1
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Jofre FM, Queiroz SDS, Sanchez DA, Arruda PV, Santos JCD, Felipe MDGDA. Biotechnological potential of yeast cell wall: An overview. Biotechnol Prog 2024:e3491. [PMID: 38934212 DOI: 10.1002/btpr.3491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 05/27/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024]
Abstract
The yeast cell wall is a complex structure whose main function is to protect the cell from physical and chemical damage, providing it with rigidity. It is composed of a matrix of covalently linked polysaccharides and proteins, including β-glucans, mannoproteins, and chitin, whose proportion can vary according to the yeast species and environmental conditions. The main components of the yeast cell wall have relevant properties that expand the possibilities of use in different industrial sectors, such as pharmaceutical, food, medical, veterinary, and cosmetic. Some applications include bioremediation, enzyme immobilization, animal feed, wine production, and hydrogel production. In the literature it is the description of the cell wall composition of model species like Saccharomyces cerevisiae and Candida albicans, however, it is important to know that this composition can vary according to the species or the culture medium conditions. Thus, understanding the structural composition of different species holds promise as an alternative to expanding the utilization of residual yeast from different bioprocesses. In the context of a circular economy, the conversion of residual yeast into valuable products is an attractive prospect for researchers aiming to develop sustainable technologies. This review provides an overview of yeast cell wall composition and its significance in biotechnological applications, considering prospects to increase the diversification of these compounds in industry.
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Affiliation(s)
- Fanny Machado Jofre
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Sarah de Souza Queiroz
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Diana Alva Sanchez
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Priscila Vaz Arruda
- Department of Bioprocess and Biotechnology Engineering, Federal University of Technology-Paraná (UTFPR), Toledo, Brazil
| | - Júlio César Dos Santos
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
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2
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Yin MQ, Xu K, Luan T, Kang XL, Yang XY, Li HX, Hou YH, Zhao JZ, Bao XM. Metabolic engineering for compartmentalized biosynthesis of the valuable compounds in Saccharomyces cerevisiae. Microbiol Res 2024; 286:127815. [PMID: 38944943 DOI: 10.1016/j.micres.2024.127815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/14/2024] [Accepted: 06/18/2024] [Indexed: 07/02/2024]
Abstract
Saccharomyces cerevisiae is commonly used as a microbial cell factory to produce high-value compounds or bulk chemicals due to its genetic operability and suitable intracellular physiological environment. The current biosynthesis pathway for targeted products is primarily rewired in the cytosolic compartment. However, the related precursors, enzymes, and cofactors are frequently distributed in various subcellular compartments, which may limit targeted compounds biosynthesis. To overcome above mentioned limitations, the biosynthesis pathways are localized in different subcellular organelles for product biosynthesis. Subcellular compartmentalization in the production of targeted compounds offers several advantages, mainly relieving competition for precursors from side pathways, improving biosynthesis efficiency in confined spaces, and alleviating the cytotoxicity of certain hydrophobic products. In recent years, subcellular compartmentalization in targeted compound biosynthesis has received extensive attention and has met satisfactory expectations. In this review, we summarize the recent advances in the compartmentalized biosynthesis of the valuable compounds in S. cerevisiae, including terpenoids, sterols, alkaloids, organic acids, and fatty alcohols, etc. Additionally, we describe the characteristics and suitability of different organelles for specific compounds, based on the optimization of pathway reconstruction, cofactor supplementation, and the synthesis of key precursors (metabolites). Finally, we discuss the current challenges and strategies in the field of compartmentalized biosynthesis through subcellular engineering, which will facilitate the production of the complex valuable compounds and offer potential solutions to improve product specificity and productivity in industrial processes.
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Affiliation(s)
- Meng-Qi Yin
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Kang Xu
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Tao Luan
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xiu-Long Kang
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Xiao-Yu Yang
- Institute of Food and Nutrition Science and Technology, Shandong Academy of Agricultural Sciences, Jinan 250100, China
| | - Hong-Xing Li
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Yun-Hua Hou
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
| | - Jian-Zhi Zhao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China; A State Key Laboratory of Microbial Technology, School of Life Science, Shandong University, Qingdao 266237, China.
| | - Xiao-Ming Bao
- State Key Laboratory of Biobased Material and Green Papermaking, School of Bioengineering, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250353, China
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3
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Arruda GL, Raymundo MTFR, Cruz-Santos MM, Shibukawa VP, Jofre FM, Prado CA, da Silva SS, Mussatto SI, Santos JC. Lignocellulosic materials valorization in second generation biorefineries: an opportunity to produce fungal biopigments. Crit Rev Biotechnol 2024:1-20. [PMID: 38817002 DOI: 10.1080/07388551.2024.2349581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/13/2024] [Indexed: 06/01/2024]
Abstract
Second generation biorefineries play an important role in the production of renewable energy and fuels, utilizing forest and agro-industrial residues and by-products as raw materials. The integration of novel bioproducts, such as: xylitol, β-carotene, xylooligosaccharides, and biopigments into the biorefinery's portfolio can offer economic benefits in the valorization of lignocellulosic materials, particularly cellulosic and hemicellulosic fractions. Fungal biopigments, known for their additional antioxidant and antimicrobial properties, are appealing to consumers and can have applications in various industrial sectors, including food and pharmaceuticals. The use of lignocellulosic materials as carbon and nutrient sources for the growth medium helps to reduce production costs, increasing the competitiveness of fungal biopigments in the market. In addition, the implementation of biopigment production in biorefineries allows the utilization of underutilized fractions, such as hemicellulose, for value-added bioproducts. This study deals with the potential of fungal biopigments production in second generation biorefineries in order to diversify the produced biomolecules together with energy generation. A comprehensive and critical review of the recent literature on this topic has been conducted, covering the major possible raw materials, general aspects of second generation biorefineries, the fungal biopigments and their potential for incorporation into biorefineries.
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Affiliation(s)
- Gabriel L Arruda
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | | | - Mónica M Cruz-Santos
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Vinícius P Shibukawa
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Fanny M Jofre
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Carina A Prado
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Silvio S da Silva
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
| | - Solange I Mussatto
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Júlio C Santos
- Department of Biotechnology, Engineering School of Lorena, University of São Paulo, Lorena, Brazil
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4
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Guo Q, Peng QQ, Li YW, Yan F, Wang YT, Ye C, Shi TQ. Advances in the metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica for the production of β-carotene. Crit Rev Biotechnol 2024; 44:337-351. [PMID: 36779332 DOI: 10.1080/07388551.2023.2166809] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 09/20/2022] [Accepted: 12/08/2022] [Indexed: 02/14/2023]
Abstract
β-Carotene is one kind of the most important carotenoids. The major functions of β-carotene include the antioxidant and anti-cardiovascular properties, which make it a growing market. Recently, the use of metabolic engineering to construct microbial cell factories to synthesize β-carotene has become the latest model for its industrial production. Among these cell factories, yeasts including Saccharomyces cerevisiae and Yarrowia lipolytica have attracted the most attention because of the: security, mature genetic manipulation tools, high flux toward carotenoids using the native mevalonate pathway and robustness for large-scale fermentation. In this review, the latest strategies for β-carotene biosynthesis, including protein engineering, promoters engineering and morphological engineering are summarized in detail. Finally, perspectives for future engineering approaches are proposed to improve β-carotene production.
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Affiliation(s)
- Qi Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, People's Republic of China
| | - Qian-Qian Peng
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Ya-Wen Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Fang Yan
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Yue-Tong Wang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Chao Ye
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
| | - Tian-Qiong Shi
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Nanjing, People's Republic of China
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5
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Lee YG, Kang NK, Kim C, Tran VG, Cao M, Yoshikuni Y, Zhao H, Jin YS. Self-Buffering system for Cost-Effective production of lactic acid from glucose and xylose using Acid-Tolerant Issatchenkia orientalis. BIORESOURCE TECHNOLOGY 2024; 399:130641. [PMID: 38552861 DOI: 10.1016/j.biortech.2024.130641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 03/24/2024] [Accepted: 03/24/2024] [Indexed: 04/05/2024]
Abstract
This study presents a cost-effective strategy for producing organic acids from glucose and xylose using the acid-tolerant yeast, Issatchenkia orientalis. I. orientalis was engineered to produce lactic acid from xylose, and the resulting strain, SD108XL, successfully converted sorghum hydrolysates into lactic acid. In order to enable low-pH fermentation, a self-buffering strategy, where the lactic acid generated by the SD108XL strain during fermentation served as a buffer, was developed. As a result, the SD108 strain produced 67 g/L of lactic acid from 73 g/L of glucose and 40 g/L of xylose, simulating a sugar composition of sorghum biomass hydrolysates. Moreover, techno-economic analysis underscored the efficiency of the self-buffering strategy in streamlining the downstream process, thereby reducing production costs. These results demonstrate the potential of I. orientalis as a platform strain for the cost-effective production of organic acids from cellulosic hydrolysates.
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Affiliation(s)
- Ye-Gi Lee
- Department of Bio and Fermentation Convergence Technology and Center for Bioconvergence, Kookmin University, Seoul 02707, Korea; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Nam Kyu Kang
- Department of Chemical Engineering, College of Engineering, Kyung Hee University, Yongin, 17104, Republic of Korea
| | - Chanwoo Kim
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Vinh G Tran
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Mingfeng Cao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yasuo Yoshikuni
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Huimin Zhao
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA; DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
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6
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Wang S, Meng D, Feng M, Li C, Wang Y. Efficient Plant Triterpenoids Synthesis in Saccharomyces cerevisiae: from Mechanisms to Engineering Strategies. ACS Synth Biol 2024; 13:1059-1076. [PMID: 38546129 DOI: 10.1021/acssynbio.4c00061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Triterpenoids possess a range of biological activities and are extensively utilized in the pharmaceutical, food, cosmetic, and chemical industries. Traditionally, they are acquired through chemical synthesis and plant extraction. However, these methods have drawbacks, including high energy consumption, environmental pollution, and being time-consuming. Recently, the de novo synthesis of triterpenoids in microbial cell factories has been achieved. This represents a promising and environmentally friendly alternative to traditional supply methods. Saccharomyces cerevisiae, known for its robustness, safety, and ample precursor supply, stands out as an ideal candidate for triterpenoid biosynthesis. However, challenges persist in industrial production and economic feasibility of triterpenoid biosynthesis. Consequently, metabolic engineering approaches have been applied to improve the triterpenoid yield, leading to substantial progress. This review explores triterpenoids biosynthesis mechanisms in S. cerevisiae and strategies for efficient production. Finally, the review also discusses current challenges and proposes potential solutions, offering insights for future engineering.
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Affiliation(s)
- Shuai Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Dong Meng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Meilin Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Chun Li
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, China
| | - Ying Wang
- Key Laboratory of Medical Molecule Science and Pharmaceutical Engineering, Ministry of Industry and Information Technology, Institute of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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Kang NK, Chau THT, Lee EY. Engineered methane biocatalysis: strategies to assimilate methane for chemical production. Curr Opin Biotechnol 2024; 85:103031. [PMID: 38101295 DOI: 10.1016/j.copbio.2023.103031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023]
Abstract
Methane (CH4), one of the greenhouse gases, is considered a promising feedstock for the biological production of fuels and chemicals. Although recent studies have demonstrated the capability of methanotrophs to convert CH4 into various bioproducts by metabolic engineering, the productivity has not reached commercial levels. As such, there is a growing interest in synthetic methanotrophic systems as an alternative. This review summarizes the strategies for enhancing native CH4 assimilation and discusses the challenges for the construction of synthetic methanotrophy into nonmethanotrophic industrial strains. Additionally, we suggest a mixed heterotrophic approach that integrates CH4 assimilation with glucose and xylose metabolism to improve productivity. The synthetic methanotrophic system presented in this review could pave the way for sustainable and efficient biomanufacturing using CH4.
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Affiliation(s)
- Nam Kyu Kang
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea
| | - Tin Hoang Trung Chau
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea
| | - Eun Yeol Lee
- Department of Chemical Engineering (BK21 FOUR Integrated Engineering Program), Kyung Hee University, 17104 Yongin-si, Gyeonggi-do, South Korea.
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8
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Zhu Z, Chen R, Zhang L. Simple phenylpropanoids: recent advances in biological activities, biosynthetic pathways, and microbial production. Nat Prod Rep 2024; 41:6-24. [PMID: 37807808 DOI: 10.1039/d3np00012e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Covering: 2000 to 2023Simple phenylpropanoids are a large group of natural products with primary C6-C3 skeletons. They are not only important biomolecules for plant growth but also crucial chemicals for high-value industries, including fragrances, nutraceuticals, biomaterials, and pharmaceuticals. However, with the growing global demand for simple phenylpropanoids, direct plant extraction or chemical synthesis often struggles to meet current needs in terms of yield, titre, cost, and environmental impact. Benefiting from the rapid development of metabolic engineering and synthetic biology, microbial production of natural products from inexpensive and renewable sources provides a feasible solution for sustainable supply. This review outlines the biological activities of simple phenylpropanoids, compares their biosynthetic pathways in different species (plants, bacteria, and fungi), and summarises key research on the microbial production of simple phenylpropanoids over the last decade, with a focus on engineering strategies that seem to hold most potential for further development. Moreover, constructive solutions to the current challenges and future perspectives for industrial production of phenylpropanoids are presented.
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Affiliation(s)
- Zhanpin Zhu
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Ruibing Chen
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
| | - Lei Zhang
- Department of Pharmaceutical Botany, School of Pharmacy, Naval Medical University, Shanghai 200433, China.
- Institute of Interdisciplinary Integrative Medicine Research, Medical School of Nantong University, Nantong 226001, China
- Innovative Drug R&D Centre, College of Life Sciences, Huaibei Normal University, Huaibei 235000, China
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9
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Liu H, Huang X, Liu Y, Jing X, Ning Y, Xu P, Deng L, Wang F. Efficient Production of Triacetic Acid Lactone from Lignocellulose Hydrolysate by Metabolically Engineered Yarrowia lipolytica. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:18909-18918. [PMID: 37999448 DOI: 10.1021/acs.jafc.3c06528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2023]
Abstract
Lignocellulose is a promising renewable feedstock for the bioproduction of high-value biochemicals. The poorly expressed xylose catabolic pathway was the bottleneck in the efficient utilization of the lignocellulose feedstock in yeast. Herein, multiple genetic and process engineering strategies were explored to debottleneck the conversion of xylose to the platform chemical triacetic acid lactone (TAL) in Yarrowia lipolytica. We identified that xylose assimilation generating more cofactor NADPH was favorable for the TAL synthesis. pH control improved the expression of acetyl-CoA carboxylase and generated more precursor malonyl-CoA. Combined with the suppression of the lipid synthesis pathway, 5.03 and 4.18 g/L TAL were produced from pure xylose and xylose-rich wheat straw hydrolysate, respectively. Our work removed the bottleneck of the xylose assimilation pathway and effectively upgraded wheat straw hydrolysate to TAL, which enabled us to build a sustainable oleaginous yeast cell factory to cost-efficiently produce green chemicals from low-cost lignocellulose by Y. lipolytica.
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Affiliation(s)
- Huan Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaolan Huang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yangming Liu
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xinyun Jing
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuchen Ning
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Peng Xu
- Department of Chemical Engineering, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
- Guangdong Provincial Key Laboratory of Materials and Technologies for Energy Conversion, Guangdong Technion-Israel Institute of Technology, Shantou, Guangdong 515063, China
| | - Li Deng
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Fang Wang
- Beijing Bioprocess Key Laboratory, State Key Laboratory of Chemical Resource Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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10
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Gao J, Yu W, Li Y, Jin M, Yao L, Zhou YJ. Engineering co-utilization of glucose and xylose for chemical overproduction from lignocellulose. Nat Chem Biol 2023; 19:1524-1531. [PMID: 37620399 DOI: 10.1038/s41589-023-01402-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 07/10/2023] [Indexed: 08/26/2023]
Abstract
Bio-refining lignocellulose could provide a sustainable supply of fuels and fine chemicals; however, the challenges associated with the co-utilization of xylose and glucose typically compromise the efficiency of lignocellulose conversion. Here we engineered the industrial yeast Ogataea polymorpha (Hansenula polymorpha) for lignocellulose biorefinery by facilitating the co-utilization of glucose and xylose to optimize the production of free fatty acids (FFAs) and 3-hydroxypropionic acid (3-HP) from lignocellulose. We rewired the central metabolism for the enhanced supply of acetyl-coenzyme A and nicotinamide adenine dinucleotide phosphate hydrogen, obtaining 30.0 g l-1 of FFAs from glucose, with productivity of up to 0.27 g l-1 h-1. Strengthening xylose uptake and catabolism promoted the synchronous utilization of glucose and xylose, which enabled the production of 38.2 g l-1 and 7.0 g l-1 FFAs from the glucose-xylose mixture and lignocellulosic hydrolysates, respectively. Finally, this efficient cell factory was metabolically transformed for 3-HP production with the highest titer of 79.6 g l-1 in fed-batch fermentation in mixed glucose and xylose.
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Affiliation(s)
- Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yunxia Li
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Mingjie Jin
- School of Environmental and Biological Engineering, Nanjing University of Science and Technology, Nanjing, PR China
| | - Lun Yao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
- Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, PR China.
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11
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Kumar V, Agrawal D, Bommareddy RR, Islam MA, Jacob S, Balan V, Singh V, Thakur VK, Navani NK, Scrutton NS. Arabinose as an overlooked sugar for microbial bioproduction of chemical building blocks. Crit Rev Biotechnol 2023:1-18. [PMID: 37932016 DOI: 10.1080/07388551.2023.2270702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 09/19/2023] [Indexed: 11/08/2023]
Abstract
The circular economy is anticipated to bring a disruptive transformation in manufacturing technologies. Robust and industrial scalable microbial strains that can simultaneously assimilate and valorize multiple carbon substrates are highly desirable, as waste bioresources contain substantial amounts of renewable and fermentable carbon, which is diverse. Lignocellulosic biomass (LCB) is identified as an inexhaustible and alternative resource to reduce global dependence on oil. Glucose, xylose, and arabinose are the major monomeric sugars in LCB. However, primary research has focused on the use of glucose. On the other hand, the valorization of pentose sugars, xylose, and arabinose, has been mainly overlooked, despite possible assimilation by vast microbial communities. The present review highlights the research efforts that have explicitly proven the suitability of arabinose as the starting feedstock for producing various chemical building blocks via biological routes. It begins by analyzing the availability of various arabinose-rich biorenewable sources that can serve as potential feedstocks for biorefineries. The subsequent section outlines the current understanding of arabinose metabolism, biochemical routes prevalent in prokaryotic and eukaryotic systems, and possible products that can be derived from this sugar. Further, currently, exemplar products from arabinose, including arabitol, 2,3-butanediol, 1,2,3-butanetriol, ethanol, lactic acid, and xylitol are discussed, which have been produced by native and non-native microbial strains using metabolic engineering and genome editing tools. The final section deals with the challenges and obstacles associated with arabinose-based production, followed by concluding remarks and prospects.
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Affiliation(s)
- Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, UK
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Dehradun, India
| | - Rajesh Reddy Bommareddy
- Department of Applied Sciences, Health and Life Sciences, Hub for Biotechnology in the Built Environment, Northumbria University, Newcastle upon Tyne, UK
| | - M Ahsanul Islam
- Department of Chemical Engineering, Loughborough University, Loughborough, UK
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, SRM Institute of Science and Technology, Kattankulathur, India
| | - Venkatesh Balan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, USA
| | - Vijai Singh
- Department of Biosciences, School of Sciences, Indrashil University, Rajpur, Mehsana, India
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Center, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Naveen Kumar Navani
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, India
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, UK
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12
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Ran Y, Yang Q, Zeng J, Li F, Cao Y, Xu Q, Qiao D, Xu H, Cao Y. Potential xylose transporters regulated by CreA improved lipid yield and furfural tolerance in oleaginous yeast Saitozyma podzolica zwy-2-3. BIORESOURCE TECHNOLOGY 2023; 386:129413. [PMID: 37390935 DOI: 10.1016/j.biortech.2023.129413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/26/2023] [Accepted: 06/27/2023] [Indexed: 07/02/2023]
Abstract
Lignocellulose's hydrolysate, a significant renewable source, contains xylose and furfural, making it challenging for industrial production of oleaginous yeast. On xylose fermentation with furfural treatment, OE::DN7263 and OE::DN7661 increased lipid yield and furfural tolerance versus WT, while, which of OE::CreA were decreased owing to CreA regulating DN7263 and DN7661 negatively. OE::CreA generated reactive oxygen species (ROS) causing oxidative damage. OE::DN7263, OE::DN7661, and ΔCreA reduced furfural via NADH; while ΔCreA produced less ROS and OE::DN7263, and OE::DN7661 scavenged ROS quickly, minimizing oxidative damage. Overall, CreA knockout increased DN7263 and DN7661 expression to facilitate xylose assimilation, enhancing NADH generation and ROS clearance. Finally, with mixed sugar fermentation, ΔCreA and OE::DN7263's biomass and lipid yield rose without furfural addition, while that of ΔCreA remained higher than WT after furfural treatment. These findings revealed how oleaginous yeast zwy-2-3 resisted furfural stress and indicated ΔCreA and OE::DN7263 might develop into robust industrial chassis strains.
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Affiliation(s)
- Yulu Ran
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingzhuoma Yang
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Jie Zeng
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Fazhi Li
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Yu Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Qingrui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Dairong Qiao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China
| | - Hui Xu
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
| | - Yi Cao
- Microbiology and Metabolic Engineering Key Laboratory of Sichuan Province, College of Life Science, Sichuan University, Chengdu, Sichuan Province 610065, PR China.
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13
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Wang M, Zhan Y, Zhao J, Li Z. Pretreatment of moso bamboo with p-toluenesulfonic acid for the recovery and depolymerization of hemicellulose. BIORESOURCE TECHNOLOGY 2023; 378:129006. [PMID: 37011848 DOI: 10.1016/j.biortech.2023.129006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 06/19/2023]
Abstract
Bamboo and its mechanical processing residues have broad prospects for high value-added utilization. In this research, p-toluenesulfonic acid was used for the pretreatment of bamboo to investigate the effects of extraction and depolymerization of hemicellulose. The response and behavior of changes of cell-wall chemical components were investigated after different solvent concentration, time, and temperature pretreatment. Results indicated that the maximum extraction yield of hemicellulose was 95.16 % with 5 % p-toluenesulfonic acid at 140 °C for 30 min. The depolymerized components of hemicellulose in the filtrate were mainly xylose and xylooligosaccharide, with xylobiose accounting for 30.77 %. The extraction of xylose from the filtrate reached a maximum of 90.16 % with 5 % p-toluenesulfonic acid at 150 °C for 30 min pretreatment. This research provided a potential strategy for the industrial production of xylose and xylooligosaccharide from bamboo and for the future conversion and utilization.
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Affiliation(s)
- Meixin Wang
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Yawei Zhan
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Jiayue Zhao
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China
| | - Zhiqiang Li
- International Centre for Bamboo and Rattan, Key Laboratory of National Forestry and Grassland Administration/Beijing for Bamboo & Rattan Science and Technology, Beijing 100102, China.
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14
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Long L, Wang W, Liu Z, Lin Y, Wang J, Lin Q, Ding S. Insights into the capability of the lignocellulolytic enzymes of Penicillium parvum 4-14 to saccharify corn bran after alkaline hydrogen peroxide pretreatment. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:79. [PMID: 37170321 PMCID: PMC10176746 DOI: 10.1186/s13068-023-02319-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/10/2023] [Indexed: 05/13/2023]
Abstract
BACKGROUND Corn bran is a major agro-industrial byproduct from corn starch processing. It contains abundant arabinoxylan that can be converted into value-added chemicals via biotechnology. Corn bran arabinoxylan (CBAX) is one of the most recalcitrant xylans for enzymatic degradation due to its particular heterogeneous nature. The present study aimed to investigate the capability of the filamentous fungus Penicillium parvum 4-14 to enzymatically saccharify CBAX and reveal the fungal carbohydrate-active enzyme (CAZyme) repertoire by genome sequencing and secretome analysis. RESULTS CBAX1 and CBAX2 with different branching degrees, together with corn bran residue (CBR) were generated from corn bran after alkaline hydrogen peroxide (AHP) pretreatment and graded ethanol precipitation. The protein blends E_CBAX1, E_CBAX2, and E_CBR were produced by the fungus grown on CBAX1, CBAX2, or CBR, respectively. Under the optimal conditions, E_CBAX1 released more than 80% xylose and arabinose from CBAX1 and CBAX2. Almost complete saccharification of the arabinoxylans was achieved by combining E_CBAX1 and a commercial enzyme cocktail Cellic®CTec3. Approximately 89% glucose, 64% xylose, and 64% arabinose were liberated from CBR by E_CBR. The combination of E_CBR with Cellic®CTec3 enhanced the saccharification of CBR, with conversion ratios of 97% for glucose, 81% for xylose, and 76% for arabinose. A total of 376 CAZymes including plentiful lignocellulolytic enzymes were predicted in P. parvum based on the fungal genomic sequence (25.8 Mb). Proteomic analysis indicated that the expression of CAZymes in P. parvum varied between CBAX1 and CBR, and the fungus produced complete cellulases, numerous hemicellulases, as well as high levels of glycosidases under the culture conditions. CONCLUSIONS This investigation disclosed the CAZyme repertoire of P. parvum at the genomic and proteomic levels, and elaborated on the promising potential of fungal lignocellulolytic enzymes upon saccharification of corn bran biomass after AHP pretreatment.
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Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China
| | - Wei Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Zhen Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Yuanxin Lin
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing, 211111, China
| | - Shaojun Ding
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing, 210037, China.
- Jiangsu Provincial Key Lab for the Chemistry and Utilization of Agro-Forest Biomass, Nanjing Forestry University, Nanjing, 210037, China.
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15
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Zhou P, Liu H, Meng X, Zuo H, Qi M, Guo L, Gao C, Song W, Wu J, Chen X, Chen W, Liu L. Engineered Artificial Membraneless Organelles in Saccharomyces cerevisiae To Enhance Chemical Production. Angew Chem Int Ed Engl 2023; 62:e202215778. [PMID: 36762978 DOI: 10.1002/anie.202215778] [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: 10/27/2022] [Revised: 02/09/2023] [Accepted: 02/10/2023] [Indexed: 02/11/2023]
Abstract
Microbial cell factories provide a green and sustainable opportunity to produce value-added products from renewable feedstock. However, the leakage of toxic or volatile intermediates decreases the efficiency of microbial cell factories. In this study, membraneless organelles (MLOs) were reconstructed in Saccharomyces cerevisiae by the disordered protein sequence A-IDPs. A regulation system was designed to spatiotemporally regulate the size and rigidity of MLOs. Manipulating the MLO size of strain ZP03-FM, the amounts of assimilated methanol and malate were increased by 162 % and 61 %, respectively. Furthermore, manipulating the MLO rigidity in strain ZP04-RB made acetyl-coA synthesis from oxidative glycolysis change to non-oxidative glycolysis; consequently, CO2 release decreased by 35 % and the n-butanol yield increased by 20 %. This artificial MLO provides a strategy for the co-localization of enzymes to channel C1 starting materials into value-added chemicals.
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Affiliation(s)
- Pei Zhou
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Hui Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Xin Meng
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Huiyun Zuo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Mengya Qi
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China
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16
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Chen S, Xu Z, Ding B, Zhang Y, Liu S, Cai C, Li M, Dale BE, Jin M. Big data mining, rational modification, and ancestral sequence reconstruction inferred multiple xylose isomerases for biorefinery. SCIENCE ADVANCES 2023; 9:eadd8835. [PMID: 36724227 PMCID: PMC9891696 DOI: 10.1126/sciadv.add8835] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 12/30/2022] [Indexed: 05/28/2023]
Abstract
The isomerization of xylose to xylulose is considered the most promising approach to initiate xylose bioconversion. Here, phylogeny-guided big data mining, rational modification, and ancestral sequence reconstruction strategies were implemented to explore new active xylose isomerases (XIs) for Saccharomyces cerevisiae. Significantly, 13 new active XIs for S. cerevisiae were mined or artificially created. Moreover, the importance of the amino-terminal fragment for maintaining basic XI activity was demonstrated. With the mined XIs, four efficient xylose-utilizing S. cerevisiae were constructed and evolved, among which the strain S. cerevisiae CRD5HS contributed to ethanol titers as high as 85.95 and 94.76 g/liter from pretreated corn stover and corn cob, respectively, without detoxifying or washing pretreated biomass. Potential genetic targets obtained from adaptive laboratory evolution were further analyzed by sequencing the high-performance strains. The combined XI mining methods described here provide practical references for mining other scarce and valuable enzymes.
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Affiliation(s)
- Sitong Chen
- 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
| | - Boning 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
| | - Yuwei Zhang
- 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
| | - Shuangmei Liu
- 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
| | - Chenggu Cai
- 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
| | - Muzi Li
- 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
| | - Bruce E. Dale
- Biomass Conversion Research Laboratory, Department of Chemical Engineering and Materials Science, Michigan State University, East Lansing, MI 48824, USA
- Great Lakes Bioenergy Research Centre (GLBRC), Michigan State University, East Lansing, MI, 48824 USA
| | - 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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17
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System analysis of Lipomyces starkeyi during growth on various plant-based sugars. Appl Microbiol Biotechnol 2022; 106:5629-5642. [PMID: 35906440 DOI: 10.1007/s00253-022-12084-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 07/14/2022] [Accepted: 07/16/2022] [Indexed: 11/02/2022]
Abstract
Oleaginous yeasts have received significant attention due to their substantial lipid storage capability. The accumulated lipids can be utilized directly or processed into various bioproducts and biofuels. Lipomyces starkeyi is an oleaginous yeast capable of using multiple plant-based sugars, such as glucose, xylose, and cellobiose. It is, however, a relatively unexplored yeast due to limited knowledge about its physiology. In this study, we have evaluated the growth of L. starkeyi on different sugars and performed transcriptomic and metabolomic analyses to understand the underlying mechanisms of sugar metabolism. Principal component analysis showed clear differences resulting from growth on different sugars. We have further reported various metabolic pathways activated during growth on these sugars. We also observed non-specific regulation in L. starkeyi and have updated the gene annotations for the NRRL Y-11557 strain. This analysis provides a foundation for understanding the metabolism of these plant-based sugars and potentially valuable information to guide the metabolic engineering of L. starkeyi to produce bioproducts and biofuels. KEY POINTS: • L. starkeyi metabolism reprograms for consumption of different plant-based sugars. • Non-specific regulation was observed during growth on cellobiose. • L. starkeyi secretes β-glucosidases for extracellular hydrolysis of cellobiose.
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18
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Wang J, Li Z, Wang W, Pang S, Yao Y, Yuan F, Wang H, Xu Z, Pan G, Liu Z, Chen Y, Fan K. Dynamic Control Strategy to Produce Riboflavin with Lignocellulose Hydrolysate in the Thermophile Geobacillus thermoglucosidasius. ACS Synth Biol 2022; 11:2163-2174. [PMID: 35677969 DOI: 10.1021/acssynbio.2c00087] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient utilization of both glucose and xylose, the two most abundant sugars in biomass hydrolysates, is one of the main objectives of biofermentation with lignocellulosic materials. The utilization of xylose is commonly inhibited by glucose, which is known as glucose catabolite repression (GCR). Here, we report a GCR-based dynamic control (GCR-DC) strategy aiming at better co-utilization of glucose and xylose, by decoupling the cell growth and biosynthesis of riboflavin as a product. Using the thermophilic strain Geobacillus thermoglucosidasius DSM 2542 as a host, we constructed additional riboflavin biosynthetic pathways that were activated by xylose but not glucose. The engineered strains showed a two-stage fermentation process. In the first stage, glucose was preferentially used for cell growth and no production of riboflavin was observed, while in the second stage where glucose was nearly depleted, xylose was effectively utilized for riboflavin biosynthesis. Using corn cob hydrolysate as a carbon source, the optimized riboflavin yields of strains DSM2542-DCall-MSS (full pathway dynamic control strategy) and DSM2542-DCrib (single-module dynamic control strategy) were 5.3- and 2.3-fold higher than that of the control strain DSM 2542 Rib-Gtg constitutively producing riboflavin, respectively. This GCR-DC strategy should also be applicable to the construction of cell factories that can efficiently use natural carbon sources with multiple sugar components for the production of high-value chemicals in future.
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Affiliation(s)
- Junyang Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zilong Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Weishan Wang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shen Pang
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yongpeng Yao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Fang Yuan
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Huizhuan Wang
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Zhen Xu
- Hebei Shengxue Dacheng Pharmaceutical Co. Ltd., Shijiazhuang 051430, Hebei, China
| | - Guohui Pan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihe Liu
- College of Life Science and Technology, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yihua Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiang Fan
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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19
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Integrated bioinformatics, modelling, and gene expression analysis of the putative pentose transporter from Candida tropicalis during xylose fermentation with and without glucose addition. Appl Microbiol Biotechnol 2022; 106:4587-4606. [PMID: 35708749 DOI: 10.1007/s00253-022-12005-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 05/18/2022] [Accepted: 05/27/2022] [Indexed: 11/02/2022]
Abstract
The transport of substrates across the cell membrane plays an essential role in nutrient assimilation by yeasts. The establishment of an efficient microbial cell factory, based on the maximum use of available carbon sources, can generate new technologies that allow the full use of lignocellulosic constituents. These technologies are of interest because they could promote the formation of added-value products with economic feasibility. In silico analyses were performed to investigate gene sequences capable of encoding xylose transporter proteins in the Candida tropicalis genome. The current study identified 11 putative transport proteins that have not yet been functionally characterized. A phylogenetic tree highlighted the potential C. tropicalis xylose-transporter proteins CtXUT1, CtXUT4, CtSTL1, CtSTL2, and CtGXT2, which were homologous to previously characterized and reported xylose transporters. Their expression was quantified through real-time qPCR at defined times, determined through a kinetic analysis of the microbial growth curve in the absence/presence of glucose supplemented with xylose as the main carbon source. The results indicated different mRNA expression levels for each gene. CtXUT1 mRNA expression was only found in the absence of glucose in the medium. Maximum CtXUT1 expression was observed in intervals of the highest xylose consumption (21 to 36 h) that corresponded to consumption rates of 1.02 and 0.82 g/L/h in the formulated media, with xylose as the only carbon source and with glucose addition. These observations indicate that CtXUT1 is an important xylose transporter in C. tropicalis. KEY POINTS: • Putative xylose transporter proteins were identified in Candida tropicalis; • The glucose concentration in the cultivation medium plays a key role in xylose transporter regulation; • The transporter gene CtXUT1 has an important role in xylose consumption by Candida tropicalis.
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20
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V Sreeharsha R, Sai Tejaswini G, Venkata Mohan S. Dual-stage biorefinery to convert spentwash hydrolysate into oleochemicals using Trichosporon cutaneum and Yarrowia lipolytica. BIORESOURCE TECHNOLOGY 2022; 354:127146. [PMID: 35421562 DOI: 10.1016/j.biortech.2022.127146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 06/14/2023]
Abstract
Yeast lipids from low-cost renewable feedstock are valuable resources for oleochemicals thus enabling circular chemistry. Current study focuses on lipid and volatile fatty acid (VFA) production through dual-stage fermentation of spentwash in a biorefinery framework with Trichosporon cutaneum (Tc) and Yarrowia lipolytica (Yl). During cell proliferation phase, Tc and Yl accumulated 2.9 and 2.5 g/L of dry biomass respectively in acid-hydrolysed spentwash (AHSW) and produced 16 and 5.5 g/L of total VFA respectively. Lipid yields (29.8%) and lipid titres (0.89 g/L) were higher in Tc/AHSW, when compared to Yl indicating the efficacy of Tc in spentwash bioremediation. Lipid accumulation was enhanced to 35% in Tc/AHSW, in presence of 0.05% NH4Cl due to oxidative stress of ammonium ions. Analysis of fatty acid composition revealed the presence of higher oleic acid, which is ideal for biodiesel production. The results demonstrate a sustainable biorefinery model for bioremediation of spentwash and its value addition.
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Affiliation(s)
- Rachapudi V Sreeharsha
- Bioengineering and Environmental Science Laboratory, Department of Energy and Environmental Engineering, CSIR- Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India; Department of Life Sciences, Chhatrapati Shahu Ji Maharaj University, Kanpur 208024, India
| | - G Sai Tejaswini
- Bioengineering and Environmental Science Laboratory, Department of Energy and Environmental Engineering, CSIR- Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India
| | - S Venkata Mohan
- Bioengineering and Environmental Science Laboratory, Department of Energy and Environmental Engineering, CSIR- Indian Institute of Chemical Technology (CSIR-IICT), Hyderabad 500 007, India.
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21
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Cheng M, Wijayawardene NN, Promputtha I, de Vries RP, Lan Y, Luo G, Wang M, Li Q, Guo X, Wang F, Liu Y, Kang Y. Potential Fungi Isolated From Anti-biodegradable Chinese Medicine Residue to Degrade Lignocellulose. Front Microbiol 2022; 13:877884. [PMID: 35620098 PMCID: PMC9127797 DOI: 10.3389/fmicb.2022.877884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 03/30/2022] [Indexed: 12/03/2022] Open
Abstract
Traditional Chinese medicine is one of the ancient medicines which is popular in Asian countries, among which the residue produced by the use of anti-biodegradables is endless, and causes significant adverse impacts on the environment. However, the high acidity of anti-biodegradable residues and some special biological activities make it difficult for microorganisms to survive, resulting in a very low degradation rate of lignocellulose in naturally stacked residues, which directly impedes the degradation of residues. We aimed to identify the fungal strains that efficiently biodegrade anti-biodegradable residue and see the possibility to improve the biodegradation of it and other agricultural wastes by co-cultivating these fungi. We isolated 302 fungal strains from anti-biodegradable residue to test hydrolysis ability. Finally, we found Coniochaeta sp., Fomitopsis sp., Nemania sp., Talaromyces sp., Phaeophlebiopsis sp. which inhabit the anti-biodegradable residues are capable of producing higher concentrations of extracellular enzymes. Synergistic fungal combinations (viz., Fomitopsis sp. + Phaeophlebiopsis sp.; Talaromyces sp. + Coniochaeta sp. + Fomitopsis sp.; Talaromyces sp. + Fomitopsis sp. + Piloderma sp. and Talaromyces sp. + Nemania sp. + Piloderma sp.) have better overall degradation effect on lignocellulose. Therefore, these fungi and their combinations have strong potential to be further developed for bioremediation and biological enzyme industrial production.
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Affiliation(s)
- Min Cheng
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Nalin N Wijayawardene
- Center for Yunnan Plateau Biological Resources Protection and Utilization, College of Biological Resource and Food Engineering, Qujing Normal University, Qujing, China.,Section of Genetics, Institute for Research and Development in Health and Social Care, Battaramulla, Sri Lanka
| | - Itthayakorn Promputtha
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Faculty of Science, Environmental Science Research Center, Chiang Mai University, Chiang Mai, Thailand
| | - Ronald P de Vries
- Fungal Physiology, Westerdijk Fungal Biodiversity Institute and Fungal Molecular Physiology, Utrecht University, Utrecht, Netherlands
| | - Yongzhe Lan
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Gang Luo
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Meizhu Wang
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Qirui Li
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Xinyao Guo
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Feng Wang
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Yanxia Liu
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
| | - Yingqian Kang
- Key Laboratory of Medical Microbiology and Parasitology and Key Laboratory of Environmental Pollution Monitoring and Disease Control, Ministry of Education, School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China.,Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, China
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22
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Smit AT, van Zomeren A, Dussan K, Riddell LA, Huijgen WJJ, Dijkstra JW, Bruijnincx PCA. Biomass Pre-Extraction as a Versatile Strategy to Improve Biorefinery Feedstock Flexibility, Sugar Yields, and Lignin Purity. ACS SUSTAINABLE CHEMISTRY & ENGINEERING 2022; 10:6012-6022. [PMID: 35571525 PMCID: PMC9092456 DOI: 10.1021/acssuschemeng.2c00838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 04/11/2022] [Indexed: 05/07/2023]
Abstract
Feedstock flexibility is highly advantageous for the viability of (solvent-based) biorefineries but comes with the considerable challenge of having to cope with the varying nature and typically high abundance of nonlignocellulose compounds in the most readily available residual biomass streams. Here, we demonstrate that mild aqueous acetone organosolv fractionation of various complex lignocellulosic raw materials (roadside grass, wheat straw, birch branches, almond shells, and a mixed stream thereof) is indeed negatively affected by these compounds and present a versatile strategy to mitigate this bottleneck in biorefining. A biomass pre-extraction approach has been developed to remove the detrimental extractives with (aqueous) acetone prior to fractionation. Pre-extraction removed organic extractives as well as minerals, primarily reducing acid dose requirements for fractionation and loss of hemicellulose sugars by degradation and improved the purity of the isolated lignin. We show how pre-extraction affects the effectiveness of the biorefinery process, including detailed mass balances for pretreatment, downstream processing, and product characteristics, and how it affects solvent and energy use with a first conceptual process design. The integrated biorefining approach allows for the improved compatibility of biorefineries with sustainable feedstock supply chains, enhanced biomass valorization (i.e., isolation of bioactive compounds from the extract), and more effective biomass processing with limited variation in product quality.
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Affiliation(s)
- Arjan T. Smit
- Unit
Energy Transition, Biobased & Circular Technologies Group, The Netherlands Organisation for Applied Scientific
Research (TNO), P.O. Box 1, 1755 ZG Petten, The Netherlands
- Organic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - André van Zomeren
- Unit
Energy Transition, Biobased & Circular Technologies Group, The Netherlands Organisation for Applied Scientific
Research (TNO), P.O. Box 1, 1755 ZG Petten, The Netherlands
| | - Karla Dussan
- Unit
Energy Transition, Biobased & Circular Technologies Group, The Netherlands Organisation for Applied Scientific
Research (TNO), P.O. Box 1, 1755 ZG Petten, The Netherlands
| | - Luke A. Riddell
- Organic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
| | - Wouter J. J. Huijgen
- Unit
Energy Transition, Biobased & Circular Technologies Group, The Netherlands Organisation for Applied Scientific
Research (TNO), P.O. Box 1, 1755 ZG Petten, The Netherlands
| | - Jan Wilco Dijkstra
- Unit
Energy Transition, Biobased & Circular Technologies Group, The Netherlands Organisation for Applied Scientific
Research (TNO), P.O. Box 1, 1755 ZG Petten, The Netherlands
| | - Pieter C. A. Bruijnincx
- Organic
Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584 CG Utrecht, The Netherlands
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23
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Deciphering Molecular Mechanism Underlying Self-Flocculation of Zymomonas mobilis for Robust Production. Appl Environ Microbiol 2022; 88:e0239821. [PMID: 35465724 DOI: 10.1128/aem.02398-21] [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: 11/20/2022] Open
Abstract
Zymomonas mobilis metabolizes sugar anaerobically through the Entner-Doudoroff pathway with less ATP generated for lower biomass accumulation to direct more sugar for product formation with improved yield, making it a suitable host to be engineered as microbial cell factories for producing bulk commodities with major costs from feedstock consumption. Self-flocculation of the bacterial cells presents many advantages, such as enhanced tolerance to environmental stresses, a prerequisite for achieving high product titers by using concentrated substrates. ZM401, a self-flocculating mutant developed from ZM4, the unicellular model strain of Z. mobilis, was employed in this work to explore the molecular mechanism underlying this self-flocculating phenotype. Comparative studies between ZM401 and ZM4 indicate that a frameshift caused by a single nucleotide deletion in the poly-T tract of ZMO1082 fused the putative gene with the open reading frame of ZMO1083, encoding the catalytic subunit BcsA of the bacterial cellulose synthase to catalyze cellulose biosynthesis. Furthermore, the single nucleotide polymorphism mutation in the open reading frame of ZMO1055, encoding a bifunctional GGDEF-EAL protein with apparent diguanylate cyclase/phosphodiesterase activities, resulted in the Ala526Val substitution, which consequently compromised in vivo specific phosphodiesterase activity for the degradation of cyclic diguanylic acid, leading to intracellular accumulation of the signaling molecule to activate cellulose biosynthesis. These discoveries are significant for engineering other unicellular strains from Z. mobilis with the self-flocculating phenotype for robust production. IMPORTANCE Stress tolerance is a prerequisite for microbial cell factories to be robust in production, particularly for biorefinery of lignocellulosic biomass to produce biofuels, bioenergy, and bio-based chemicals for sustainable socioeconomic development, since various inhibitors are released during the pretreatment to destroy the recalcitrant lignin-carbohydrate complex for sugar production through enzymatic hydrolysis of the cellulose component, and their detoxification is too costly for producing bulk commodities. Although tolerance to individual stress has been intensively studied, the progress seems less significant since microbial cells are inevitably suffering from multiple stresses simultaneously under production conditions. When self-flocculating, microbial cells are more tolerant to multiple stresses through the general stress response due to enhanced quorum sensing associated with the morphological change for physiological and metabolic advantages. Therefore, elucidation of the molecular mechanism underlying such a self-flocculating phenotype is significant for engineering microbial cells with the unique multicellular morphology through rational design to boost their production performance.
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24
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Songdech P, Intasit R, Yingchutrakul Y, Butkinaree C, Ratanakhanokchai K, Soontorngun N. Activation of cryptic xylose metabolism by a transcriptional activator Znf1 boosts up xylitol production in the engineered Saccharomyces cerevisiae lacking xylose suppressor BUD21 gene. Microb Cell Fact 2022; 21:32. [PMID: 35248023 PMCID: PMC8897867 DOI: 10.1186/s12934-022-01757-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/14/2022] [Indexed: 11/10/2022] Open
Abstract
Abstract
Background
Xylitol is a valuable pentose sugar alcohol, used in the food and pharmaceutical industries. Biotechnological xylitol production is currently attractive due to possible conversion from abundant and low-cost industrial wastes or agricultural lignocellulosic biomass. In this study, the transcription factor Znf1 was characterised as being responsible for the activation of cryptic xylose metabolism in a poor xylose-assimilating S. cerevisiae for xylitol production.
Results
The results suggest that the expression of several xylose-utilising enzyme genes, encoding xylose reductases for the reduction of xylose to xylitol was derepressed by xylose. Their expression and those of a pentose phosphate shunt and related pathways required for xylose utilisation were strongly activated by the transcription factor Znf1. Using an engineered S. cerevisiae strain overexpressing ZNF1 in the absence of the xylose suppressor bud21Δ, xylitol production was maximally by approximately 1200% to 12.14 g/L of xylitol, corresponding to 0.23 g/g xylose consumed, during 10% (w/v) xylose fermentation. Proteomic analysis supported the role of Znf1 and Bud21 in modulating levels of proteins associated with carbon metabolism, xylose utilisation, ribosomal protein synthesis, and others. Increased tolerance to lignocellulosic inhibitors and improved cell dry weight were also observed in this engineered bud21∆ + pLJ529-ZNF1 strain. A similar xylitol yield was achieved using fungus-pretreated rice straw hydrolysate as an eco-friendly and low-cost substrate.
Conclusions
Thus, we identified the key modulators of pentose sugar metabolism, namely the transcription factor Znf1 and the suppressor Bud21, for enhanced xylose utilisation, providing a potential application of a generally recognised as safe yeast in supporting the sugar industry and the sustainable lignocellulose-based bioeconomy.
Graphical Abstract
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25
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Krujatz F, Dani S, Windisch J, Emmermacher J, Hahn F, Mosshammer M, Murthy S, Steingroewer J, Walther T, Kühl M, Gelinsky M, Lode A. Think outside the box: 3D bioprinting concepts for biotechnological applications – recent developments and future perspectives. Biotechnol Adv 2022; 58:107930. [DOI: 10.1016/j.biotechadv.2022.107930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/17/2022] [Indexed: 12/14/2022]
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26
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Wang XH, Zhao C, Lu XY, Zong H, Zhuge B. Production of Caffeic Acid with Co-fermentation of Xylose and Glucose by Multi-modular Engineering in Candida glycerinogenes. ACS Synth Biol 2022; 11:900-908. [PMID: 35138824 DOI: 10.1021/acssynbio.1c00535] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Caffeic acid (CA), a natural phenolic compound, has important medicinal value and market potential. In this study, we report a metabolic engineering strategy for the biosynthesis of CA in Candida glycerinogenes using xylose and glucose. The availability of precursors was increased by optimization of the shikimate (SA) pathway and the aromatic amino acid pathway. Subsequently, the carbon flux into the SA pathway was maximized by introducing a xylose metabolic pathway and optimizing the xylose assimilation pathway. Eventually, a high yielding strain CG19 was obtained, which reached a yield of 4.61 mg/g CA from mixed sugar, which was 1.2-fold higher than that of glucose. The CA titer in the 5 L bioreactor reached 431.45 mg/L with a yield of 8.63 mg/g of mixed sugar. These promising results demonstrate the great advantages of mixed sugar over glucose for high-yield production of CA. This is the first report to produce CA in C. glycerinogenes with xylose and glucose as carbon sources, which developed a promising strategy for the efficient production of high-value aromatic compounds.
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Affiliation(s)
- Xi-Hui Wang
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Cui Zhao
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Xin-Yao Lu
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Hong Zong
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
| | - Bin Zhuge
- The Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- The Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi 214122, China
- Research Centre of Industrial Microbiology, School of Biotechnology, Jiangnan University, Wuxi 214122, China
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27
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Sun Y, Kong M, Li X, Li Q, Xue Q, Hou J, Jia Z, Lei Z, Xiao W, Shi S, Cao L. Metabolic and Evolutionary Engineering of Diploid Yeast for the Production of First- and Second-Generation Ethanol. Front Bioeng Biotechnol 2022; 9:835928. [PMID: 35155419 PMCID: PMC8831863 DOI: 10.3389/fbioe.2021.835928] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 12/31/2021] [Indexed: 11/13/2022] Open
Abstract
Despite a growing preference for second-generation (2G) ethanol in industries, its application is severely restricted owing to a major obstacle of developing a suitable yeast strain for fermentation using feedstock biomasses. In this study, a yeast strain, Saccharomyces cerevisiae A31Z, for 2G bioethanol production was developed from an industrial strain, Angel, using metabolic engineering by the incorporation of gene clusters involved in the xylose metabolism combined with adaptive evolution for evolving its anti-inhibitory properties. This strain outcompeted its ancestors in xylose utilization and subsequent ethanol production and manifested higher tolerance against common inhibitors from lignocellulosic hydrolysates, and also it lowered the production of glycerol by-product. Furthermore, A31Z outperformed in ethanol production using industrial hydrolysate from dried distillers grains with solubles and whole corn. Overall, this study provided a promising path for improving 2G bioethanol production in industries using S. cerevisiae.
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Affiliation(s)
- Yang Sun
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Science, Jilin Agricultural University, Changchun, China
| | - Meilin Kong
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Xiaowei Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Qi Li
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Qian Xue
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Junyan Hou
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zefang Jia
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Zhipeng Lei
- Key Laboratory of Straw Comprehensive Utilization and Black Soil Conservation, Ministry of Education, College of Life Science, Jilin Agricultural University, Changchun, China
| | - Wei Xiao
- College of Life Sciences, Capital Normal University, Beijing, China
| | - Shuobo Shi
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
- *Correspondence: Shuobo Shi, ; Limin Cao,
| | - Limin Cao
- College of Life Sciences, Capital Normal University, Beijing, China
- *Correspondence: Shuobo Shi, ; Limin Cao,
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28
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Oreoluwa Jokodola E, Narisetty V, Castro E, Durgapal S, Coulon F, Sindhu R, Binod P, Rajesh Banu J, Kumar G, Kumar V. Process optimisation for production and recovery of succinic acid using xylose-rich hydrolysates by Actinobacillus succinogenes. BIORESOURCE TECHNOLOGY 2022; 344:126224. [PMID: 34751156 PMCID: PMC8683751 DOI: 10.1016/j.biortech.2021.126224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 05/05/2023]
Abstract
Succinic acid (SA) is a top platform chemical obtainable from biomass. The current study evaluated the potential of Actinobacillus succinogenes for SA production using xylose-rich hemicellulosic fractions of two important lignocellulosic feedstocks, olive pits (OP) and sugarcane bagasse (SCB) and the results were compared with pure xylose. Initial experiments were conducted in shake flask followed by batch and fed-batch cultivation in bioreactor. Further separation of SA from the fermented broth was carried out by adapting direct crystallisation method. During fed-batch culture, maximum SA titers of 36.7, 33.6, and 28.7 g/L was achieved on pure xylose, OP and SCB hydrolysates, respectively, with same conversion yield of 0.27 g/g. The recovery yield of SA accumulated on pure xylose, OP and SCB hydrolysates was 79.1, 76.5, and 75.2%, respectively. The results obtained are of substantial value and pave the way for development of sustainable SA biomanufacturing in an integrated biorefinery.
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Affiliation(s)
| | - Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Eulogio Castro
- Department of Chemical, Environmental and Materials Engineering, Universidad de Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Sumit Durgapal
- Department of Pharmaceutical Sciences, Kumaun University, Bhimtal, Nainital 263136, Uttarakhand, India
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Raveendran Sindhu
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram 695 019, Kerala, India
| | - J Rajesh Banu
- Department of Life Sciences, Central University of Tamil Nadu, Neelakudi, Thiruvarur, Tamil Nadu 610005, India
| | - Gopalakrishnan Kumar
- School of Civil and Environmental Engineering, Yonsei University, Seoul 03722, Republic of Korea
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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29
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Narisetty V, Cox R, Bommareddy R, Agrawal D, Ahmad E, Pant KK, Chandel AK, Bhatia SK, Kumar D, Binod P, Gupta VK, Kumar V. Valorisation of xylose to renewable fuels and chemicals, an essential step in augmenting the commercial viability of lignocellulosic biorefineries. SUSTAINABLE ENERGY & FUELS 2021; 6:29-65. [PMID: 35028420 PMCID: PMC8691124 DOI: 10.1039/d1se00927c] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/25/2021] [Indexed: 05/30/2023]
Abstract
Biologists and engineers are making tremendous efforts in contributing to a sustainable and green society. To that end, there is growing interest in waste management and valorisation. Lignocellulosic biomass (LCB) is the most abundant material on the earth and an inevitable waste predominantly originating from agricultural residues, forest biomass and municipal solid waste streams. LCB serves as the renewable feedstock for clean and sustainable processes and products with low carbon emission. Cellulose and hemicellulose constitute the polymeric structure of LCB, which on depolymerisation liberates oligomeric or monomeric glucose and xylose, respectively. The preferential utilization of glucose and/or absence of the xylose metabolic pathway in microbial systems cause xylose valorization to be alienated and abandoned, a major bottleneck in the commercial viability of LCB-based biorefineries. Xylose is the second most abundant sugar in LCB, but a non-conventional industrial substrate unlike glucose. The current review seeks to summarize the recent developments in the biological conversion of xylose into a myriad of sustainable products and associated challenges. The review discusses the microbiology, genetics, and biochemistry of xylose metabolism with hurdles requiring debottlenecking for efficient xylose assimilation. It further describes the product formation by microbial cell factories which can assimilate xylose naturally and rewiring of metabolic networks to ameliorate xylose-based bioproduction in native as well as non-native strains. The review also includes a case study that provides an argument on a suitable pathway for optimal cell growth and succinic acid (SA) production from xylose through elementary flux mode analysis. Finally, a product portfolio from xylose bioconversion has been evaluated along with significant developments made through enzyme, metabolic and process engineering approaches, to maximize the product titers and yield, eventually empowering LCB-based biorefineries. Towards the end, the review is wrapped up with current challenges, concluding remarks, and prospects with an argument for intense future research into xylose-based biorefineries.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
| | - Rylan Cox
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- School of Aerospace, Transport and Manufacturing, Cranfield University Cranfield MK43 0AL UK
| | - Rajesh Bommareddy
- Department of Applied Sciences, Northumbria University Newcastle upon Tyne NE1 8ST UK
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR- Indian Institute of Petroleum Mohkampur Dehradun 248005 India
| | - Ejaz Ahmad
- Department of Chemical Engineering, Indian Institute of Technology (ISM) Dhanbad 826004 India
| | - Kamal Kumar Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
| | - Anuj Kumar Chandel
- Department of Biotechnology, Engineering School of Lorena (EEL), University of São Paulo Lorena 12.602.810 Brazil
| | - Shashi Kant Bhatia
- Department of Biological Engineering, College of Engineering, Konkuk University Seoul 05029 Republic of Korea
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences Solan 173229 Himachal Pradesh India
| | - Parmeswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST) Thiruvananthapuram 695 019 Kerala India
| | | | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University Cranfield MK43 0AL UK +44 (0)1234754786
- Department of Chemical Engineering, Indian Institute of Technology Delhi New Delhi 110016 India
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30
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Tan YS, Wang L, Wang YY, He QE, Liu ZH, Zhu Z, Song K, Li BZ, Yuan YJ. Protein acetylation regulates xylose metabolism during adaptation of Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:241. [PMID: 34920742 PMCID: PMC8684234 DOI: 10.1186/s13068-021-02090-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 12/04/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND As the second most abundant polysaccharide in nature, hemicellulose can be degraded to xylose as the feedstock for bioconversion to fuels and chemicals. To enhance xylose conversion, the engineered Saccharomyces cerevisiae with xylose metabolic pathway is usually adapted with xylose as the carbon source in the laboratory. However, the mechanism under the adaptation phenomena of the engineered strain is still unclear. RESULTS In this study, xylose-utilizing S. cerevisiae was constructed and used for the adaptation study. It was found that xylose consumption rate increased 1.24-fold in the second incubation of the yYST12 strain in synthetic complete-xylose medium compared with the first incubation. The study figured out that it was observed at the single-cell level that the stagnation time for xylose utilization was reduced after adaptation with xylose medium in the microfluidic device. Such transient memory of xylose metabolism after adaptation with xylose medium, named "xylose consumption memory", was observed in the strains with both xylose isomerase pathway and xylose reductase and xylitol dehydrogenase pathways. In further, the proteomic acetylation of the strains before and after adaptation was investigated, and it was revealed that H4K5 was one of the most differential acetylation sites related to xylose consumption memory of engineered S. cerevisiae. We tested 8 genes encoding acetylase or deacetylase, and it was found that the knockout of the GCN5 and HPA2 encoding acetylases enhanced the xylose consumption memory. CONCLUSIONS The behavior of xylose consumption memory in engineered S. cerevisiae can be successfully induced with xylose in the adaptation. H4K5Ac and two genes of GCN5 and HPA2 are related to xylose consumption memory of engineered S. cerevisiae during adaptation. This study provides valuable insights into the xylose adaptation of engineered S. cerevisiae.
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Affiliation(s)
- Yong-Shui Tan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Li Wang
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Ying Wang
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Qi-En He
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhi-Hua Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Zhen Zhu
- Key Laboratory of MEMS of Ministry of Education, Southeast University, Nanjing, 210096 People’s Republic of China
| | - Kai Song
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Bing-Zhi Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
| | - Ying-Jin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 People’s Republic of China
- Synthetic Biology Research Platform, Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), Tianjin University, Tianjin, 300072 People’s Republic of China
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Long L, Sun L, Liu Z, Lin Q, Wang J, Ding S. Functional characterization of a GH62 family α-L-arabinofuranosidase from Eupenicillium parvum suitable for monosaccharification of corncob arabinoxylan in combination with key enzymes. Enzyme Microb Technol 2021; 154:109965. [PMID: 34933174 DOI: 10.1016/j.enzmictec.2021.109965] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/20/2021] [Accepted: 12/06/2021] [Indexed: 11/30/2022]
Abstract
Corncob rich in arabinoxylan is an important raw material widely used in bio-refinery. Complete saccharification of arabinoxylan depends on the synergism of different enzymes including α-L-arabinofuranosidase (ABF). This study aimed to investigate the functional characteristics of a new ABF EpABF62A belonging to glycoside hydrolase (GH) 62 family from the fungus Eupenicillium parvum, and to explore its potential in the saccharification of corncob arabinoxylan. The recombinant EpABF62A showed high activity against wheat arabinoxylan and rye arabinoxylan, with the optimal temperature of 55 °C and pH of 4.5. The protein contains an N-terminal cellulose-binding domain family 1 (CBM_1) domain, and displayed a 59.5% absorption rate to phosphoric acid swollen cellulose. Regioselectivity analysis indicated that the enzyme selectively removed α-1,2 or α-1,3 linked arabinofuranosyl residues on mono-substituted xylose residues on arabinoxylan. Corncob arabinoxylans (CAX1 or CAX2) with different (low or high) branching degrees were extracted from the raw material by alkaline hydrogen peroxide pretreatment and graded ethanol precipitation. Single EpABF62A removed 69.5% or 67.1% arabinose from CAX1 or CAX2, respectively. EpABF62A combined with a GH10 xylanase, a GH43 β-D-xylosidase and a GH67 α-glucuronidase released 75.0% or 64.5% xylose from CAX1 or CAX2, respectively. The addition of the four hemicellulases enhanced the saccharification the solid fraction of the pretreated corncob by the commercial cellulase Cellic® CTec2, and the conversion ratios of glucose, xylose and arabinose were up to 94.0%, 91.8% and 82.6%, respectively.
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Affiliation(s)
- Liangkun Long
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing 210037, China
| | - Lu Sun
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Zhen Liu
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Qunying Lin
- Nanjing Institute for the Comprehensive Utilization of Wild Plants, Nanjing 211111, China
| | - Jing Wang
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China
| | - Shaojun Ding
- Jiangsu Co-Innovation Center for Efficient Processing and Utilization of Forest Resources, College of Chemical Engineering, Nanjing Forestry University, Nanjing 210037, China; Jiangsu Key Lab for the Chemistry & Utilization of Agricultural and Forest Biomass, Nanjing 210037, China.
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32
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Lou J, Wang J, Yang Y, Yang Q, LI R, Hu M, He Q, Du J, Wang X, Li M, Yang S. Development and characterization of efficient xylose utilization strains of Zymomonas mobilis. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:231. [PMID: 34863266 PMCID: PMC8645129 DOI: 10.1186/s13068-021-02082-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/19/2021] [Indexed: 05/15/2023]
Abstract
BACKGROUND Efficient use of glucose and xylose is a key for the economic production of lignocellulosic biofuels and biochemicals, and different recombinant strains have been constructed for xylose utilization including those using Zymomonas mobilis as the host. However, the xylose utilization efficiency still needs to be improved. In this work, the strategy of combining metabolic engineering and adaptive laboratory evolution (ALE) was employed to develop recombinant Z. mobilis strains that can utilize xylose efficiently at high concentrations, and NGS-based genome resequencing and RNA-Seq transcriptomics were performed for strains evolved after serial transfers in different media to understand the impact of xylose and differences among strains with different xylose-utilization capabilities at molecular level. RESULTS Heterologous genes encoding xylose isomerase and xylulokinase were evaluated, which were then introduced into xylose-utilizing strain Z. mobilis 8b to enhance its capacity of xylose utilization. The results demonstrated that the effect of three xylose isomerases on xylose utilization was different, and the increase of copy number of xylose metabolism genes can improve xylose utilization. Among various recombinant strains constructed, the xylose utilization capacity of the recombinant strain 8b-RsXI-xylB was the best, which was further improved through continuous adaption with 38 transfers over 100 days in 50 g/L xylose media. The fermentation performances of the parental strain 8b, the evolved 8b-S38 strain with the best xylose utilization capability, and the intermediate strain 8b-S8 in different media were compared, and the results showed that only 8b-S38 could completely consume xylose at 50 g/L and 100 g/L concentrations. In addition, the xylose consumption rate of 8b-S38 was faster than that of 8b at different xylose concentrations from 50 to 150 g/L, and the ethanol yield increased by 16 ~ 40%, respectively. The results of the mixed-sugar fermentation also demonstrated that 8b-S38 had a higher xylose consumption rate than 8b, and its maximum ethanol productivity was 1.2 ~ 1.4 times higher than that of 8b and 8b-S8. Whole-genome resequencing identified three common genetic changes in 8b-S38 compared with 8b and 8b-S8. RNA-Seq study demonstrated that the expression levels of genes encoding chaperone proteins, ATP-dependent proteases, phage shock proteins, ribosomal proteins, flagellar operons, and transcriptional regulators were significantly increased in xylose media in 8b-S38. The up-regulated expression of these genes may therefore contribute to the efficient xylose utilization of 8b-S38 by maintaining the normal cell metabolism and growth, repairing cellular damages, and rebalancing cellular energy to help cells resist the stressful environment. CONCLUSIONS This study provides gene candidates to improve xylose utilization, and the result of expressing an extra copy of xylose isomerase and xylulokinase improved xylose utilization also provides a direction for efficient xylose-utilization strain development in other microorganisms. In addition, this study demonstrated the necessity to combine metabolic engineering and ALE for industrial strain development. The recombinant strain 8b-S38 can efficiently metabolize xylose for ethanol fermentation at high xylose concentrations as well as in mixed sugars of glucose and xylose, which could be further developed as the microbial biocatalyst for the production of lignocellulosic biofuels and biochemicals.
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Affiliation(s)
- Jiyun Lou
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Jingwen Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Qing Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Runxia LI
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Mimi Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Qiaoning He
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Jun Du
- China Biotech Fermentation Industry Association, Beijing, 100833 China
| | - Xia Wang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Mian Li
- Zhejiang Huakang Pharmaceutical Co., Ltd., Kaihua County, Zhejiang, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan, 430062 China
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Narisetty V, Castro E, Durgapal S, Coulon F, Jacob S, Kumar D, Kumar Awasthi M, Kishore Pant K, Parameswaran B, Kumar V. High level xylitol production by Pichia fermentans using non-detoxified xylose-rich sugarcane bagasse and olive pits hydrolysates. BIORESOURCE TECHNOLOGY 2021; 342:126005. [PMID: 34592613 PMCID: PMC8651628 DOI: 10.1016/j.biortech.2021.126005] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/16/2021] [Accepted: 09/19/2021] [Indexed: 05/22/2023]
Abstract
Hemicellulosic sugars, the overlooked fraction of lignocellulosic residues can serve as potential and cost-effective raw material that can be exploited for xylitol production. Xylitol is a top platform chemical with applications in food and pharmaceutical industries. Sugarcane bagasse (SCB) and olive pits (OP) are the major waste streams from sugar and olive oil industries, respectively. The current study evaluated the potential of Pichia fermentans for manufacturing of xylitol from SCB and OP hydrolysates through co-fermentation strategy. The highest xylitol accumulation was noticed with a glucose and xylose ratio of 1:10 followed by feeding with xylose alone. The fed-batch cultivation using pure xylose, SCB, and OP hydrolysates, resulted in xylitol accumulation of 102.5, 86.6 and 71.9 g/L with conversion yield of 0.78, 0.75 and 0.74 g/g, respectively. The non-pathogenic behaviour and ability to accumulate high xylitol levels from agro-industrial residues demonstrates the potential of P. fermentans as microbial cell factory.
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Affiliation(s)
- Vivek Narisetty
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Eulogio Castro
- Department of Chemical, Environmental and Materials Engineering, Universidad de Jaén, Campus Las Lagunillas, 23071 Jaén, Spain
| | - Sumit Durgapal
- Department of Pharmaceutical Sciences, Kumaun University, Bhimtal, Nainital 263136, Uttarakhand, India
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK
| | - Samuel Jacob
- Department of Biotechnology, School of Bioengineering, College of Engineering and Technology, Faculty of Engineering and Technology, SRM Institute of Science and Technology, SRM Nagar, Kattankulathur, Chengalpattu District, Tamil Nadu, 603203, India
| | - Dinesh Kumar
- School of Bioengineering & Food Technology, Shoolini University of Biotechnology and Management Sciences, Solan 173229, Himachal Pradesh, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province 712100, China
| | - Kamal Kishore Pant
- Department of Chemical Engineering, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Binod Parameswaran
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology (CSIR-NIIST), Thiruvananthapuram, Kerala 695019, India
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield MK43 0AL, UK.
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Zhang Q, Zeng W, Xu S, Zhou J. Metabolism and strategies for enhanced supply of acetyl-CoA in Saccharomyces cerevisiae. BIORESOURCE TECHNOLOGY 2021; 342:125978. [PMID: 34598073 DOI: 10.1016/j.biortech.2021.125978] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Acetyl-CoA is a kind of important cofactor that is involved in many metabolic pathways. It serves as the precursor for many interesting commercial products, such as terpenes, flavonoids and anthraquinones. However, the insufficient supply of acetyl-CoA limits biosynthesis of its derived compounds in the intracellular. In this review, we outlined metabolic pathways involved in the catabolism and anabolism of acetyl-CoA, as well as some important derived products. We examined several strategies for the enhanced supply of acetyl-CoA, and provided insight into pathways that generate acetyl-CoA to balance metabolism, which can be harnessed to improve the titer, yield and productivities of interesting products in Saccharomyces cerevisiae and other eukaryotic microorganisms. We believe that peroxisomal fatty acid β-oxidation could be an attractive strategy for enhancing the supply of acetyl-CoA.
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Affiliation(s)
- Qian Zhang
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Weizhu Zeng
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Sha Xu
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Jingwen Zhou
- National Engineering Laboratory for Cereal Fermentation Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Science Center for Future Foods, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China; Jiangsu Provisional Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China.
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35
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Lee YG, Kim C, Sun L, Lee TH, Jin YS. Selective production of retinol by engineered Saccharomyces cerevisiae through the expression of retinol dehydrogenase. Biotechnol Bioeng 2021; 119:399-410. [PMID: 34850377 DOI: 10.1002/bit.28004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 11/23/2021] [Accepted: 11/27/2021] [Indexed: 11/06/2022]
Abstract
Retinol is a fat-soluble vitamin A that is widely used in the food and pharmaceutical industries. Currently, retinol is commercially produced by chemical synthesis. Microbial production of retinol has been alternatively explored but restricted to a mixture of retinoids including retinol, retinal, and retinoic acid. Thus, we introduced heterologous retinol dehydrogenase into retinoids mixture-producing Saccharomyces cerevisiae for the selective production of retinol using xylose. Expression of human RDH10 and Escherichia coli ybbO led to increase in retinol production, but retinal remained as a major product. In contrast, S. cerevisiae harboring human RDH12 produced retinol selectively with negligible production of retinal. The resulting strain (SR8A-RDH12) produced retinol only. However, more glycerol was accumulated due to intracellular redox imbalance. Therefore, Lactococcus lactis noxE coding for H2 O-forming NADH oxidase was additionally introduced to resolve the redox imbalance. The resulting strain produced 52% less glycerol and more retinol with a 30% higher yield than a parental strain. As the produced retinol was not stable, we examined culture and storage conditions including temperature, light, and antioxidants for the optimal production of retinol. In conclusion, we achieved selective production of retinol efficiently from xylose by introducing human RDH12 and NADH oxidase into S. cerevisiae.
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Affiliation(s)
- Ye-Gi Lee
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Chanwoo Kim
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Tae-Hee Lee
- Solus BioTech, Yongin, Gyeonggi-do, South Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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Kuschmierz L, Shen L, Bräsen C, Snoep J, Siebers B. Workflows for optimization of enzyme cascades and whole cell catalysis based on enzyme kinetic characterization and pathway modelling. Curr Opin Biotechnol 2021; 74:55-60. [PMID: 34794111 DOI: 10.1016/j.copbio.2021.10.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 10/22/2021] [Indexed: 12/18/2022]
Abstract
To move towards a circular bioeconomy, sustainable strategies for the utilization of renewable, non-food biomass wastes such as lignocellulose, are needed. To this end, an efficient bioconversion of d-xylose - after d-glucose the most abundant sugar in lignocellulose - is highly desirable. Most standard organisms used in biotechnology are limited in metabolising d-xylose, and also in vitro enzymatic strategies for its conversion have not been very successful. We herein discuss that bioconversion of d-xylose is mostly hampered by missing knowledge on the kinetic properties of the enzymes involved in its metabolism. We propose a combination of classical enzyme characterizations and mathematical modelling approaches as a workflow for rational, model-based design to optimize enzyme cascades and/or whole cell biocatalysts for efficient d-xylose metabolism.
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Affiliation(s)
- Laura Kuschmierz
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Lu Shen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Christopher Bräsen
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany
| | - Jacky Snoep
- Department of Biochemistry, University of Stellenbosch, Private Bag X1, Matieland, 7602, South Africa; Department of Molecular Cell Physiology, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
| | - Bettina Siebers
- Molecular Enzyme Technology and Biochemistry (MEB), Environmental Microbiology and Biotechnology (EMB), Centre for Water and Environmental Research (CWE), University of Duisburg-Essen, Universitätsstraße 5, 45141, Essen, Germany.
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37
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Fast filtration with a vacuum manifold system as a rapid and robust metabolome sampling method for Saccharomyces cerevisiae. Process Biochem 2021. [DOI: 10.1016/j.procbio.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Xylitol Production by Candida Species from Hydrolysates of Agricultural Residues and Grasses. FERMENTATION-BASEL 2021. [DOI: 10.3390/fermentation7040243] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Xylitol is an industrially important chemical due to its commercial applications. The use of xylitol as a sweetener as well as its utilization in biomedical applications has made it a high value specialty chemical. Although several species of yeast synthesize xylitol, this review focusses on the species of the genus Candida. The importance of the enzyme xylitol reductase present in Candida species as it relates to their ability to synthesize xylitol was examined. Another focus of this work was to review prior studies examining the ability of the Candida species to synthesize xylitol effectively from hydrolysates of agricultural residues and grasses. An advantage of utilizing such a hydrolysate as a substrate for yeast xylitol production would be decreasing the overall cost of synthesizing xylitol. The intent of this review was to learn if such hydrolysates could substitute for xylose as a substrate for the yeast when producing xylitol. In addition, a comparison of xylitol production by Candida species should indicate which hydrolysate of agricultural residues and grasses would be the best substrate for xylitol production. From studies analyzing previous hydrolysates of agricultural residues and grasses, it was concluded that a hydrolysate of sugarcane bagasse supported the highest level of xylitol by Candida species, although corncob hydrolysates also supported significant yeast xylitol production. It was also concluded that fewer studies examined yeast xylitol production on hydrolysates of grasses and that further research on grasses may provide hydrolysates with a higher xylose content, which could support greater yeast xylitol production.
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Miyamoto RY, de Melo RR, de Mesquita Sampaio IL, de Sousa AS, Morais ER, Sargo CR, Zanphorlin LM. Paradigm shift in xylose isomerase usage: a novel scenario with distinct applications. Crit Rev Biotechnol 2021; 42:693-712. [PMID: 34641740 DOI: 10.1080/07388551.2021.1962241] [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: 10/20/2022]
Abstract
Isomerases are enzymes that induce physical changes in a molecule without affecting the original molecular formula. Among this class of enzymes, xylose isomerases (XIs) are the most studied to date, partly due to their extensive application in industrial processes to produce high-fructose corn sirups. In recent years, the need for sustainable initiatives has triggered efforts to improve the biobased economy through the use of renewable raw materials. In this context, D-xylose usage is crucial as it is the second-most abundant sugar in nature. The application of XIs in biotransforming xylose, enabling downstream metabolism in several microorganisms, is a smart strategy for ensuring a low-carbon footprint and producing several value-added biochemicals with broad industrial applications such as in the food, cosmetics, pharmaceutical, and polymer industries. Considering recent advancements that have expanded the range of applications of XIs, this review provides a comprehensive and concise overview of XIs, from their primary sources to the biochemical and structural features that influence their mechanisms of action. This comprehensive review may help address the challenges involved in XI applications in different industries and facilitate the exploitation of xylose bioprocesses.
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Affiliation(s)
- Renan Yuji Miyamoto
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Pharmaceutical Sciences (FCF), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Ricardo Rodrigues de Melo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Isabelle Lobo de Mesquita Sampaio
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Amanda Silva de Sousa
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Edvaldo Rodrigo Morais
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.,Faculty of Food Engineering (FEA), State University of Campinas (UNICAMP), Campinas, Brazil
| | - Cintia Regina Sargo
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Leticia Maria Zanphorlin
- Brazilian Biorenewables National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
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Simultaneous Production of Bioethanol and Bioelectricity in a Membrane-Less Single-Chambered Yeast Fuel Cell by Saccharomyces cerevisiae and Pichia fermentans. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2021. [DOI: 10.1007/s13369-021-06248-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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41
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Sun T, Yu Y, Wang K, Ledesma-Amaro R, Ji XJ. Engineering Yarrowia lipolytica to produce fuels and chemicals from xylose: A review. BIORESOURCE TECHNOLOGY 2021; 337:125484. [PMID: 34320765 DOI: 10.1016/j.biortech.2021.125484] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/26/2021] [Accepted: 06/28/2021] [Indexed: 06/13/2023]
Abstract
The production of chemicals and fuels from lignocellulosic biomass has great potential industrial applications due to its economic feasibility and environmental attractiveness. However, the utilized microorganisms must be able to use all the sugars present in lignocellulosic hydrolysates, especially xylose, the second most plentiful monosaccharide on earth. Yarrowia lipolytica is a good candidate for producing various valuable products from biomass, but this yeast is unable to catabolize xylose efficiently. The development of metabolic engineering facilitated the application of Y. lipolytica as a platform for the bioconversion of xylose into various value-added products. Here, we reviewed the research progress on natural xylose-utilization pathways and their reconstruction in Y. lipolytica. The progress and emerging trends in metabolic engineering of Y. lipolytica for producing chemicals and fuels are further introduced. Finally, challenges and future perspectives of using lignocellulosic hydrolysate as substrate for Y. lipolytica are discussed.
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Affiliation(s)
- Tao Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Yizi Yu
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Kaifeng Wang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, UK
| | - Xiao-Jun Ji
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing 211816, People's Republic of China.
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42
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Complete and efficient conversion of plant cell wall hemicellulose into high-value bioproducts by engineered yeast. Nat Commun 2021; 12:4975. [PMID: 34404791 PMCID: PMC8371099 DOI: 10.1038/s41467-021-25241-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 07/27/2021] [Indexed: 11/26/2022] Open
Abstract
Plant cell wall hydrolysates contain not only sugars but also substantial amounts of acetate, a fermentation inhibitor that hinders bioconversion of lignocellulose. Despite the toxic and non-consumable nature of acetate during glucose metabolism, we demonstrate that acetate can be rapidly co-consumed with xylose by engineered Saccharomyces cerevisiae. The co-consumption leads to a metabolic re-configuration that boosts the synthesis of acetyl-CoA derived bioproducts, including triacetic acid lactone (TAL) and vitamin A, in engineered strains. Notably, by co-feeding xylose and acetate, an enginered strain produces 23.91 g/L TAL with a productivity of 0.29 g/L/h in bioreactor fermentation. This strain also completely converts a hemicellulose hydrolysate of switchgrass into 3.55 g/L TAL. These findings establish a versatile strategy that not only transforms an inhibitor into a valuable substrate but also expands the capacity of acetyl-CoA supply in S. cerevisiae for efficient bioconversion of cellulosic biomass. Cellulosic hydrolysates contain substantial amounts of acetate, which is toxic to fermenting microorganisms. Here, the authors engineer Baker’s yeast to co-consume xylose and acetate for triacetic acid lactone production from a hemicellulose hydrolysate of switchgrass.
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43
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Kang NK, Lee JW, Ort DR, Jin YS. L-malic acid production from xylose by engineered Saccharomyces cerevisiae. Biotechnol J 2021; 17:e2000431. [PMID: 34390209 DOI: 10.1002/biot.202000431] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 07/14/2021] [Accepted: 07/28/2021] [Indexed: 11/07/2022]
Abstract
L-malic acid is widely used in the food, chemical, and pharmaceutical industries. Here, we report on production of malic acid from xylose, the second most abundant sugar in lignocellulosic hydrolysates, by engineered Saccharomyces cerevisiae. To enable malic acid production in a xylose-assimilating S. cerevisiae, we overexpressed PYC1 and PYC2, coding for pyruvate carboxylases, a truncated MDH3 coding for malate dehydrogenase, and SpMAE1, coding for a Schizosaccharomyces pombe malate transporter. Additionally, both the ethanol and glycerol-producing pathways were blocked to enhance malic acid production. The resulting strain produced malic acid from both glucose and xylose, but it produced much higher titers of malic acid from xylose than glucose. Interestingly, the engineered strain had higher malic acid yield from lower concentrations (10 g/L) of xylose, with no ethanol production, than from higher xylose concentrations (20 g/L and 40 g/L). As such, a fed-batch culture maintaining xylose concentrations at low levels was conducted and 61.2 g/L of malic acid was produced, with a productivity of 0.32 g/L∙h. These results represent successful engineering of S. cerevisiae for the production of malic acid from xylose, confirming that that xylose offers the efficient production of various biofuels and chemicals by engineered S. cerevisiae. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Nam Kyu Kang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Jae Won Lee
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Donald R Ort
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Departments of Plant Biology and Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, USA.,Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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44
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Ning P, Yang G, Hu L, Sun J, Shi L, Zhou Y, Wang Z, Yang J. Recent advances in the valorization of plant biomass. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:102. [PMID: 33892780 PMCID: PMC8063360 DOI: 10.1186/s13068-021-01949-3] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 04/07/2021] [Indexed: 05/28/2023]
Abstract
Plant biomass is a highly abundant renewable resource that can be converted into several types of high-value-added products, including chemicals, biofuels and advanced materials. In the last few decades, an increasing number of biomass species and processing techniques have been developed to enhance the application of plant biomass followed by the industrial application of some of the products, during which varied technologies have been successfully developed. In this review, we summarize the different sources of plant biomass, the evolving technologies for treating it, and the various products derived from plant biomass. Moreover, the challenges inherent in the valorization of plant biomass used in high-value-added products are also discussed. Overall, with the increased use of plant biomass, the development of treatment technologies, and the solution of the challenges raised during plant biomass valorization, the value-added products derived from plant biomass will become greater in number and more valuable.
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Affiliation(s)
- Peng Ning
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Guofeng Yang
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China
| | - Lihong Hu
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Jingxin Sun
- College of Food Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Lina Shi
- Agricultural Integrated Service Center of Zhuyouguan, Longkou, Yantai, China
| | - Yonghong Zhou
- Institute of Chemical Industry of Forest Products, Key Laboratory of Biomass Energy and Material, CAF, Nanjing, China
| | - Zhaobao Wang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
| | - Jianming Yang
- Energy-rich Compounds Production by Photosynthetic Carbon Fixation Research Center, Shandong Key Lab of Applied Mycology, Qingdao Agricultural University, No. 700 Changcheng Road, Chengyang District, Qingdao, 266109, China.
- College of Life Sciences, Qingdao Agricultural University, Qingdao, China.
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Hernández-Fernández M, Cordero-Bueso G, Ruiz-Muñoz M, Cantoral JM. Culturable Yeasts as Biofertilizers and Biopesticides for a Sustainable Agriculture: A Comprehensive Review. PLANTS (BASEL, SWITZERLAND) 2021; 10:822. [PMID: 33919047 PMCID: PMC8142971 DOI: 10.3390/plants10050822] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 04/07/2021] [Accepted: 04/19/2021] [Indexed: 01/18/2023]
Abstract
The extensive use of synthetic fertilizers and pesticides has negative consequences in terms of soil microbial biodiversity and environmental contamination. Faced with this growing concern, a proposed alternative agricultural method is the use of microorganisms as biofertilizers. Many works have been focused on bacteria, but the limited literature on yeasts and their potential ability to safely promote plant growth is gaining particular attention in recent years. Thus, the objective of this review is to highlight the application of yeasts as biological agents in different sectors of sustainable agricultural practices through direct or indirect mechanisms of action. Direct mechanisms include the ability of yeasts to provide soluble nutrients to plants, produce organic acids and phytohormones (indole-3-acetic acid). Indirect mechanisms involve the ability for yeasts to act as biocontrol agents through their high antifungal activity and lower insecticidal and herbicidal activity, and as soil bioremediating agents. They also act as protective agents against extreme environmental factors by activating defense mechanisms. It is evident that all the aspects that yeasts offer could be useful in the creation of quality biofertilizers and biopesticides. Hence, extensive research on yeasts could be promising and potentially provide an environmentally friendly solution to the increased crop production that will be required with a growing population.
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Affiliation(s)
| | - Gustavo Cordero-Bueso
- Laboratory of Microbiology, Department Biomedicine, Biotechnology and Public Health, University of Cádiz, Puerto Real, 11510 Cádiz, Spain; (M.H.-F.); (M.R.-M.); (J.M.C.)
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46
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Recent insights, applications and prospects of xylose reductase: a futuristic enzyme for xylitol production. Eur Food Res Technol 2021. [DOI: 10.1007/s00217-020-03674-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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47
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Zha J, Yuwen M, Qian W, Wu X. Yeast-Based Biosynthesis of Natural Products From Xylose. Front Bioeng Biotechnol 2021; 9:634919. [PMID: 33614617 PMCID: PMC7886706 DOI: 10.3389/fbioe.2021.634919] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Accepted: 01/11/2021] [Indexed: 12/28/2022] Open
Abstract
Xylose is the second most abundant sugar in lignocellulosic hydrolysates. Transformation of xylose into valuable chemicals, such as plant natural products, is a feasible and sustainable route to industrializing biorefinery of biomass materials. Yeast strains, including Saccharomyces cerevisiae, Scheffersomyces stipitis, and Yarrowia lipolytica, display some paramount advantages in expressing heterologous enzymes and pathways from various sources and have been engineered extensively to produce natural products. In this review, we summarize the advances in the development of metabolically engineered yeasts to produce natural products from xylose, including aromatics, terpenoids, and flavonoids. The state-of-the-art metabolic engineering strategies and representative examples are reviewed. Future challenges and perspectives are also discussed on yeast engineering for commercial production of natural products using xylose as feedstocks.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
| | | | | | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an, China
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Nitzsche R, Köchermann J, Gröngröft A, Kraume M. Nanofiltration of Organosolv Hemicellulose Hydrolyzate: Influence of Hydrothermal Pretreatment and Membrane Characteristics on Filtration Performance and Fouling. Ind Eng Chem Res 2021. [DOI: 10.1021/acs.iecr.0c03256] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Roy Nitzsche
- DBFZ—Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Jakob Köchermann
- DBFZ—Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Arne Gröngröft
- DBFZ—Deutsches Biomasseforschungszentrum gemeinnützige GmbH, Torgauer Straße 116, 04347 Leipzig, Germany
| | - Matthias Kraume
- Chair of Chemical and Process Engineering, Technische Universität Berlin, Fraunhoferstraße 33-36, 10587 Berlin, Germany
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Prabhu AA, Bosakornranut E, Amraoui Y, Agrawal D, Coulon F, Vivekanand V, Thakur VK, Kumar V. Enhanced xylitol production using non-detoxified xylose rich pre-hydrolysate from sugarcane bagasse by newly isolated Pichia fermentans. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:209. [PMID: 33375948 PMCID: PMC7772924 DOI: 10.1186/s13068-020-01845-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 11/28/2020] [Indexed: 05/09/2023]
Abstract
BACKGROUND Integrated management of hemicellulosic fraction and its economical transformation to value-added products is the key driver towards sustainable lignocellulosic biorefineries. In this aspect, microbial cell factories are harnessed for the sustainable production of commercially viable biochemicals by valorising C5 and C6 sugars generated from agro-industrial waste. However, in the terrestrial ecosystem, microbial systems can efficiently consume glucose. On the contrary, pentose sugars are less preferred carbon source as most of the microbes lack metabolic pathway for their utilization. The effective utilization of both pentose and hexose sugars is key for economical biorefinery. RESULTS Bioprospecting the food waste and selective enrichment on xylose-rich medium led to screening and isolation of yeast which was phylogenetically identified as Pichia fermentans. The newly isolated xylose assimilating yeast was explored for xylitol production. The wild type strain robustly grew on xylose and produced xylitol with > 40% conversion yield. Chemical mutagenesis of isolated yeast with ethyl methanesulphonate (EMS) yielded seven mutants. The mutant obtained after 15 min EMS exposure, exhibited best xylose bioconversion efficiency. This mutant under shake flask conditions produced maximum xylitol titer and yield of 34.0 g/L and 0.68 g/g, respectively. However, under the same conditions, the control wild type strain accumulated 27.0 g/L xylitol with a conversion yield of 0.45 g/g. Improved performance of the mutant was attributed to 34.6% activity enhancement in xylose reductase with simultaneous reduction of xylitol dehydrogenase activity by 22.9%. Later, the culture medium was optimized using statistical design and validated at shake flask and bioreactor level. Bioreactor studies affirmed the competence of the mutant for xylitol accumulation. The xylitol titer and yield obtained with pure xylose were 98.9 g/L and 0.67 g/g, respectively. In comparison, xylitol produced using non-detoxified xylose rich pre-hydrolysate from sugarcane bagasse was 79.0 g/L with an overall yield of 0.54 g/g. CONCLUSION This study demonstrates the potential of newly isolated P. fermentans in successfully valorising the hemicellulosic fraction for the sustainable xylitol production.
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Affiliation(s)
- Ashish A Prabhu
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Ekkarin Bosakornranut
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Yassin Amraoui
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Deepti Agrawal
- Biochemistry and Biotechnology Area, Material Resource Efficiency Division, CSIR-Indian Institute of Petroleum, Mohkampur, Dehradun, 248005, India
| | - Frederic Coulon
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK
| | - Vivekanand Vivekanand
- Centre for Energy and Environment, Malaviya National Institute of Technology, Jaipur, Rajasthan, 302017, India
| | - Vijay Kumar Thakur
- Biorefining and Advanced Materials Research Centre, Scotland's Rural College (SRUC), Edinburgh, UK
| | - Vinod Kumar
- School of Water, Energy and Environment, Cranfield University, Cranfield, MK43 0AL, UK.
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Zhang Y, Nielsen J, Liu Z. Yeast based biorefineries for oleochemical production. Curr Opin Biotechnol 2020; 67:26-34. [PMID: 33360103 DOI: 10.1016/j.copbio.2020.11.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Revised: 10/04/2020] [Accepted: 11/22/2020] [Indexed: 12/17/2022]
Abstract
Biosynthesis of oleochemicals enables sustainable production of natural and unnatural alternatives from renewable feedstocks. Yeast cell factories have been extensively studied and engineered to produce a variety of oleochemicals, focusing on both central carbon metabolism and lipid metabolism. Here, we review recent progress towards oleochemical synthesis in yeast based biorefineries, as well as utilization of alternative renewable feedstocks, such as xylose and l-arabinose. We also review recent studies of C1 compound utilization or co-utilization and discuss how these studies can lead to third generation yeast based biorefineries for oleochemical production.
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Affiliation(s)
- Yiming Zhang
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China
| | - Jens Nielsen
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China; Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden; BioInnovation Institute, Ole Maaløes Vej 3, DK2200 Copenhagen N, Denmark.
| | - Zihe Liu
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, China.
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