from the laboratory scale and the pilot plant. Ethanol yields from pretreated starch are comparable with those in commercial industries that use molasses and hydrolyzed starch as raw materials. RESULTS Before the pilot-scale bioethanol production, studies of starch extraction and dilute sulfuric acid-based pretreatment was carefully conducted. The amount of starch extracted from dry and fresh avocado seed was 16.85 g ± 0.34 g and 29.79 ± 3.18 g of dry starch, representing a yield of ∼17% and 30%, respectively. After a dilute sulfuric acid pretreatment of starch, the released reducing sugars (RRS) were obtained and the hydrolysate slurries containing glucose (109.79 ± 1.14 g/L), xylose (0.99 ± 0.06 g/L), and arabinose (0.38 ± 0.01 g/L). The efficiency of total sugar conversion was 73.40%, with a productivity of 9.26 g/L/h. The ethanol fermentation in a 125 mL flask fermenter showed that Saccharomyces cerevisiae (Fali, active dry yeast) produced the maximum ethanol concentration, pmax at 49.05 g/L (6.22% v/v) with a yield coefficient, Yp/s of 0.44 gEthanol/gGlucose, a productivity or production rate, rp at 2.01 g/L/h and an efficiency, Ef of 85.37%. The pilot scale experiments of the ethanol fermentation using the 40-L fermenter were also successfully achieved with essentially good results. The values of pmax,Yp/s, rp, and Ef of the 40-L scale were at 50.94 g/L (6.46% v/v), 0.45 gEthanol/gGlucose, 2.11 g/L/h, and 88.74%, respectively. Because of using raw starch, major by-products, i.e., acetic acid in the two scales were very low, in ranges of 0.88-2.45 g/L, and lactic acid was not produced, which are less than those values in the industries. CONCLUSIONS The sequential hydrolysis and fermentation process of two scales for ethanol production using the combination of hydrolysis by utilizing dilute sulfuric acid-based pretreatment and fermentation by a single yeast Saccharomyces cerevisiae strain is practicable and feasible for realistic and effective scale-up strategies of bioethanol production from the starch of avocado seeds.
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Affiliation(s)
- Luis Caballero-Sanchez
- Posgrado de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica S/N, Ciudad Universitaria, 58030, Morelia, Mich, México
| | - Pedro E Lázaro-Mixteco
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica S/N, Ciudad Universitaria, 58030, Morelia, Mich, México
| | - Alejandra Vargas-Tah
- Facultad de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica S/N, Ciudad Universitaria, 58030, Morelia, Mich, México.
| | - Agustín J Castro-Montoya
- Posgrado de Ingeniería Química, Universidad Michoacana de San Nicolás de Hidalgo, Francisco J. Múgica S/N, Ciudad Universitaria, 58030, Morelia, Mich, México.
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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.
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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
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