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Sornlek W, Sonthirod C, Tangphatsornruang S, Ingsriswang S, Runguphan W, Eurwilaichtr L, Champreda V, Tanapongpipat S, Schaap PJ, Martins Dos Santos VAP. Genes controlling hydrolysate toxin tolerance identified by QTL analysis of the natural Saccharomyces cerevisiae BCC39850. Appl Microbiol Biotechnol 2024; 108:21. [PMID: 38159116 DOI: 10.1007/s00253-023-12843-3] [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: 04/17/2023] [Revised: 09/21/2023] [Accepted: 09/30/2023] [Indexed: 01/03/2024]
Abstract
Lignocellulosic material can be converted to valorized products such as fuels. Pretreatment is an essential step in conversion, which is needed to increase the digestibility of the raw material for microbial fermentation. However, pretreatment generates by-products (hydrolysate toxins) that are detrimental to microbial growth. In this study, natural Saccharomyces strains isolated from habitats in Thailand were screened for their tolerance to synthetic hydrolysate toxins (synHTs). The Saccharomyces cerevisiae natural strain BCC39850 (toxin-tolerant) was crossed with the laboratory strain CEN.PK2-1C (toxin-sensitive), and quantitative trait locus (QTL) analysis was performed on the segregants using phenotypic scores of growth (OD600) and glucose consumption. VMS1, DET1, KCS1, MRH1, YOS9, SYO1, and YDR042C were identified from QTLs as candidate genes associated with the tolerance trait. CEN.PK2-1C knockouts of the VMS1, YOS9, KCS1, and MRH1 genes exhibited significantly greater hydrolysate toxin sensitivity to growth, whereas CEN.PK2-1C knock-ins with replacement of VMS1 and MRH1 genes from the BCC39850 alleles showed significant increased ethanol production titers compared with the CEN.PK2-1C parental strain in the presence of synHTs. The discovery of VMS1, YOS9, MRH1, and KCS1 genes associated with hydrolysate toxin tolerance in S. cerevisiae indicates the roles of the endoplasmic-reticulum-associated protein degradation pathway, plasma membrane protein association, and the phosphatidylinositol signaling system in this trait. KEY POINTS: • QTL analysis was conducted using a hydrolysate toxin-tolerant S. cerevisiae natural strain • Deletion of VMS1, YOS9, MRH1, and KCS1 genes associated with hydrolysate toxin-sensitivity • Replacement of VMS1 and MRH1 with natural strain alleles increased ethanol production titers in the presence of hydrolysate toxins.
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Affiliation(s)
- Warasirin Sornlek
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Supawadee Ingsriswang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Lily Eurwilaichtr
- National Energy Technology Center, 114 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand
| | - Sutipa Tanapongpipat
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Road, Khlong Nueng, Khlong Luang, 12120, Pathum Thani, Thailand.
| | - Peter J Schaap
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Vitor A P Martins Dos Santos
- The Laboratory of Systems and Synthetic Biology, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Bioprocess Engineering Group, Wageningen University and Research, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
- LifeGlimmer GmbH, Markelstrasse 38, 12163, Berlin, Germany.
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Ilhamzah, Tsukuda Y, Yamaguchi Y, Ogita A, Fujita KI. Persimmon tannin promotes the growth of Saccharomyces cerevisiae under ethanol stress. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:6118-6126. [PMID: 38445539 DOI: 10.1002/jsfa.13439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 02/27/2024] [Accepted: 03/06/2024] [Indexed: 03/07/2024]
Abstract
BACKGROUND Saccharomyces cerevisiae plays a pivotal role in various industrial processes, including bioethanol production and alcoholic beverage fermentation. However, during these fermentations, yeasts are subjected to various environmental stresses, such as ethanol stress, which hinder cell growth and ethanol production. Genetic manipulations and the addition of natural ingredients rich in antioxidants to the culture have been shown to overcome this. Here, we investigated the potential of persimmon tannins, known for their antioxidative properties, to enhance the ethanol stress tolerance of yeast. RESULTS Assessment of the effects of 6.25 mg mL-1 persimmon tannins after 48 h incubation revealed cell viability to be increased by 8.9- and 6.5-fold compared to the control treatment with and without 12.5% ethanol, respectively. Furthermore, persimmon tannins reduced ethanol-induced oxidative stress, including the production of cellular reactive oxygen species and acceleration of lipid peroxidation. However, persimmon tannins could hardly overcome ethanol-induced cell membrane damage. CONCLUSION The findings herein indicate the potential of persimmon tannin as a protective agent for increasing yeast tolerance to ethanol stress by restricting oxidative damage but not membrane damage. Overall, this study unveils the implications of persimmon tannins for industries relying on yeast. © 2024 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.
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Affiliation(s)
- Ilhamzah
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | - Yuka Tsukuda
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
| | | | - Akira Ogita
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
- Research Center for Urban Health and Sports, Osaka Metropolitan University, Osaka, Japan
| | - Ken-Ichi Fujita
- Graduate School of Science, Osaka Metropolitan University, Osaka, Japan
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3
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Fang L, Chen Y, He Q, Wang L, Duan Q, Huang C, Song H, Cao Y. Mining novel gene targets for improving tolerance to furfural and acetic acid in Yarrowia lipolytica using whole-genome CRISPRi library. BIORESOURCE TECHNOLOGY 2024; 403:130764. [PMID: 38718903 DOI: 10.1016/j.biortech.2024.130764] [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: 02/03/2024] [Revised: 03/25/2024] [Accepted: 04/28/2024] [Indexed: 05/20/2024]
Abstract
Abundant renewable resource lignocellulosic biomass possesses tremendous potential for green biomanufacturing, while its efficient utilization by Yarrowia lipolytica, an attractive biochemical production host, is restricted since the presence of inhibitors furfural and acetic acid in lignocellulosic hydrolysate. Given deficient understanding of inherent interactions between inhibitors and cellular metabolism, sufficiently mining relevant genes is necessary. Herein, 14 novel gene targets were discovered using clustered regularly interspaced short palindromic repeats interference library in Y. lipolytica, achieving tolerance to 0.35 % (v/v) acetic acid (the highest concentration reported in Y. lipolytica), 4.8 mM furfural, or a combination of 2.4 mM furfural and 0.15 % (v/v) acetic acid. The tolerance mechanism might involve improvement of cell division and decrease of reactive oxygen species level. Transcriptional repression of effective gene targets still enabled tolerance when xylose was a carbon source. This work forms a robust foundation for improving microbial tolerance to lignocellulose-derived inhibitors and revealing underlying mechanism.
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Affiliation(s)
- Lixia Fang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yaru Chen
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qianxi He
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Luxin Wang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Qiyang Duan
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Congcong Huang
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Hao Song
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingxiu Cao
- Frontier Science Center for Synthetic Biology (Ministry of Education), Key Laboratory of Systems Bioengineering, and School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
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Lechtenberg T, Wynands B, Müller MF, Polen T, Noack S, Wierckx N. Improving 5-(hydroxymethyl)furfural (HMF) tolerance of Pseudomonas taiwanensis VLB120 by automated adaptive laboratory evolution (ALE). Metab Eng Commun 2024; 18:e00235. [PMID: 38832093 PMCID: PMC11144800 DOI: 10.1016/j.mec.2024.e00235] [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: 03/19/2024] [Revised: 04/29/2024] [Accepted: 05/07/2024] [Indexed: 06/05/2024] Open
Abstract
The aldehyde 5-(hydroxymethyl)furfural (HMF) is of great importance for a circular bioeconomy. It is a renewable platform chemical that can be converted into a range of useful compounds to replace petroleum-based products such as the green plastic monomer 2,5-furandicarboxylic acid (FDCA). However, it also exhibits microbial toxicity for example hindering the efficient biotechnological valorization of lignocellulosic hydrolysates. Thus, there is an urgent need for tolerance-improved organisms applicable to whole-cell biocatalysis. Here, we engineer an oxidation-deficient derivative of the naturally robust and emerging biotechnological workhorse P. taiwanensis VLB120 by robotics-assisted adaptive laboratory evolution (ALE). The deletion of HMF-oxidizing enzymes enabled for the first time evolution under constant selection pressure by the aldehyde, yielding strains with consistently improved growth characteristics in presence of the toxicant. Genome sequencing of evolved clones revealed loss-of function mutations in the LysR-type transcriptional regulator-encoding mexT preventing expression of the associated efflux pump mexEF-oprN. This knowledge allowed reverse engineering of strains with enhanced aldehyde tolerance, even in a background of active or overexpressed HMF oxidation machinery, demonstrating a synergistic effect of two distinct tolerance mechanisms.
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Affiliation(s)
- Thorsten Lechtenberg
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Benedikt Wynands
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Moritz-Fabian Müller
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Tino Polen
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Stephan Noack
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
| | - Nick Wierckx
- Institute of Bio- and Geosciences IBG-1: Biotechnology, Forschungszentrum Jülich, 52425 Jülich, Germany
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5
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Hou S, Wang S, Zheng C, Zhou Y, Yu C, Li H. Hexadecanoic acid produced in the co-culture of S. cerevisiae and E.coli promotes oxidative stress tolerance of the S.cerevisiae cells. World J Microbiol Biotechnol 2024; 40:213. [PMID: 38789629 DOI: 10.1007/s11274-024-04004-z] [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: 03/18/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Co-fermentation performed by Saccharomyces cerevisiae and Escherichia coli or other microbes has been widely used in industrial fermentation. Meanwhile, the co-cultured microbes might regulate each other's metabolisms or cell behaviors including oxidative stress tolerance through secreting molecules. Here, results based on the co-culture system of S. cerevisiae and E. coli suggested the promoting effect of E. coli on the oxidative stress tolerance of S. cerevisiae cells. The co-cultured E. coli could enhance S. cerevisiae cell viability through improving its membrane stability and reducing the oxidized lipid level. Meanwhile, promoting effect of the co-cultured supernatant on the oxidative stress tolerance of S. cerevisiae illustrated by the supernatant substitution strategy suggested that secreted compounds contained in the co-cultured supernatant contributed to the higher oxidative stress tolerance of S. cerevisiae. The potential key regulatory metabolite (i.e., hexadecanoic acid) with high content difference between co-cultured supernatant and the pure-cultured S. cerevisiae supernatant was discovered by GC-MS-based metabolomics strategy. And exogenous addition of hexadecanoic acid did suggest its contribution to higher oxidative stress tolerance of S. cerevisiae. Results presented here would contribute to the understanding of the microbial interactions and provide the foundation for improving the efficiency of co-fermentation performed by S. cerevisiae and E. coli.
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Affiliation(s)
- Shuxin Hou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shihui Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Caijuan Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yu Zhou
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Hao Li
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China.
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6
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Parmaki S, Vasquez MI, Patsalou M, Gomes RFA, Simeonov SP, Afonso CAM, Koutinas M. Ecotoxicological assessment of biomass-derived furan platform chemicals using aquatic and terrestrial bioassays. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2024; 26:686-699. [PMID: 38372577 DOI: 10.1039/d3em00552f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
An environmental toxicological assessment of fourteen furanic compounds serving as valuable building blocks produced from biomass was performed. The molecules selected included well studied compounds serving as control examples to compare the toxicity exerted against a variety of highly novel furans which have been additionally targeted as potential or current alternatives to biofuels, building blocks and polymer monomers. The impact of the furan platform chemicals targeted on widely applied ecotoxicity model organisms was determined employing the marine bioluminescent bacterium Aliivibrio fischeri and the freshwater green microalgae Raphidocelis subcapitata, while their ecotoxicity effects on plants were assessed using dicotyledonous plants Sinapis alba and Lepidium sativum. Regarding the specific endpoints evaluated, the furans tested were slightly toxic or practically nontoxic for A. fischeri following 5 and 15 min of exposure. Moreover, most of the building blocks did not affect the growth of L. sativum and S. alba at 150 mg L-1 for 72 h of exposure. Specifically, 9 and 11 out of the 14 furan platform chemicals tested were non-effective or stimulant for L. sativum and S. alba respectively. Given that furans comprise common inhibitors in biorefinery fermentations, the growth inhibition of the specific building blocks was studied using the industrial workhorse yeast Saccharomyces cerevisiae, demonstrating insignificant inhibition on eukaryotic cell growth following 6, 12 and 16 h of exposure at a concentration of 500 mg L-1. The study provides baseline information to unravel the ecotoxic effects and to confirm the green aspects of a range of versatile biobased platform molecules.
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Affiliation(s)
- Stella Parmaki
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
| | - Marlen I Vasquez
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
- European University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus
| | - Maria Patsalou
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
| | - Rafael F A Gomes
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Svilen P Simeonov
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
- Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, Acad. G. Bonchev str., bl. 9, 1113, Sofia, Bulgaria
| | - Carlos A M Afonso
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Prof. Gama Pinto, 1649-003, Lisbon, Portugal
| | - Michalis Koutinas
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3036, Limassol, Cyprus.
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7
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Singh S, Arya SK, Krishania M. Bioprocess optimization for enhanced xylitol synthesis by new isolate Meyerozyma caribbica CP02 using rice straw. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2024; 17:31. [PMID: 38402217 PMCID: PMC10894501 DOI: 10.1186/s13068-024-02475-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/10/2024] [Indexed: 02/26/2024]
Abstract
The present work models the fermentation process parameters of the newly isolated, Meyerozyma caribbica CP02 for enhanced xylitol production and its fermentability study on rice straw hydrolysate. The study examined the impact of each of the process variables by one variable at a time optimization followed by statistical validation. Temperature of 32 °C, pH of 3.5, agitation of 200 rpm, 1.5% (v/v) inoculum, 80 gL-1 initial xylose was optimized. Subsequently, a sequential two-stage agitation approach was adopted for fermentation. At these optimized conditions, xylitol yield of 0.77 gg-1 and 0.64 gg-1 was achieved using media containing commercial and rice straw derived xylose, respectively. For scale up, in 3L batch bioreactor, the highest xylitol yield (0.63 gg-1) was attained at 72 h with rice straw hydrolysate media containing initial xylose (59.48 ± 0.82 gL-1) along with inhibitors (1.55 ± 0.10 gL-1 aliphatic acids, 0.0.048 ± 0.11 gL-1 furans, 0.64 ± 0.23 gL-1 total phenols). The results imply that even under circumstances characterized by an acidic pH and elevated initial xylose level, M. caribbica CP02, as an isolate, displays robustness and shows favorable fermentability of rice straw hydrolysate. Therefore, isolate CP02 has potential to be used in bio-refineries for high yield xylitol production with minimal hydrolysate processing requirements.
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Affiliation(s)
- Saumya Singh
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81 (Knowledge City), Mohali, 140306, India
| | - Shailendra Kumar Arya
- Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Meena Krishania
- Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector-81 (Knowledge City), Mohali, 140306, India.
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Henriques D, Minebois R, dos Santos D, Barrio E, Querol A, Balsa-Canto E. A Dynamic Genome-Scale Model Identifies Metabolic Pathways Associated with Cold Tolerance in Saccharomyces kudriavzevii. Microbiol Spectr 2023; 11:e0351922. [PMID: 37227304 PMCID: PMC10269563 DOI: 10.1128/spectrum.03519-22] [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: 09/04/2022] [Accepted: 05/10/2023] [Indexed: 05/26/2023] Open
Abstract
Saccharomyces kudriavzevii is a cold-tolerant species identified as a good alternative for industrial winemaking. Although S. kudriavzevii has never been found in winemaking, its co-occurrence with Saccharomyces cerevisiae in Mediterranean oaks is well documented. This sympatric association is believed to be possible due to the different growth temperatures of the two yeast species. However, the mechanisms behind the cold tolerance of S. kudriavzevii are not well understood. In this work, we propose the use of a dynamic genome-scale model to compare the metabolic routes used by S. kudriavzevii at two temperatures, 25°C and 12°C, to decipher pathways relevant to cold tolerance. The model successfully recovered the dynamics of biomass and external metabolites and allowed us to link the observed phenotype with exact intracellular pathways. The model predicted fluxes that are consistent with previous findings, but it also led to novel results which we further confirmed with intracellular metabolomics and transcriptomic data. The proposed model (along with the corresponding code) provides a comprehensive picture of the mechanisms of cold tolerance that occur within S. kudriavzevii. The proposed strategy offers a systematic approach to explore microbial diversity from extracellular fermentation data at low temperatures. IMPORTANCE Nonconventional yeasts promise to provide new metabolic pathways for producing industrially relevant compounds and tolerating specific stressors such as cold temperatures. The mechanisms behind the cold tolerance of S. kudriavzevii or its sympatric relationship with S. cerevisiae in Mediterranean oaks are not well understood. This study proposes a dynamic genome-scale model to investigate metabolic pathways relevant to cold tolerance. The predictions of the model would indicate the ability of S. kudriavzevii to produce assimilable nitrogen sources from extracellular proteins present in its natural niche. These predictions were further confirmed with metabolomics and transcriptomic data. This finding suggests that not only the different growth temperature preferences but also this proteolytic activity may contribute to the sympatric association with S. cerevisiae. Further exploration of these natural adaptations could lead to novel engineering targets for the biotechnological industry.
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Affiliation(s)
- David Henriques
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
| | - Romain Minebois
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | | | - Eladio Barrio
- Genomics Department, Universitat de València, Valencia, Spain
| | - Amparo Querol
- Systems Biology of Yeasts of Biotechnological Interest, IATA-CSIC, Paterna, Spain
| | - Eva Balsa-Canto
- Bioprocess and Biosystems Engineering, IIM-CSIC, Vigo, Spain
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da Silva RR, Zaiter MA, Boscolo M, da Silva R, Gomes E. Xylose consumption and ethanol production by Pichia guilliermondii and Candida oleophila in the presence of furans, phenolic compounds, and organic acids commonly produced during the pre-treatment of plant biomass. Braz J Microbiol 2023; 54:753-759. [PMID: 36826705 PMCID: PMC10234969 DOI: 10.1007/s42770-023-00937-z] [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: 07/13/2022] [Accepted: 02/15/2023] [Indexed: 02/25/2023] Open
Abstract
For 2G ethanol production, pentose fermentation and yeast tolerance to lignocellulosic hydrolyzate components are essential to improve biorefinery yields. Generally, physicochemical pre-treatment methodologies are used to facilitate access to cellulose and hemicellulose in plant material, which consequently can generate microbial growth inhibitory compounds, such as furans, weak acids, and phenolic compounds. Because of the unsatisfactory yield of wild-type Saccharomyces cerevisiae during pentose fermentation, the search for xylose-fermenting yeasts tolerant to microbial growth inhibitors has gained attention. In this study, we investigated the ability of the yeasts Pichia guilliermondii G1.2 and Candida oleophila G10.1 to produce ethanol from xylose and tolerate the inhibitors furfural, 5-hydroxymethylfurfural (HMF), acetic acid, formic acid, ferulic acid, and vanillin. We demonstrated that both yeasts were able to grow and consume xylose in the presence of all single inhibitors, with greater growth limitation in media containing furfural, acetic acid, and vanillin. In saline medium containing a mixture of these inhibitors (2.5-3.5 mM furfural and HMF, 1 mM ferulic acid, 1-1.5 mM vanillin, 10-13 mM acetic acid, and 5-7 mM formic acid), both yeasts were able to produce ethanol from xylose, similar to that detected in the control medium (without inhibitors). In future studies, the proteins involved in the transport of pentose and tolerance to these inhibitors need to be investigated.
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Affiliation(s)
- Ronivaldo Rodrigues da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil.
| | - Mohammed Anas Zaiter
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Maurício Boscolo
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Roberto da Silva
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
| | - Eleni Gomes
- Instituto de Biociencias, Letras e Ciencias Exatas, Universidade Estadual Paulista "Julio de Mesquita Filho", Cristovao Colombo, 2265, Jd Nazareth, Ibilce‑Unesp, Sao Jose do Rio Preto, São Paulo, Brazil
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10
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Guo H, Zhao Y, Chang JS, Lee DJ. Inhibitor formation and detoxification during lignocellulose biorefinery: A review. BIORESOURCE TECHNOLOGY 2022; 361:127666. [PMID: 35878776 DOI: 10.1016/j.biortech.2022.127666] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/16/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
Abstract
For lignocellulose biorefinery, pretreatment is needed to maximize the cellulose accessibility, frequently generating excess inhibitory substances to decline the efficiency of the subsequent fermentation processes. This mini-review updates the current research efforts to detoxify the adverse impacts of generated inhibitors on the performance of biomass biorefinery. The lignocellulose pretreatment processes are first reviewed. The generation of inhibitors, furans, furfural, phenols, formic acid, and acetic acid, from the lignocellulose, with their action mechanisms, are listed. Then the detoxification processes are reviewed, from which the biological detoxification processes are noted as promising and worth further study. The challenges and prospects for applying biological detoxification in lignocellulose biorefinery are outlined. Integrated studies considering the entire biorefinery should be performed on a case-by-case basis.
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Affiliation(s)
- Hongliang Guo
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Ying Zhao
- College of Forestry, Northeast Forestry University, Harbin 150040, China
| | - Jo-Shu Chang
- Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan
| | - Duu-Jong Lee
- Department of Mechanical Engineering, City University of Hong Kong, Kowloon Tong, Hong Kong; Department of Chemical Engineering and Materials Science, Yuan Ze University, Chung-li 32003, Taiwan.
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Yang T, Zhang S, Li L, Tian J, Li X, Pan Y. Screening and transcriptomic analysis of the ethanol-tolerant mutant Saccharomyces cerevisiae YN81 for high-gravity brewing. Front Microbiol 2022; 13:976321. [PMID: 36090078 PMCID: PMC9453260 DOI: 10.3389/fmicb.2022.976321] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Ethanol stress is one of the major limiting factors for high-gravity brewing. Breeding of yeast strain with high ethanol tolerance, and revealing the ethanol tolerance mechanism of Saccharomyces cerevisiae is of great significance to the production of high-gravity beer. In this study, the mutant YN81 was obtained by ultraviolet-diethyl sulfate (UV-DES) cooperative mutagenesis from parental strain CS31 used in high-gravity craft beer brewing. The ethanol tolerance experiment results showed that cell growth and viability of YN81 were significantly greater than that of CS31 under ethanol stress. The ethanol tolerance mechanisms of YN81 were studied through observation of cell morphology, intracellular trehalose content, and transcriptomic analysis. Results from scanning electron microscope (SEM) showed alcohol toxicity caused significant changes in the cell morphology of CS31, while the cell morphology of YN81 changed slightly, indicating the cell morphology of CS31 got worse (the formation of hole and cell wrinkle). In addition, compared with ethanol-free stress, the trehalose content of YN81 and CS31 increased dramatically under ethanol stress, but there was no significant difference between YN81 and CS31, whether with or without ethanol stress. GO functional annotation analysis showed that under alcohol stress, the number of membrane-associated genes in YN81 was higher than that without alcohol stress, as well as CS31, while membrane-associated genes in YN81 were expressed more than CS31 under alcohol stress. KEGG functional enrichment analysis showed unsaturated fatty acid synthesis pathways and amino acid metabolic pathways were involved in ethanol tolerance of YN81. The mutant YN81 and its ethanol tolerance mechanism provide an optimal strain and theoretical basis for high-gravity craft beer brewing.
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D-Lactic Acid Production from Sugarcane Bagasse by Genetically Engineered Saccharomyces cerevisiae. J Fungi (Basel) 2022; 8:jof8080816. [PMID: 36012804 PMCID: PMC9410322 DOI: 10.3390/jof8080816] [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: 06/06/2022] [Revised: 07/26/2022] [Accepted: 07/29/2022] [Indexed: 11/25/2022] Open
Abstract
Lactic acid (LA) is a promising bio-based chemical that has broad applications in food, nutraceutical, and bioplastic industries. However, production of the D-form of LA (D-LA) from fermentative organisms is lacking. In this study, Saccharomyces cerevisiae harboring the D-lactate dehydrogenase (DLDH) gene from Leuconostoc mesenteroides was constructed (CEN.PK2_DLDH). To increase D-LA production, the CRISPR/Cas12a system was used for the deletion of gpd1, gpd2, and adh1 to minimize glycerol and ethanol production. Although an improved D-LA titer was observed for both CEN.PK2_DLDHΔgpd and CEN.PK2_DLDHΔgpdΔadh1, growth impairment was observed. To enhance the D-LA productivity, CEN.PK2_DLDHΔgpd was crossed with the weak acid-tolerant S. cerevisiae BCC39850. The isolated hybrid2 showed a maximum D-LA concentration of 23.41 ± 1.65 g/L, equivalent to the improvement in productivity and yield by 2.2 and 1.5 folds, respectively. The simultaneous saccharification and fermentation using alkaline pretreated sugarcane bagasse by the hybrid2 led to an improved D-LA conversion yield on both the washed solid and whole slurry (0.33 and 0.24 g/g glucan). Our findings show the exploitation of natural yeast diversity and the potential strategy of gene editing combined with conventional breeding on improving the performance of S. cerevisiae for the production of industrially potent products.
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Improving Lipid Production of Yarrowia lipolytica by the Aldehyde Dehydrogenase-Mediated Furfural Detoxification. Int J Mol Sci 2022; 23:ijms23094761. [PMID: 35563152 PMCID: PMC9102794 DOI: 10.3390/ijms23094761] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/23/2022] [Accepted: 04/25/2022] [Indexed: 02/01/2023] Open
Abstract
Yarrowia lipolytica, the non-conventional yeast capable of high lipogenesis, is a microbial chassis for producing lipid-based biofuels and chemicals from renewable resources such as lignocellulosic biomass. However, the low tolerance of Y. lipolytica against furfural, a major inhibitory furan aldehyde derived from the pretreatment processes of lignocellulosic biomass, has restricted the efficient conversion of lignocellulosic hydrolysates. In this study, the furfural tolerance of Y. lipolytica has been improved by supporting its endogenous detoxification mechanism. Specifically, the endogenous genes encoding the aldehyde dehydrogenase family proteins were overexpressed in Y. lipolytica to support the conversion of furfural to furoic acid. Among them, YALI0E15400p (FALDH2) has shown the highest conversion rate of furfural to furoic acid and resulted in two-fold increased cell growth and lipid production in the presence of 0.4 g/L of furfural. To our knowledge, this is the first report to identify the native furfural detoxification mechanism and increase furfural resistance through rational engineering in Y. lipolytica. Overall, these results will improve the potential of Y. lipolytica to produce lipids and other value-added chemicals from a carbon-neutral feedstock of lignocellulosic biomass.
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Li B, Liu N, Zhao X. Response mechanisms of Saccharomyces cerevisiae to the stress factors present in lignocellulose hydrolysate and strategies for constructing robust strains. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:28. [PMID: 35292082 PMCID: PMC8922928 DOI: 10.1186/s13068-022-02127-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 03/01/2022] [Indexed: 11/19/2022]
Abstract
Bioconversion of lignocellulosic biomass to biofuels such as bioethanol and high value-added products has attracted great interest in recent decades due to the carbon neutral nature of biomass feedstock. However, there are still many key technical difficulties for the industrial application of biomass bioconversion processes. One of the challenges associated with the microorganism Saccharomyces cerevisiae that is usually used for bioethanol production refers to the inhibition of the yeast by various stress factors. These inhibitive effects seriously restrict the growth and fermentation performance of the strains, resulting in reduced bioethanol production efficiency. Therefore, improving the stress response ability of the strains is of great significance for industrial production of bioethanol. In this article, the response mechanisms of S. cerevisiae to various hydrolysate-derived stress factors including organic acids, furan aldehydes, and phenolic compounds have been reviewed. Organic acids mainly stimulate cells to induce intracellular acidification, furan aldehydes mainly break the intracellular redox balance, and phenolic compounds have a greater effect on membrane homeostasis. These damages lead to inadequate intracellular energy supply and dysregulation of transcription and translation processes, and then activate a series of stress responses. The regulation mechanisms of S. cerevisiae in response to these stress factors are discussed with regard to the cell wall/membrane, energy, amino acids, transcriptional and translational, and redox regulation. The reported key target genes and transcription factors that contribute to the improvement of the strain performance are summarized. Furthermore, the genetic engineering strategies of constructing multilevel defense and eliminating stress effects are discussed in order to provide technical strategies for robust strain construction. It is recommended that robust S. cerevisiae can be constructed with the intervention of metabolic regulation based on the specific stress responses. Rational design with multilevel gene control and intensification of key enzymes can provide good strategies for construction of robust strains.
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Affiliation(s)
- Bo Li
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Nan Liu
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China.,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China
| | - Xuebing Zhao
- Key Laboratory of Industrial Biocatalysis, Ministry of Education, Tsinghua University, Beijing, 100084, China. .,Institute of Applied Chemistry, Department of Chemical Engineering, Tsinghua University, Beijing, 100084, China.
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