1
|
Zhang ZX, Xu YS, Li ZJ, Xu LW, Ma W, Li YF, Guo DS, Sun XM, Huang H. Turning waste into treasure: A new direction for low-cost production of lipid chemicals from Thraustochytrids. Biotechnol Adv 2024; 73:108354. [PMID: 38588906 DOI: 10.1016/j.biotechadv.2024.108354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 03/29/2024] [Accepted: 04/03/2024] [Indexed: 04/10/2024]
Abstract
Thraustochytrids are marine microorganisms known for their fast growth and ability to store lipids, making them useful for producing polyunsaturated fatty acids (PUFAs), biodiesel, squalene, and carotenoids. However, the high cost of production, mainly due to expensive fermentation components, limits their wider use. A significant challenge in this context is the need to balance production costs with the value of the end products. This review focuses on integrating the efficient utilization of waste with Thraustochytrids fermentation, including the economic substitution of carbon sources, nitrogen sources, and fermentation water. This approach aligns with the 3Rs principles (reduction, recycling, and reuse). Furthermore, it emphasizes the role of Thraustochytrids in converting waste into lipid chemicals and promoting sustainable circular production models. The aim of this review is to emphasize the value of Thraustochytrids in converting waste into treasure, providing precise cost reduction strategies for future commercial production.
Collapse
Affiliation(s)
- Zi-Xu Zhang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Ying-Shuang Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Zi-Jia Li
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Lu-Wei Xu
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Wang Ma
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| | - Ying-Feng Li
- Zhihe Biotechnology (Changzhou) Co. Ltd, 1 Hanshan Road, Xuejia Town, Xinbei District, Changzhou, People's Republic of China
| | - Dong-Sheng Guo
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China; Zhihe Biotechnology (Changzhou) Co. Ltd, 1 Hanshan Road, Xuejia Town, Xinbei District, Changzhou, People's Republic of China
| | - Xiao-Man Sun
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China.
| | - He Huang
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, People's Republic of China
| |
Collapse
|
2
|
Qiu Y, Liu W, Wu M, Bao H, Sun X, Dou Q, Jia H, Liu W, Shen Y. Construction of an alternative NADPH regeneration pathway improves ethanol production in Saccharomyces cerevisiae with xylose metabolic pathway. Synth Syst Biotechnol 2024; 9:269-276. [PMID: 38469586 PMCID: PMC10926300 DOI: 10.1016/j.synbio.2024.02.004] [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: 12/19/2023] [Revised: 02/05/2024] [Accepted: 02/19/2024] [Indexed: 03/13/2024] Open
Abstract
Full conversion of glucose and xylose from lignocellulosic hydrolysates is required for obtaining a high ethanol yield. However, glucose and xylose share flux in the pentose phosphate pathway (PPP) and glycolysis pathway (EMP), with glucose having a competitive advantage in the shared metabolic pathways. In this work, we knocked down ZWF1 to preclude glucose from entering the PPP. This reduced the [NADPH] level and disturbed growth on both glucose or xylose, confirming that the oxidative PPP, which begins with Zwf1p and ultimately leads to CO2 production, is the primary source of NADPH in both glucose and xylose. Upon glucose depletion, gluconeogenesis is necessary to generate glucose-6-phosphate, the substrate of Zwf1p. We re-established the NADPH regeneration pathway by replacing the endogenous NAD+-dependent glyceraldehyde-3-phosphate dehydrogenase (GAPDH) gene TDH3 with heterogenous NADP + -GAPDH genes GDH, gapB, and GDP1. Among the resulting strains, the strain BZP1 (zwf1Δ, tdh3::GDP1) exhibited a similar xylose consumption rate before glucose depletion, but a 1.6-fold increased xylose consumption rate following glucose depletion compared to the original strain BSGX001, and the ethanol yield for total consumed sugars of BZP1 was 13.5% higher than BSGX001. This suggested that using the EMP instead of PPP to generate NADPH reduces the wasteful metabolic cycle and excess CO2 release from oxidative PPP. Furthermore, we used a copper-repressing promoter to modulate the expression of ZWF1 and optimize the timing of turning off the ZWF1, therefore, to determine the competitive equilibrium between glucose-xylose co-metabolism. This strategy allowed fast growth in the early stage of fermentation and low waste in the following stages of fermentation.
Collapse
Affiliation(s)
- Yali Qiu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Wei Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Meiling Wu
- Advanced Medical Research Institute, Shandong University, Jinan, 250012, China
| | - Haodong Bao
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xinhua Sun
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Qin Dou
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Hongying Jia
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao, 266237, China
| |
Collapse
|
3
|
Das S, Chandukishore T, Ulaganathan N, Dhodduraj K, Gorantla SS, Chandna T, Gupta LK, Sahoo A, Atheena PV, Raval R, Anjana PA, DasuVeeranki V, Prabhu AA. Sustainable biorefinery approach by utilizing xylose fraction of lignocellulosic biomass. Int J Biol Macromol 2024; 266:131290. [PMID: 38569993 DOI: 10.1016/j.ijbiomac.2024.131290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/20/2024] [Accepted: 03/29/2024] [Indexed: 04/05/2024]
Abstract
Lignocellulosic biomass (LCB) has been a lucrative feedstock for developing biochemical products due to its rich organic content, low carbon footprint and abundant accessibility. The recalcitrant nature of this feedstock is a foremost bottleneck. It needs suitable pretreatment techniques to achieve a high yield of sugar fractions such as glucose and xylose with low inhibitory components. Cellulosic sugars are commonly used for the bio-manufacturing process, and the xylose sugar, which is predominant in the hemicellulosic fraction, is rejected as most cell factories lack the five‑carbon metabolic pathways. In the present review, more emphasis was placed on the efficient pretreatment techniques developed for disintegrating LCB and enhancing xylose sugars. Further, the transformation of the xylose to value-added products through chemo-catalytic routes was highlighted. In addition, the review also recapitulates the sustainable production of biochemicals by native xylose assimilating microbes and engineering the metabolic pathway to ameliorate biomanufacturing using xylose as the sole carbon source. Overall, this review will give an edge on the bioprocessing of microbial metabolism for the efficient utilization of xylose in the LCB.
Collapse
Affiliation(s)
- Satwika Das
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - T Chandukishore
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Nivedhitha Ulaganathan
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Kawinharsun Dhodduraj
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Sai Susmita Gorantla
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Teena Chandna
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Laxmi Kumari Gupta
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - P V Atheena
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - Ritu Raval
- Department of Biotechnology, Manipal Institute of Technology, Manipal 576104, Karnataka, India
| | - P A Anjana
- Department of Chemical Engineering, National Institute of Technology Warangal, Warangal 506004, Telangana, India
| | - Venkata DasuVeeranki
- Biochemical Engineering Laboratory, Department of Bioscience and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ashish A Prabhu
- Bioprocess Development Research Laboratory, Department of Biotechnology, National Institute of Technology Warangal, Warangal 506004, Telangana, India.
| |
Collapse
|
4
|
Li F, Bai W, Zhang Y, Zhang Z, Zhang D, Shen N, Yuan J, Zhao G, Wang X. Construction of an economical xylose-utilizing Saccharomyces cerevisiae and its ethanol fermentation. FEMS Yeast Res 2024; 24:foae001. [PMID: 38268490 PMCID: PMC10855017 DOI: 10.1093/femsyr/foae001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 01/03/2024] [Accepted: 01/23/2024] [Indexed: 01/26/2024] Open
Abstract
Traditional industrial Saccharomyces cerevisiae could not metabolize xylose due to the lack of a specific enzyme system for the reaction from xylose to xylulose. This study aims to metabolically remould industrial S. cerevisiae for the purpose of utilizing both glucose and xylose with high efficiency. Heterologous gene xylA from Piromyces and homologous genes related to xylose utilization were selected to construct expression cassettes and integrated into genome. The engineered strain was domesticated with industrial material under optimizing conditions subsequently to further improve xylose utilization rates. The resulting S. cerevisiae strain ABX0928-0630 exhibits a rapid growth rate and possesses near 100% xylose utilization efficiency to produce ethanol with industrial material. Pilot-scale fermentation indicated the predominant feature of ABX0928-0630 for industrial application, with ethanol yield of 0.48 g/g sugars after 48 hours and volumetric xylose consumption rate of 0.87 g/l/h during the first 24 hours. Transcriptome analysis during the modification and domestication process revealed a significant increase in the expression level of pathways associated with sugar metabolism and sugar sensing. Meanwhile, genes related to glycerol lipid metabolism exhibited a pattern of initial increase followed by a subsequent decrease, providing a valuable reference for the construction of efficient xylose-fermenting strains.
Collapse
Affiliation(s)
- Fan Li
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Wenxin Bai
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Yuan Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Zijian Zhang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
| | - Deguo Zhang
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
- COFCO Biotechnology Co., Ltd., No. 1, Zhongliang Avenue, Yuhui District, Bengbu, Anhui 233010, China
| | - Naidong Shen
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Jingwei Yuan
- COFCO Biochemical and Bioenergy (Zhaodong) Co., Ltd., No. 24, Zhaolan Road, Zhaodong City, Suihua, Heilongjiang 151100, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Guomiao Zhao
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| | - Xiaoyan Wang
- Nutrition and Health Research Institute, COFCO Corporation, No. 4 Road, South District, Beiqijia Town, Changping District, Beijing 102209, China
- COFCO Corporation, COFCO Fortune Plaza, No.8, Chao Yang Men South St., Chao Yang District, Beijing 100020, China
| |
Collapse
|
5
|
Deng Z, Mu Y, Chen Z, Yan L, Ju X, Li L. Construction of a xylose metabolic pathway in Trichosporonoides oedocephalis ATCC 16958 for the production of erythritol and xylitol. Biotechnol Lett 2023; 45:1529-1539. [PMID: 37831286 DOI: 10.1007/s10529-023-03428-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 05/18/2023] [Accepted: 07/15/2023] [Indexed: 10/14/2023]
Abstract
PURPOSE Erythritol is a valuable compound as sweetener and chemical material however cannot be fermented from the abundant substrate xylose. METHODS The strain Trichosporonoides oedocephalis ATCC 16958 was employed to produce polyols including xylitol and erythritol by metabolic engineering approaches. RESULTS The introduction of a substrate-specific ribose-5-phosphate isomerase endowed T. oedocephalis with xylose-assimilation activity to produce xylitol, and eliminated glycerol production simultaneously. A more value-added product, erythritol was produced by further introducing a homologous xylulose kinase. The carbon flux was redirected from xylitol to erythritol by adding high osmotic pressure. The production of erythritol was improved to 46.5 g/L in flasks by fermentation adjustment, and the process was scaled up in a 5-L fermentor, with a 40 g/L erythritol production after 120 h, and a time-space yield of 0.56 g/L/h. CONCLUSION This study demonstrated the potential of T. oedocephalis in the synthesis of multiple useful products from xylose.
Collapse
Affiliation(s)
- Zhou Deng
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China
| | - Yinghui Mu
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China
| | - Zhi Chen
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China
| | - Lishi Yan
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China
| | - Xin Ju
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China.
| | - Liangzhi Li
- School of Chemistry and Life Sciences, Suzhou University of Science and Technology, No. 99 Xuefu Rd., Huqiu District, Suzhou, 215009, Jiangsu, People's Republic of China.
| |
Collapse
|
6
|
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.
Collapse
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.
| |
Collapse
|
7
|
Vargas BDO, dos Santos JR, Pereira GAG, de Mello FDSB. An atlas of rational genetic engineering strategies for improved xylose metabolism in Saccharomyces cerevisiae. PeerJ 2023; 11:e16340. [PMID: 38047029 PMCID: PMC10691383 DOI: 10.7717/peerj.16340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 10/03/2023] [Indexed: 12/05/2023] Open
Abstract
Xylose is the second most abundant carbohydrate in nature, mostly present in lignocellulosic material, and representing an appealing feedstock for molecule manufacturing through biotechnological routes. However, Saccharomyces cerevisiae-a microbial cell widely used industrially for ethanol production-is unable to assimilate this sugar. Hence, in a world with raising environmental awareness, the efficient fermentation of pentoses is a crucial bottleneck to producing biofuels from renewable biomass resources. In this context, advances in the genetic mapping of S. cerevisiae have contributed to noteworthy progress in the understanding of xylose metabolism in yeast, as well as the identification of gene targets that enable the development of tailored strains for cellulosic ethanol production. Accordingly, this review focuses on the main strategies employed to understand the network of genes that are directly or indirectly related to this phenotype, and their respective contributions to xylose consumption in S. cerevisiae, especially for ethanol production. Altogether, the information in this work summarizes the most recent and relevant results from scientific investigations that endowed S. cerevisiae with an outstanding capability for commercial ethanol production from xylose.
Collapse
Affiliation(s)
- Beatriz de Oliveira Vargas
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Jade Ribeiro dos Santos
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | - Gonçalo Amarante Guimarães Pereira
- Department of Genetics, Evolution, Microbiology, and Immunology, Institute of Biology, Universidade Estadual de Campinas, Campinas, Brazil
| | | |
Collapse
|
8
|
Saxena A, Hussain A, Parveen F, Ashfaque M. Current status of metabolic engineering of microorganisms for bioethanol production by effective utilization of pentose sugars of lignocellulosic biomass. Microbiol Res 2023; 276:127478. [PMID: 37625339 DOI: 10.1016/j.micres.2023.127478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 08/01/2023] [Accepted: 08/09/2023] [Indexed: 08/27/2023]
Abstract
Lignocellulosic biomass, consisting of homo- and heteropolymeric sugars, acts as a substrate for the generation of valuable biochemicals and biomaterials. The readily available hexoses are easily utilized by microbes due to the presence of transporters and native metabolic pathways. But, utilization of pentose sugar viz., xylose and arabinose are still challenging due to several reasons including (i) the absence of the particular native pathways and transporters, (ii) the presence of inhibitors, and (iii) lower uptake of pentose sugars. These challenges can be overcome by manipulating metabolic pathways/glycosidic enzymes cascade by using genetic engineering tools involving inverse-metabolic engineering, ex-vivo isomerization, Adaptive Laboratory Evolution, Directed Metabolic Engineering, etc. Metabolic engineering of bacteria and fungi for the utilization of pentose sugars for bioethanol production is the focus area of research in the current decade. This review outlines current approaches to biofuel development and strategies involved in the metabolic engineering of different microbes that can uptake pentose for bioethanol production.
Collapse
Affiliation(s)
- Ayush Saxena
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Akhtar Hussain
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Fouziya Parveen
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| | - Mohammad Ashfaque
- Lignocellulose & Biofuel Laboratory, Department of Biosciences, Integral University, Lucknow 226026, Uttar Pradesh, India.
| |
Collapse
|
9
|
Sullivan SF, Shetty A, Bharadwaj T, Krishna N, Trivedi VD, Endalur Gopinarayanan V, Chappell TC, Sellers DM, Pravin Kumar R, Nair NU. Towards universal synthetic heterotrophy using a metabolic coordinator. Metab Eng 2023; 79:14-26. [PMID: 37406763 PMCID: PMC10529783 DOI: 10.1016/j.ymben.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 06/13/2023] [Accepted: 07/03/2023] [Indexed: 07/07/2023]
Abstract
Engineering the utilization of non-native substrates, or synthetic heterotrophy, in proven industrial microbes such as Saccharomyces cerevisiae represents an opportunity to valorize plentiful and renewable sources of carbon and energy as inputs to bioprocesses. We previously demonstrated that activation of the galactose (GAL) regulon, a regulatory structure used by this yeast to coordinate substrate utilization with biomass formation during growth on galactose, during growth on the non-native substrate xylose results in a vastly altered gene expression profile and faster growth compared with constitutive overexpression of the same heterologous catabolic pathway. However, this effort involved the creation of a xylose-inducible variant of Gal3p (Gal3pSyn4.1), the sensor protein of the GAL regulon, preventing this semi-synthetic regulon approach from being easily adapted to additional non-native substrates. Here, we report the construction of a variant Gal3pMC (metabolic coordinator) that exhibits robust GAL regulon activation in the presence of structurally diverse substrates and recapitulates the dynamics of the native system. Multiple molecular modeling studies suggest that Gal3pMC occupies conformational states corresponding to galactose-bound Gal3p in an inducer-independent manner. Using Gal3pMC to test a regulon approach to the assimilation of the non-native lignocellulosic sugars xylose, arabinose, and cellobiose yields higher growth rates and final cell densities when compared with a constitutive overexpression of the same set of catabolic genes. The subsequent demonstration of rapid and complete co-utilization of all three non-native substrates suggests that Gal3pMC-mediated dynamic global gene expression changes by GAL regulon activation may be universally beneficial for engineering synthetic heterotrophy.
Collapse
Affiliation(s)
- Sean F Sullivan
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Anuj Shetty
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Tharun Bharadwaj
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Naveen Krishna
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Vikas D Trivedi
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA; Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Todd C Chappell
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - Daniel M Sellers
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA
| | - R Pravin Kumar
- Kcat Enzymatic Private Limited, Bengaluru, Karnataka, 560005, India
| | - Nikhil U Nair
- Department of Chemical & Biological Engineering, Tufts University, Medford, MA, 02155, USA.
| |
Collapse
|
10
|
Kim GB, Choi SY, Cho IJ, Ahn DH, Lee SY. Metabolic engineering for sustainability and health. Trends Biotechnol 2023; 41:425-451. [PMID: 36635195 DOI: 10.1016/j.tibtech.2022.12.014] [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: 11/09/2022] [Revised: 12/17/2022] [Accepted: 12/21/2022] [Indexed: 01/12/2023]
Abstract
Bio-based production of chemicals and materials has attracted much attention due to the urgent need to establish sustainability and enhance human health. Metabolic engineering (ME) allows purposeful modification of cellular metabolic, regulatory, and signaling networks to achieve enhanced production of desired chemicals and degradation of environmentally harmful chemicals. ME has significantly progressed over the past 30 years through further integration of the strategies of synthetic biology, systems biology, evolutionary engineering, and data science aided by artificial intelligence. Here we review the field of ME from its emergence to the current state-of-the-art, highlighting its contribution to sustainable production of chemicals, health, and the environment through representative examples. Future challenges of ME and perspectives are also discussed.
Collapse
Affiliation(s)
- Gi Bae Kim
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - So Young Choi
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - In Jin Cho
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Da-Hee Ahn
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Sang Yup Lee
- Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 four), Institute for the BioCentury, Korea Advanced Institute of Science and Technology (KAIST), 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; Systems Metabolic Engineering and Systems Healthcare Cross-Generation Collaborative Laboratory, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea; BioProcess Engineering Research Center and BioInformatics Research Center, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea.
| |
Collapse
|
11
|
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.
Collapse
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
| |
Collapse
|
12
|
Madhavan A, Arun KB, Sindhu R, Nair BG, Pandey A, Awasthi MK, Szakacs G, Binod P. Design and genome engineering of microbial cell factories for efficient conversion of lignocellulose to fuel. BIORESOURCE TECHNOLOGY 2023; 370:128555. [PMID: 36586428 DOI: 10.1016/j.biortech.2022.128555] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/26/2022] [Accepted: 12/27/2022] [Indexed: 06/17/2023]
Abstract
The gradually increasing need for fossil fuels demands renewable biofuel substitutes. This has fascinated an increasing investigation to design innovative energy fuels that have comparable Physico-chemical and combustion characteristics with fossil-derived fuels. The efficient microbes for bioenergy synthesis desire the proficiency to consume a large quantity of carbon substrate, transfer various carbohydrates through efficient metabolic pathways, capability to withstand inhibitory components and other degradation compounds, and improve metabolic fluxes to synthesize target compounds. Metabolically engineered microbes could be an efficient methodology for synthesizing biofuel from cellulosic biomass by cautiously manipulating enzymes and metabolic pathways. This review offers a comprehensive perspective on the trends and advances in metabolic and genetic engineering technologies for advanced biofuel synthesis by applying various heterologous hosts. Probable technologies include enzyme engineering, heterologous expression of multiple genes, CRISPR-Cas technologies for genome editing, and cell surface display.
Collapse
Affiliation(s)
- Aravind Madhavan
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India.
| | - K B Arun
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru 560029, Karnataka, India
| | - Raveendran Sindhu
- Department of Food Technology, TKM Institute of Technology, Kollam 689 122, India
| | - Bipin G Nair
- School of Biotechnology, Amrita Vishwa Vidyapeetham, Amritapuri, Kollam 690525 Kerala, India
| | - Ashok Pandey
- Center for Innovation and Translational Research, CSIR-Indian Institute of Toxicology Research, Lucknow 226 001, India; Sustainability Cluster, School of Engineering, University of Petroleum and Energy Studies, Dehradun 248007, Uttarkhand, India; Centre for Energy and Environmental Sustainability, Lucknow 226 029, Uttar Pradesh, India
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A & F University, Yangling, Shaanxi 712 100, China
| | - George Szakacs
- Budapest University of Technology and Economics, Department of Applied Biotechnology and Food Science, 1111 Budapest, Szent Gellert ter 4, Hungary
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary Science and Technology, Trivandrum 695 019, India
| |
Collapse
|
13
|
Coimbra L, Malan K, Fagúndez A, Guigou M, Lareo C, Fernández B, Pratto M, Batista S. Fermentation of D-xylose to Ethanol by Saccharomyces cerevisiae CAT-1 Recombinant Strains. BIOENERGY RESEARCH 2023; 16:1001-1012. [PMID: 36248719 PMCID: PMC9540035 DOI: 10.1007/s12155-022-10514-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/27/2022] [Indexed: 05/09/2023]
Abstract
Ethanol production by the D-xylose fermentation of lignocellulosic biomass would augment environmental sustainability by increasing the yield of biofuel obtained per cultivated area. A set of recombinant strains derived from the industrial strain Saccharomyces cerevisiae CAT-1 was developed for this purpose. First, two recombinant strains were obtained by the chromosomal insertion of genes involved in the assimilation and transport of D-xylose (Gal2-N376F). Strain CAT-1-XRT was developed with heterologous genes for D-xylose metabolism from the oxo-reductive pathway of Scheffersomyces stipitis (XYL1-K270R, XYL2); and strain CAT-1-XIT, with D-xylose isomerase (xylA gene, XI) from Streptomyces coelicolor. Moreover, both recombinant strains contained extra copies of homologous genes for xylulose kinase (XK) and transaldolase (TAL1). Furthermore, plasmid (pRS42K::XI) was constructed with xylA from Piromyces sp. transferred to CAT-1, CAT-1-XRT, and CAT-1-XIT, followed by an evolution protocol. After 10 subcultures, CAT-1-XIT (pRS42K::XI) consumed 74% of D-xylose, producing 12.6 g/L ethanol (0.31 g ethanol/g D-xylose). The results of this study show that CAT-1-XIT (pRS42K::XI) is a promising recombinant strain for the efficient utilization of D-xylose to produce ethanol from lignocellulosic materials.
Collapse
Affiliation(s)
- Lucía Coimbra
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Karen Malan
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Alejandra Fagúndez
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Mairan Guigou
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Claudia Lareo
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Belén Fernández
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| | - Martín Pratto
- Departamento de Bioingeniería, Facultad de Ingeniería, Instituto de Ingeniería Química, Universidad de La República. Julio Herrera Y Reissig 565, 11300 Montevideo, CP Uruguay
| | - Silvia Batista
- Laboratorio de Microbiología Molecular, Departamento BIOGEM, Instituto de Investigaciones Biológicas Clemente Estable, Avenida Italia 3318, 11600 Montevideo, CP Uruguay
| |
Collapse
|
14
|
Identification of Mutations Responsible for Improved Xylose Utilization in an Adapted Xylose Isomerase Expressing Saccharomyces cerevisiae Strain. FERMENTATION 2022. [DOI: 10.3390/fermentation8120669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Economic conversion of biomass to biofuels and chemicals requires efficient and complete utilization of xylose. Saccharomyces cerevisiae strains engineered for xylose utilization are still considerably limited in their overall ability to metabolize xylose. In this study, we identified causative mutations resulting in improved xylose fermentation of an adapted S. cerevisiae strain expressing codon-optimized xylose isomerase and xylulokinase genes from the rumen bacterium Prevotella ruminicola. Genome sequencing identified single-nucleotide polymorphisms in seven open reading frames. Tetrad analysis showed that mutations in both PBS2 and PHO13 genes were required for increased xylose utilization. Single deletion of either PBS2 or PHO13 did not improve xylose utilization in strains expressing the xylose isomerase pathway. Saccharomyces can also be engineered for xylose metabolism using the xylose reductase/xylitol dehydrogenase genes from Scheffersomyces stipitis. In strains expressing the xylose reductase pathway, single deletion of PHO13 did show a significant increase xylose utilization, and further improvement in growth and fermentation was seen when PBS2 was also deleted. These findings will extend the understanding of metabolic limitations for xylose utilization in S. cerevisiae as well as understanding of how they differ among strains engineered with two different xylose utilization pathways.
Collapse
|
15
|
Wang LR, Zhang ZX, Nong FT, Li J, Huang PW, Ma W, Zhao QY, Sun XM. Engineering the xylose metabolism in Schizochytrium sp. to improve the utilization of lignocellulose. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:114. [PMID: 36289497 PMCID: PMC9609267 DOI: 10.1186/s13068-022-02215-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 10/15/2022] [Indexed: 11/05/2022]
Abstract
Background Schizochytrium sp. is a heterotrophic, oil-producing microorganism that can efficiently produce lipids. However, the industrial production of bulk chemicals using Schizochytrium sp. is still not economically viable due to high-cost culture medium. Replacing glucose with cheap and renewable lignocellulose is a highly promising approach to reduce production costs, but Schizochytrium sp. cannot efficiently metabolize xylose, a major pentose in lignocellulosic biomass. Results In order to improve the utilization of lignocellulose by Schizochytrium sp., we cloned and functionally characterized the genes encoding enzymes involved in the xylose metabolism. The results showed that the endogenous xylose reductase and xylulose kinase genes possess corresponding functional activities. Additionally, attempts were made to construct a strain of Schizochytrium sp. that can effectively use xylose by using genetic engineering techniques to introduce exogenous xylitol dehydrogenase/xylose isomerase; however, the introduction of heterologous xylitol dehydrogenase did not produce a xylose-utilizing engineered strain, whereas the introduction of xylose isomerase did. The results showed that the engineered strain 308-XI with an exogenous xylose isomerase could consume 8.2 g/L xylose over 60 h of cultivation. Xylose consumption was further elevated to 11.1 g/L when heterologous xylose isomerase and xylulose kinase were overexpressed simultaneously. Furthermore, cultivation of 308-XI-XK(S) using lignocellulosic hydrolysates, which contained glucose and xylose, yielded a 22.4 g/L of dry cell weight and 5.3 g/L of total lipid titer, respectively, representing 42.7 and 30.4% increases compared to the wild type. Conclusion This study shows that engineering of Schizochytrium sp. to efficiently utilize xylose is conducive to improve its utilization of lignocellulose, which can reduce the costs of industrial lipid production. Supplementary Information The online version contains supplementary material available at 10.1186/s13068-022-02215-w.
Collapse
Affiliation(s)
- Ling-Ru Wang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Zi-Xu Zhang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Fang-Tong Nong
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Jin Li
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Peng-Wei Huang
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Wang Ma
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| | - Quan-Yu Zhao
- grid.412022.70000 0000 9389 5210School of Pharmaceutical Science, Nanjing Tech University, No. 30 Puzhu South Road, Pukou District, Nanjing, Jiangsu China
| | - Xiao-Man Sun
- grid.260474.30000 0001 0089 5711School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, 2 Xuelin Road, Qixia District, Nanjing, Jiangsu China
| |
Collapse
|
16
|
Geng B, Jia X, Peng X, Han Y. Biosynthesis of value-added bioproducts from hemicellulose of biomass through microbial metabolic engineering. Metab Eng Commun 2022; 15:e00211. [PMID: 36311477 PMCID: PMC9597109 DOI: 10.1016/j.mec.2022.e00211] [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: 08/04/2022] [Revised: 10/02/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022] Open
Abstract
Hemicellulose is the second most abundant carbohydrate in lignocellulosic biomass and has extensive applications. In conventional biomass refinery, hemicellulose is easily converted to unwanted by-products in pretreatment and therefore can't be fully utilized. The present study aims to summarize the most recent development of lignocellulosic polysaccharide degradation and fully convert it to value-added bioproducts through microbial and enzymatic catalysis. Firstly, bioprocess and microbial metabolic engineering for enhanced utilization of lignocellulosic carbohydrates were discussed. The bioprocess for degradation and conversion of natural lignocellulose to monosaccharides and organic acids using anaerobic thermophilic bacteria and thermostable glycoside hydrolases were summarized. Xylose transmembrane transporting systems in natural microorganisms and the latest strategies for promoting the transporting capacity by metabolic engineering were summarized. The carbon catabolite repression effect restricting xylose utilization in microorganisms, and metabolic engineering strategies developed for co-utilization of glucose and xylose were discussed. Secondly, the metabolic pathways of xylose catabolism in microorganisms were comparatively analyzed. Microbial metabolic engineering for converting xylose to value-added bioproducts based on redox pathways, non-redox pathways, pentose phosphate pathway, and improving inhibitors resistance were summarized. Thirdly, strategies for degrading lignocellulosic polysaccharides and fully converting hemicellulose to value-added bioproducts through microbial metabolic engineering were proposed. Hemicellulose is the main carbohydrate of biomass and has valuable applications. Hemicellulose is underutilized in conventional biomass refinery and pretreatment. Microbial and enzymatic catalysis were applied for hemicellulose utilization. Xylose is converted to value-added bioproducts by metabolic engineering.
Collapse
Affiliation(s)
- Biao Geng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojing Jia
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaowei Peng
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yejun Han
- National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China,School of Chemical Engineering, University of Chinese Academy of Sciences, Beijing, 100049, China,Corresponding author. National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, Beijing, 100190, China.
| |
Collapse
|
17
|
Balagurunathan B, Ling H, Choi WJ, Chang MW. Potential use of microbial engineering in single-cell protein production. Curr Opin Biotechnol 2022; 76:102740. [PMID: 35660478 DOI: 10.1016/j.copbio.2022.102740] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 04/08/2022] [Accepted: 04/28/2022] [Indexed: 12/16/2022]
Abstract
Single-cell proteins (SCPs) have been widely used in human food and animal feed applications, still, there are challenges in their production and commercialization. Recently, advances in microbial synthetic biology, genomic engineering, and biofoundry technologies have offered capabilities to effectively and rapidly engineer microorganisms for improving the productivity, nutritional, and functional quality of SCPs. In this review, we discuss various synthetic biology, genomic engineering, and biofoundry tools that can be harnessed for SCP production and genetic modification. We also describe the current and potential applications of genetic modification in producing intermediate feedstocks, as well as biomass-based and multifunctional SCPs. Finally, we discuss the technological and policy-control related challenges encountered when deploying genetic modification in SCP production for animal feed and human food applications.
Collapse
Affiliation(s)
- Balaji Balagurunathan
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A⁎STAR) 1, Pesek Road, Jurong Island, 627833, Singapore.
| | - Hua Ling
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| | - Won Jae Choi
- Singapore Institute of Food and Biotechnology Innovation, Agency for Science, Technology and Research (A⁎STAR) 1, Pesek Road, Jurong Island, 627833, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; Institute of Chemical and Engineering Sciences, Agency for Science, Technology and Research in Singapore (A⁎STAR), 1 Pesek Road, Jurong Island, Singapore 627833, Singapore; Singapore Institute of Technology, 10 Dover Dr, Singapore 138683, Singapore
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Synthetic Biology Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 28 Medical Drive, Singapore 117456, Singapore; Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, 8 Medical Drive, Singapore 117597, Singapore; Wilmar-NUS Corporate Laboratory (WIL@NUS), National University of Singapore, 14 Medical Drive, Singapore 117599, Singapore.
| |
Collapse
|
18
|
Peng B, Esquirol L, Lu Z, Shen Q, Cheah LC, Howard CB, Scott C, Trau M, Dumsday G, Vickers CE. An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae. Nat Commun 2022; 13:2895. [PMID: 35610221 PMCID: PMC9130285 DOI: 10.1038/s41467-022-30529-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Bottlenecks in metabolic pathways due to insufficient gene expression levels remain a significant problem for industrial bioproduction using microbial cell factories. Increasing gene dosage can overcome these bottlenecks, but current approaches suffer from numerous drawbacks. Here, we describe HapAmp, a method that uses haploinsufficiency as evolutionary force to drive in vivo gene amplification. HapAmp enables efficient, titratable, and stable integration of heterologous gene copies, delivering up to 47 copies onto the yeast genome. The method is exemplified in metabolic engineering to significantly improve production of the sesquiterpene nerolidol, the monoterpene limonene, and the tetraterpene lycopene. Limonene titre is improved by 20-fold in a single engineering step, delivering ∼1 g L-1 in the flask cultivation. We also show a significant increase in heterologous protein production in yeast. HapAmp is an efficient approach to unlock metabolic bottlenecks rapidly for development of microbial cell factories.
Collapse
Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia. .,CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Lygie Esquirol
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Qianyi Shen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia.,Biocatalysis and Synthetic Biology Team, CSIRO Land and Water, Black Mountain Science and Innovation Park, Canberra, ACT, 2061, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia.
| |
Collapse
|
19
|
Xylitol production by Pseudomonas gessardii VXlt-16 from sugarcane bagasse hydrolysate and cost analysis. Bioprocess Biosyst Eng 2022; 45:1019-1031. [PMID: 35355104 DOI: 10.1007/s00449-022-02721-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 03/13/2022] [Indexed: 12/28/2022]
Abstract
Xylitol is a well-known sugar alcohol with exponentially rising market demand due to its diverse industrial applications. Organic agro-industrial residues (OAIR) are economic alternative for the cost-effective production of commodity products along with addressing environmental pollution. The present study aimed to design a process for xylitol production from OAIR via microbial fermentation with Pseudomonas gessardii VXlt-16. Parametric analysis with Taguchi orthogonal array approach resulted in a conversion factor of 0.64 g xylitol/g xylose available in untreated sugarcane bagasse hydrolysate (SBH). At bench scale, the product yield increased to 71.98/100 g (0.66 g/L h). 48.49 g of xylitol crystals of high purity (94.56%) were recovered after detoxification with 2% activated carbon. Cost analysis identified downstream operations as one of the cost-intensive parts that can be countered by adsorbent recycling. Spent carbon, regenerated with acetic acid washing can be reused for six cycles effectively and reduced downstream cost by about ≈32%. The strategy would become useful in the cost-effective production of several biomass-dependent products like proteins, enzymes, organic acids, as well.
Collapse
|
20
|
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
Collapse
|
21
|
de Hulster E, Mooiman C, Timmermans R, Mans R. Automated Evolutionary Engineering of Yeasts. Methods Mol Biol 2022; 2513:255-270. [PMID: 35781210 DOI: 10.1007/978-1-0716-2399-2_15] [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: 06/15/2023]
Abstract
Evolutionary engineering of microbes provides a powerful tool for untargeted optimization of (engineered) cell factories and identification of genetic targets for further research. Directed evolution is an intrinsically time-intensive effort, and automated methods can significantly reduce manual labor. Here, design considerations for various evolutionary engineering methods are described, and generic workflows for batch-, chemostat-, and accelerostat-based evolution in automated bioreactors are provided. These methods can be used to evolve yeast cultures for >1000 generations and are designed to require minimal manual intervention.
Collapse
Affiliation(s)
- Erik de Hulster
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | - Christiaan Mooiman
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands
| | | | - Robert Mans
- Department of Biotechnology, Delft University of Technology, Delft, The Netherlands.
| |
Collapse
|
22
|
Brink DP, Borgström C, Persson VC, Ofuji Osiro K, Gorwa-Grauslund MF. D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers. Int J Mol Sci 2021; 22:12410. [PMID: 34830296 PMCID: PMC8625115 DOI: 10.3390/ijms222212410] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/11/2021] [Accepted: 11/12/2021] [Indexed: 11/17/2022] Open
Abstract
Extension of the substrate range is among one of the metabolic engineering goals for microorganisms used in biotechnological processes because it enables the use of a wide range of raw materials as substrates. One of the most prominent examples is the engineering of baker's yeast Saccharomyces cerevisiae for the utilization of d-xylose, a five-carbon sugar found in high abundance in lignocellulosic biomass and a key substrate to achieve good process economy in chemical production from renewable and non-edible plant feedstocks. Despite many excellent engineering strategies that have allowed recombinant S. cerevisiae to ferment d-xylose to ethanol at high yields, the consumption rate of d-xylose is still significantly lower than that of its preferred sugar d-glucose. In mixed d-glucose/d-xylose cultivations, d-xylose is only utilized after d-glucose depletion, which leads to prolonged process times and added costs. Due to this limitation, the response on d-xylose in the native sugar signaling pathways has emerged as a promising next-level engineering target. Here we review the current status of the knowledge of the response of S. cerevisiae signaling pathways to d-xylose. To do this, we first summarize the response of the native sensing and signaling pathways in S. cerevisiae to d-glucose (the preferred sugar of the yeast). Using the d-glucose case as a point of reference, we then proceed to discuss the known signaling response to d-xylose in S. cerevisiae and current attempts of improving the response by signaling engineering using native targets and synthetic (non-native) regulatory circuits.
Collapse
Affiliation(s)
- Daniel P. Brink
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- BioZone Centre for Applied Bioscience and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College St., Toronto, ON M5S 3E5, Canada
| | - Viktor C. Persson
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| | - Karen Ofuji Osiro
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
- Genetics and Biotechnology Laboratory, Embrapa Agroenergy, Brasília 70770-901, DF, Brazil
| | - Marie F. Gorwa-Grauslund
- Applied Microbiology, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00 Lund, Sweden; (C.B.); (V.C.P.); (K.O.O.)
| |
Collapse
|
23
|
Kuanyshev N, Deewan A, Jagtap SS, Liu J, Selvam B, Chen LQ, Shukla D, Rao CV, Jin YS. Identification and analysis of sugar transporters capable of co-transporting glucose and xylose simultaneously. Biotechnol J 2021; 16:e2100238. [PMID: 34418308 DOI: 10.1002/biot.202100238] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 08/04/2021] [Accepted: 08/18/2021] [Indexed: 11/09/2022]
Abstract
Simultaneous co-fermentation of glucose and xylose is a key desired trait of engineered Saccharomyces cerevisiae for efficient and rapid production of biofuels and chemicals. However, glucose strongly inhibits xylose transport by endogenous hexose transporters of S. cerevisiae. We identified structurally distant sugar transporters (Lipomyces starkeyi LST1_205437 and Arabidopsis thaliana AtSWEET7) capable of co-transporting glucose and xylose from previously unexplored oleaginous yeasts and plants. Kinetic analysis showed that LST1_205437 had lenient glucose inhibition on xylose transport and AtSWEET7 transported glucose and xylose simultaneously with no inhibition. Modelling studies of LST1_205437 revealed that Ala335 residue at sugar binding site can accommodates both glucose and xylose. Docking studies with AtSWEET7 revealed that Trp59, Trp183, Asn145, and Asn179 residues stabilized the interactions with sugars, allowing both xylose and glucose to be co-transported. In addition, we altered sugar preference of LST1_205437 by single amino acid mutation at Asn365. Our findings provide a new mechanistic insight on glucose and xylose transport mechanism of sugar transporters and the identified sugar transporters can be employed to develop engineered yeast strains for producing cellulosic biofuels and chemicals.
Collapse
Affiliation(s)
- Nurzhan Kuanyshev
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Anshu Deewan
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Sujit Sadashiv Jagtap
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Jingjing Liu
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Balaji Selvam
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Li-Qing Chen
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Diwakar Shukla
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,NIH Center for Macromolecular Modeling and Bioinformatics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Christopher V Rao
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation University of Illinois at Urbana-Champaign, Urbana, Illinois, USA.,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
| |
Collapse
|
24
|
Konstantinidis D, Pereira F, Geissen EM, Grkovska K, Kafkia E, Jouhten P, Kim Y, Devendran S, Zimmermann M, Patil KR. Adaptive laboratory evolution of microbial co-cultures for improved metabolite secretion. Mol Syst Biol 2021; 17:e10189. [PMID: 34370382 PMCID: PMC8351387 DOI: 10.15252/msb.202010189] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 07/02/2021] [Accepted: 07/07/2021] [Indexed: 12/13/2022] Open
Abstract
Adaptive laboratory evolution has proven highly effective for obtaining microorganisms with enhanced capabilities. Yet, this method is inherently restricted to the traits that are positively linked to cell fitness, such as nutrient utilization. Here, we introduce coevolution of obligatory mutualistic communities for improving secretion of fitness‐costly metabolites through natural selection. In this strategy, metabolic cross‐feeding connects secretion of the target metabolite, despite its cost to the secretor, to the survival and proliferation of the entire community. We thus co‐evolved wild‐type lactic acid bacteria and engineered auxotrophic Saccharomyces cerevisiae in a synthetic growth medium leading to bacterial isolates with enhanced secretion of two B‐group vitamins, viz., riboflavin and folate. The increased production was specific to the targeted vitamin, and evident also in milk, a more complex nutrient environment that naturally contains vitamins. Genomic, proteomic and metabolomic analyses of the evolved lactic acid bacteria, in combination with flux balance analysis, showed altered metabolic regulation towards increased supply of the vitamin precursors. Together, our findings demonstrate how microbial metabolism adapts to mutualistic lifestyle through enhanced metabolite exchange.
Collapse
Affiliation(s)
- Dimitrios Konstantinidis
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Filipa Pereira
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eva-Maria Geissen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kristina Grkovska
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Eleni Kafkia
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Medical Research Council Toxicology Unit, Cambridge, UK
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd, Espoo, Finland
| | - Yongkyu Kim
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Saravanan Devendran
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Michael Zimmermann
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Kiran Raosaheb Patil
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.,Medical Research Council Toxicology Unit, Cambridge, UK
| |
Collapse
|
25
|
Palermo GCDL, Coutouné N, Bueno JGR, Maciel LF, Dos Santos LV. Exploring metal ion metabolisms to improve xylose fermentation in Saccharomyces cerevisiae. Microb Biotechnol 2021; 14:2101-2115. [PMID: 34313008 PMCID: PMC8449651 DOI: 10.1111/1751-7915.13887] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 06/25/2021] [Indexed: 01/22/2023] Open
Abstract
The development of high‐performance xylose‐fermenting yeast is essential to achieve feasible conversion of biomass‐derived sugars in lignocellulose‐based biorefineries. However, engineered C5‐strains of Saccharomyces cerevisiae still present low xylose consumption rates under anaerobic conditions. Here, we explore alternative metabolisms involved in metal homeostasis, which positively affect C5 fermentation and analyse the non‐obvious regulatory network connection of both metabolisms using time‐course transcriptome analysis. Our results indicated the vacuolar Fe2+/Mn2+ transporter CCC1, and the protein involved in heavy metal ion homeostasis BSD2, as promising new targets for rational metabolic engineering strategies, enhancing xylose consumption in nine and 2.3‐fold compared with control. Notably, intracellular metal concentration levels were affected differently by mutations and the results were compared with positive controls isu1Δ, a Fe‐S cluster scaffold protein, and ssk2Δ, a component of HOG pathway. Temporal expression profiles indicate a metabolic remodelling in response to xylose, demonstrating changes in the main sugar sensing signalling pathways.
Collapse
Affiliation(s)
- Gisele Cristina de Lima Palermo
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Natalia Coutouné
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - João Gabriel Ribeiro Bueno
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| | - Lucas Ferreira Maciel
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil
| | - Leandro Vieira Dos Santos
- Brazilian Biorenewable National Laboratory (LNBR), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, São Paulo, 13083-100, Brazil.,Genetics and Molecular Biology Graduate Program, Institute of Biology, University of Campinas (UNICAMP), Campinas, São Paulo, Brazil
| |
Collapse
|
26
|
Adebami GE, Kuila A, Ajunwa OM, Fasiku SA, Asemoloye MD. Genetics and metabolic engineering of yeast strains for efficient ethanol production. J FOOD PROCESS ENG 2021. [DOI: 10.1111/jfpe.13798] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Arindam Kuila
- Department of Bioscience and Biotechnology Banasthali University Vanasthali India
| | - Obinna M. Ajunwa
- Department of Microbiology Modibbo Adama University of Technology Yola Nigeria
| | - Samuel A. Fasiku
- Department of Biological Sciences Ajayi Crowther University Oyo Nigeria
| | - Michael D. Asemoloye
- Department of Pharmaceutical Science and Technology Tianjin University Tianjin China
| |
Collapse
|
27
|
Lam FH, Turanlı-Yıldız B, Liu D, Resch MG, Fink GR, Stephanopoulos G. Engineered yeast tolerance enables efficient production from toxified lignocellulosic feedstocks. SCIENCE ADVANCES 2021; 7:7/26/eabf7613. [PMID: 34172441 PMCID: PMC8232913 DOI: 10.1126/sciadv.abf7613] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 05/13/2021] [Indexed: 05/03/2023]
Abstract
Lignocellulosic biomass remains unharnessed for the production of renewable fuels and chemicals due to challenges in deconstruction and the toxicity its hydrolysates pose to fermentation microorganisms. Here, we show in Saccharomyces cerevisiae that engineered aldehyde reduction and elevated extracellular potassium and pH are sufficient to enable near-parity production between inhibitor-laden and inhibitor-free feedstocks. By specifically targeting the universal hydrolysate inhibitors, a single strain is enhanced to tolerate a broad diversity of highly toxified genuine feedstocks and consistently achieve industrial-scale titers (cellulosic ethanol of >100 grams per liter when toxified). Furthermore, a functionally orthogonal, lightweight design enables seamless transferability to existing metabolically engineered chassis strains: We endow full, multifeedstock tolerance on a xylose-consuming strain and one producing the biodegradable plastics precursor lactic acid. The demonstration of "drop-in" hydrolysate competence enables the potential of cost-effective, at-scale biomass utilization for cellulosic fuel and nonfuel products alike.
Collapse
Affiliation(s)
- Felix H Lam
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Burcu Turanlı-Yıldız
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Dany Liu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA
| | - Michael G Resch
- National Bioenergy Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
| | - Gerald R Fink
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
| | - Gregory Stephanopoulos
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| |
Collapse
|
28
|
The Pentose Phosphate Pathway in Yeasts-More Than a Poor Cousin of Glycolysis. Biomolecules 2021; 11:biom11050725. [PMID: 34065948 PMCID: PMC8151747 DOI: 10.3390/biom11050725] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/04/2021] [Accepted: 05/10/2021] [Indexed: 01/14/2023] Open
Abstract
The pentose phosphate pathway (PPP) is a route that can work in parallel to glycolysis in glucose degradation in most living cells. It has a unidirectional oxidative part with glucose-6-phosphate dehydrogenase as a key enzyme generating NADPH, and a non-oxidative part involving the reversible transketolase and transaldolase reactions, which interchange PPP metabolites with glycolysis. While the oxidative branch is vital to cope with oxidative stress, the non-oxidative branch provides precursors for the synthesis of nucleic, fatty and aromatic amino acids. For glucose catabolism in the baker’s yeast Saccharomyces cerevisiae, where its components were first discovered and extensively studied, the PPP plays only a minor role. In contrast, PPP and glycolysis contribute almost equally to glucose degradation in other yeasts. We here summarize the data available for the PPP enzymes focusing on S. cerevisiae and Kluyveromyces lactis, and describe the phenotypes of gene deletions and the benefits of their overproduction and modification. Reference to other yeasts and to the importance of the PPP in their biotechnological and medical applications is briefly being included. We propose future studies on the PPP in K. lactis to be of special interest for basic science and as a host for the expression of human disease genes.
Collapse
|
29
|
Ruchala J, Sibirny AA. Pentose metabolism and conversion to biofuels and high-value chemicals in yeasts. FEMS Microbiol Rev 2020; 45:6034013. [PMID: 33316044 DOI: 10.1093/femsre/fuaa069] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 12/09/2020] [Indexed: 12/15/2022] Open
Abstract
Pentose sugars are widespread in nature and two of them, D-xylose and L-arabinose belong to the most abundant sugars being the second and third by abundance sugars in dry plant biomass (lignocellulose) and in general on planet. Therefore, it is not surprising that metabolism and bioconversion of these pentoses attract much attention. Several different pathways of D-xylose and L-arabinose catabolism in bacteria and yeasts are known. There are even more common and really ubiquitous though not so abundant pentoses, D-ribose and 2-deoxy-D-ribose, the constituents of all living cells. Thus, ribose metabolism is example of endogenous metabolism whereas metabolism of other pentoses, including xylose and L-arabinose, represents examples of the metabolism of foreign exogenous compounds which normally are not constituents of yeast cells. As a rule, pentose degradation by the wild-type strains of microorganisms does not lead to accumulation of high amounts of valuable substances; however, productive strains have been obtained by random selection and metabolic engineering. There are numerous reviews on xylose and (less) L-arabinose metabolism and conversion to high value substances; however, they mostly are devoted to bacteria or the yeast Saccharomyces cerevisiae. This review is devoted to reviewing pentose metabolism and bioconversion mostly in non-conventional yeasts, which naturally metabolize xylose. Pentose metabolism in the recombinant strains of S. cerevisiae is also considered for comparison. The available data on ribose, xylose, L-arabinose transport, metabolism, regulation of these processes, interaction with glucose catabolism and construction of the productive strains of high-value chemicals or pentose (ribose) itself are described. In addition, genome studies of the natural xylose metabolizing yeasts and available tools for their molecular research are reviewed. Metabolism of other pentoses (2-deoxyribose, D-arabinose, lyxose) is briefly reviewed.
Collapse
Affiliation(s)
- Justyna Ruchala
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| | - Andriy A Sibirny
- Department of Microbiology and Molecular Genetics, University of Rzeszow, Zelwerowicza 4, Rzeszow 35-601, Poland.,Department of Molecular Genetics and Biotechnology, Institute of Cell Biology NAS of Ukraine, Drahomanov Street, 14/16, Lviv 79005, Ukraine
| |
Collapse
|
30
|
Biorefinery: The Production of Isobutanol from Biomass Feedstocks. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10228222] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Environmental issues have prompted the vigorous development of biorefineries that use agricultural waste and other biomass feedstock as raw materials. However, most current biorefinery products are cellulosic ethanol. There is an urgent need for biorefineries to expand into new bioproducts. Isobutanol is an important bulk chemical with properties that are close to gasoline, making it a very promising biofuel. The use of microorganisms to produce isobutanol has been extensively studied, but there is still a considerable gap to achieving the industrial production of isobutanol from biomass. This review summarizes current metabolic engineering strategies that have been applied to biomass isobutanol production and recent advances in the production of isobutanol from different biomass feedstocks.
Collapse
|
31
|
Sun L, Jin YS. Xylose Assimilation for the Efficient Production of Biofuels and Chemicals by Engineered Saccharomyces cerevisiae. Biotechnol J 2020; 16:e2000142. [PMID: 33135317 DOI: 10.1002/biot.202000142] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 10/15/2020] [Indexed: 11/09/2022]
Abstract
Microbial conversion of plant biomass into fuels and chemicals offers a practical solution to global concerns over limited natural resources, environmental pollution, and climate change. Pursuant to these goals, researchers have put tremendous efforts and resources toward engineering the yeast Saccharomyces cerevisiae to efficiently convert xylose, the second most abundant sugar in lignocellulosic biomass, into various fuels and chemicals. Here, recent advances in metabolic engineering of yeast is summarized to address bottlenecks on xylose assimilation and to enable simultaneous co-utilization of xylose and other substrates in lignocellulosic hydrolysates. Distinct characteristics of xylose metabolism that can be harnessed to produce advanced biofuels and chemicals are also highlighted. Although many challenges remain, recent research investments have facilitated the efficient fermentation of xylose and simultaneous co-consumption of xylose and glucose. In particular, understanding xylose-induced metabolic rewiring in engineered yeast has encouraged the use of xylose as a carbon source for producing various non-ethanol bioproducts. To boost the lignocellulosic biomass-based bioeconomy, much attention is expected to promote xylose-utilizing efficiency via reprogramming cellular regulatory networks, to attain robust co-fermentation of xylose and other cellulosic carbon sources under industrial conditions, and to exploit the advantageous traits of yeast xylose metabolism for producing diverse fuels and chemicals.
Collapse
Affiliation(s)
- Liang Sun
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,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
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,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
| |
Collapse
|
32
|
Qin L, Dong S, Yu J, Ning X, Xu K, Zhang SJ, Xu L, Li BZ, Li J, Yuan YJ, Li C. Stress-driven dynamic regulation of multiple tolerance genes improves robustness and productive capacity of Saccharomyces cerevisiae in industrial lignocellulose fermentation. Metab Eng 2020; 61:160-170. [DOI: 10.1016/j.ymben.2020.06.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 06/01/2020] [Accepted: 06/07/2020] [Indexed: 12/20/2022]
|
33
|
Jeong D, Oh EJ, Ko JK, Nam JO, Park HS, Jin YS, Lee EJ, Kim SR. Metabolic engineering considerations for the heterologous expression of xylose-catabolic pathways in Saccharomyces cerevisiae. PLoS One 2020; 15:e0236294. [PMID: 32716960 PMCID: PMC7384654 DOI: 10.1371/journal.pone.0236294] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 07/01/2020] [Indexed: 11/18/2022] Open
Abstract
Xylose, the second most abundant sugar in lignocellulosic biomass hydrolysates, can be fermented by Saccharomyces cerevisiae expressing one of two heterologous xylose pathways: a xylose oxidoreductase pathway and a xylose isomerase pathway. Depending on the type of the pathway, its optimization strategies and the fermentation efficiencies vary significantly. In the present study, we constructed two isogenic strains expressing either the oxidoreductase pathway (XYL123) or the isomerase pathway (XI-XYL3), and delved into simple and reproducible ways to improve the resulting strains. First, the strains were subjected to the deletion of PHO13, overexpression of TAL1, and adaptive evolution, but those individual approaches were only effective in the XYL123 strain but not in the XI-XYL3 strain. Among other optimization strategies of the XI-XYL3 strain, we found that increasing the copy number of the xylose isomerase gene (xylA) is the most promising but yet preliminary strategy for the improvement. These results suggest that the oxidoreductase pathway might provide a simpler metabolic engineering strategy than the isomerase pathway for the development of efficient xylose-fermenting strains under the conditions tested in the present study.
Collapse
Affiliation(s)
- Deokyeol Jeong
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Eun Joong Oh
- Renewable and Sustainable Energy Institute (RASEI), University of Colorado Boulder, Boulder, Colorado, United States of America
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, Republic of Korea
| | - Ju-Ock Nam
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Hee-Soo Park
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Eun Jung Lee
- Department of Chemical Engineering, School of Applied Chemical Engineering, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
| | - Soo Rin Kim
- School of Food Science and Biotechnology, Kyungpook National University, Daegu, Republic of Korea
- * E-mail: (EJL); (SRK)
| |
Collapse
|
34
|
Improving Xylose Fermentation in Saccharomyces cerevisiae by Expressing Nuclear-Localized Hexokinase 2. Microorganisms 2020; 8:microorganisms8060856. [PMID: 32517148 PMCID: PMC7356972 DOI: 10.3390/microorganisms8060856] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/03/2020] [Accepted: 06/04/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding the relationship between xylose and the metabolic regulatory systems is a prerequisite to enhance xylose utilization in recombinant S. cerevisiae strains. Hexokinase 2 (Hxk2p) is an intracellular glucose sensor that localizes to the cytoplasm or the nucleus depending on the carbon source. Hxk2p interacts with Mig1p to regulate gene transcription in the nucleus. Here, we investigated the effect of nucleus-localized Hxk2p and Mig1p on xylose fermentation. The results show that the expression of HXK2S14A, which encodes a constitutively nucleus-localized Hxk2p, increased the xylose consumption rate, the ethanol production rate, and the ethanol yield of the engineered yeast strain by 23.5%, 78.6% and 42.6%, respectively. The deletion of MIG1 decreased xylose utilization and eliminated the positive effect of Hxk2p. We then performed RNA-seq and found that the targets of Hxk2pS14A on xylose were mainly genes that encode RNA-binding proteins. This is very different from the known targets of Mig1p and supports the notion that the Hxk2p-Mig1p interaction is abolished in the presence of xylose. These results will improve our understanding of the interrelation between the Snf1p-Mig1p-Hxk2p glucose signaling pathway and xylose utilization in S. cerevisiae and suggests that the expression of HXK2S14A could be a viable strategy to improve xylose utilization.
Collapse
|
35
|
Crystal structure of a novel xylose isomerase from Streptomyces sp. F-1 revealed the presence of unique features that differ from conventional classes. Biochim Biophys Acta Gen Subj 2020; 1864:129549. [DOI: 10.1016/j.bbagen.2020.129549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/24/2020] [Accepted: 02/04/2020] [Indexed: 01/12/2023]
|
36
|
Claes A, Deparis Q, Foulquié-Moreno MR, Thevelein JM. Simultaneous secretion of seven lignocellulolytic enzymes by an industrial second-generation yeast strain enables efficient ethanol production from multiple polymeric substrates. Metab Eng 2020; 59:131-141. [DOI: 10.1016/j.ymben.2020.02.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Revised: 02/01/2020] [Accepted: 02/18/2020] [Indexed: 01/22/2023]
|
37
|
Zhao Z, Xian M, Liu M, Zhao G. Biochemical routes for uptake and conversion of xylose by microorganisms. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:21. [PMID: 32021652 PMCID: PMC6995148 DOI: 10.1186/s13068-020-1662-x] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/21/2020] [Indexed: 05/23/2023]
Abstract
Xylose is a major component of lignocellulose and the second most abundant sugar present in nature. Efficient utilization of xylose is required for the development of economically viable processes to produce biofuels and chemicals from biomass. However, there are still some bottlenecks in the bioconversion of xylose, including the fact that some microorganisms cannot assimilate xylose naturally and that the uptake and metabolism of xylose are inhibited by glucose, which is usually present with xylose in lignocellulose hydrolysate. To overcome these issues, numerous efforts have been made to discover, characterize, and engineer the transporters and enzymes involved in xylose utilization to relieve glucose inhibition and to develop recombinant microorganisms to produce fuels and chemicals from xylose. Here we describe a recent advancement focusing on xylose-utilizing pathways, biosynthesis of chemicals from xylose, and engineering strategies used to improve the conversion efficiency of xylose.
Collapse
Affiliation(s)
- Zhe Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Mo Xian
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Min Liu
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| | - Guang Zhao
- CAS Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, 266101 China
| |
Collapse
|
38
|
Nijland JG, Driessen AJM. Engineering of Pentose Transport in Saccharomyces cerevisiae for Biotechnological Applications. Front Bioeng Biotechnol 2020; 7:464. [PMID: 32064252 PMCID: PMC7000353 DOI: 10.3389/fbioe.2019.00464] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 12/19/2019] [Indexed: 01/05/2023] Open
Abstract
Lignocellulosic biomass yields after hydrolysis, besides the hexose D-glucose, D-xylose, and L-arabinose as main pentose sugars. In second generation bioethanol production utilizing the yeast Saccharomyces cerevisiae, it is critical that all three sugars are co-consumed to obtain an economically feasible and robust process. Since S. cerevisiae is unable to metabolize pentose sugars, metabolic pathway engineering has been employed to introduce the respective pathways for D-xylose and L-arabinose metabolism. However, S. cerevisiae lacks specific pentose transporters, and these sugars enter the cell with low affinity via glucose transporters of the Hxt family. Therefore, in the presence of D-glucose, utilization of D-xylose and L-arabinose is poor as the Hxt transporters prefer D-glucose. To solve this problem, heterologous expression of pentose transporters has been attempted but often with limited success due to poor expression and stability, and/or low turnover. A more successful approach is the engineering of the endogenous Hxt transporter family and evolutionary selection for D-glucose insensitive growth on pentose sugars. This has led to the identification of a critical and conserved asparagine residue in Hxt transporters that, when mutated, reduces the D-glucose affinity while leaving the D-xylose affinity mostly unaltered. Likewise, mutant Gal2 transporter have been selected supporting specific uptake of L-arabinose. In fermentation experiments, the transporter mutants support efficient uptake and consumption of pentose sugars, and even co-consumption of D-xylose and D-glucose when used at industrial concentrations. Further improvements are obtained by interfering with the post-translational inactivation of Hxt transporters at high or low D-glucose concentrations. Transporter engineering solved major limitations in pentose transport in yeast, now allowing for co-consumption of sugars that is limited only by the rates of primary metabolism. This paves the way for a more economical second-generation biofuels production process.
Collapse
Affiliation(s)
- Jeroen G Nijland
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
| | - Arnold J M Driessen
- Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology, University of Groningen, Groningen, Netherlands
| |
Collapse
|
39
|
Lee M, Rozeboom HJ, Keuning E, de Waal P, Janssen DB. Structure-based directed evolution improves S. cerevisiae growth on xylose by influencing in vivo enzyme performance. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:5. [PMID: 31938040 PMCID: PMC6954610 DOI: 10.1186/s13068-019-1643-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 12/22/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Efficient bioethanol production from hemicellulose feedstocks by Saccharomyces cerevisiae requires xylose utilization. Whereas S. cerevisiae does not metabolize xylose, engineered strains that express xylose isomerase can metabolize xylose by converting it to xylulose. For this, the type II xylose isomerase from Piromyces (PirXI) is used but the in vivo activity is rather low and very high levels of the enzyme are needed for xylose metabolism. In this study, we explore the use of protein engineering and in vivo selection to improve the performance of PirXI. Recently solved crystal structures were used to focus mutagenesis efforts. RESULTS We constructed focused mutant libraries of Piromyces xylose isomerase by substitution of second shell residues around the substrate- and metal-binding sites. Following library transfer to S. cerevisiae and selection for enhanced xylose-supported growth under aerobic and anaerobic conditions, two novel xylose isomerase mutants were obtained, which were purified and subjected to biochemical and structural analysis. Apart from a small difference in response to metal availability, neither the new mutants nor mutants described earlier showed significant changes in catalytic performance under various in vitro assay conditions. Yet, in vivo performance was clearly improved. The enzymes appeared to function suboptimally in vivo due to enzyme loading with calcium, which gives poor xylose conversion kinetics. The results show that better in vivo enzyme performance is poorly reflected in kinetic parameters for xylose isomerization determined in vitro with a single type of added metal. CONCLUSION This study shows that in vivo selection can identify xylose isomerase mutants with only minor changes in catalytic properties measured under standard conditions. Metal loading of xylose isomerase expressed in yeast is suboptimal and strongly influences kinetic properties. Metal uptake, distribution and binding to xylose isomerase are highly relevant for rapid xylose conversion and may be an important target for optimizing yeast xylose metabolism.
Collapse
Affiliation(s)
- Misun Lee
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Henriëtte J. Rozeboom
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Eline Keuning
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Paul de Waal
- DSM Biotechnology Center, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Dick B. Janssen
- Biochemical Laboratory, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| |
Collapse
|
40
|
Simulating Extracellular Glucose Signals Enhances Xylose Metabolism in Recombinant Saccharomyces cerevisiae. Microorganisms 2020; 8:microorganisms8010100. [PMID: 31936831 PMCID: PMC7022881 DOI: 10.3390/microorganisms8010100] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 12/30/2019] [Accepted: 01/08/2020] [Indexed: 12/24/2022] Open
Abstract
Efficient utilization of both glucose and xylose from lignocellulosic biomass would be economically beneficial for biofuel production. Recombinant Saccharomyces cerevisiae strains with essential genes and metabolic networks for xylose metabolism can ferment xylose; however, the efficiency of xylose fermentation is much lower than that of glucose, the preferred carbon source of yeast. Implications from our previous work suggest that activation of the glucose sensing system may benefit xylose metabolism. Here, we show that deleting cAMP phosphodiesterase genes PDE1 and PDE2 increased PKA activity of strains, and consequently, increased xylose utilization. Compared to the wild type strain, the specific xylose consumption rate (rxylose) of the pde1Δ pde2Δ mutant strains increased by 50%; the specific ethanol-producing rate (rethanol) of the strain increased by 70%. We also show that HXT1 and HXT2 transcription levels slightly increased when xylose was present. We also show that HXT1 and HXT2 transcription levels slightly increased when xylose was present. Deletion of either RGT2 or SNF3 reduced expression of HXT1 in strains cultured in 1 g L−1 xylose, which suggests that xylose can bind both Snf3 and Rgt2 and slightly alter their conformations. Deletion of SNF3 significantly weakened the expression of HXT2 in the yeast cultured in 40 g L−1 xylose, while deletion of RGT2 did not weaken expression of HXT2, suggesting that S. cerevisiae mainly depends on Snf3 to sense a high concentration of xylose (40 g L−1). Finally, we show that deletion of Rgt1, increased rxylose by 24% from that of the control. Our findings indicate how S. cerevisiae may respond to xylose and this study provides novel targets for further engineering of xylose-fermenting strains.
Collapse
|
41
|
Hoang Nguyen Tran P, Ko JK, Gong G, Um Y, Lee SM. Improved simultaneous co-fermentation of glucose and xylose by Saccharomyces cerevisiae for efficient lignocellulosic biorefinery. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:12. [PMID: 31993090 PMCID: PMC6975041 DOI: 10.1186/s13068-019-1641-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 12/19/2019] [Indexed: 05/22/2023]
Abstract
BACKGROUND Lignocellulosic biorefinery offers economical and sustainable production of fuels and chemicals. Saccharomyces cerevisiae, a promising industrial host for biorefinery, has been intensively developed to expand its product profile. However, the sequential and slow conversion of xylose into target products remains one of the main challenges for realizing efficient industrial lignocellulosic biorefinery. RESULTS In this study, we developed a powerful mixed-sugar co-fermenting strain of S. cerevisiae, XUSEA, with improved xylose conversion capacity during simultaneous glucose/xylose co-fermentation. To reinforce xylose catabolism, the overexpression target in the pentose phosphate pathway was selected using a DNA assembler method and overexpressed increasing xylose consumption and ethanol production by twofold. The performance of the newly engineered strain with improved xylose catabolism was further boosted by elevating fermentation temperature and thus significantly reduced the co-fermentation time by half. Through combined efforts of reinforcing the pathway of xylose catabolism and elevating the fermentation temperature, XUSEA achieved simultaneous co-fermentation of lignocellulosic hydrolysates, composed of 39.6 g L-1 glucose and 23.1 g L-1 xylose, within 24 h producing 30.1 g L-1 ethanol with a yield of 0.48 g g-1. CONCLUSIONS Owing to its superior co-fermentation performance and ability for further engineering, XUSEA has potential as a platform in a lignocellulosic biorefinery toward realizing a more economical and sustainable process for large-scale bioethanol production.
Collapse
Affiliation(s)
- Phuong Hoang Nguyen Tran
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Ja Kyong Ko
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
| | - Gyeongtaek Gong
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and Technology (KIST), Seoul, 02792 Republic of Korea
- Division of Energy and Environment Technology, University of Science and Technology (UST), Daejeon, 34113 Republic of Korea
- Green School, Korea University, Seoul, 02841 Republic of Korea
| |
Collapse
|
42
|
Tang R, Ye P, Alper HS, Liu Z, Zhao X, Bai F. Identification and characterization of novel xylose isomerases from a Bos taurus fecal metagenome. Appl Microbiol Biotechnol 2019; 103:9465-9477. [PMID: 31701197 DOI: 10.1007/s00253-019-10161-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 09/08/2019] [Accepted: 09/28/2019] [Indexed: 12/31/2022]
Abstract
Discovering sugar metabolism genes is of great interest for lignocellulosic biorefinery. Xylose isomerases (XIs) were commonly screened from metagenomes derived from bovine rumen, soil, and other sources. However, so far, XIs and other sugar-utilizing enzymes have not been discovered from fecal metagenomes. In this study, environmental DNA from the fecal samples collected from yellow cattle (Bos taurus) was sequenced and analyzed. In the whole 14.26 Gbp clean data, 92 putative XIs were annotated. After sequence analysis, seven putative XIs were heterologously expressed in Escherichia coli and characterized in vitro. The XIs 58444 and 58960 purified from E. coli exhibited 22% higher enzyme activity when compared with that of the native E. coli XI. The XI 58444, similar to the XI from Lachnospira multipara, exhibited a relatively stable activity profile across different pH conditions. Four XIs were further investigated in budding yeast Saccharomyces cerevisiae after codon optimization. Overexpression of the codon-optimized 58444 enabled S. cerevisiae to utilize 6.4 g/L xylose after 96 h without any other genetic manipulations, which is 56% higher than the control yeast strain overexpressing an optimized XI gene xylA*3 selected by three rounds of mutation. Our results provide evidence that a bovine fecal metagenome is a novel and valuable source of XIs and other industrial enzymes for biotechnology applications.
Collapse
Affiliation(s)
- Ruiqi Tang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Peiliang Ye
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Hal S Alper
- McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Zhanying Liu
- School of Chemical Engineering, Inner Mongolia University of Technology, Hohhot, 010051, China.,Center for Conservation and Emission Reductioin in Fermentation Industry, Inner Mongolia, Hohhot, 010051, China
| | - Xinqing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Fengwu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| |
Collapse
|
43
|
Zhang Y, Lane S, Chen JM, Hammer SK, Luttinger J, Yang L, Jin YS, Avalos JL. Xylose utilization stimulates mitochondrial production of isobutanol and 2-methyl-1-butanol in Saccharomyces cerevisiae. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:223. [PMID: 31548865 PMCID: PMC6753614 DOI: 10.1186/s13068-019-1560-2] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/31/2019] [Indexed: 05/12/2023]
Abstract
BACKGROUND Branched-chain higher alcohols (BCHAs), including isobutanol and 2-methyl-1-butanol, are promising advanced biofuels, superior to ethanol due to their higher energy density and better compatibility with existing gasoline infrastructure. Compartmentalizing the isobutanol biosynthetic pathway in yeast mitochondria is an effective way to produce BCHAs from glucose. However, to improve the sustainability of biofuel production, there is great interest in developing strains and processes to utilize lignocellulosic biomass, including its hemicellulose component, which is mostly composed of the pentose xylose. RESULTS In this work, we rewired the xylose isomerase assimilation and mitochondrial isobutanol production pathways in the budding yeast Saccharomyces cerevisiae. We then increased the flux through these pathways by making gene deletions of BAT1, ALD6, and PHO13, to develop a strain (YZy197) that produces as much as 4 g/L of BCHAs (3.10 ± 0.18 g isobutanol/L and 0.91 ± 0.02 g 2-methyl-1-butanol/L) from xylose. This represents approximately a 28-fold improvement on the highest isobutanol titers obtained from xylose previously reported in yeast and the first report of 2-methyl-1-butanol produced from xylose. The yield of total BCHAs is 57.2 ± 5.2 mg/g xylose, corresponding to ~ 14% of the maximum theoretical yield. Respirometry experiments show that xylose increases mitochondrial activity by as much as 7.3-fold compared to glucose. CONCLUSIONS The enhanced levels of mitochondrial BCHA production achieved, even without disrupting ethanol byproduct formation, arise mostly from xylose activation of mitochondrial activity and are correlated with slow rates of sugar consumption.
Collapse
Affiliation(s)
- Yanfei Zhang
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Stephan Lane
- Carl R. Woese Institute for Genomic Biology, 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
| | - Jhong-Min Chen
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Sarah K. Hammer
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Jake Luttinger
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
| | - Lifeng Yang
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ USA
- Department of Chemistry, Princeton University, Princeton, NJ USA
| | - Yong-Su Jin
- Carl R. Woese Institute for Genomic Biology, 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
| | - José L. Avalos
- Department of Chemical and Biological Engineering, Princeton University, 101 Hoyt Laboratory, William Street, Princeton, NJ 08544 USA
- Andlinger Center for Energy and the Environment, Princeton, NJ USA
- Department of Molecular Biology, Princeton University, Princeton, NJ USA
| |
Collapse
|
44
|
Fernández-Sandoval MT, Galíndez-Mayer J, Bolívar F, Gosset G, Ramírez OT, Martinez A. Xylose-glucose co-fermentation to ethanol by Escherichia coli strain MS04 using single- and two-stage continuous cultures under micro-aerated conditions. Microb Cell Fact 2019; 18:145. [PMID: 31443652 PMCID: PMC6706898 DOI: 10.1186/s12934-019-1191-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 08/10/2019] [Indexed: 12/19/2022] Open
Abstract
Background Simultaneous co-fermentation of mixed sugars is an important feature to consider in the production of ethanol from lignocellulosic biomass hydrolysates because it enhances the overall ethanol yield and volumetric productivity during fermentation. Continuous cultures can be used during ethanol production from lignocellulosic hydrolysates to prevent catabolite repression by glucose on other sugars, such as xylose, and thus promote the simultaneous and total consumption of sugars and reduce fermentation time. The use of single- and two-stage continuous cultures under micro-aerated conditions for simultaneous consumption of xylose and glucose, and fermentation to ethanol by ethanologenic Escherichia coli strain MS04 was studied. Mineral medium supplemented with glucose, xylose and sodium acetate, was used to compare continuous cultures performance to batch cultures. Results Single-stage continuous cultures under micro-aerated conditions allowed the total co-consumption of a mixture of glucose and xylose (7.5 and 42.5 g/L, respectively) in mineral medium, with steady state ethanol production of 18 g/L, and a volumetric ethanol productivity of 0.9 g/L h, when low dilution rates (0.05 h−1) were used. However, the volumetric productivity was lower than the batch process under similar conditions (1.3 g/L h). Conversely, micro-aerated two-stage continuous culture enhanced the volumetric productivity up to 1.6 g/L h at a dilution rate of 0.15 h−1, with a total consumption of sugars and a slight reduction of the overall ethanol yield. Conclusions The total and simultaneous consumption of glucose and xylose by the ethanologenic E. coli strain MS04 was accomplished by using two-stage continuous culture under micro-aerated conditions with an increase in the volumetric ethanol productivity of 23% and 78% when compared to batch and single-stage continuous cultures, respectively. Multi-stage continuous cultivation can be used to promote the simultaneous consumption of all sugars contained in biomass hydrolysates, and thus increase the volumetric ethanol productivity of the fermentation process.
Collapse
Affiliation(s)
- Marco T Fernández-Sandoval
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Juvencio Galíndez-Mayer
- Laboratorio de Bioingeniería, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Carpio y Plan de Ayala, Col. Santo Tomás, CP 11340, Mexico, D.F., Mexico
| | - Francisco Bolívar
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Guillermo Gosset
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Octavio T Ramírez
- Departamento de Medicina Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Alfredo Martinez
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Av. Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
45
|
Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM. The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology. Metab Eng 2019; 56:1-16. [PMID: 31401242 DOI: 10.1016/j.ymben.2019.08.004] [Citation(s) in RCA: 250] [Impact Index Per Article: 50.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 12/21/2022]
Abstract
Harnessing the process of natural selection to obtain and understand new microbial phenotypes has become increasingly possible due to advances in culturing techniques, DNA sequencing, bioinformatics, and genetic engineering. Accordingly, Adaptive Laboratory Evolution (ALE) experiments represent a powerful approach both to investigate the evolutionary forces influencing strain phenotypes, performance, and stability, and to acquire production strains that contain beneficial mutations. In this review, we summarize and categorize the applications of ALE to various aspects of microbial physiology pertinent to industrial bioproduction by collecting case studies that highlight the multitude of ways in which evolution can facilitate the strain construction process. Further, we discuss principles that inform experimental design, complementary approaches such as computational modeling that help maximize utility, and the future of ALE as an efficient strain design and build tool driven by growing adoption and improvements in automation.
Collapse
Affiliation(s)
- Troy E Sandberg
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Michael J Salazar
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Liam L Weng
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA
| | - Bernhard O Palsson
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Adam M Feist
- Department of Bioengineering, University of California, San Diego, CA, 92093, USA; Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Lyngby, Denmark.
| |
Collapse
|
46
|
McDonald MJ. Microbial Experimental Evolution - a proving ground for evolutionary theory and a tool for discovery. EMBO Rep 2019; 20:e46992. [PMID: 31338963 PMCID: PMC6680118 DOI: 10.15252/embr.201846992] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 03/23/2019] [Accepted: 06/28/2019] [Indexed: 01/21/2023] Open
Abstract
Microbial experimental evolution uses controlled laboratory populations to study the mechanisms of evolution. The molecular analysis of evolved populations enables empirical tests that can confirm the predictions of evolutionary theory, but can also lead to surprising discoveries. As with other fields in the life sciences, microbial experimental evolution has become a tool, deployed as part of the suite of techniques available to the molecular biologist. Here, I provide a review of the general findings of microbial experimental evolution, especially those relevant to molecular microbiologists that are new to the field. I also relate these results to design considerations for an evolution experiment and suggest future directions for those working at the intersection of experimental evolution and molecular biology.
Collapse
Affiliation(s)
- Michael J McDonald
- School of Biological Sciences, Monash University, Melbourne, Vic., Australia
| |
Collapse
|
47
|
Wei S, Bai P, Liu Y, Yang M, Ma J, Hou J, Liu W, Bao X, Shen Y. A Thi2p Regulatory Network Controls the Post-glucose Effect of Xylose Utilization in Saccharomyces cerevisiae. Front Microbiol 2019; 10:1649. [PMID: 31379793 PMCID: PMC6660263 DOI: 10.3389/fmicb.2019.01649] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/03/2019] [Indexed: 12/16/2022] Open
Abstract
The complete and efficient utilization of both glucose and xylose is necessary for the economically viable production of biofuels and chemicals using lignocellulosic feedstocks. Although recently obtained recombinant Saccharomyces cerevisiae strains metabolize xylose well when xylose is the sole carbon source in the medium (henceforth referred to as "X stage"), their xylose consumption rate is significantly reduced during the xylose-only consumption phase of glucose-xylose co-fermentation ("GX stage"). This post-glucose effect seriously decreases overall fermentation efficiency. We showed in previous work that THI2 deletion can alleviate this post-glucose effect, but the underlying mechanisms were ill-defined. In the present study, we profiled the transcriptome of a thi2Δ strain growing at the GX stage. Thi2p in GX stage cells regulates genes involved in the cell cycle, stress tolerance, and cell viability. Importantly, the regulation of Thi2p differs from a previous regulatory network that functions when glucose is the sole carbon source, which suggests that the function of Thi2p depends on the carbon source. Modeling research seeking to optimize metabolic engineering via TFs should account for this important carbon source difference. Building on our initial study, we confirmed that several identified factors did indeed increase fermentation efficiency. Specifically, overexpressing STT4, RGI2, and TFC3 increases specific xylose utilization rate of the strain by 36.9, 29.7, 42.8%, respectively, in the GX stage of anaerobic fermentation. Our study thus illustrates a promising strategy for the rational engineering of yeast for lignocellulosic ethanol production.
Collapse
Affiliation(s)
- Shan Wei
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Penggang Bai
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Yanan Liu
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Mengdan Yang
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Juanzhen Ma
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Weifeng Liu
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| | - Xiaoming Bao
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China.,Shandong Provincial Key Laboratory of Microbial Engineering, Qi Lu University of Technology, Jinan, China
| | - Yu Shen
- State Key Laboratory of Microbial Technology, Microbiology and Biotechnology Institute, Shandong University, Qingdao, China
| |
Collapse
|
48
|
Bracher JM, Martinez-Rodriguez OA, Dekker WJC, Verhoeven MD, van Maris AJA, Pronk JT. Reassessment of requirements for anaerobic xylose fermentation by engineered, non-evolved Saccharomyces cerevisiae strains. FEMS Yeast Res 2019; 19:5106349. [PMID: 30252062 PMCID: PMC6240133 DOI: 10.1093/femsyr/foy104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 09/21/2018] [Indexed: 01/03/2023] Open
Abstract
Expression of a heterologous xylose isomerase, deletion of the GRE3 aldose-reductase gene and overexpression of genes encoding xylulokinase (XKS1) and non-oxidative pentose-phosphate-pathway enzymes (RKI1, RPE1, TAL1, TKL1) enables aerobic growth of Saccharomyces cerevisiae on d-xylose. However, literature reports differ on whether anaerobic growth on d-xylose requires additional mutations. Here, CRISPR-Cas9-assisted reconstruction and physiological analysis confirmed an early report that this basic set of genetic modifications suffices to enable anaerobic growth on d-xylose in the CEN.PK genetic background. Strains that additionally carried overexpression cassettes for the transaldolase and transketolase paralogs NQM1 and TKL2 only exhibited anaerobic growth on d-xylose after a 7–10 day lag phase. This extended lag phase was eliminated by increasing inoculum concentrations from 0.02 to 0.2 g biomass L−1. Alternatively, a long lag phase could be prevented by sparging low-inoculum-density bioreactor cultures with a CO2/N2-mixture, thus mimicking initial CO2 concentrations in high-inoculum-density, nitrogen-sparged cultures, or by using l-aspartate instead of ammonium as nitrogen source. This study resolves apparent contradictions in the literature on the genetic interventions required for anaerobic growth of CEN.PK-derived strains on d-xylose. Additionally, it indicates the potential relevance of CO2 availability and anaplerotic carboxylation reactions for anaerobic growth of engineered S. cerevisiae strains on d-xylose.
Collapse
Affiliation(s)
- Jasmine M Bracher
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | | | - Wijb J C Dekker
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| | - Maarten D Verhoeven
- DSM Biotechnology Centre, Alexander Fleminglaan 1, 2613 AX Delft, The Netherlands
| | - Antonius J A van Maris
- Department of Industrial Biotechnology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, AlbaNova University Center, SE 106 91, Stockholm, Sweden
| | - Jack T Pronk
- Department of Biotechnology, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands
| |
Collapse
|
49
|
Osiro KO, Borgström C, Brink DP, Fjölnisdóttir BL, Gorwa-Grauslund MF. Exploring the xylose paradox in Saccharomyces cerevisiae through in vivo sugar signalomics of targeted deletants. Microb Cell Fact 2019; 18:88. [PMID: 31122246 PMCID: PMC6532234 DOI: 10.1186/s12934-019-1141-x] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2019] [Accepted: 05/17/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There have been many successful strategies to implement xylose metabolism in Saccharomyces cerevisiae, but no effort has so far enabled xylose utilization at rates comparable to that of glucose (the preferred sugar of this yeast). Many studies have pointed towards the engineered yeast not sensing that xylose is a fermentable carbon source despite growing and fermenting on it, which is paradoxical. We have previously used fluorescent biosensor strains to in vivo monitor the sugar signalome in yeast engineered with xylose reductase and xylitol dehydrogenase (XR/XDH) and have established that S. cerevisiae senses high concentrations of xylose with the same signal as low concentration of glucose, which may explain the poor utilization. RESULTS In the present study, we evaluated the effects of three deletions (ira2∆, isu1∆ and hog1∆) that have recently been shown to display epistatic effects on a xylose isomerase (XI) strain. Through aerobic and anaerobic characterization, we showed that the proposed effects in XI strains were for the most part also applicable in the XR/XDH background. The ira2∆isu1∆ double deletion led to strains with the highest specific xylose consumption- and ethanol production rates but also the lowest biomass titre. The signalling response revealed that ira2∆isu1∆ changed the low glucose-signal in the background strain to a simultaneous signalling of high and low glucose, suggesting that engineering of the signalome can improve xylose utilization. CONCLUSIONS The study was able to correlate the previously proposed beneficial effects of ira2∆, isu1∆ and hog1∆ on S. cerevisiae xylose uptake, with a change in the sugar signalome. This is in line with our previous hypothesis that the key to resolve the xylose paradox lies in the sugar sensing and signalling networks. These results indicate that the future engineering targets for improved xylose utilization should probably be sought not in the metabolic networks, but in the signalling ones.
Collapse
Affiliation(s)
- Karen O Osiro
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Celina Borgström
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | - Daniel P Brink
- Applied Microbiology, Department of Chemistry, Lund University, Lund, Sweden
| | | | | |
Collapse
|
50
|
Sunwoo I, Kwon JE, Nguyen TH, Jeong GT, Kim SK. Ethanol production from water hyacinth (Eichhornia crassipes) hydrolysate by hyper-thermal acid hydrolysis, enzymatic saccharification and yeasts adapted to high concentration of xylose. Bioprocess Biosyst Eng 2019; 42:1367-1374. [DOI: 10.1007/s00449-019-02136-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Accepted: 04/24/2019] [Indexed: 11/24/2022]
|