1
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Liu X, Sun Y, Lv X, Song M, Sun J, Sun Y. Targeting lipid peroxidation-associated ferroptosis suppresses lung carcinoma progression by regulating cell cycle arrest. Int Immunopharmacol 2024; 138:112518. [PMID: 38917528 DOI: 10.1016/j.intimp.2024.112518] [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: 04/11/2024] [Revised: 05/29/2024] [Accepted: 06/16/2024] [Indexed: 06/27/2024]
Abstract
Lung carcinoma is a frequently encountered cancerous growth that affects the respiratory tract and has a high occurrence rate globally. In light of the ongoing worldwide health emergency, the significance of efficient therapeutic agents and strategies is of utmost importance. A meticulous control of the cell cycle is crucial for comprehending the pathophysiology and molecular causes of lung cancer, as well as for the formulation of efficacious therapeutic medicines. The mechanism by which cells synchronize cell cycle with cell survival and death is still not fully understood. In this study, we demonstrate that the halting of the cell cycle has a strong inhibitory impact on ferroptosis, a specific type of controlled cell death triggered by excessive lipid peroxidation at the membranes of cells. Ferroptosis is halted through the mechanism of cell cycle arrest, which involves the deposition of intracellular lipids mediated by diacylglycerol acyltransferase (DGAT). Excessive amounts of polyunsaturated fatty acids (PUFAs) are stored as triacylglycerols (TAGs) within inactive cells. As a result, inhibiting DGAT causes a rearrangement of PUFAs from TAGs to phospholipids and makes arrested cells more susceptible to ferroptosis. We demonstrate that certain lung cancer cells that are resistant to antimitotic drugs and have a slow-cycling behavior exhibit an increase in lipid droplets. Furthermore, we find that the growth of tumors resistant to 5-fluorouracil, lorlatinib, and docetaxel can be effectively suppressed by a combination treatment involving the use of ferroptosis inducers and DGAT inhibitors, which induces ferroptosis. Collectively, these findings demonstrate the involvement of cell cycle arrest in conferring resistance to ferroptosis and propose a potential therapeutic approach for addressing the challenge of slow-cycling malignancies that exhibit resistance to ferroptosis.
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Affiliation(s)
- Xiuju Liu
- Department of Respiratory Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, PR China
| | - Yuhui Sun
- Department of Medical Administration, Tai'an Hospital of Traditional Chinese Medicine (TCM), Tai'an 271000, PR China
| | - Xue Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Shandong University of Traditional Chinese Medicine, Jinan 250117, PR China
| | - Mengmeng Song
- Department of Hematology & Oncology, Tai'an Hospital of Traditional Chinese Medicine (TCM), Tai'an 271000, PR China
| | - Jian Sun
- Department of Oncology, Shouguang People's Hospital, Shouguang 262700, PR China
| | - Yulan Sun
- Department of Respiratory Medicine, Shandong Cancer Hospital and Institute, Shandong First Medical University and Shandong Academy of Medical Sciences, Jinan 250117, PR China.
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2
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Xie CY, Su RR, Wu B, Sun ZY, Tang YQ. Response mechanisms of different Saccharomyces cerevisiae strains to succinic acid. BMC Microbiol 2024; 24:158. [PMID: 38720268 PMCID: PMC11077785 DOI: 10.1186/s12866-024-03314-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 04/25/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The production of succinic acid (SA) from biomass has attracted worldwide interest. Saccharomyces cerevisiae is preferred for SA production due to its strong tolerance to low pH conditions, ease of genetic manipulation, and extensive application in industrial processes. However, when compared with bacterial producers, the SA titers and productivities achieved by engineered S. cerevisiae strains were relatively low. To develop efficient SA-producing strains, it's necessary to clearly understand how S. cerevisiae cells respond to SA. RESULTS In this study, we cultivated five S. cerevisiae strains with different genetic backgrounds under different concentrations of SA. Among them, KF7 and NBRC1958 demonstrated high tolerance to SA, whereas NBRC2018 displayed the least tolerance. Therefore, these three strains were chosen to study how S. cerevisiae responds to SA. Under a concentration of 20 g/L SA, only a few differentially expressed genes were observed in three strains. At the higher concentration of 60 g/L SA, the response mechanisms of the three strains diverged notably. For KF7, genes involved in the glyoxylate cycle were significantly downregulated, whereas genes involved in gluconeogenesis, the pentose phosphate pathway, protein folding, and meiosis were significantly upregulated. For NBRC1958, genes related to the biosynthesis of vitamin B6, thiamin, and purine were significantly downregulated, whereas genes related to protein folding, toxin efflux, and cell wall remodeling were significantly upregulated. For NBRC2018, there was a significant upregulation of genes connected to the pentose phosphate pathway, gluconeogenesis, fatty acid utilization, and protein folding, except for the small heat shock protein gene HSP26. Overexpression of HSP26 and HSP42 notably enhanced the cell growth of NBRC1958 both in the presence and absence of SA. CONCLUSIONS The inherent activities of small heat shock proteins, the levels of acetyl-CoA and the strains' potential capacity to consume SA all seem to affect the responses and tolerances of S. cerevisiae strains to SA. These factors should be taken into consideration when choosing host strains for SA production. This study provides a theoretical basis and identifies potential host strains for the development of robust and efficient SA-producing strains.
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Affiliation(s)
- Cai-Yun Xie
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Ran-Ran Su
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Bo Wu
- Biogas Institute of Ministry of Agriculture, Renmin Rd. 4-13, Chengdu, 610041, Sichuan, China
| | - Zhao-Yong Sun
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China
| | - Yue-Qin Tang
- College of Architecture and Environment, Sichuan University, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Sichuan Environmental Protection Key Laboratory of Organic Wastes Valorization, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
- Engineering Research Center of Alternative Energy Materials & Devices, Ministry of Education, No. 24 South Section 1 First Ring Road, Chengdu, 610065, Sichuan, China.
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3
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Zeng DW, Yang YQ, Wang Q, Zhang FL, Zhang MD, Liao S, Liu ZQ, Fan YC, Liu CG, Zhang L, Zhao XQ. Transcriptome analysis of Kluyveromyces marxianus under succinic acid stress and development of robust strains. Appl Microbiol Biotechnol 2024; 108:293. [PMID: 38592508 PMCID: PMC11003901 DOI: 10.1007/s00253-024-13097-3] [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: 10/17/2023] [Revised: 02/22/2024] [Accepted: 02/28/2024] [Indexed: 04/10/2024]
Abstract
Kluyveromyces marxianus has become an attractive non-conventional yeast cell factory due to its advantageous properties such as high thermal tolerance and rapid growth. Succinic acid (SA) is an important platform molecule that has been applied in various industries such as food, material, cosmetics, and pharmaceuticals. SA bioproduction may be compromised by its toxicity. Besides, metabolite-responsive promoters are known to be important for dynamic control of gene transcription. Therefore, studies on global gene transcription under various SA concentrations are of great importance. Here, comparative transcriptome changes of K. marxianus exposed to various concentrations of SA were analyzed. Enrichment and analysis of gene clusters revealed repression of the tricarboxylic acid cycle and glyoxylate cycle, also activation of the glycolysis pathway and genes related to ergosterol synthesis. Based on the analyses, potential SA-responsive promoters were investigated, among which the promoter strength of IMTCP2 and KLMA_50231 increased 43.4% and 154.7% in response to 15 g/L SA. In addition, overexpression of the transcription factors Gcr1, Upc2, and Ndt80 significantly increased growth under SA stress. Our results benefit understanding SA toxicity mechanisms and the development of robust yeast for organic acid production. KEY POINTS: • Global gene transcription of K. marxianus is changed by succinic acid (SA) • Promoter activities of IMTCP2 and KLMA_50123 are regulated by SA • Overexpression of Gcr1, Upc2, and Ndt80 enhanced SA tolerance.
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Affiliation(s)
- Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yong-Qiang Yang
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Qi Wang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Mao-Dong Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Zhi-Qiang Liu
- School of Life Sciences, Hainan University, Haikou, 570228, China
| | - Ya-Chao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China
| | - Chen-Guang Liu
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd, Dalian, 116045, China.
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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4
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Zhang MM, Yuan B, Wang YT, Zhang FL, Liu CG, Zhao XQ. Differential Protein Expression in Set5p-Mediated Acetic Acid Stress Response and Novel Targets for Engineering Yeast Stress Tolerance. J Proteome Res 2024. [PMID: 38396335 DOI: 10.1021/acs.jproteome.3c00617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2024]
Abstract
Acetic acid is a prevalent inhibitor in lignocellulosic hydrolysate, which represses microbial growth and bioproduction. Histone modification and chromatin remodeling have been revealed to be critical for regulating eukaryotic metabolism. However, related studies in chronic acetic acid stress responses remain unclear. Our previous studies revealed that overexpression of the histone H4 methyltransferase Set5p enhanced acetic acid stress tolerance of the budding yeast Saccharomyces cerevisiae. In this study, we examined the role of Set5p in acetic acid stress by analyzing global protein expression. Significant activation of intracellular protein expression under the stress was discovered, and the functions of the differential proteins were mainly involved in chromatin modification, signal transduction, and carbohydrate metabolism. Notably, a substantial increase of Set5p expression was observed in response to acetic acid stress. Functional studies demonstrated that the restriction of the telomere capping protein Rtc3p, as well as Ies3p and Taf14p, which are related to chromatin regulation, was critical for yeast stress response. This study enriches the understanding of the epigenetic regulatory mechanisms underlying yeast stress response mediated by histone-modifying enzymes. The results also benefit the development of robust yeast strains for lignocellulosic bioconversion.
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Affiliation(s)
- Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Ya-Ting Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Feng-Li Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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5
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Yuan B, Wang WB, Wang XQ, Liu CG, Hasunuma T, Kondo A, Zhao XQ. The chromatin remodeler Ino80 regulates yeast stress tolerance and cell metabolism through modulating nitrogen catabolite repression. Int J Biol Macromol 2024; 258:129041. [PMID: 38154715 DOI: 10.1016/j.ijbiomac.2023.129041] [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: 06/08/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 12/30/2023]
Abstract
Chromatin remodelers are important in maintaining the dynamic chromatin state in eukaryotic cells, which is essential for epigenetic regulation. Among the remodelers, the multi-subunits complex INO80 plays crucial roles in transcriptional regulation. However, current knowledge of chromatin regulation of the core subunit Ino80 on stress adaptation remains mysterious. Here we revealed that overexpressing the chromatin remodeler Ino80 elevated tolerance to multiple stresses in budding yeast Saccharomyces cerevisiae. Analyses of differential chromatin accessibility and global transcription levels revealed an enrichment of genes involved in NCR (nitrogen catabolite repression) under acetic acid stress. We demonstrated that Ino80 overexpression reduced the histone H3 occupancy in the promoter region of the glutamate dehydrogenase gene GDH2 and the allantoinase gene DAL1. Consistently, the decreased occupancy of nucleosome was revealed in the Ino80-inactivation mutant. Further analyses showed that Ino80 was recruited to the specific DNA locus in the promoter region of GDH2. Consistently, Ino80 overexpression facilitated the utilization of non-preferred nitrogen source to enhance ethanol yield under prolonged acetic acid stress. These results demonstrate that Ino80 plays a crucial role in coordinating carbon and nitrogen metabolism during stress adaptation.
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Affiliation(s)
- Bing Yuan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xue-Qing Wang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Tomohisa Hasunuma
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan; Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Akihiko Kondo
- Graduate School of Science, Technology and Innovation, Kobe University, Kobe 657-8501, Japan; Engineering Biology Research Center, Kobe University, Kobe 657-8501, Japan; RIKEN Center for Sustainable Resource Science, Kanagawa 230-0045, Japan
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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6
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Li M, Chu Y, Dong X, Ji H. General mechanisms of weak acid-tolerance and current strategies for the development of tolerant yeasts. World J Microbiol Biotechnol 2023; 40:49. [PMID: 38133718 DOI: 10.1007/s11274-023-03875-y] [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: 11/01/2023] [Accepted: 12/16/2023] [Indexed: 12/23/2023]
Abstract
Yeast cells are often subjected to various types of weak acid stress in the process of industrial production, food processing, and preservation, resulting in growth inhibition and reduced fermentation performance. Under acidic conditions, weak acids enter the near-neutral yeast cytoplasm and dissociate into protons and anions, leading to cytoplasmic acidification and cell damage. Although some yeast strains have developed the ability to survive weak acids, the complexity and diversity of stresses during industrial production still require the application of appropriate strategies for phenotypes improvement. In this review, we summarized current knowledge concerning weak acid stress response and resistance, which may suggest important targets for further construction of more robust strains. We also highlight current feasible strategies for improving the weak acid resistance of yeasts, such as adaptive laboratory evolution, transcription factors engineering, and cell membrane/wall engineering. Moreover, the challenges and perspectives associated with improving the competitiveness of industrial strains are also discussed. This review provides effective strategies for improving the industrial phenotypes of yeast from multiple dimensions in future studies.
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Affiliation(s)
- Mengmeng Li
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Yunfei Chu
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China
| | - Xiameng Dong
- Department of Agriculture and Biotechnology, Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, 325006, PR China.
| | - Hao Ji
- Institute of Life Sciences, College of Life and Environmental Science, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
- Biomedical Collaborative Innovation Center of Zhejiang Province & Engineering Laboratory of Zhejiang Province for Pharmaceutical Development of Growth Factors, Wenzhou University, Wenzhou, Zhejiang, 325035, PR China.
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7
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Asemoloye MD, Bello TS, Oladoye PO, Remilekun Gbadamosi M, Babarinde SO, Ebenezer Adebami G, Olowe OM, Temporiti MEE, Wanek W, Marchisio MA. Engineered yeasts and lignocellulosic biomaterials: shaping a new dimension for biorefinery and global bioeconomy. Bioengineered 2023; 14:2269328. [PMID: 37850721 PMCID: PMC10586088 DOI: 10.1080/21655979.2023.2269328] [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: 06/24/2023] [Accepted: 10/03/2023] [Indexed: 10/19/2023] Open
Abstract
The next milestone of synthetic biology research relies on the development of customized microbes for specific industrial purposes. Metabolic pathways of an organism, for example, depict its chemical repertoire and its genetic makeup. If genes controlling such pathways can be identified, scientists can decide to enhance or rewrite them for different purposes depending on the organism and the desired metabolites. The lignocellulosic biorefinery has achieved good progress over the past few years with potential impact on global bioeconomy. This principle aims to produce different bio-based products like biochemical(s) or biofuel(s) from plant biomass under microbial actions. Meanwhile, yeasts have proven very useful for different biotechnological applications. Hence, their potentials in genetic/metabolic engineering can be fully explored for lignocellulosic biorefineries. For instance, the secretion of enzymes above the natural limit (aided by genetic engineering) would speed-up the down-line processes in lignocellulosic biorefineries and the cost. Thus, the next milestone would greatly require the development of synthetic yeasts with much more efficient metabolic capacities to achieve basic requirements for particular biorefinery. This review gave comprehensive overview of lignocellulosic biomaterials and their importance in bioeconomy. Many researchers have demonstrated the engineering of several ligninolytic enzymes in heterologous yeast hosts. However, there are still many factors needing to be well understood like the secretion time, titter value, thermal stability, pH tolerance, and reactivity of the recombinant enzymes. Here, we give a detailed account of the potentials of engineered yeasts being discussed, as well as the constraints associated with their development and applications.
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Affiliation(s)
- Michael Dare Asemoloye
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, Nankai District, China
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Tunde Sheriffdeen Bello
- Department of Plant Biology, School of Life Sciences, Federal University of Technology Minna, Minna Niger State, Nigeria
| | | | | | - Segun Oladiran Babarinde
- Department of Plant, Food and Environmental Sciences, Faculty of Agriculture, Dalhousie University, Truro, Nova Scotia, Canada
| | | | - Olumayowa Mary Olowe
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Mail Bag, Mmabatho, South Africa
| | | | - Wolfgang Wanek
- Department of Microbiology and Ecosystem Science, University of Vienna, Vienna, Austria
| | - Mario Andrea Marchisio
- School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, Nankai District, China
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8
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Zhang FL, Zhang L, Zeng DW, Liao S, Fan Y, Champreda V, Runguphan W, Zhao XQ. Engineering yeast cell factories to produce biodegradable plastics and their monomers: Current status and prospects. Biotechnol Adv 2023; 68:108222. [PMID: 37516259 DOI: 10.1016/j.biotechadv.2023.108222] [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: 04/23/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 07/31/2023]
Abstract
Traditional plastic products have caused serious environmental pollution due to difficulty to be degraded in the natural environment. In the recent years, biodegradable plastics are receiving increasing attention due to advantages in natural degradability and environmental friendliness. Biodegradable plastics have potential to be used in food, agriculture, industry, medicine and other fields. However, the high production cost of such plastics is the bottleneck that limits their commercialization and application. Yeasts, including budding yeast and non-conventional yeasts, are widely studied to produce biodegradable plastics and their organic acid monomers. Compared to bacteria, yeast strains are more tolerable to multiple stress conditions including low pH and high temperature, and also have other advantages such as generally regarded as safe, and no phage infection. In addition, synthetic biology and metabolic engineering of yeast have enabled its rapid and efficient engineering for bioproduction using various renewable feedstocks, especially lignocellulosic biomass. This review focuses on the recent progress in biosynthesis technology and strategies of monomeric organic acids for biodegradable polymers, including polylactic acid (PLA), polyhydroxyalkanoate (PHA), polybutylene succinate (PBS), and polybutylene adipate terephthalate (PBAT) using yeast cell factories. Improving the performance of yeast as a cell factory and strategies to improve yeast acid stress tolerance are also discussed. In addition, the critical challenges and future prospects for the production of biodegradable plastic monomer using yeast are also discussed.
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Affiliation(s)
- Feng-Li Zhang
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin Zhang
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Du-Wen Zeng
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Sha Liao
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Yachao Fan
- SINOPEC Dalian Research Institute of Petroleum and Petrochemicals Co., Ltd., Dalian 116045, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Weerawat Runguphan
- National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phaholyothin Road, Khlong Luang, Pathumthani 12120, Thailand
| | - Xin-Qing Zhao
- Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China.
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9
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Minnaar L, den Haan R. Engineering natural isolates of Saccharomyces cerevisiae for consolidated bioprocessing of cellulosic feedstocks. Appl Microbiol Biotechnol 2023; 107:7013-7028. [PMID: 37688599 PMCID: PMC10589140 DOI: 10.1007/s00253-023-12729-4] [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: 05/19/2023] [Revised: 08/03/2023] [Accepted: 08/06/2023] [Indexed: 09/11/2023]
Abstract
Saccharomyces cerevisiae has gained much attention as a potential host for cellulosic bioethanol production using consolidated bioprocessing (CBP) methodologies, due to its high-ethanol-producing titres, heterologous protein production capabilities, and tolerance to various industry-relevant stresses. Since the secretion levels of heterologous proteins are generally low in domesticated strains of S. cerevisiae, natural isolates may offer a more diverse genetic background for improved heterologous protein secretion, while also displaying greater robustness to process stresses. In this study, the potential of natural and industrial S. cerevisiae strains to secrete a core set of cellulases (CBH1, CBH2, EG2, and BGL1), encoded by genes integrated using CRISPR/Cas9 tools, was evaluated. High levels of heterologous protein production were associated with a reduced maximal growth rate and with slight changes in overall strain robustness, compared to the parental strains. The natural isolate derivatives YI13_BECC and YI59_BECC displayed superior secretion capacity for the heterologous cellulases at high incubation temperature and in the presence of acetic acid, respectively, compared to the reference industrial strain MH1000_BECC. These strains also exhibited multi-tolerance to several fermentation-associated and secretion stresses. Cultivation of the strains on crystalline cellulose in oxygen-limited conditions yielded ethanol concentrations in the range of 4-4.5 g/L, representing 35-40% of the theoretical maximum ethanol yield after 120 h, without the addition of exogenous enzymes. This study therefore highlights the potential of these natural isolates to be used as chassis organisms in CBP bioethanol production. KEY POINTS: • Process-related fermentation stresses influence heterologous protein production. • Transformants produced up to 4.5 g/L ethanol, ~ 40% of the theoretical yield in CBP. • CRISPR/Cas9 was feasible for integrating genes in natural S. cerevisiae isolates.
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Affiliation(s)
- Letitia Minnaar
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Riaan den Haan
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa.
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10
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Jilani SB, Olson DG. Mechanism of furfural toxicity and metabolic strategies to engineer tolerance in microbial strains. Microb Cell Fact 2023; 22:221. [PMID: 37891678 PMCID: PMC10612203 DOI: 10.1186/s12934-023-02223-x] [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: 08/29/2023] [Accepted: 10/05/2023] [Indexed: 10/29/2023] Open
Abstract
Lignocellulosic biomass represents a carbon neutral cheap and versatile source of carbon which can be converted to biofuels. A pretreatment step is frequently used to make the lignocellulosic carbon bioavailable for microbial metabolism. Dilute acid pretreatment at high temperature and pressure is commonly utilized to efficiently solubilize the pentose fraction by hydrolyzing the hemicellulose fibers and the process results in formation of furans-furfural and 5-hydroxymethyl furfural-and other inhibitors which are detrimental to metabolism. The presence of inhibitors in the medium reduce productivity of microbial biocatalysts and result in increased production costs. Furfural is the key furan inhibitor which acts synergistically along with other inhibitors present in the hydrolysate. In this review, the mode of furfural toxicity on microbial metabolism and metabolic strategies to increase tolerance is discussed. Shared cellular targets between furfural and acetic acid are compared followed by discussing further strategies to engineer tolerance. Finally, the possibility to use furfural as a model inhibitor of dilute acid pretreated lignocellulosic hydrolysate is discussed. The furfural tolerant strains will harbor an efficient lignocellulosic carbon to pyruvate conversion mechanism in presence of stressors in the medium. The pyruvate can be channeled to any metabolite of interest by appropriate modulation of downstream pathway of interest. The aim of this review is to emphasize the use of hydrolysate as a carbon source for bioproduction of biofuels and other compounds of industrial importance.
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Affiliation(s)
- S Bilal Jilani
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH, 03755, USA.
| | - Daniel G Olson
- Thayer School of Engineering, Dartmouth College, 15 Thayer Drive, Hanover, NH, 03755, USA
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
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11
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Nguyen TP, Meng DR, Chang CH, Su PY, Ou CA, Hou PF, Sung HM, Chou CH, Ohme-Takagi M, Huang HJ. Antifungal mechanism of volatile compounds emitted by Actinomycetota Paenarthrobacter ureafaciens from a disease-suppressive soil on Saccharomyces cerevisiae. mSphere 2023; 8:e0032423. [PMID: 37750721 PMCID: PMC10597458 DOI: 10.1128/msphere.00324-23] [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: 06/18/2023] [Accepted: 08/07/2023] [Indexed: 09/27/2023] Open
Abstract
Increasing evidence suggests that in disease-suppressive soils, microbial volatile compounds (mVCs) released from bacteria may inhibit the growth of plant-pathogenic fungi. However, the antifungal activities and molecular responses of fungi to different mVCs remain largely undescribed. In this study, we first evaluated the responses of pathogenic fungi to treatment with mVCs from Paenarthrobacter ureafaciens. Then, we utilized the well-characterized fungal model organism Saccharomyces cerevisiae to study the potential mechanistic effects of the mVCs. Our data showed that exposure to P. ureafaciens mVCs leads to reduced growth of several pathogenic fungi, and in yeast cells, mVC exposure prompts the accumulation of reactive oxygen species. Further experiments with S. cerevisiae deletion mutants indicated that Slt2/Mpk1 and Hog1 MAPKs play major roles in the yeast response to P. ureafaciens mVCs. Transcriptomic analysis revealed that exposure to mVCs was associated with 1,030 differentially expressed genes (DEGs) in yeast. According to gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses, many of these DEGs are involved in mitochondrial dysfunction, cell integrity, mitophagy, cellular metabolism, and iron uptake. Genes encoding antimicrobial proteins were also significantly altered in the yeast after exposure to mVCs. These findings suggest that oxidative damage and mitochondrial dysfunction are major contributors to the fungal toxicity of mVCs. Furthermore, our data showed that cell wall, antioxidant, and antimicrobial defenses are induced in yeast exposed to mVCs. Thus, our findings expand upon previous research by delineating the transcriptional responses of the fungal model. IMPORTANCE Since the use of bacteria-emitted volatile compounds in phytopathogen control is of considerable interest, it is important to understand the molecular mechanisms by which fungi may adapt to microbial volatile compounds (mVCs). Paenarthrobacter ureafaciens is an isolated bacterium from disease-suppressive soil that belongs to the Actinomycetota phylum. P. ureafaciens mVCs showed a potent antifungal effect on phytopathogens, which may contribute to disease suppression in soil. However, our knowledge about the antifungal mechanism of mVCs is limited. This study has proven that mVCs are toxic to fungi due to oxidative stress and mitochondrial dysfunction. To deal with mVC toxicity, antioxidants and physical defenses are required. Furthermore, iron uptake and CAP proteins are required for antimicrobial defense, which is necessary for fungi to deal with the thread from mVCs. This study provides essential foundational knowledge regarding the molecular responses of fungi to inhibitory mVCs.
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Affiliation(s)
- Tri-Phuong Nguyen
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - De-Rui Meng
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ching-Han Chang
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
| | - Pei-Yu Su
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chieh-An Ou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Ping-Fu Hou
- Kaohsiung District Agricultural Research and Extension Station, Pingtung, Taiwan
| | - Huang-Mo Sung
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chang-Hung Chou
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Masaru Ohme-Takagi
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Hao-Jen Huang
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
- Graduate Program in Translational Agricultural Sciences, National Cheng Kung University and Academia Sinica, Tainan, Taiwan
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12
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Liu L, Helal SE, Peng N. CRISPR-Cas-Based Engineering of Probiotics. BIODESIGN RESEARCH 2023; 5:0017. [PMID: 37849462 PMCID: PMC10541000 DOI: 10.34133/bdr.0017] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 08/30/2023] [Indexed: 10/19/2023] Open
Abstract
Probiotics are the treasure of the microbiology fields. They have been widely used in the food industry, clinical treatment, and other fields. The equivocal health-promoting effects and the unknown action mechanism were the largest obstacles for further probiotic's developed applications. In recent years, various genome editing techniques have been developed and applied to explore the mechanisms and functional modifications of probiotics. As important genome editing tools, CRISPR-Cas systems that have opened new improvements in genome editing dedicated to probiotics. The high efficiency, flexibility, and specificity are the advantages of using CRISPR-Cas systems. Here, we summarize the classification and distribution of CRISPR-Cas systems in probiotics, as well as the editing tools developed on the basis of them. Then, we discuss the genome editing of probiotics based on CRISPR-Cas systems and the applications of the engineered probiotics through CRISPR-Cas systems. Finally, we proposed a design route for CRISPR systems that related to the genetically engineered probiotics.
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Affiliation(s)
- Ling Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
- CABIO Biotech (Wuhan) Co. Ltd., Wuhan, China
| | - Shimaa Elsayed Helal
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
| | - Nan Peng
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, Hubei, China
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13
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Sha Y, Zhou L, Wang Z, Ding Y, Lu M, Xu Z, Zhai R, Jin M. Adaptive laboratory evolution boost Yarrowia lipolytica tolerance to vanillic acid. J Biotechnol 2023; 367:42-52. [PMID: 36965629 DOI: 10.1016/j.jbiotec.2023.03.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 02/18/2023] [Accepted: 03/17/2023] [Indexed: 03/27/2023]
Abstract
Microbial tolerance to lignocellulose-derived inhibitors, such as aromatic acids, is critical for the economical production of biofuels and biochemicals. Here, adaptive laboratory evolution was applied to improve the tolerance of Yarrowia lipolytica to a representative aromatic acid inhibitor vanillic acid. The transcriptome profiling of evolved strain suggested that the tolerance could be related to the up-regulation of RNA processing and multidrug transporting pathways. Further analysis by reverse engineering confirmed that the amplification of YALI0_F13475g coding for transcriptional coactivator and YALI0_E25201g coding for multidrug transporter conferred tolerance not only to vanillic acid but also towards ferulic acid, p-coumaric acid, p-hydroxybenzoic acid and syringic acid. These findings suggested that regulation of RNA processing and multidrug transporting pathways may be important for enhanced aromatic acid tolerance in Y. lipolytica. This study provides valuable genetic information for robust strain construction for lignocellulosic biorefinery.
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Affiliation(s)
- Yuanyuan Sha
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Linlin Zhou
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zedi Wang
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Ying Ding
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Minrui Lu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Zhaoxian Xu
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Rui Zhai
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing 210094, China; Biorefinery Research Institution, Nanjing University of Science and Technology, Nanjing 210094, China.
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14
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Effect of Short-Chain Fatty Acids on the Yield of 2,3-Butanediol by Saccharomyces cerevisiae W141: The Synergistic Effect of Acetic Acid and Dissolved Oxygen. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9030236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
As a platform chemical, 2,3-butanediol (2,3-BDO) has been widely used in various industrial fields. To improve the yield of 2,3-BDO produced by Saccharomyces cerevisiae W141, this paper explored the effects of exogenous short-chain fatty acids (SCFAs) as well as the synergistic effects of acetic acid and dissolved oxygen content on the yield of 2,3-BDO from the perspective of physiological metabolism. The results indicated that different SCFAs had different effects on the production of 2,3-BDO, and higher or lower concentrations of SCFAs were not conducive to the generation of 2,3-BDO. However, exogenically adding 1.0 g/L acetic acid significantly increased the yield of 2,3-BDO and the expression level of bdh1, a key gene in the synthesis of 2,3-BDO (p < 0.05). In addition, a dissolved oxygen concentration of 4.52 mg/L was proven to be the optimal condition for 2,3-BDO production. When the dissolved oxygen content and acetic acid concentration were 4.52 mg/L and 1.0 g/L, respectively, the maximum yield of 2,3-BDO was 3.25 ± 0.03 g/L, which was 66.59% higher than that produced by S. cerevisiae W141 alone. These results provide methodological guidance for the industrial production of 2,3-BDO by S. cerevisiae.
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15
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Ciamponi FE, Procópio DP, Murad NF, Franco TT, Basso TO, Brandão MM. Multi-omics network model reveals key genes associated with p-coumaric acid stress response in an industrial yeast strain. Sci Rep 2022; 12:22466. [PMID: 36577778 PMCID: PMC9797568 DOI: 10.1038/s41598-022-26843-2] [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: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 12/30/2022] Open
Abstract
The production of ethanol from lignocellulosic sources presents increasingly difficult issues for the global biofuel scenario, leading to increased production costs of current second-generation (2G) ethanol when compared to first-generation (1G) plants. Among the setbacks encountered in industrial processes, the presence of chemical inhibitors from pre-treatment processes severely hinders the potential of yeasts in producing ethanol at peak efficiency. However, some industrial yeast strains have, either naturally or artificially, higher tolerance levels to these compounds. Such is the case of S. cerevisiae SA-1, a Brazilian fuel ethanol industrial strain that has shown high resistance to inhibitors produced by the pre-treatment of cellulosic complexes. Our study focuses on the characterization of the transcriptomic and physiological impact of an inhibitor of this type, p-coumaric acid (pCA), on this strain under chemostat cultivation via RNAseq and quantitative physiological data. It was found that strain SA-1 tend to increase ethanol yield and production rate while decreasing biomass yield when exposed to pCA, in contrast to pCA-susceptible strains, which tend to decrease their ethanol yield and fermentation efficiency when exposed to this substance. This suggests increased metabolic activity linked to mitochondrial and peroxisomal processes. The transcriptomic analysis also revealed a plethora of differentially expressed genes located in co-expressed clusters that are associated with changes in biological pathways linked to biosynthetic and energetical processes. Furthermore, it was also identified 20 genes that act as interaction hubs for these clusters, while also having association with altered pathways and changes in metabolic outputs, potentially leading to the discovery of novel targets for metabolic engineering toward a more robust industrial yeast strain.
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Affiliation(s)
- F. E. Ciamponi
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - D. P. Procópio
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - N. F. Murad
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
| | - T. T. Franco
- grid.411087.b0000 0001 0723 2494School of Chemical Engineering (FEQ), State University of Campinas (Unicamp), Av. Albert Einstein, 500, Campinas, SP 13083-852 Brazil
| | - T. O. Basso
- grid.11899.380000 0004 1937 0722Department of Chemical Engineering, University of São Paulo (USP), Av. Prof. Luciano Gualberto, 380, São Paulo, SP 05508-010 Brazil
| | - M. M. Brandão
- grid.411087.b0000 0001 0723 2494Center for Molecular Biology and Genetic Engineering (CBMEG), State University of Campinas (Unicamp), Av. Cândido Rondon, 400, Campinas, SP 13083-875 Brazil
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16
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Fang Y, Xiao H. The Aspartic Protease Yps3p and Cell Wall Glucanase Scw10p Are Novel Determinants That Enhance the Secretion of the Antitumor Triterpenoid GA-HLDOA in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:2917-2926. [PMID: 35969118 DOI: 10.1021/acssynbio.2c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Efficient bioproduction of triterpenoids is gaining increasing interest because of their significant biological applications; however, the secretion and bioproduction of triterpenoids are hindered by untapped genetic determinants. In our previous study, we observed that different engineered Saccharomyces cerevisiae strains exhibit different abilities for secreting the antitumor triterpenoid ganoderic acid 3-hydroxy-lanosta-8,24-dien-26-oic acid (GA-HLDOA). In the present study, we performed comparative proteomics analyses of the engineered strains and identified two genes, encoding an aspartic protease, YPS3, and a cell wall glucanase, SCW10, as the most effective determinants that enhance the secretion of GA-HLDOA. Compared with this control strain, strain BJ5464-r demonstrated an overexpression of YPS3 and SCW10 resulting in 3.9-fold and 4.7-fold higher secretion of GA-HLDOA, respectively, and these increases were accompanied by an increase in cell permeability. Moreover, compared with the YPS3-overexpressing strain, the SCW10-overexpressing strain had a thinner outer mannan layer. Our findings offer valuable insights into designing microbial cell factories for the efficient secretion of triterpenoids.
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Affiliation(s)
- Yubo Fang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-chuan Road, Shanghai, 200240, China
| | - Han Xiao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, and Laboratory of Molecular Biochemical Engineering, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, 800 Dong-chuan Road, Shanghai, 200240, China
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17
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Cheng C, Wang WB, Sun ML, Tang RQ, Bai L, Alper HS, Zhao XQ. Deletion of NGG1 in a recombinant Saccharomyces cerevisiae improved xylose utilization and affected transcription of genes related to amino acid metabolism. Front Microbiol 2022; 13:960114. [PMID: 36160216 PMCID: PMC9493327 DOI: 10.3389/fmicb.2022.960114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 08/09/2022] [Indexed: 11/16/2022] Open
Abstract
Production of biofuels and biochemicals from xylose using yeast cell factory is of great interest for lignocellulosic biorefinery. Our previous studies revealed that a natural yeast isolate Saccharomyces cerevisiae YB-2625 has superior xylose-fermenting ability. Through integrative omics analysis, NGG1, which encodes a transcription regulator as well as a subunit of chromatin modifying histone acetyltransferase complexes was revealed to regulate xylose metabolism. Deletion of NGG1 in S. cerevisiae YRH396h, which is the haploid version of the recombinant yeast using S. cerevisiae YB-2625 as the host strain, improved xylose consumption by 28.6%. Comparative transcriptome analysis revealed that NGG1 deletion down-regulated genes related to mitochondrial function, TCA cycle, ATP biosynthesis, respiration, as well as NADH generation. In addition, the NGG1 deletion mutant also showed transcriptional changes in amino acid biosynthesis genes. Further analysis of intracellular amino acid content confirmed the effect of NGG1 on amino acid accumulation during xylose utilization. Our results indicated that NGG1 is one of the core nodes for coordinated regulation of carbon and nitrogen metabolism in the recombinant S. cerevisiae. This work reveals novel function of Ngg1p in yeast metabolism and provides basis for developing robust yeast strains to produce ethanol and biochemicals using lignocellulosic biomass.
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Affiliation(s)
- Cheng Cheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- School of Life Sciences, Hefei Normal University, Hefei, China
| | - Wei-Bin Wang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Meng-Lin Sun
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Rui-Qi Tang
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Long Bai
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Hal S. Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, United States
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- *Correspondence: Xin-Qing Zhao,
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18
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De Novo Purine Nucleotide Biosynthesis Pathway Is Required for Development and Pathogenicity in Magnaporthe oryzae. J Fungi (Basel) 2022; 8:jof8090915. [PMID: 36135640 PMCID: PMC9502316 DOI: 10.3390/jof8090915] [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: 06/24/2022] [Revised: 08/25/2022] [Accepted: 08/26/2022] [Indexed: 12/04/2022] Open
Abstract
Purine nucleotides are indispensable compounds for many organisms and participate in basic vital activities such as heredity, development, and growth. Blocking of purine nucleotide biosynthesis may inhibit proliferation and development and is commonly used in cancer therapy. However, the function of the purine nucleotide biosynthesis pathway in the pathogenic fungus Magnaporthe oryzae is not clear. In this study, we focused on the de novo purine biosynthesis (DNPB) pathway and characterized MoAde8, a phosphoribosylglycinamide formyltransferase, catalyzing the third step of the DNPB pathway in M. oryzae. MoAde8 was knocked out, and the mutant (∆Moade8) exhibited purine auxotroph, defects in aerial hyphal growth, conidiation, and pathogenicity, and was more sensitive to hyperosmotic stress and oxidative stress. Moreover, ∆Moade8 caused decreased activity of MoTor kinase due to blocked purine nucleotide synthesis. The autophagy level was also impaired in ∆Moade8. Additionally, MoAde5, 7, 6, and 12, which are involved in de novo purine nucleotide biosynthesis, were also analyzed, and the mutants showed defects similar to the defects of ∆Moade8. In summary, de novo purine nucleotide biosynthesis is essential for conidiation, development, and pathogenicity in M. oryzae.
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19
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How adaptive laboratory evolution can boost yeast tolerance to lignocellulosic hydrolyses. Curr Genet 2022; 68:319-342. [PMID: 35362784 DOI: 10.1007/s00294-022-01237-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/01/2022] [Accepted: 03/06/2022] [Indexed: 12/25/2022]
Abstract
The yeast Saccharomyces cerevisiae is an excellent candidate for establishing cell factories to convert lignocellulosic biomass into chemicals and fuels. To enable this technology, yeast robustness must be improved to withstand the fermentation inhibitors (e.g., weak organic acids, phenols, and furan aldehydes) resulting from biomass pretreatment and hydrolysis. Here, we discuss how evolution experiments performed in the lab, a method commonly known as adaptive laboratory evolution (ALE), may contribute to lifting yeast tolerance against the inhibitors of lignocellulosic hydrolysates (LCHs). The key is that, through the combination of whole-genome sequencing and reverse engineering, ALE provides a robust platform for discovering and testing adaptive alleles, allowing to explore the genetic underpinnings of yeast responses to LCHs. We review the insights gained from past evolution experiments with S. cerevisiae in LCH inhibitors and propose experimental designs to optimise the discovery of genetic variants adaptive to biomass toxicity. The knowledge gathered through ALE projects is envisaged as a roadmap to engineer superior yeast strains for biomass-based bioprocesses.
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20
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Chen HQ, Xing Q, Cheng C, Zhang MM, Liu CG, Champreda V, Zhao XQ. Identification of Kic1p and Cdc42p as Novel Targets to Engineer Yeast Acetic Acid Stress Tolerance. Front Bioeng Biotechnol 2022; 10:837813. [PMID: 35402407 PMCID: PMC8992792 DOI: 10.3389/fbioe.2022.837813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/09/2022] [Indexed: 11/13/2022] Open
Abstract
Robust yeast strains that are tolerant to multiple stress environments are desired for an efficient biorefinery. Our previous studies revealed that zinc sulfate serves as an important nutrient for stress tolerance of budding yeast Saccharomyces cerevisiae. Acetic acid is a common inhibitor in cellulosic hydrolysate, and the development of acetic acid-tolerant strains is beneficial for lignocellulosic biorefineries. In this study, comparative proteomic studies were performed using S. cerevisiae cultured under acetic acid stress with or without zinc sulfate addition, and novel zinc-responsive proteins were identified. Among the differentially expressed proteins, the protein kinase Kic1p and the small rho-like GTPase Cdc42p, which is required for cell integrity and regulation of cell polarity, respectively, were selected for further studies. Overexpression of KIC1 and CDC42 endowed S. cerevisiae with faster growth and ethanol fermentation under the stresses of acetic acid and mixed inhibitors, as well as in corncob hydrolysate. Notably, the engineered yeast strains showed a 12 h shorter lag phase under the three tested conditions, leading to up to 52.99% higher ethanol productivity than that of the control strain. Further studies showed that the transcription of genes related to stress response was significantly upregulated in the engineered strains under the stress condition. Our results in this study provide novel insights in exploring zinc-responsive proteins for applications of synthetic biology in developing a robust industrial yeast.
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Affiliation(s)
- Hong-Qi Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Qi Xing
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Cheng Cheng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ming-Ming Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Verawat Champreda
- National Center for Genetic Engineering and Biotechnology, Pathumthani, Thailand
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
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21
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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: 17] [Impact Index Per Article: 8.5] [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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22
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Data mining of Saccharomyces cerevisiae mutants engineered for increased tolerance towards inhibitors in lignocellulosic hydrolysates. Biotechnol Adv 2022; 57:107947. [DOI: 10.1016/j.biotechadv.2022.107947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/15/2022] [Accepted: 03/15/2022] [Indexed: 12/15/2022]
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23
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Stovicek V, Dato L, Almqvist H, Schöpping M, Chekina K, Pedersen LE, Koza A, Figueira D, Tjosås F, Ferreira BS, Forster J, Lidén G, Borodina I. Rational and evolutionary engineering of Saccharomyces cerevisiae for production of dicarboxylic acids from lignocellulosic biomass and exploring genetic mechanisms of the yeast tolerance to the biomass hydrolysate. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:22. [PMID: 35219341 PMCID: PMC8882276 DOI: 10.1186/s13068-022-02121-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 02/12/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Lignosulfonates are significant wood chemicals with a $700 million market, produced by sulfite pulping of wood. During the pulping process, spent sulfite liquor (SSL) is generated, which in addition to lignosulfonates contains hemicellulose-derived sugars-in case of hardwoods primarily the pentose sugar xylose. The pentoses are currently underutilized. If they could be converted into value-added chemicals, overall economic profitability of the process would increase. SSLs are typically very inhibitory to microorganisms, which presents a challenge for a biotechnological process. The aim of the present work was to develop a robust yeast strain able to convert xylose in SSL to carboxylic acids. RESULTS The industrial strain Ethanol Red of the yeast Saccharomyces cerevisiae was engineered for efficient utilization of xylose in a Eucalyptus globulus lignosulfonate stream at low pH using CRISPR/Cas genome editing and adaptive laboratory evolution. The engineered strain grew in synthetic medium with xylose as sole carbon source with maximum specific growth rate (µmax) of 0.28 1/h. Selected evolved strains utilized all carbon sources in the SSL at pH 3.5 and grew with µmax between 0.05 and 0.1 1/h depending on a nitrogen source supplement. Putative genetic determinants of the increased tolerance to the SSL were revealed by whole genome sequencing of the evolved strains. In particular, four top-candidate genes (SNG1, FIT3, FZF1 and CBP3) were identified along with other gene candidates with predicted important roles, based on the type and distribution of the mutations across different strains and especially the best performing ones. The developed strains were further engineered for production of dicarboxylic acids (succinic and malic acid) via overexpression of the reductive branch of the tricarboxylic acid cycle (TCA). The production strain produced 0.2 mol and 0.12 mol of malic acid and succinic acid, respectively, per mol of xylose present in the SSL. CONCLUSIONS The combined metabolic engineering and adaptive evolution approach provided a robust SSL-tolerant industrial strain that converts fermentable carbon content of the SSL feedstock into malic and succinic acids at low pH.in production yields reaching 0.1 mol and 0.065 mol per mol of total consumed carbon sources.. Moreover, our work suggests potential genetic background of the tolerance to the SSL stream pointing out potential gene targets for improving the tolerance to inhibitory industrial feedstocks.
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Affiliation(s)
- Vratislav Stovicek
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Laura Dato
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,River Stone Biotech ApS, Fruebjergvej 3, 2100, Copenhagen, Denmark
| | - Henrik Almqvist
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Marie Schöpping
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark.,Division of Industrial Biotechnology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96, Gothenburg, Sweden
| | - Ksenia Chekina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Lasse Ebdrup Pedersen
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Anna Koza
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.,Chr. Hansen A/S, Boge Alle 10-12, 2970, Hørsholm, Denmark
| | - Diogo Figueira
- Biotrend S.A., Biocant Park Núcleo 04, Lote 2, 3060-197, Cantanhede, Portugal
| | - Freddy Tjosås
- Borregaard ApS, Hjalmar Wessels vei 6, 1721, Sarpsborg, Norway
| | | | - Jochen Forster
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark
| | - Gunnar Lidén
- Department of Chemical Engineering, Lund University, P.O. Box 124, 221 00, Lund, Sweden
| | - Irina Borodina
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, Building 220, 2800, Kgs. Lyngby, Denmark.
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Strategies to increase tolerance and robustness of industrial microorganisms. Synth Syst Biotechnol 2022; 7:533-540. [PMID: 35024480 PMCID: PMC8718811 DOI: 10.1016/j.synbio.2021.12.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 12/17/2021] [Accepted: 12/17/2021] [Indexed: 01/06/2023] Open
Abstract
The development of a cost-competitive bioprocess requires that the cell factory converts the feedstock into the product of interest at high rates and yields. However, microbial cell factories are exposed to a variety of different stresses during the fermentation process. These stresses can be derived from feedstocks, metabolism, or industrial production processes, limiting production capacity and diminishing competitiveness. Improving stress tolerance and robustness allows for more efficient production and ultimately makes a process more economically viable. This review summarises general trends and updates the most recent developments in technologies to improve the stress tolerance of microorganisms. We first look at evolutionary, systems biology and computational methods as examples of non-rational approaches. Then we review the (semi-)rational approaches of membrane and transcription factor engineering for improving tolerance phenotypes. We further discuss challenges and perspectives associated with these different approaches.
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25
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Kang J, Zhou X, Zhang W, Pei F, Ge J. Transcriptomic analysis of bacteriocin synthesis and stress response in Lactobacillus paracasei HD1.7 under acetic acid stress. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112897] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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26
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Chen HQ, Zhang MM, Xing Q, Ye PL, Hasunuma T, Kondo A, Zhao XQ. Improved ethanol fermentation by promoter replacement of zinc responsive genes IPL1, PRP6 and RTC1 in Saccharomyces cerevisiae. Biochem Eng J 2022. [DOI: 10.1016/j.bej.2021.108274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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27
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Brandt BA, García-Aparicio MDP, Görgens JF, van Zyl WH. Rational engineering of Saccharomyces cerevisiae towards improved tolerance to multiple inhibitors in lignocellulose fermentations. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:173. [PMID: 34454598 PMCID: PMC8403374 DOI: 10.1186/s13068-021-02021-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 08/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND The fermentation of lignocellulose hydrolysates to ethanol requires robust xylose-capable Saccharomyces cerevisiae strains able to operate in the presence of microbial inhibitory stresses. This study aimed at developing industrial S. cerevisiae strains with enhanced tolerance towards pretreatment-derived microbial inhibitors, by identifying novel gene combinations that confer resistance to multiple inhibitors (thus cumulative inhibitor resistance phenotype) with minimum impact on the xylose fermentation ability. The strategy consisted of multiple sequential delta-integrations of double-gene cassettes containing one gene conferring broad inhibitor tolerance (ARI1, PAD1 or TAL1) coupled with an inhibitor-specific gene (ADH6, FDH1 or ICT1). The performances of the transformants were compared with the parental strain in terms of biomass growth, ethanol yields and productivity, as well as detoxification capacities in a synthetic inhibitor cocktail, sugarcane bagasse hydrolysate as well as hardwood spent sulphite liquor. RESULTS The first and second round of delta-integrated transformants exhibited a trade-off between biomass and ethanol yield. Transformants showed increased inhibitor resistance phenotypes relative to parental controls specifically in fermentations with concentrated spent sulphite liquors at 40% and 80% v/v concentrations in 2% SC media. Unexpectedly, the xylose fermentation capacity of the transformants was reduced compared to the parental control, but certain combinations of genes had a minor impact (e.g. TAL1 + FDH1). The TAL1 + ICT1 combination negatively impacted on both biomass growth and ethanol yield, which could be linked to the ICT1 protein increasing transformant susceptibility to weak acids and temperature due to cell membrane changes. CONCLUSIONS The integration of the selected genes was proven to increase tolerance to pretreatment inhibitors in synthetic or industrial hydrolysates, but they were limited to the fermentation of glucose. However, some gene combination sequences had a reduced impact on xylose conversion.
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Affiliation(s)
- Bianca A Brandt
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Maria D P García-Aparicio
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Johann F Görgens
- Department of Process Engineering, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Willem H van Zyl
- Department of Microbiology, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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28
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Gao X, Xu K, Ahmad N, Qin L, Li C. Recent advances in engineering of microbial cell factories for intelligent pH regulation and tolerance. Biotechnol J 2021; 16:e2100151. [PMID: 34164941 DOI: 10.1002/biot.202100151] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 06/09/2021] [Accepted: 06/11/2021] [Indexed: 11/12/2022]
Abstract
pH regulation is a serious concern in the industrial fermentation process as pH adjustment heavily utilizes acid/base and pollutes the environment. Under pH-stress conditions, microbial growth and production of valuable target products may be severely affected. Furthermore, some strains generating acidic or alkaline products require self pH regulation and increased tolerance against pH-stress. For pH control, synthetic biology has provided advanced engineering approaches to construct robust and more intelligent microbial strains, exhibiting tolerance to pH-stress to cope with limitations of pH regulation. This study reviewed the current progress of advanced strain evolution strategies to engineer pH-stress tolerant strains via synthetic biology. In addition, a large number of pH-responsive elements, including promoters, riboswitches, and some proteins have been investigated and applied for construction of pH-responsive genetic circuits and intelligent pH-responsive microbial strains.
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Affiliation(s)
- Xiaopeng Gao
- 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, PR China.,School of Life Science, Yan'an University, Shanxi, PR China
| | - Ke Xu
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China.,Tangshan Key Laboratory of Agricultural Pathogenic Fungi and Toxins, Department of Life Science, Tangshan Normal University, Tangshan, PR China
| | - Nadeem Ahmad
- 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, PR China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR 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, PR China.,School of Life Science, Yan'an University, Shanxi, PR China.,Key Lab for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing, PR China
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29
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Stress modulation as a means to improve yeasts for lignocellulose bioconversion. Appl Microbiol Biotechnol 2021; 105:4899-4918. [PMID: 34097119 DOI: 10.1007/s00253-021-11383-y] [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: 02/21/2021] [Revised: 05/20/2021] [Accepted: 05/28/2021] [Indexed: 12/15/2022]
Abstract
The second-generation (2G) fermentation environment for lignocellulose conversion presents unique challenges to the fermentative organism that do not necessarily exist in other industrial fermentations. While extreme osmotic, heat, and nutrient starvation stresses are observed in sugar- and starch-based fermentation environments, additional pre-treatment-derived inhibitor stress, potentially exacerbated by stresses such as pH and product tolerance, exist in the 2G environment. Furthermore, in a consolidated bioprocessing (CBP) context, the organism is also challenged to secrete enzymes that may themselves lead to unfolded protein response and other stresses. This review will discuss responses of the yeast Saccharomyces cerevisiae to 2G-specific stresses and stress modulation strategies that can be followed to improve yeasts for this application. We also explore published -omics data and discuss relevant rational engineering, reverse engineering, and adaptation strategies, with the view of identifying genes or alleles that will make positive contributions to the overall robustness of 2G industrial strains. KEYPOINTS: • Stress tolerance is a key driver to successful application of yeast strains in biorefineries. • A wealth of data regarding stress responses has been gained through omics studies. • Integration of this knowledge could inform engineering of fit for purpose strains.
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30
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Improving Acetic Acid and Furfural Resistance of Xylose-Fermenting Saccharomyces cerevisiae Strains by Regulating Novel Transcription Factors Revealed via Comparative Transcriptomic Analysis. Appl Environ Microbiol 2021; 87:AEM.00158-21. [PMID: 33712428 DOI: 10.1128/aem.00158-21] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 03/04/2021] [Indexed: 11/20/2022] Open
Abstract
Acetic acid and furfural are the two prevalent inhibitors coexisting with glucose and xylose in lignocellulosic hydrolysate. The transcriptional regulations of Saccharomyces cerevisiae in response to acetic acid (Aa), furfural (Fur), and the mixture of acetic acid and furfural (Aa_Fur) were revealed during mixed glucose and xylose fermentation. Carbohydrate metabolism pathways were significantly enriched in response to Aa, while pathways of xenobiotic biodegradation and metabolism were significantly enriched in response to Fur. In addition to these pathways, other pathways were activated in response to Aa_Fur, i.e., cofactor and vitamin metabolism and lipid metabolism. Overexpression of Haa1p or Tye7p improved xylose consumption rates by nearly 50%, while the ethanol yield was enhanced by nearly 8% under acetic acid and furfural stress conditions. Co-overexpression of Haa1p and Tye7p resulted in a 59% increase in xylose consumption rate and a 12% increase in ethanol yield, revealing the beneficial effects of Haa1p and Tye7p on improving the tolerance of yeast to mixed acetic acid and furfural.IMPORTANCE Inhibitor tolerance is essential for S. cerevisiae when fermenting lignocellulosic hydrolysate with various inhibitors, including weak acids, furans, and phenols. The details regarding how xylose-fermenting S. cerevisiae strains respond to multiple inhibitors during fermenting mixed glucose and xylose are still unknown. This study revealed the transcriptional regulation mechanism of an industrial xylose-fermenting S. cerevisiae strain in response to acetic acid and furfural. The transcription factor Haa1p was found to be involved in both acetic acid and furfural tolerance. In addition to Haa1p, four other transcription factors, Hap4p, Yox1p, Tye7p, and Mga1p, were identified as able to improve the resistance of yeast to these two inhibitors. This study underscores the feasibility of uncovering effective transcription factors for constructing robust strains for lignocellulosic bioethanol production.
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Qiao Y, Zhou J, Lu X, Zong H, Zhuge B. Improving the productivity of Candida glycerinogenes in the fermentation of ethanol from non-detoxified sugarcane bagasse hydrolysate by a hexose transporter mutant. J Appl Microbiol 2021; 131:1787-1799. [PMID: 33694233 DOI: 10.1111/jam.15059] [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: 11/21/2020] [Revised: 02/09/2021] [Accepted: 03/02/2021] [Indexed: 11/27/2022]
Abstract
AIMS In this study, we attempted to increase the productivity of Candida glycerinogenes yeast for ethanol production from non-detoxified sugarcane bagasse hydrolysates (NDSBH) by identifying the hexose transporter in this yeast that makes a high contribution to glucose consumption, and by adding additional copies of this transporter and enhancing its membrane localisation stability (MLS). METHODS AND RESULTS Based on the knockout and overexpression of key hexose transporter genes and the characterisation of their promoter properties, we found that Cghxt4 and Cghxt6 play major roles in the early and late stages of fermentation, respectively, with Cghxt4 contributing most to glucose consumption. Next, subcellular localisation analysis revealed that a common mutation of two ubiquitination sites (K9 and K538) in Cghxt4 improved its MLS. Finally, we overexpressed this Cghxt4 mutant (Cghxt4.2A) using a strong promoter, PCgGAP , which resulted in a significant increase in the ethanol productivity of C. glycerinogenes in the NDSBH medium. Specifically, the recombinant strain showed 18 and 25% higher ethanol productivity than the control in two kinds of YP-NDSBH medium (YP-NDSBH1G160 and YP-NDSBH2G160 ), respectively. CONCLUSIONS The hexose transporter mutant Cghxt4.2A (Cghxt4K9A,K538A ) with multiple copies and high MLS was able to significantly increase the ethanol productivity of C. glycerinogenes in NDSBH. SIGNIFICANCE AND IMPACT OF THE STUDY Our results provide a promising strategy for constructing efficient strains for ethanol production.
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Affiliation(s)
- Y Qiao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - J Zhou
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China
| | - X Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - H Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - B Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
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32
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Li P, Tan X, Fu X, Dang Y, Li S. Metabolomic analysis reveals Kluyveromyces marxianus’s stress responses during high-temperature ethanol fermentation. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.01.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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33
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Wang L, Li B, Wang SP, Xia ZY, Gou M, Tang YQ. Improving multiple stress-tolerance of a flocculating industrial Saccharomyces cerevisiae strain by random mutagenesis and hybridization. Process Biochem 2021. [DOI: 10.1016/j.procbio.2020.12.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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34
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Kim IS, Choi W, Son J, Lee JH, Lee H, Lee J, Shin SC, Kim HW. Screening and Genetic Network Analysis of Genes Involved in Freezing and Thawing Resistance in DaMDHAR-Expressing Saccharomyces cerevisiae Using Gene Expression Profiling. Genes (Basel) 2021; 12:genes12020219. [PMID: 33546197 PMCID: PMC7913288 DOI: 10.3390/genes12020219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 01/28/2021] [Accepted: 01/30/2021] [Indexed: 01/24/2023] Open
Abstract
The cryoprotection of cell activity is a key determinant in frozen-dough technology. Although several factors that contribute to freezing tolerance have been reported, the mechanism underlying the manner in which yeast cells respond to freezing and thawing (FT) stress is not well established. Therefore, the present study demonstrated the relationship between DaMDHAR encoding monodehydroascorbate reductase from Antarctic hairgrass Deschampsia antarctica and stress tolerance to repeated FT cycles (FT2) in transgenic yeast Saccharomyces cerevisiae. DaMDHAR-expressing yeast (DM) cells identified by immunoblotting analysis showed high tolerance to FT stress conditions, thereby causing lower damage for yeast cells than wild-type (WT) cells with empty vector alone. To detect FT2 tolerance-associated genes, 3′-quant RNA sequencing was employed using mRNA isolated from DM and WT cells exposed to FT (FT2) conditions. Approximately 332 genes showed ≥2-fold changes in DM cells and were classified into various groups according to their gene expression. The expressions of the changed genes were further confirmed using western blot analysis and biochemical assay. The upregulated expression of 197 genes was associated with pentose phosphate pathway, NADP metabolic process, metal ion homeostasis, sulfate assimilation, β-alanine metabolism, glycerol synthesis, and integral component of mitochondrial and plasma membrane (PM) in DM cells under FT2 stress, whereas the expression of the remaining 135 genes was partially related to protein processing, selenocompound metabolism, cell cycle arrest, oxidative phosphorylation, and α-glucoside transport under the same condition. With regard to transcription factors in DM cells, MSN4 and CIN5 were activated, but MSN2 and MGA1 were not. Regarding antioxidant systems and protein kinases in DM cells under FT stress, CTT1, GTO, GEX1, and YOL024W were upregulated, whereas AIF1, COX2, and TRX3 were not. Gene activation represented by transcription factors and enzymatic antioxidants appears to be associated with FT2-stress tolerance in transgenic yeast cells. RCK1, MET14, and SIP18, but not YPK2, have been known to be involved in the protein kinase-mediated signalling pathway and glycogen synthesis. Moreover, SPI18 and HSP12 encoding hydrophilin in the PM were detected. Therefore, it was concluded that the genetic network via the change of gene expression levels of multiple genes contributing to the stabilization and functionality of the mitochondria and PM, not of a single gene, might be the crucial determinant for FT tolerance in DaMDAHR-expressing transgenic yeast. These findings provide a foundation for elucidating the DaMDHAR-dependent molecular mechanism of the complex functional resistance in the cellular response to FT stress.
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Affiliation(s)
- Il-Sup Kim
- Advanced Bio-Resource Research Center, Kyungpook National University, Daegu 41566, Korea;
| | - Woong Choi
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Jonghyeon Son
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Jun Hyuck Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Hyoungseok Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Jungeun Lee
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
| | - Seung Chul Shin
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
| | - Han-Woo Kim
- Korea Polar Research Institute, Incheon 21990, Korea; (W.C.); (J.S.); (J.H.L.); (H.L.); (J.L.); (S.C.S.)
- Department of Polar Science, University of Science and Technology, Incheon 21990, Korea
- Correspondence:
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Choi KR, Jiao S, Lee SY. Metabolic engineering strategies toward production of biofuels. Curr Opin Chem Biol 2020; 59:1-14. [DOI: 10.1016/j.cbpa.2020.02.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 02/14/2020] [Accepted: 02/20/2020] [Indexed: 10/24/2022]
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36
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Liu CG, Cao LY, Wen Y, Li K, Mehmood MA, Zhao XQ, Bai FW. Intracellular redox manipulation of Zymomonas mobilis for improving tolerance against lignocellulose hydrolysate-derived stress. Chem Eng Sci 2020. [DOI: 10.1016/j.ces.2020.115933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Danchin A, Sekowska A, You C. One-carbon metabolism, folate, zinc and translation. Microb Biotechnol 2020; 13:899-925. [PMID: 32153134 PMCID: PMC7264889 DOI: 10.1111/1751-7915.13550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Accepted: 02/17/2020] [Indexed: 12/16/2022] Open
Abstract
The translation process, central to life, is tightly connected to the one-carbon (1-C) metabolism via a plethora of macromolecule modifications and specific effectors. Using manual genome annotations and putting together a variety of experimental studies, we explore here the possible reasons of this critical interaction, likely to have originated during the earliest steps of the birth of the first cells. Methionine, S-adenosylmethionine and tetrahydrofolate dominate this interaction. Yet, 1-C metabolism is unlikely to be a simple frozen accident of primaeval conditions. Reactive 1-C species (ROCS) are buffered by the translation machinery in a way tightly associated with the metabolism of iron-sulfur clusters, zinc and potassium availability, possibly coupling carbon metabolism to nitrogen metabolism. In this process, the highly modified position 34 of tRNA molecules plays a critical role. Overall, this metabolic integration may serve both as a protection against the deleterious formation of excess carbon under various growth transitions or environmental unbalanced conditions and as a regulator of zinc homeostasis, while regulating input of prosthetic groups into nascent proteins. This knowledge should be taken into account in metabolic engineering.
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Affiliation(s)
- Antoine Danchin
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
- School of Biomedical SciencesLi Ka Shing Faculty of MedicineThe University of Hong KongS.A.R. Hong KongChina
| | - Agnieszka Sekowska
- AMAbiotics SASInstitut Cochin24 rue du Faubourg Saint‐Jacques75014ParisFrance
| | - Conghui You
- Shenzhen Key Laboratory of Microbial Genetic EngineeringCollege of Life Sciences and OceanologyShenzhen University1066 Xueyuan Rd518055ShenzhenChina
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Chen H, Li J, Wan C, Fang Q, Bai F, Zhao X. Improvement of inhibitor tolerance in Saccharomyces cerevisiae by overexpression of the quinone oxidoreductase family gene YCR102C. FEMS Yeast Res 2020; 19:5543220. [PMID: 31374572 DOI: 10.1093/femsyr/foz055] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 07/31/2019] [Indexed: 12/14/2022] Open
Abstract
Budding yeast Saccharomyces cerevisiae is widely used for lignocellulosic biorefinery. However, its fermentation efficiency is challenged by various inhibitors (e.g. weak acids, furfural) in the lignocellulosic hydrolysate, and acetic acid is commonly present as a major inhibitor. The effects of oxidoreductases on the inhibitor tolerance of S. cerevisiae have mainly focused on furfural and vanillin, whereas the influence of quinone oxidoreductase on acetic acid tolerance is still unknown. In this study, we show that overexpression of a quinone oxidoreductase-encoding gene, YCR102C, in S. cerevisiae, significantly enhanced ethanol production under acetic acid stress as well as in the inhibitor mixture, and also improved resistance to simultaneous stress of 40°C and 3.6 g/L acetic acid. Increased catalase activities, NADH/NAD+ ratio and contents of several metals, especially potassium, were observed by YCR102C overexpression under acetic acid stress. To our knowledge, this is the first report that the quinone oxidoreductase family protein is related to acid stress tolerance. Our study provides a novel strategy to increase lignocellulosic biorefinery efficiency using yeast cell factory.
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Affiliation(s)
- Hongqi Chen
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jie Li
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Chun Wan
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qing Fang
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian 116024, China
| | - Fengwu Bai
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xinqing Zhao
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
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Li B, Xie CY, Yang BX, Gou M, Xia ZY, Sun ZY, Tang YQ. The response mechanisms of industrial Saccharomyces cerevisiae to acetic acid and formic acid during mixed glucose and xylose fermentation. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.01.002] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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40
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Li Y, Wu Z, Li R, Miao Y, Weng P, Wang L. Integrated transcriptomic and proteomic analysis of the acetic acid stress in Issatchenkia orientalis. J Food Biochem 2020; 44:e13203. [PMID: 32232868 DOI: 10.1111/jfbc.13203] [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: 07/11/2019] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 11/30/2022]
Abstract
Issatchenkia orientalis known as a multi-tolerant non-Saccharomyces yeast, which tolerant environmental stresses, exhibits potential in wine making and bioethanol production. It is essential for the growth of I. orientalis to tolerant acetic acid in the mixed cultures with Saccharomyces cerevisiae. In this work, RNA-sequence and TMT (Tandem Mass Tag) were used to examine the comprehensive transcriptomic and proteomic profiles of I. orientalis in response to acetic acid. The results showed that 876 genes were identified differentially transcribed in I. orientalis genome and 399 proteins expressed in proteome after 4 hr acetic acid (90 mM, pH 4.5). The comprehensive analysis showed a series of determinants of acetic acid tolerance: Glycolysis and TCA cycle provide enough nicotinamide adenine dinucleotide to effectively convert acetic acid. Genes associated with potassium, iron, zinc, and glutathione synthesis were upregulated. The same changes of differentially expressed genes and proteins were mainly concentrated in chaperones, coenzyme, energy production, and transformation. PRACTICAL APPLICATIONS: In addition to the main fermentation products, wine yeast also produces metabolite acetic acid in the fermentation process, and yeast cells are exposed to acetic acid stress, which restrains cell proliferation. Issatchenkia orientalis exhibits great potential in winemaking and bioethanol production. The yeast is known as a multi-tolerant non-Saccharomyces yeast that can tolerate a variety of environmental stresses. In this study, RNA-Seq and TMT were conducted to investigate the changes in transcriptional and proteomic profile of I. orientalis under acetic acid stress. The knowledge of the transcription and expression changes of the I. orientalis is expected to understand the tolerance mechanisms in I. orientalis and to guide traditional fermentation processes by Saccharomyces cerevisiae improving its high resistance to acetic acid stress.
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Affiliation(s)
- Yingdi Li
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Zufang Wu
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China.,Key Laboratory of Animal Protein Deep Processing Technology of Zhejiang Province, Ningbo University, Ningbo, P.R. China
| | - Ruoyun Li
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Yingjie Miao
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Peifang Weng
- Department of Food Science and Engineering, School of Food and Pharmaceutical Sciences, Ningbo University, Ningbo, P.R. China
| | - Liping Wang
- School of Food Science and Technology, Shanghai Ocean University, Shanghai, China
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41
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Wang Y, Zhang Z, Lu X, Zong H, Zhuge B. Transcription factor Hap5 induces gsh2 expression to enhance 2-phenylethanol tolerance and production in an industrial yeast Candida glycerinogenes. Appl Microbiol Biotechnol 2020; 104:4093-4107. [PMID: 32162090 DOI: 10.1007/s00253-020-10509-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Revised: 02/13/2020] [Accepted: 02/28/2020] [Indexed: 02/07/2023]
Abstract
2-Phenylethanol (2-PE) is an important flavor compound but also impairs cell growth severely, which in turn blocks its bioproduction. However, the molecular mechanism of 2-PE tolerance is unclear. In this study, a superb 2-PE stress-tolerant and producing yeast, Candida glycerinogenes, was selected to uncover the underlying mechanism of 2-PE tolerance. We discovered that Hap5 is an essential regulator to 2-PE resistance, and its induction by 2-PE stress occurs at the post-transcriptional level, rather than at the transcriptional level. Under 2-PE stress, Hap5 is activated and imported into the nucleus rapidly. Then, the nuclear Hap5 binds to the glutathione synthetase (gsh2) promoter via CCAAT box, to induce the expression of gsh2 gene. The increased gsh2 expression contributes to enhanced cellular glutathione content, and consequently alleviates ROS accumulation, lipid peroxidation, and cell membrane damage caused by 2-PE toxicity. Specifically, increasing the expression of gsh2 is effective in improving not just 2-PE tolerance (33.7% higher biomass under 29 mM 2-PE), but also 2-PE production (16.2% higher). This study extends our knowledge of 2-PE tolerance mechanism and also provides a promising strategy to improve 2-PE production.
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Affiliation(s)
- Yuqin Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Zhongyuan Zhang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Xinyao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China.
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China.,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China. .,Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi, China.
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High Gravity Fermentation of Sugarcane Bagasse Hydrolysate by Saccharomyces pastorianus to Produce Economically Distillable Ethanol Concentrations: Necessity of Medium Components Examined. FERMENTATION-BASEL 2020. [DOI: 10.3390/fermentation6010008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A major economic obstacle in lignocellulosic ethanol production is the low sugar concentrations in the hydrolysate and subsequent fermentation to economically distillable ethanol concentrations. We have previously demonstrated a two-stage fermentation process that recycles xylose with xylose isomerase to increase ethanol productivity, where the low sugar concentrations in the hydrolysate limit the final ethanol concentrations. In this study, three approaches are combined to increase ethanol concentrations. First, the medium-additive requirements were investigated to reduce ethanol dilution. Second, methods to increase the sugar concentrations in the sugarcane bagasse hydrolysate were undertaken. Third, the two-stage fermentation process was recharacterized with high gravity hydrolysate. It was determined that phosphate and magnesium sulfate are essential to the ethanol fermentation. Additionally, the Escherichia coli extract and xylose isomerase additions were shown to significantly increase ethanol productivity. Finally, the fermentation on hydrolysate had only slightly lower productivity than the reagent-grade sugar fermentation; however, both fermentations had similar final ethanol concentrations. The present work demonstrates the capability to produce ethanol from high gravity sugarcane bagasse hydrolysate using Saccharomyces pastorianus with low yeast inoculum in minimal medium. Moreover, ethanol productivities were on par with pilot-scale commercial starch-based facilities, even when the yeast biomass production stage was included.
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43
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Shinkawa S, Mitsuzawa S. Feasibility study of on-site solid-state enzyme production by Aspergillus oryzae. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:31. [PMID: 32127918 PMCID: PMC7045521 DOI: 10.1186/s13068-020-1669-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/28/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND The development of biorefinery systems that use lignocellulosic biomass as a renewable carbon source to produce fuels and chemicals is attracting increasing attention. The process cost of enzymatic saccharification of biomass is a major challenge for commercialization. To decrease this cost, researchers have proposed on-site solid-state fermentation (SSF). This study investigated the feasibility of using Aspergillus oryzae as a host microorganism for SSF recombinant enzyme production with ammonia-treated rice straw as model biomass. Eight A. oryzae strains were tested, all of which are used in the food industry. We evaluated the effects of acetic acid, a fermentation inhibitor. We also developed a platform strain for targeted recombinant enzyme production by gene engineering technologies. RESULTS The SSF validation test showed variation in the visibility of mycelium growth and secreted protein in all eight A. oryzae strains. The strains used to produce shoyu and miso grew better under test conditions. The ammonia-treated rice straw contained noticeable amounts of acetic acid. This acetic acid enhanced the protein production by A. oryzae in a liquid-state fermentation test. The newly developed platform strain successfully secreted three foreign saccharifying enzymes. CONCLUSIONS A. oryzae is a promising candidate as a host microorganism for on-site SSF recombinant enzyme production, which bodes well for the future development of a more cost-efficient saccharifying enzyme production system.
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Affiliation(s)
- Satoru Shinkawa
- Fundamental Technology Center, Honda R&D Co., Ltd., 1-4-1 Chuo, Wako-shi, Saitama, 351-0113 Japan
- Present Address: Honda Research Institute Japan Co., Ltd., 8-1 Honcho, Wako-shi, Saitama, 351-0188 Japan
| | - Shigenobu Mitsuzawa
- Fundamental Technology Center, Honda R&D Co., Ltd., 1-4-1 Chuo, Wako-shi, Saitama, 351-0113 Japan
- Present Address: Honda Research Institute Japan Co., Ltd., 8-1 Honcho, Wako-shi, Saitama, 351-0188 Japan
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44
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Hu J, Dong Y, Wang W, Zhang W, Lou H, Chen Q. Deletion of Atg22 gene contributes to reduce programmed cell death induced by acetic acid stress in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:298. [PMID: 31890026 PMCID: PMC6933646 DOI: 10.1186/s13068-019-1638-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 12/12/2019] [Indexed: 05/27/2023]
Abstract
BACKGROUND Programmed cell death (PCD) induced by acetic acid, the main by-product released during cellulosic hydrolysis, cast a cloud over lignocellulosic biofuel fermented by Saccharomyces cerevisiae and became a burning problem. Atg22p, an ignored integral membrane protein located in vacuole belongs to autophagy-related genes family; prior study recently reported that it is required for autophagic degradation and efflux of amino acids from vacuole to cytoplasm. It may alleviate the intracellular starvation of nutrition caused by Ac and increase cell tolerance. Therefore, we investigate the role of atg22 in cell death process induced by Ac in which attempt is made to discover new perspectives for better understanding of the mechanisms behind tolerance and more robust industrial strain construction. RESULTS In this study, we compared cell growth, physiological changes in the absence and presence of Atg22p under Ac exposure conditions. It is observed that disruption and overexpression of Atg22p delays and enhances acetic acid-induced PCD, respectively. The deletion of Atg22p in S. cerevisiae maintains cell wall integrity, and protects cytomembrane integrity, fluidity and permeability upon Ac stress by changing cytomembrane phospholipids, sterols and fatty acids. More interestingly, atg22 deletion increases intracellular amino acids to aid yeast cells for tackling amino acid starvation and intracellular acidification. Further, atg22 deletion upregulates series of stress response genes expression such as heat shock protein family, cell wall integrity and autophagy. CONCLUSIONS The findings show that Atg22p possessed the new function related to cell resistance to Ac. This may help us have a deeper understanding of PCD induced by Ac and provide a new strategy to improve Ac resistance in designing industrial yeast strains for bioethanol production during lignocellulosic biofuel fermentation.
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Affiliation(s)
- Jingjin Hu
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Yachen Dong
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Wei Wang
- Institute of Quality and Standard for Agriculture Products, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021 China
| | - Wei Zhang
- Department of Cardiovascular & Metabolic Sciences, The Lerner Research Institute, Cleveland Clinic, Cleveland, OH USA
| | - Hanghang Lou
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
| | - Qihe Chen
- Department of Food Science and Nutrition, Key Laboratory for Food Microbial Technology of Zhejiang Province, Zhejiang University, Hangzhou, 310058 China
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45
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Dakal TC, Dhabhai B. Current status of genetic & metabolic engineering and novel QTL mapping-based strategic approach in bioethanol production. GENE REPORTS 2019. [DOI: 10.1016/j.genrep.2019.100497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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46
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Tang R, Ye P, Alper HS, Liu Z, Zhao X, Bai F. Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome. Appl Microbiol Biotechnol 2019; 103:9465-9477. [PMID: 31701197 DOI: 10.1007/s00253-019-10161-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/31/2022]
Abstract
Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.
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Affiliation(s)
- Ruiqi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peiliang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Zhanying Liu
- School of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, 010051, China.,Center for Conservation and Emission Reductioin in Fermentation Industry, Inner Mongolia, Hohhot, 010051, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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47
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Improved cellulase production in recombinant Saccharomyces cerevisiae by disrupting the cell wall protein-encoding gene CWP2. J Biosci Bioeng 2019; 129:165-171. [PMID: 31537451 DOI: 10.1016/j.jbiosc.2019.08.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/23/2019] [Accepted: 08/23/2019] [Indexed: 12/27/2022]
Abstract
Budding yeast Saccharomyces cerevisiae has been widely used for heterologous protein production. However, low protein production titer and secretion levels continue to challenge its practical applications. The yeast cell wall plays important roles in yeast cell growth and environmental responses. Nevertheless, the effects of yeast cell wall proteins on heterologous protein production and secretion remain unclear. CWP2 encodes a mannoprotein that is the major component of the yeast cell wall. So far, studies on its function have been very limited. Here we show that CWP2 disruption improved extracellular cellobiohydrolase activity by 85.9%. A calcofluor white hypersensitivity assay revealed increased sensitivity of the mutant compared to the parental strain, indicating impaired cell wall integrity. However, no changes were observed in normal cell growth or growth stressed by tunicamycin and dithiothreitol, suggesting that the unfolded protein response pathway was not affected by the gene disruption. Comparative transcriptome analysis revealed changes in multiple genes involved in cell wall structure, biosynthesis, and cell wall integrity induced by CWP2 disruption, suggesting a pivotal role of Cwp2p in yeast cell wall organization. Notably, CWP2 disruption also led to elevated transcription of a large number of genes involved in ribosome biogenesis, which indicated that CWP2 is not only in yeast cell wall biosynthesis, but also in protein translation. This work reveals novel insights into the functions of CWP2 and also presents a new strategy to increase heterologous protein production in yeast strains by manipulating cell wall-related proteins.
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