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Guo Q, Xu J, Li J, Tang S, Cheng Y, Gao B, Xiong LB, Xiong J, Wang FQ, Wei DZ. Synergistic increase in coproporphyrin III biosynthesis by mitochondrial compartmentalization in engineered Saccharomyces cerevisiae. Synth Syst Biotechnol 2024; 9:834-841. [PMID: 39113689 PMCID: PMC11305229 DOI: 10.1016/j.synbio.2024.07.001] [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: 05/15/2024] [Revised: 07/04/2024] [Accepted: 07/10/2024] [Indexed: 08/10/2024] Open
Abstract
Coproporphyrin III (CP III), a natural porphyrin derivative, has extensive applications in the biomedical and material industries. S. cerevisiae has previously been engineered to highly accumulate the CP III precursor 5-aminolevulinic acid (ALA) through the C4 pathway. In this study, a combination of cytoplasmic metabolic engineering and mitochondrial compartmentalization was used to enhance CP III production in S. cerevisiae. By integrating pathway genes into the chromosome, the CP III titer gradually increased to 32.5 ± 0.5 mg/L in shake flask cultivation. Nevertheless, increasing the copy number of pathway genes did not consistently enhance CP III synthesis. Hence, the partial synthesis pathway was compartmentalized in mitochondria to evaluate its effectiveness in increasing CP III production. Subsequently, by superimposing the mitochondrial compartmentalization strategy on cytoplasmic metabolic engineered strains, the CP III titer was increased to 64.3 ± 1.9 mg/L. Furthermore, augmenting antioxidant pathway genes to reduce reactive oxygen species (ROS) levels effectively improved the growth of engineered strains, resulting in a further increase in the CP III titer to 82.9 ± 1.4 mg/L. Fed-batch fermentations in a 5 L bioreactor achieved a titer of 402.8 ± 9.3 mg/L for CP III. This study provides a new perspective on engineered yeast for the microbial production of porphyrins.
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Affiliation(s)
- Qidi Guo
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Jiaqi Xu
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jiacun Li
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Shuyan Tang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuhui Cheng
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Bei Gao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Liang-Bin Xiong
- Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai, 201318, China
| | - Jie Xiong
- Department of Gastroenterology, Tongji Institute of Digestive Disease, Tongji Hospital, School of Medicine, TongJi University, Shanghai, 200065, China
| | - Feng-Qing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Dong-Zhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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Azambuja SPH, de Mélo AHF, Bertozzi BG, Inoue HP, Egawa VY, Rosa CA, Rocha LO, Teixeira GS, Goldbeck R. Performance of Saccharomyces cerevisiae strains against the application of adaptive laboratory evolution strategies for butanol tolerance. Food Res Int 2024; 190:114637. [PMID: 38945626 DOI: 10.1016/j.foodres.2024.114637] [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: 12/05/2023] [Revised: 06/08/2024] [Accepted: 06/09/2024] [Indexed: 07/02/2024]
Abstract
Although the industrial production of butanol has been carried out for decades by bacteria of the Clostridium species, recent studies have shown the use of the yeast Saccharomyces cerevisiae as a promising alternative. While the production of n-butanol by this yeast is still very far from its tolerability (up to 2% butanol), the improvement in the tolerance can lead to an increase in butanol production. The aim of the present work was to evaluate the adaptive capacity of the laboratory strain X2180-1B and the Brazilian ethanol-producing strain CAT-1 when submitted to two strategies of adaptive laboratory Evolution (ALE) in butanol. The strains were submitted, in parallel, to ALE with successive passages or with UV irradiation, using 1% butanol as selection pressure. Despite initially showing greater tolerance to butanol, the CAT-1 strain did not show great improvements after being submitted to ALE. Already the laboratory strain X2180-1B showed an incredible increase in butanol tolerance, starting from a condition of inability to grow in 1% butanol, to the capacity to grow in this same condition. With emphasis on the X2180_n100#28 isolated colony that presented the highest maximum specific growth rate among all isolated colonies, we believe that this colony has good potential to be used as a model yeast for understanding the mechanisms that involve tolerance to alcohols and other inhibitory compounds.
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Affiliation(s)
- Suéllen P H Azambuja
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Allan H F de Mélo
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Bruno G Bertozzi
- Food Microbiology Laboratory I, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Heitor P Inoue
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Viviane Y Egawa
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Carlos A Rosa
- Departament of Microbiology, Federal University of Minas Gerais, Belo Horizonte, MG, Brazil
| | - Liliana O Rocha
- Food Microbiology Laboratory I, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Gleidson S Teixeira
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil
| | - Rosana Goldbeck
- Laboratory of Bioprocesses and Metabolic Engineering, Department of Food Engineering, School of Food Engineering, University of Campinas, Campinas, SP, Brazil.
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Hou R, Shan M, Liu X, Yao M, Yang K, Wang Y, Sui Z, Liang Z, Zhang Y, Zhang L. Proteomic analysis reveals that the co-ordination of cytosolic and mitochondrial pathways is beneficial for sabinene biosynthesis in engineered Saccharomyces cerevisiae. Biotechnol J 2024; 19:e2300710. [PMID: 38581096 DOI: 10.1002/biot.202300710] [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: 12/15/2023] [Revised: 03/08/2024] [Accepted: 03/09/2024] [Indexed: 04/08/2024]
Abstract
Reconstruction and optimization of biosynthetic pathways can help to overproduce target chemicals in microbial cell factories based on genetic engineering. However, the perturbation of biosynthetic pathways on cellular metabolism is not well investigated and profiling the engineered microbes remains challenging. The rapid development of omics tools has the potential to characterize the engineered microbial cell factory. Here, we performed label-free quantitative proteomic analysis and metabolomic analysis of engineered sabinene overproducing Saccharomyces cerevisiae strains. Combined metabolic analysis andproteomic analysis of targeted mevalonate (MVA) pathway showed that co-ordination of cytosolic and mitochondrial pathways had balanced metabolism, and genome integration of biosynthetic genes had higher sabinene production with less MVA enzymes. Furthermore, comparative proteomic analysis showed that compartmentalized mitochondria pathway had perturbation on central cellular metabolism. This study provided an omics analysis example for characterizing engineered cell factory, which can guide future regulation of the cellular metabolism and maintaining optimal protein expression levels for the synthesis of target products.
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Affiliation(s)
- Rui Hou
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Mengying Shan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Xinxin Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Mingdong Yao
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Kaiguang Yang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Ying Wang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, China
| | - Zhigang Sui
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhen Liang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Yukui Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Lihua Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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Zheng C, Hou S, Zhou Y, Yu C, Li H. Regulation of the PFK1 gene on the interspecies microbial competition behavior of Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2024; 108:272. [PMID: 38517486 PMCID: PMC10959778 DOI: 10.1007/s00253-024-13091-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/24/2024]
Abstract
Saccharomyces cerevisiae is a widely used strain for ethanol fermentation; meanwhile, efficient utilization of glucose could effectively promote ethanol production. The PFK1 gene is a key gene for intracellular glucose metabolism in S. cerevisiae. Our previous work suggested that although deletion of the PFK1 gene could confer higher oxidative tolerance to S. cerevisiae cells, the PFK1Δ strain was prone to contamination by other microorganisms. High interspecies microbial competition ability is vital for the growth and survival of microorganisms in co-cultures. The result of our previous studies hinted us a reasonable logic that the EMP (i.e., the Embden-Meyerhof-Parnas pathway, the glycolytic pathway) key gene PFK1 could be involved in regulating interspecies competitiveness of S. cerevisiae through the regulation of glucose utilization and ethanol production efficiency. The results suggest that under 2% and 5% glucose, the PFK1Δ strain showed slower growth than the S288c wild-type and TDH1Δ strains in the lag and exponential growth stages, but realized higher growth in the stationary stage. However, relative high supplement of glucose (10%) eliminated this phenomenon, suggesting the importance of glucose in the regulation of PFK1 in yeast cell growth. Furthermore, during the lag growth phase, the PFK1Δ strain displayed a decelerated glucose consumption rate (P < 0.05). The expression levels of the HXT2, HXT5, and HXT6 genes decreased by approximately 0.5-fold (P < 0.05) and the expression level of the ZWF1 exhibited a onefold increase in the PFK1Δ strain compared to that in the S. cerevisiae S288c wild-type strain (P < 0.05).These findings suggested that the PFK1 inhibited the uptake and utilization of intracellular glucose by yeast cells, resulting in a higher amount of residual glucose in the medium for the PFK1Δ strain to utilize for growth during the reverse overshoot stage in the stationary phase. The results presented here also indicated the potential of ethanol as a defensive weapon against S. cerevisiae. The lower ethanol yield in the early stage of the PFK1Δ strain (P < 0.001) and the decreased expression levels of the PDC5 and PDC6 (P < 0.05), which led to slower growth, resulted in the strain being less competitive than the wild-type strain when co-cultured with Escherichia coli. The lower interspecies competitiveness of the PFK1Δ strain further promoted the growth of co-cultured E. coli, which in turn activated the ethanol production efficiency of the PFK1Δ strain to antagonize it from E. coli at the stationary stage. The results presented clarified the regulation of the PFK1 gene on the growth and interspecies microbial competition behavior of S. cerevisiae and would help us to understand the microbial interactions between S. cerevisiae and other microorganisms. KEY POINTS: • PFK1Δ strain could realize reverse growth overshoot at the stationary stage • PFK1 deletion decreased ethanol yield and interspecific competitiveness • Proportion of E. coli in co-culture affected ethanol yield capacity of yeast cells.
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Affiliation(s)
- Caijuan Zheng
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Shuxin Hou
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Yu Zhou
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China
| | - Changyuan Yu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, 100029, People's Republic of China
| | - Hao Li
- School of Public Health, Jining Medical University, Jining, 272067, People's Republic of China.
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Shin J, Liao S, Kuanyshev N, Xin Y, Kim C, Lu T, Jin YS. Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium. Nat Commun 2024; 15:781. [PMID: 38278783 PMCID: PMC10817915 DOI: 10.1038/s41467-024-45011-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 01/11/2024] [Indexed: 01/28/2024] Open
Abstract
Synthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
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Affiliation(s)
- Jonghyeok Shin
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, Republic of Korea
| | - Siqi Liao
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Nurzhan Kuanyshev
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongping Xin
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Chanwoo Kim
- 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
| | - Ting Lu
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL, 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.
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Samakkarn W, Vandecruys P, Moreno MRF, Thevelein J, Ratanakhanokchai K, Soontorngun N. New biomarkers underlying acetic acid tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Appl Microbiol Biotechnol 2024; 108:153. [PMID: 38240846 PMCID: PMC10799125 DOI: 10.1007/s00253-023-12946-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 10/16/2023] [Accepted: 10/17/2023] [Indexed: 01/22/2024]
Abstract
Evolutionary engineering experiments, in combination with omics technologies, revealed genetic markers underpinning the molecular mechanisms behind acetic acid stress tolerance in the probiotic yeast Saccharomyces cerevisiae var. boulardii. Here, compared to the ancestral Ent strain, evolved yeast strains could quickly adapt to high acetic acid levels (7 g/L) and displayed a shorter lag phase of growth. Bioinformatic-aided whole-genome sequencing identified genetic changes associated with enhanced strain robustness to acetic acid: a duplicated sequence in the essential endocytotic PAN1 gene, mutations in a cell wall mannoprotein (dan4Thr192del), a lipid and fatty acid transcription factor (oaf1Ser57Pro) and a thiamine biosynthetic enzyme (thi13Thr332Ala). Induction of PAN1 and its associated endocytic complex SLA1 and END3 genes was observed following acetic acid treatment in the evolved-resistant strain when compared to the ancestral strain. Genome-wide transcriptomic analysis of the evolved Ent acid-resistant strain (Ent ev16) also revealed a dramatic rewiring of gene expression among genes associated with cellular transport, metabolism, oxidative stress response, biosynthesis/organization of the cell wall, and cell membrane. Some evolved strains also displayed better growth at high acetic acid concentrations and exhibited adaptive metabolic profiles with altered levels of secreted ethanol (4.0-6.4% decrease), glycerol (31.4-78.5% increase), and acetic acid (53.0-60.3% increase) when compared to the ancestral strain. Overall, duplication/mutations and transcriptional alterations are key mechanisms driving improved acetic acid tolerance in probiotic strains. We successfully used adaptive evolutionary engineering to rapidly and effectively elucidate the molecular mechanisms behind important industrial traits to obtain robust probiotic yeast strains for myriad biotechnological applications. KEY POINTS: •Acetic acid adaptation of evolutionary engineered robust probiotic yeast S. boulardii •Enterol ev16 with altered genetic and transcriptomic profiles survives in up to 7 g/L acetic acid •Improved acetic acid tolerance of S. boulardii ev16 with mutated PAN1, DAN4, OAF1, and THI13 genes.
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Affiliation(s)
- Wiwan Samakkarn
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Paul Vandecruys
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Maria Remedios Foulquié Moreno
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
| | - Johan Thevelein
- Laboratory of Molecular Cell Biology, Institute of Botany and Microbiology, KU Leuven, Leuven, Heverlee, Belgium
- Center for Microbiology, VIB, Leuven, Flanders, Belgium
- NovelYeast Bv, Open Bio-Incubator, Erasmus High School, (Jette), Brussels, Belgium
| | - Khanok Ratanakhanokchai
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
- Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi, Bangkok, Thailand
| | - Nitnipa Soontorngun
- Excellent Research Laboratory for Yeast Innovation, Division of Biochemical Technology, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi, Bangkok, Thailand.
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Haresh Liya D, Elanchezhian M, Pahari M, Mouroug Anand N, Suresh S, Balaji N, Kumar Jainarayanan A. QPromoters: sequence based prediction of promoter strength in Saccharomyces cesrevisiae. ALL LIFE 2023. [DOI: 10.1080/26895293.2023.2168304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- Devang Haresh Liya
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mirudula Elanchezhian
- Department of Biological Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Mukulika Pahari
- Department of Computer Engineering, Ramrao Adik Institute of Technology, DY Patil Deemed to be University, Navi Mumbai, India
| | - Nithishwer Mouroug Anand
- Department of Physical Sciences, Indian Institute of Science Education and Research, Mohali, India
| | - Shivani Suresh
- Sheffield Institute for Translational Neuroscience (SITraN), University of Sheffield, Sheffield, UK
| | - Nivedha Balaji
- School of Biology and Environmental Sciences (SBES), University College Dublin, Dublin, Ireland
| | - Ashwin Kumar Jainarayanan
- Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK
- Interdisciplinary Bioscience Doctoral Training Program and Exeter College, University of Oxford, Oxford, UK
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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.
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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
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Cho Y, Kim JH, Choi W, Park DY, Cho BK, Kim YH, Min J. Reassembled Vacuoles for Drug Delivery Carriers Using Yeast Vacuoles for Enhanced Antibacterial Activity. Biomacromolecules 2023; 24:4915-4922. [PMID: 37861681 DOI: 10.1021/acs.biomac.3c00616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
In this study, we aimed to develop an efficient drug delivery system by reassembling vacuoles isolated from Saccharomyces cerevisiae. Initially, we assessed the impact of vacuolar enzymes on the efficacy of the loaded antibiotic polymyxin B (PMB), by conducting antibacterial activity tests using Shigella flexneri and Salmonella enteritidis. The results showed that vacuolar enzymes inhibited the effectiveness of PMB, highlighting the limitations of using natural vacuoles as drug carriers. To overcome this, we proposed a new drug delivery system called reassembled vacuoles (ReV). ReV particles were created by removing vacuolar enzymes and reassembling the vacuolar membrane through extrusion. ReV demonstrated improved structural stability, a more uniform size, and enhanced PMB release compared to natural vacuoles. Encapsulation efficiency tests revealed high loading efficiency for both normal vacuoles (NorV) and ReV, with over 80% efficiency at concentrations up to 600 μg/mL. The antibacterial activity of PMB-loaded ReV showed comparable results to PMB alone, indicating the potential of ReV as a drug delivery system. In conclusion, reassembled vacuoles offer a promising approach for drug delivery, addressing the limitations of natural vacuoles and providing opportunities for targeted and efficient drug release.
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Affiliation(s)
- Yunyoung Cho
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-Gu Jeonju, Jeonbuk 54896, South Korea
| | - Ji Hun Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Wooil Choi
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-Gu Jeonju, Jeonbuk 54896, South Korea
| | - Dae-Young Park
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, 291 Daehak-ro, Yuseong-Gu, Daejeon 34141, South Korea
| | - Yang-Hoon Kim
- School of Biological Sciences, Chungbuk National University, 1 Chungdae-Ro, Seowon-Gu, Cheongju 28644, South Korea
| | - Jiho Min
- Graduate School of Semiconductor and Chemical Engineering, Jeonbuk National University, 567 Baekje-daero, Deokjin-Gu Jeonju, Jeonbuk 54896, South Korea
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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.
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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.
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Özçelik C, Beğli Ö, Hınçer A, Ahan RE, Kesici MS, Oğuz O, Kasırga TS, Özçubukçu S, Şeker UÖŞ. Synergistic Screening of Peptide-Based Biotechnological Drug Candidates for Neurodegenerative Diseases Using Yeast Display and Phage Display. ACS Chem Neurosci 2023; 14:3609-3621. [PMID: 37638647 PMCID: PMC10557061 DOI: 10.1021/acschemneuro.3c00248] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 08/14/2023] [Indexed: 08/29/2023] Open
Abstract
Peptide therapeutics are robust and promising molecules for treating diverse disease conditions. These molecules can be developed from naturally occurring or mimicking native peptides, through rational design and peptide libraries. We developed a new platform for the rapid screening of the peptide therapeutics for disease targets. In the course of the study, we aimed to employ our platform to screen a new generation of peptide therapeutic candidates against aggregation-prone protein targets. Two peptide drug candidates were screened for protein aggregation-prone diseases, namely, Parkinson's and Alzheimer's diseases. Currently, there are several therapeutic applications that are only effective in masking or slowing down symptom development. Nonetheless, different approaches are being developed for inhibiting amyloid aggregation in the secondary nucleation phase, which is critical for amyloid fibril formation. Instead of targeting secondary nucleated protein structures, we tried to inhibit the aggregation of monomeric amyloid units as a novel approach for halting the disease condition. To achieve this, we combined yeast surface display and phage display library platforms. We expressed α-synuclein, amyloid β40, and amyloid β42 on the yeast surface, and we selected peptides by using phage display library. After iterative biopanning cycles optimized for yeast cells, several peptides were selected for interaction studies. All of the peptides have been used for in vitro characterization methods, which are quartz crystal microbalance-dissipation (QCM-D) measurement, atomic force microscopy (AFM) imaging, dot-blotting, and ThT assay, and some of them have yielded promising results in blocking fibrillization. The rest of the peptides, although, interacted with amyloid units which made them usable as a sensor molecule candidate. Therefore, peptides selected by yeast surface display and phage display library combination are good choice for diverse disease-prone molecule inhibition, particularly those inhibiting fibrillization. Additionally, these selected peptides can be used as drugs and sensors to detect diseases quickly and halt disease progression.
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Affiliation(s)
- Cemile
Elif Özçelik
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Özge Beğli
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Ahmet Hınçer
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Recep Erdem Ahan
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Mehmet Seçkin Kesici
- Department
of Chemistry, Faculty of Science, Middle
East Technical University, Ankara 06800, Turkey
| | - Oğuzhan Oğuz
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Talip Serkan Kasırga
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
| | - Salih Özçubukçu
- Department
of Chemistry, Faculty of Science, Middle
East Technical University, Ankara 06800, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM
− Institute of Materials Science and Nanotechnology, Bilkent University, Ankara 06800, Turkey
- Interdisciplinary
Program in Neuroscience, Bilkent University, Ankara 06800, Turkey
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12
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Wang B, Zhao X, Fu T, Chen X, Guo X, Li X, Yang F. Glucose Starvation Stimulates the Promoting Strength of a Novel Evolved Suc2 Promoter. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:13838-13847. [PMID: 37669532 DOI: 10.1021/acs.jafc.3c03699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
Promoters are essential for designing Saccharomyces cerevisiae cell factories. Identifying novel promoters tuned to produce specific metabolites under increasingly diverse industrial stresses is required to improve the economic feasibility of whole fermentation processes. In this study, a positively evolved Suc2 promoter (SUC 2p) with promoter activity stronger than that of the wild-type Suc2 promoter (SUC 2wtp) was obtained. Quantitative real-time PCR, fluorescence analysis, Western blotting, and a β-galactosidase activity assay revealed that SUC 2p is a medium-strength promoter compared with eight reported promoters at a medium glucose concentration (2% (w/v)). Different glucose concentrations modulated the strength of SUC 2p. Low glucose concentrations (0.05 and 0.5% (w/v)) enhanced the promoter strength of SUC 2p dramatically, with promoter activity higher than that of reported strong promoters. Glucose starvation resulted in the formation of a new Msn2/4 binding site on SUC 2p. Our work should facilitate the development of promoters with novel fine-tuning properties and the construction of S. cerevisiae cell factories suitable for the industrial production of essential chemicals under glucose-deprived conditions.
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Affiliation(s)
- Biying Wang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoya Zhao
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Tong Fu
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyi Chen
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xiaoyu Guo
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Xianzhen Li
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
| | - Fan Yang
- School of Biological Engineering, Dalian Polytechnic University, Ganjingziqu, Dalian 116034, P. R. China
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13
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Wayllace NM, Martín M, Busi MV, Gomez-Casati DF. Microbial glucoamylases: structural and functional properties and biotechnological uses. World J Microbiol Biotechnol 2023; 39:293. [PMID: 37653355 DOI: 10.1007/s11274-023-03731-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 08/14/2023] [Indexed: 09/02/2023]
Abstract
Glucoamylases (GAs) are one of the principal groups of enzymes involved in starch hydrolysis and belong to the glycosylhydrolase family. They are classified as exo-amylases due to their ability to hydrolyze α-1,4 glycosidic bonds from the non-reducing end of starch, maltooligosaccharides, and related substrates, releasing β-D-glucose. Structurally, GAs possess a characteristic catalytic domain (CD) with an (α/α)6 fold and exhibit five conserved regions within this domain. The CD may or may not be linked to a non-catalytic domain with variable functions depending on its origin. GAs are versatile enzymes with diverse applications in food, biofuel, bioplastic and other chemical industries. Although fungal GAs are commonly employed for these purposes, they have limitations such as their low thermostability and an acidic pH requirement. Alternatively, GAs derived from prokaryotic organisms are a good option to save costs as they exhibit greater thermostability compared to fungal GAs. Moreover, a group of cold-adapted GAs from psychrophilic organisms demonstrates intriguing properties that make them suitable for application in various industries. This review provides a comprehensive overview of the structural and sequential properties as well as biotechnological applications of GAs in different industrial processes.
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Affiliation(s)
- Natael M Wayllace
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - Mariana Martín
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina
| | - María V Busi
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
| | - Diego F Gomez-Casati
- CEFOBI-CONICET. Centro de Estudios Fotosintéticos y Bioquímicos - Consejo Nacional de Investigaciones Científicas y Técnicas. Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Suipacha 531, Rosario, Santa Fe, Argentina.
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14
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Petroleum Hydrocarbon Catabolic Pathways as Targets for Metabolic Engineering Strategies for Enhanced Bioremediation of Crude-Oil-Contaminated Environments. FERMENTATION-BASEL 2023. [DOI: 10.3390/fermentation9020196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Anthropogenic activities and industrial effluents are the major sources of petroleum hydrocarbon contamination in different environments. Microbe-based remediation techniques are known to be effective, inexpensive, and environmentally safe. In this review, the metabolic-target-specific pathway engineering processes used for improving the bioremediation of hydrocarbon-contaminated environments have been described. The microbiomes are characterised using environmental genomics approaches that can provide a means to determine the unique structural, functional, and metabolic pathways used by the microbial community for the degradation of contaminants. The bacterial metabolism of aromatic hydrocarbons has been explained via peripheral pathways by the catabolic actions of enzymes, such as dehydrogenases, hydrolases, oxygenases, and isomerases. We proposed that by using microbiome engineering techniques, specific pathways in an environment can be detected and manipulated as targets. Using the combination of metabolic engineering with synthetic biology, systemic biology, and evolutionary engineering approaches, highly efficient microbial strains may be utilised to facilitate the target-dependent bioprocessing and degradation of petroleum hydrocarbons. Moreover, the use of CRISPR-cas and genetic engineering methods for editing metabolic genes and modifying degradation pathways leads to the selection of recombinants that have improved degradation abilities. The idea of growing metabolically engineered microbial communities, which play a crucial role in breaking down a range of pollutants, has also been explained. However, the limitations of the in-situ implementation of genetically modified organisms pose a challenge that needs to be addressed in future research.
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15
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Steyn A, Viljoen-Bloom M, Van Zyl WH. Constructing recombinant Saccharomyces cerevisiae strains for malic-to-fumaric acid conversion. FEMS Microbiol Lett 2023; 370:6988173. [PMID: 36646426 PMCID: PMC10086307 DOI: 10.1093/femsle/fnad003] [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: 09/15/2022] [Revised: 12/09/2022] [Accepted: 01/13/2023] [Indexed: 01/18/2023] Open
Abstract
Saccharomyces cerevisiae with its robustness and good acid tolerance, is an attractive candidate for use in various industries, including waste-based biorefineries where a high-value organic acid is produced, such as fumaric acid could be beneficial. However, this yeast is not a natural producer of dicarboxylic acids, and genetic engineering of S. cerevisiae strains is required to achieve this outcome. Disruption of the natural FUM1 gene and the recombinant expression of fumarase and malate transporter genes improved the malic acid-to-fumaric acid conversion by engineered S. cerevisiae strains. The efficacy of the strains was significantly influenced by the source of the fumarase gene (yeast versus bacterial), the presence of the XYNSEC signal secretion signal and the available oxygen in synthetic media cultivations. The ΔFUM1Ckr_fum + mae1 and ΔFUM1(ss)Ckr_fum + mae1 strains converted extracellular malic acid into 0.98 and 1.11 g/L fumaric acid under aerobic conditions.
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Affiliation(s)
- Annica Steyn
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Marinda Viljoen-Bloom
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
| | - Willem Heber Van Zyl
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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16
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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.
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17
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Yang P, Jiang S, Lu S, Jiang S, Jiang S, Deng Y, Lu J, Wang H, Zhou Y. Ethanol yield improvement in Saccharomyces cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta mutant and molecular mechanism exploration based on the metabolic flux and transcriptomics approaches. Microb Cell Fact 2022; 21:160. [PMID: 35964044 PMCID: PMC9375381 DOI: 10.1186/s12934-022-01885-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 08/05/2022] [Indexed: 11/10/2022] Open
Abstract
Background Saccharomyces cerevisiae generally consumes glucose to produce ethanol accompanied by the main by-products of glycerol, acetic acid, and lactic acid. The minimization of the formation of by-products in S. cerevisiae was an effective way to improve the economic viability of the bioethanol industry. In this study, S. cerevisiae GPD2, FPS1, ADH2, and DLD3 genes were knocked out by the Clustered Regularly Interspaced Short Palindromic Repeats Cas9 (CRISPR-Cas9) approach. The mechanism of gene deletion affecting ethanol metabolism was further elucidated based on metabolic flux and transcriptomics approaches. Results The engineered S. cerevisiae with gene deletion of GPD2, FPS1, ADH2, and DLD3 was constructed by the CRISPR-Cas9 approach. The ethanol content of engineered S. cerevisiae GPD2 Delta FPS1 Delta ADH2 Delta DLD3 Delta increased by 18.58% with the decrease of glycerol, acetic acid, and lactic acid contents by 22.32, 8.87, and 16.82%, respectively. The metabolic flux analysis indicated that the carbon flux rethanol in engineered strain increased from 60.969 to 63.379. The sequencing-based RNA-Seq transcriptomics represented 472 differential expression genes (DEGs) were identified in engineered S. cerevisiae, in which 195 and 277 genes were significantly up-regulated and down-regulated, respectively. The enriched pathways of up-regulated genes were mainly involved in the energy metabolism of carbohydrates, while the down-regulated genes were mainly enriched in acid metabolic pathways. Conclusions The yield of ethanol in engineered S. cerevisiae increased with the decrease of the by-products including glycerol, acetic acid, and lactic acid. The deletion of genes GPD2, FPS1, ADH2, and DLD3 resulted in the redirection of carbon flux. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01885-3.
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Affiliation(s)
- Peizhou Yang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China.
| | - Shuying Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Shuhua Lu
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Suwei Jiang
- Department of Biological, Food and Environment Engineering, Hefei University, 158 Jinxiu Avenue, Hefei, 230601, China
| | - Shaotong Jiang
- College of Food and Biological Engineering, Anhui Key Laboratory of Intensive Processing of Agricultural Products, Hefei University of Technology, 420 Feicui Road, Shushan District, Hefei, 230601, Anhui, China
| | - Yanhong Deng
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Jiuling Lu
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Hu Wang
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
| | - Yong Zhou
- Suzhou Cofco Biochemical Co., Ltd., Suzhou, 234001, China
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18
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Current Ethanol Production Requirements for the Yeast Saccharomyces cerevisiae. Int J Microbiol 2022; 2022:7878830. [PMID: 35996633 PMCID: PMC9392646 DOI: 10.1155/2022/7878830] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 06/28/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022] Open
Abstract
An increase in global energy demand has caused oil prices to reach record levels in recent times. High oil prices together with concerns over CO2 emissions have resulted in renewed interest in renewable energy. Nowadays, ethanol is the principal renewable biofuel. However, the industrial need for increased productivity, wider substrate range utilization, and the production of novel compounds leads to renewed interest in further extending the use of current industrial strains by exploiting the immense, and still unknown, potential of natural yeast strains. This review seeks to answer the following questions: (a) which characteristics should S. cerevisiae have for the current production of first- and second-generation ethanol? (b) Why are alcohol-tolerance and thermo-tolerance characteristics required? (c) Which genes are related to these characteristics? (d) What are the advances that can be achieved with the isolation of new organisms from the environment?
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19
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Identification of the sesquiterpene synthase AcTPS1 and high production of (-)-germacrene D in metabolically engineered Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:89. [PMID: 35585553 PMCID: PMC9115970 DOI: 10.1186/s12934-022-01814-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 05/03/2022] [Indexed: 12/04/2022] Open
Abstract
Background The sesquiterpene germacrene D is a highly promising product due to its wide variety of insecticidal activities and ability to serve as a precursor for many other sesquiterpenes. Biosynthesis of high value compounds through genome mining for synthases and metabolic engineering of microbial factories, especially Saccharomyces cerevisiae, has been proven to be an effective strategy. However, there have been no studies on the de novo synthesis of germacrene D from carbon sources in microbes. Hence, the construction of the S. cerevisiae cell factory to achieve high production of germacrene D is highly desirable. Results We identified five putative sesquiterpene synthases (AcTPS1 to AcTPS5) from Acremonium chrysogenum and the major product of AcTPS1 characterized by in vivo, in vitro reaction and NMR detection was revealed to be (–)-germacrene D. After systematically comparing twenty-one germacrene D synthases, AcTPS1 was found to generate the highest amount of (–)-germacrene D and was integrated into the terpene precursor-enhancing yeast strain, achieving 376.2 mg/L of (–)-germacrene D. Iterative engineering was performed to improve the production of (–)-germacrene D, including increasing the copy numbers of AcTPS1, tHMG1 and ERG20, and downregulating or knocking out other inhibitory factors (such as erg9, rox1, dpp1). Finally, the optimal strain LSc81 achieved 1.94 g/L (–)-germacrene D in shake-flask fermentation and 7.9 g/L (–)-germacrene D in a 5-L bioreactor, which is the highest reported (–)-germacrene D titer achieved to date. Conclusion We successfully achieved high production of (–)-germacrene D in S. cerevisiae through terpene synthase mining and metabolic engineering, providing an impressive example of microbial overproduction of high-value compounds. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01814-4.
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Das PK, Sahoo A, Dasu VV. Current status, and the developments of hosts and expression systems for the production of recombinant human cytokines. Biotechnol Adv 2022; 59:107969. [PMID: 35525478 DOI: 10.1016/j.biotechadv.2022.107969] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 02/07/2023]
Abstract
Cytokines consist of peptides, proteins and glycoproteins, which are biological signaling molecules, and boost cell-cell communication in immune reactions to stimulate cellular movements in the place of trauma, inflammation and infection. Recombinant cytokines are designed in such a way that they have generalized immunostimulation action or stimulate specific immune cells when the body encounters immunosuppressive signals from exogenous pathogens or other tumor microenvironments. Recombinant cytokines have improved the treatment processes for numerous diseases. They are also beneficial against novel toxicities that arise due to pharmacologic immunostimulators that lead to an imbalance in the regulation of cytokine. So, the production and use of recombinant human cytokines as therapeutic proteins are significant for medical treatment purposes. For the improved production of recombinant human cytokines, the development of host cells such as bacteria, yeast, fungi, insect, mammal and transgenic plants, and the specific expression systems for individual hosts is necessary. The recent advancements in the field of genetic engineering are beneficial for easy and efficient genetic manipulations for hosts as well as expression cassettes. The use of metabolic engineering and systems biology approaches have tremendous applications in recombinant protein production by generating mathematical models, and analyzing complex biological networks and metabolic pathways via simulations to understand the interconnections between metabolites and genetic behaviors. Further, the bioprocess developments and the optimization of cell culture conditions would enhance recombinant cytokines productivity on large scales.
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Affiliation(s)
- Prabir Kumar Das
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Ansuman Sahoo
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Veeranki Venkata Dasu
- Biochemical Engineering Laboratory, Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India.
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Abid R, Waseem H, Ali J, Ghazanfar S, Muhammad Ali G, Elasbali AM, Alharethi SH. Probiotic Yeast Saccharomyces: Back to Nature to Improve Human Health. J Fungi (Basel) 2022; 8:jof8050444. [PMID: 35628700 PMCID: PMC9147304 DOI: 10.3390/jof8050444] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/11/2022] [Accepted: 03/18/2022] [Indexed: 02/02/2023] Open
Abstract
Saccharomyces cerevisiae var. boulardii is best known for its treatment efficacy against different gastrointestinal diseases. This probiotic yeast can significantly protect the normal microbiota of the human gut and inhibit the pathogenicity of different diarrheal infections. Several clinical investigations have declared S. cerevisiae var. boulardii a biotherapeutic agent due to its antibacterial, antiviral, anti-carcinogenic, antioxidant, anti-inflammatory and immune-modulatory properties. Oral or intramuscular administration of S. cerevisiae var. boulardii can remarkably induce health-promoting effects in the host body. Different intrinsic and extrinsic factors are responsible for its efficacy against acute and chronic gut-associated diseases. This review will discuss the clinical and beneficial effects of S. cerevisiae var. boulardii in the treatment and prevention of different metabolic diseases and highlight some of its health-promising properties. This review article will provide fundamental insights for new avenues in the fields of biotherapeutics, antimicrobial resistance and one health.
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Affiliation(s)
- Rameesha Abid
- Department of Biotechnology, University of Sialkot, Sialkot 51310, Pakistan;
- National Agriculture Research Center, National Institute of Genomics and Agriculture Biotechnology (NIGAB), Islamabad 44100, Pakistan;
- Correspondence: (A.M.E.); (R.A.)
| | - Hassan Waseem
- Department of Biological Sciences, Muslim Youth University, Islamabad 44100, Pakistan;
| | - Jafar Ali
- Department of Biotechnology, University of Sialkot, Sialkot 51310, Pakistan;
- Department of Biological Sciences, Muslim Youth University, Islamabad 44100, Pakistan;
| | - Shakira Ghazanfar
- National Agriculture Research Center, National Institute of Genomics and Agriculture Biotechnology (NIGAB), Islamabad 44100, Pakistan;
| | - Ghulam Muhammad Ali
- Pakistan Agricultural Research Council (PARC) 20, Ataturk Avenue, G-5/1, Islamabad 44000, Pakistan;
| | - Abdelbaset Mohamed Elasbali
- Department of Clinical Laboratory Science, College of Applied Sciences-Qurayyat, Jouf University, Al-Jouf P.O. Box 2014, Saudi Arabia
- Correspondence: (A.M.E.); (R.A.)
| | - Salem Hussain Alharethi
- Department of Biological Science, College of Arts and Science, Najran University, Najran 66262, Saudi Arabia;
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22
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Incorporating, Quantifying, and Leveraging Noncanonical Amino Acids in Yeast. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2022; 2394:377-432. [PMID: 35094338 DOI: 10.1007/978-1-0716-1811-0_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Genetic code expansion has allowed for extraordinary advances in enhancing protein chemical diversity and functionality, but there remains a critical need for understanding and engineering genetic code expansion systems for improved efficiency. Incorporation of noncanonical amino acids (ncAAs) at stop codons provides a site-specific method for introducing unique chemistry into proteins, though often at reduced yields compared to wild-type proteins. A powerful platform for ncAA incorporation supports both the expression and evaluation of chemically diverse proteins for a broad range of applications. In yeast, ncAAs have been used to study dynamic cellular processes such as protein-protein interactions and also allow for exploration of eukaryotic-specific biology such as epigenetics. Furthermore, yeast display is an advantageous technology for engineering and screening the properties of proteins in high throughput. The protocols presented in this chapter describe detailed methods for the yeast-based genetic encoding of ncAAs in proteins intracellularly or on the yeast surface. In addition, methods are presented for modifying proteins on the yeast surface using bioorthogonal chemical reactions and evaluating reaction efficiency. Finally, protocols are included for the preparation of libraries that involve genetic code expansion. Libraries of proteins that contain ncAAs or libraries of the cellular machinery required to encode ncAAs can be constructed and screened in high throughput for many biological and chemical applications. Efficient incorporation of ncAAs facilitates elucidation of fundamental eukaryotic biology and advances tools for enzyme and genome engineering to evolve host cells that are better able to accommodate alternative genetic codes.
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23
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Li S, Ma L, Fu W, Su R, Zhao Y, Deng Y. Programmable Synthetic Upstream Activating Sequence Library for Fine-Tuning Gene Expression Levels in Saccharomyces cerevisiae. ACS Synth Biol 2022; 11:1228-1239. [PMID: 35195994 DOI: 10.1021/acssynbio.1c00511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A wide dynamic range of promoters is necessary for fine-tuning transcription levels. However, weak intensity and narrow dynamic range limit transcriptional regulation via constitutive promoters. The upstream activation sequence (UAS) located upstream of the core promoter is a crucial region that could obviously enhance promoter strength. Herein, we created a random mutagenesis library consisting of 330 different variants based on the UAS of the TDH3 promoter with an ∼37-fold dynamic range by error-prone polymerase chain reaction (PCR) and obtained strong intensity mutant UAS, which was ∼12-fold greater than the wild-type UASTDH3. Analysis of the mutant library revealed 15 strength-enhancing sites and their corresponding bases of the UASTDH3 regions, which provided the impetus for a synthetic library. The resulting 32 768 mutant UAS library was constructed by permutation and combination of the bases of the 15 enhancing sites. To characterize the library, a strength prediction model was built by correlating DNA structural features and UAS strength, which provided a model between UAS sequence and intensity. Following characterization, the UAS library was applied to precisely regulate gene expression in the production of β-carotene, proving that the UAS library would be a useful tool for gene tuning in metabolic engineering. In summary, we designed, constructed, and characterized a UAS library that facilitated precise tuning of transcription levels of target proteins.
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Affiliation(s)
- Shiyun Li
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Lizhou Ma
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Wenxuan Fu
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Ruifang Su
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yunying Zhao
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
| | - Yu Deng
- National Engineering Laboratory for Cereal Fermentation Technology (NELCF), Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
- Jiangsu Provincial Research Center for Bioactive Product Processing Technology, Jiangnan University, 1800 Lihu Road, Wuxi, Jiangsu 214122, China
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Physiological comparisons among Spathaspora passalidarum, Spathaspora arborariae, and Scheffersomyces stipitis reveal the bottlenecks for their use in the production of second-generation ethanol. Braz J Microbiol 2022; 53:977-990. [PMID: 35174461 PMCID: PMC9151973 DOI: 10.1007/s42770-022-00693-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 12/21/2021] [Indexed: 02/01/2023] Open
Abstract
The microbial conversion of pentoses to ethanol is one of the major drawbacks that limits the complete use of lignocellulosic sugars. In this study, we compared the yeast species Spathaspora arborariae, Spathaspora passalidarum, and Sheffersomyces stipitis regarding their potential use for xylose fermentation. Herein, we evaluated the effects of xylose concentration, presence of glucose, and temperature on ethanol production. The inhibitory effects of furfural, hydroxymethylfurfural (HMF), acetic acid, and ethanol were also determined. The highest ethanol yield (0.44 g/g) and productivity (1.02 g/L.h) were obtained using Sp. passalidarum grown in 100 g/L xylose at 32 °C. The rate of xylose consumption was reduced in the presence of glucose for the species tested. Hydroxymethylfurfural did not inhibit the growth of yeasts, whereas furfural extended their lag phase. Acetic acid inhibited the growth and fermentation of all yeasts. Furthermore, we showed that these xylose-fermenting yeasts do not produce ethanol concentrations greater than 4% (v/v), probably due to the inhibitory effects of ethanol on yeast physiology. Our data confirm that among the studied yeasts, Sp. passalidarum is the most promising for xylose fermentation, and the low tolerance to ethanol is an important aspect to be improved to increase its performance for second-generation (2G) ethanol production. Our molecular data showed that this yeast failed to induce the expression of some classical genes involved in ethanol tolerance. These findings suggest that Sp. passalidarum may have not activated a proper response to the stress, impacting its ability to overcome the negative effects of ethanol on the cells.
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Procópio DP, Kendrick E, Goldbeck R, Damasio ARDL, Franco TT, Leak DJ, Jin YS, Basso TO. Xylo-Oligosaccharide Utilization by Engineered Saccharomyces cerevisiae to Produce Ethanol. Front Bioeng Biotechnol 2022; 10:825981. [PMID: 35242749 PMCID: PMC8886126 DOI: 10.3389/fbioe.2022.825981] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/18/2022] [Indexed: 11/26/2022] Open
Abstract
The engineering of xylo-oligosaccharide-consuming Saccharomyces cerevisiae strains is a promising approach for more effective utilization of lignocellulosic biomass and the development of economic industrial fermentation processes. Extending the sugar consumption range without catabolite repression by including the metabolism of oligomers instead of only monomers would significantly improve second-generation ethanol production This review focuses on different aspects of the action mechanisms of xylan-degrading enzymes from bacteria and fungi, and their insertion in S. cerevisiae strains to obtain microbial cell factories able of consume these complex sugars and convert them to ethanol. Emphasis is given to different strategies for ethanol production from both extracellular and intracellular xylo-oligosaccharide utilization by S. cerevisiae strains. The suitability of S. cerevisiae for ethanol production combined with its genetic tractability indicates that it can play an important role in xylan bioconversion through the heterologous expression of xylanases from other microorganisms.
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Affiliation(s)
- Dielle Pierotti Procópio
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, Brazil
| | - Emanuele Kendrick
- Department of Biology and Biochemistry, Faculty of Sciences, University of Bath, Bath, United Kingdom
| | - Rosana Goldbeck
- School of Food Engineering, University of Campinas, Campinas, Brazil
| | | | - Telma Teixeira Franco
- Interdisciplinary Center of Energy Planning, University of Campinas, Campinas, Brazil
- School of Chemical Engineering, University of Campinas, Campinas, Brazil
| | - David J. Leak
- Department of Biology and Biochemistry, Faculty of Sciences, University of Bath, Bath, United Kingdom
| | - Yong-Su Jin
- DOE Center for Advanced Bioenergy and Bioproducts Innovation, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- Department of Food Science and Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Thiago Olitta Basso
- Department of Chemical Engineering, Escola Politécnica, University of São Paulo, São Paulo, Brazil
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26
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Kumar V, Bansal V, Madhavan A, Kumar M, Sindhu R, Awasthi MK, Binod P, Saran S. Active pharmaceutical ingredient (API) chemicals: a critical review of current biotechnological approaches. Bioengineered 2022; 13:4309-4327. [PMID: 35135435 PMCID: PMC8973766 DOI: 10.1080/21655979.2022.2031412] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The aim of this article was to generate a framework of bio-based economy by an effective utilization of biomass from the perspectives of agriculture for developing potential end bio-based products (e.g. pharmaceuticals, active pharmaceutical ingredients). Our discussion is also extended to the conservatory ways of bioenergy along with development of bio-based products and biofuels. This review article further showcased the fundamental principles for producing these by-products. Thereby, the necessity of creating these products is to be efficaciously utilization by small-scale farmers that can aid the local needs for bio-based materials and energy. Concurrently, the building up of small markets will open up the avenues and linkages for bigger markets. In nutshell, the aim of the review is to explore the pathway of the biotechnological approaches so that less chosen producers and underdeveloped areas can be allied so that pressure on the systems of biomass production can be relaxed.
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Affiliation(s)
- Vinod Kumar
- Fermentation Technology and Microbial Biotechnology Division, Csir- Indian Institute of Integrative Medicine (Csir-iiim), J & K, India.,Academy of Scientific and Innovative Research (Acsir), Ghaziabad-India
| | - Vasudha Bansal
- Department of Foods and Nutrition, Government Home Science College, Affiliated to Panjab University, Chandigarh, India
| | - Aravind Madhavan
- Division of Infectious Disease Biology, Rajiv Gandhi Centre for Biotechnology, - Trivandrum- India
| | - Manoj Kumar
- Fermentation Technology and Microbial Biotechnology Division, Csir- Indian Institute of Integrative Medicine (Csir-iiim), J & K, India.,Academy of Scientific and Innovative Research (Acsir), Ghaziabad-India
| | - Raveendran Sindhu
- Deapartment of Food Technology, Tkm Institute of Technology, Kollam-India
| | - Mukesh Kumar Awasthi
- Department of Resource and Environmental Science, College of Natural Resources and Environment, Northwest A&f University, Shaanxi Province, Yangling, PR China
| | - Parameswaran Binod
- Microbial Processes and Technology Division, CSIR-National Institute for Interdisciplinary, Science and Technology (Csir-niist), Trivandrum- India
| | - Saurabh Saran
- Fermentation Technology and Microbial Biotechnology Division, Csir- Indian Institute of Integrative Medicine (Csir-iiim), J & K, India
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Sengupta S, Nath R, Bhattacharjee A. Characterizing the effect of S-nitrosoglutathione on Saccharomyces cerevisiae: Upregulation of alcohol dehydrogenase and inactivation of aconitase. Process Biochem 2022. [DOI: 10.1016/j.procbio.2021.12.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Jayakody LN, Chinmoy B, Turner TL. Trends in valorization of highly-toxic lignocellulosic biomass derived-compounds via engineered microbes. BIORESOURCE TECHNOLOGY 2022; 346:126614. [PMID: 34954359 DOI: 10.1016/j.biortech.2021.126614] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2021] [Revised: 12/18/2021] [Accepted: 12/19/2021] [Indexed: 05/26/2023]
Abstract
Lignocellulosic biomass-derived fuels, chemicals, and materials are promising sustainable solutions to replace the current petroleum-based production. The direct microbial conversion of thermos-chemically pretreated lignocellulosic biomass is hampered by the presence of highly toxic chemical compounds. Also, thermo-catalytic upgrading of lignocellulosic biomass generates wastewater that contains heterogeneous toxic chemicals, a mixture of unutilized carbon. Metabolic engineering efforts have primarily focused on the conversion of carbohydrates in lignocellulose biomass; substantial opportunities exist to harness value from toxic lignocellulose-derived toxic compounds. This article presents the comprehensive metabolic routes and tolerance mechanisms to develop robust synthetic microbial cell factories to valorize the highly toxic compounds to advanced-platform chemicals. The obtained platform chemicals can be used to manufacture high-value biopolymers and biomaterials via a hybrid biochemical approach for replacing petroleum-based incumbents. The proposed strategy enables a sustainable bio-based materials economy by microbial biofunneling of lignocellulosic biomass-derived toxic molecules, an untapped biogenic carbon.
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Affiliation(s)
- Lahiru N Jayakody
- School of Biological Science, Southern Illinois University Carbondale, Carbondale, IL, USA; Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
| | - Baroi Chinmoy
- Illinois Sustainable Technology Center, University of Illinois Urbana Champaign, IL, USA
| | - Timothy L Turner
- Northwestern University Feinberg School of Medicine, Chicago, IL, USA
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Semumu T, Gamero A, Boekhout T, Zhou N. Evolutionary engineering to improve Wickerhamomyces subpelliculosus and Kazachstania gamospora for baking. World J Microbiol Biotechnol 2022; 38:48. [PMID: 35089427 DOI: 10.1007/s11274-021-03226-9] [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: 10/26/2021] [Accepted: 12/30/2021] [Indexed: 10/19/2022]
Abstract
The conventional baker's yeast, Saccharomyces cerevisiae, is the indispensable baking yeast of all times. Its monopoly coupled to its major drawbacks, such as streamlined carbon substrate utilisation base and a poor ability to withstand a number of baking associated stresses, prompt the need to search for alternative yeasts to leaven bread in the era of increasingly complex consumer lifestyles. Our previous work identified the inefficient baking attributes of Wickerhamomyces subpelliculosus and Kazachstania gamospora as well as preliminarily observations of improving the fermentative capacity of these potential alternative baker's yeasts using evolutionary engineering. Here we report on the characterisation and improvement in baking traits in five out of six independently evolved lines incubated for longer time and passaged for at least 60 passages relative to their parental strains as well as the conventional baker's yeast. In addition, the evolved clones produced bread with a higher loaf volume when compared to bread baked with either the ancestral strain or the control conventional baker's yeast. Remarkably, our approach improved the yeasts' ability to withstand baking associated stresses, a key baking trait exhibited poorly in both the conventional baker's yeast and their ancestral strains. W. subpelliculosus evolved the best characteristics attractive for alternative baker's yeasts as compared to the evolved K. gamospora strains. These results demonstrate the robustness of evolutionary engineering in development of alternative baker's yeasts.
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Affiliation(s)
- Thandiwe Semumu
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana.
| | - Amparo Gamero
- Department of Preventive Medicine and Public Health, Food Science, Toxicology and Forensic Medicine, Faculty of Pharmacy, University of Valencia, Avda. Vicent Andrés Estellés S/N, Burjassot, 46100, València, Spain
| | - Teun Boekhout
- Westerdijk Fungal Biodiversity Institute, Utrecht, The Netherlands.,Institute of Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
| | - Nerve Zhou
- Department of Biological Sciences and Biotechnology, Botswana International University of Science and Technology, Private Bag 16, Central District, Palapye, Botswana.
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Biosensor for branched-chain amino acid metabolism in yeast and applications in isobutanol and isopentanol production. Nat Commun 2022; 13:270. [PMID: 35022416 PMCID: PMC8755756 DOI: 10.1038/s41467-021-27852-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/15/2021] [Indexed: 11/30/2022] Open
Abstract
Branched-chain amino acid (BCAA) metabolism fulfills numerous physiological roles and can be harnessed to produce valuable chemicals. However, the lack of eukaryotic biosensors specific for BCAA-derived products has limited the ability to develop high-throughput screens for strain engineering and metabolic studies. Here, we harness the transcriptional regulator Leu3p from Saccharomyces cerevisiae to develop a genetically encoded biosensor for BCAA metabolism. In one configuration, we use the biosensor to monitor yeast production of isobutanol, an alcohol derived from valine degradation. Small modifications allow us to redeploy Leu3p in another biosensor configuration that monitors production of the leucine-derived alcohol, isopentanol. These biosensor configurations are effective at isolating high-producing strains and identifying enzymes with enhanced activity from screens for branched-chain higher alcohol (BCHA) biosynthesis in mitochondria as well as cytosol. Furthermore, this biosensor has the potential to assist in metabolic studies involving BCAA pathways, and offers a blueprint to develop biosensors for other products derived from BCAA metabolism. There are a lack of eukaryotic biosensors specific for branched-chain amino acid (BCAA)-derived products. Here the authors report a genetically encoded biosensor for BCAA metabolism based on the Leu3p transcriptional regulator; they use this to monitor yeast production of isobutanol and isopentanol.
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31
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Seo SO, Jin YS. Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annu Rev Food Sci Technol 2022; 13:463-488. [DOI: 10.1146/annurev-food-052720-012228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Nutrition, Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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32
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Lorrine OE, Raja Abd. Rahman RNZ, Tan JS, Raja Khairuddin RF, Salleh AB, Oslan SN. Determination of Putative Vacuolar Proteases, PEP4 and PRB1 in a Novel Yeast Expression Host Meyerozyma guilliermondii Strain SO Using Bioinformatics Tools. PERTANIKA JOURNAL OF SCIENCE AND TECHNOLOGY 2022. [DOI: 10.47836/pjst.30.1.42] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Meyerozyma guilliermondii strain SO, a newly isolated yeast species from spoilt orange, has been used as a host to express the recombinant proteins using methylotrophic yeast promoters. However, as a novel yeast expression system, the vacuolar proteases of this yeast have not been determined, which may have contributed to the low level of heterologous protein secretions. Thus, this study aimed to determine intra- and extracellular proteolytic activity and identify the putative vacuolar proteases using bioinformatics techniques. A clear zone was observed from the nutrient agar skimmed milk screening plate. Proteolytic activity of 117.30 U/ml and 75 U/ml were obtained after 72 h of cultivation for both extracellular and intracellular proteins, respectively. Next, the Hidden Markov model (HMM) was used to detect the presence of the vacuolar proteases (PEP4 and PRB1) from the strain SO proteome. Aspartyl protease (PEP4) with 97.55% identity to Meyerozyma sp. JA9 and a serine protease (PRB1) with 70.91% identity to Candida albicans were revealed. The homology with other yeast vacuolar proteases was confirmed via evolutionary analysis. PROSPER tool prediction of cleavage sites postulated that PEP4 and PRB1 might have caused proteolysis of heterologous proteins in strain SO. In conclusion, two putative vacuolar proteases (PEP4 and PRB1) were successfully identified in strain SO. Further characterization can be done to understand their specific properties, and their effects on heterologous protein expression can be conducted via genome editing.
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Otto M, Liu D, Siewers V. Saccharomyces cerevisiae as a Heterologous Host for Natural Products. Methods Mol Biol 2022; 2489:333-367. [PMID: 35524059 DOI: 10.1007/978-1-0716-2273-5_18] [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: 06/14/2023]
Abstract
Cell factories can provide a sustainable supply of natural products with applications as pharmaceuticals, food-additives or biofuels. Besides being an important model organism for eukaryotic systems, Saccharomyces cerevisiae is used as a chassis for the heterologous production of natural products. Its success as a cell factory can be attributed to the vast knowledge accumulated over decades of research, its overall ease of engineering and its robustness. Many methods and toolkits have been developed by the yeast metabolic engineering community with the aim of simplifying and accelerating the engineering process.In this chapter, a range of methodologies are highlighted, which can be used to develop novel natural product cell factories or to improve titer, rate and yields of an existing cell factory with the goal of developing an industrially relevant strain. The addressed topics are applicable for different stages of a cell factory engineering project and include the choice of a natural product platform strain, expression cassette design for heterologous or native genes, basic and advanced genetic engineering strategies, and library screening methods using biosensors. The many engineering methods available and the examples of yeast cell factories underline the importance and future potential of this host for industrial production of natural products.
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Affiliation(s)
- Maximilian Otto
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Dany Liu
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden
| | - Verena Siewers
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden.
- Novo Nordisk Foundation Center for Biosustainability, Chalmers University of Technology, Gothenburg, Sweden.
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Yaakoub H, Sanchez NS, Ongay-Larios L, Courdavault V, Calenda A, Bouchara JP, Coria R, Papon N. The high osmolarity glycerol (HOG) pathway in fungi †. Crit Rev Microbiol 2021; 48:657-695. [PMID: 34893006 DOI: 10.1080/1040841x.2021.2011834] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
While fungi are widely occupying nature, many species are responsible for devastating mycosis in humans. Such niche diversity explains how quick fungal adaptation is necessary to endow the capacity of withstanding fluctuating environments and to cope with host-imposed conditions. Among all the molecular mechanisms evolved by fungi, the most studied one is the activation of the phosphorelay signalling pathways, of which the high osmolarity glycerol (HOG) pathway constitutes one of the key molecular apparatus underpinning fungal adaptation and virulence. In this review, we summarize the seminal knowledge of the HOG pathway with its more recent developments. We specifically described the HOG-mediated stress adaptation, with a particular focus on osmotic and oxidative stress, and point out some lags in our understanding of its involvement in the virulence of pathogenic species including, the medically important fungi Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus, compared to the model yeast Saccharomyces cerevisiae. Finally, we also highlighted some possible applications of the HOG pathway modifications to improve the fungal-based production of natural products in the industry.
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Affiliation(s)
- Hajar Yaakoub
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
| | - Norma Silvia Sanchez
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Laura Ongay-Larios
- Unidad de Biología Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Vincent Courdavault
- EA2106 "Biomolécules et Biotechnologies Végétales", Université de Tours, Tours, France
| | | | | | - Roberto Coria
- Departamento de Genética Molecular, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Mexico City, Mexico
| | - Nicolas Papon
- Univ Angers, Univ Brest, GEIHP, SFR ICAT, Angers, France
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Ravi S, Gunawan R. ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data. PLoS Comput Biol 2021; 17:e1009589. [PMID: 34758020 PMCID: PMC8608322 DOI: 10.1371/journal.pcbi.1009589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/22/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022] Open
Abstract
Genome-scale metabolic models (GEMs) provide a powerful framework for simulating the entire set of biochemical reactions in a cell using a constraint-based modeling strategy called flux balance analysis (FBA). FBA relies on an assumed metabolic objective for generating metabolic fluxes using GEMs. But, the most appropriate metabolic objective is not always obvious for a given condition and is likely context-specific, which often complicate the estimation of metabolic flux alterations between conditions. Here, we propose a new method, called ΔFBA (deltaFBA), that integrates differential gene expression data to evaluate directly metabolic flux differences between two conditions. Notably, ΔFBA does not require specifying the cellular objective. Rather, ΔFBA seeks to maximize the consistency and minimize inconsistency between the predicted flux differences and differential gene expression. We showcased the performance of ΔFBA through several case studies involving the prediction of metabolic alterations caused by genetic and environmental perturbations in Escherichia coli and caused by Type-2 diabetes in human muscle. Importantly, in comparison to existing methods, ΔFBA gives a more accurate prediction of flux differences. Metabolic alterations are often used as hallmarks of observable phenotypes. In this regard, reconstructed genome-scale metabolic models (GEMs) provide a rich and computable representation of the entire set of biochemical reactions in a cell. However, the performance of analytical tools for predicting metabolic reaction rates or fluxes using GEMs is sensitive to the assumed metabolic objective that is often unknown and likely context-specific. Here, we propose a novel method called ΔFBA that combines differential gene expression data and GEMs to evaluate differences in the metabolic fluxes between two conditions (perturbation vs. control) without the need for specifying a metabolic objective. In our demonstration, ΔFBA outperformed other existing methods in predicting metabolic flux alterations.
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Affiliation(s)
- Sudharshan Ravi
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America
- Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Rudiyanto Gunawan
- Department of Chemical and Biological Engineering, University at Buffalo-SUNY, Buffalo, New York, United States of America
- * E-mail:
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36
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Deng J, Wu Y, Zheng Z, Chen N, Luo X, Tang H, Keasling JD. A synthetic promoter system for well-controlled protein expression with different carbon sources in Saccharomyces cerevisiae. Microb Cell Fact 2021; 20:202. [PMID: 34663323 PMCID: PMC8522093 DOI: 10.1186/s12934-021-01691-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Accepted: 09/27/2021] [Indexed: 11/24/2022] Open
Abstract
Background Saccharomyces cerevisiae is an important synthetic biology chassis for microbial production of valuable molecules. Promoter engineering has been frequently applied to generate more synthetic promoters with a variety of defined characteristics in order to achieve a well-regulated genetic network for high production efficiency. Galactose-inducible (GAL) expression systems, composed of GAL promoters and multiple GAL regulators, have been widely used for protein overexpression and pathway construction in S. cerevisiae. However, the function of each element in synthetic promoters and how they interact with GAL regulators are not well known. Results Here, a library of synthetic GAL promoters demonstrate that upstream activating sequences (UASs) and core promoters have a synergistic relationship that determines the performance of each promoter under different carbon sources. We found that the strengths of synthetic GAL promoters could be fine-tuned by manipulating the sequence, number, and substitution of UASs. Core promoter replacement generated synthetic promoters with a twofold strength improvement compared with the GAL1 promoter under multiple different carbon sources in a strain with GAL1 and GAL80 engineering. These results represent an expansion of the classic GAL expression system with an increased dynamic range and a good tolerance of different carbon sources. Conclusions In this study, the effect of each element on synthetic GAL promoters has been evaluated and a series of well-controlled synthetic promoters are constructed. By studying the interaction of synthetic promoters and GAL regulators, synthetic promoters with an increased dynamic range under different carbon sources are created. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01691-3.
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Affiliation(s)
- Jiliang Deng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,State Key Laboratory of Hybrid Rice, Department of Plant Science, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yanling Wu
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Zhaohui Zheng
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Nanzhu Chen
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiaozhou Luo
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Hongting Tang
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Jay D Keasling
- Center for Synthetic Biochemistry, Shenzhen Institute of Synthetic Biology, Shenzhen Institute for Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.,Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.,Department of Chemical and Biomolecular Engineering & Department of Bioengineering, University of California, Berkeley, CA, 94720, USA.,Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kgs. Lyngby, Denmark
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Perpelea A, Wijaya AW, Martins LC, Rippert D, Klein M, Angelov A, Peltonen K, Teleki A, Liebl W, Richard P, Thevelein JM, Takors R, Sá-Correia I, Nevoigt E. Towards valorization of pectin-rich agro-industrial residues: Engineering of Saccharomyces cerevisiae for co-fermentation of d-galacturonic acid and glycerol. Metab Eng 2021; 69:1-14. [PMID: 34648971 DOI: 10.1016/j.ymben.2021.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/08/2021] [Accepted: 10/01/2021] [Indexed: 10/20/2022]
Abstract
Pectin-rich plant biomass residues represent underutilized feedstocks for industrial biotechnology. The conversion of the oxidized monomer d-galacturonic acid (d-GalUA) to highly reduced fermentation products such as alcohols is impossible due to the lack of electrons. The reduced compound glycerol has therefore been considered an optimal co-substrate, and a cell factory able to efficiently co-ferment these two carbon sources is in demand. Here, we inserted the fungal d-GalUA pathway in a strain of the yeast S. cerevisiae previously equipped with an NAD-dependent glycerol catabolic pathway. The constructed strain was able to consume d-GalUA with the highest reported maximum specific rate of 0.23 g gCDW-1 h-1 in synthetic minimal medium when glycerol was added. By means of a 13C isotope-labelling analysis, carbon from both substrates was shown to end up in pyruvate. The study delivers the proof of concept for a co-fermentation of the two 'respiratory' carbon sources to ethanol and demonstrates a fast and complete consumption of d-GalUA in crude sugar beet pulp hydrolysate under aerobic conditions. The future challenge will be to achieve co-fermentation under industrial, quasi-anaerobic conditions.
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Affiliation(s)
- Andreea Perpelea
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Andy Wiranata Wijaya
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany; Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Luís C Martins
- iBB - Institute for Bioengineering and Biosciences/i4HB-Associate Laboratory Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Dorthe Rippert
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany
| | - Angel Angelov
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str 4, 85354, Freising-Weihenstephan, Germany; NGS Competence Center Tübingen, Universitätsklinikum Tübingen, Calwerstraße 7, 72076, Tübingen, Germany
| | - Kaisa Peltonen
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, VTT Espoo, Finland
| | - Attila Teleki
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Wolfgang Liebl
- Chair of Microbiology, TUM School of Life Sciences, Technical University of Munich, Emil-Ramann-Str 4, 85354, Freising-Weihenstephan, Germany
| | - Peter Richard
- VTT Technical Research Centre of Finland Ltd., P.O. Box 1000, 02044, VTT Espoo, Finland
| | - Johan M Thevelein
- NovelYeast bv, Open Bio-Incubator, Erasmus High School, Laarbeeklaan 121, 1090, Brussels (Jette), Belgium
| | - Ralf Takors
- Institute of Biochemical Engineering, University of Stuttgart, Allmandring 31, 70569, Stuttgart, Germany
| | - Isabel Sá-Correia
- iBB - Institute for Bioengineering and Biosciences/i4HB-Associate Laboratory Institute for Health and Bioeconomy at Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal; Department of Bioengineering, Instituto Superior Técnico, Universidade de Lisboa, Av. Rovisco Pais, 1049-001, Lisbon, Portugal
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759, Bremen, Germany.
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38
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An integrated in vivo/in vitro framework to enhance cell-free biosynthesis with metabolically rewired yeast extracts. Nat Commun 2021; 12:5139. [PMID: 34446711 PMCID: PMC8390474 DOI: 10.1038/s41467-021-25233-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 07/30/2021] [Indexed: 02/07/2023] Open
Abstract
Cell-free systems using crude cell extracts present appealing opportunities for designing biosynthetic pathways and enabling sustainable chemical synthesis. However, the lack of tools to effectively manipulate the underlying host metabolism in vitro limits the potential of these systems. Here, we create an integrated framework to address this gap that leverages cell extracts from host strains genetically rewired by multiplexed CRISPR-dCas9 modulation and other metabolic engineering techniques. As a model, we explore conversion of glucose to 2,3-butanediol in extracts from flux-enhanced Saccharomyces cerevisiae strains. We show that cellular flux rewiring in several strains of S. cerevisiae combined with systematic optimization of the cell-free reaction environment significantly increases 2,3-butanediol titers and volumetric productivities, reaching productivities greater than 0.9 g/L-h. We then show the generalizability of the framework by improving cell-free itaconic acid and glycerol biosynthesis. Our coupled in vivo/in vitro metabolic engineering approach opens opportunities for synthetic biology prototyping efforts and cell-free biomanufacturing.
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39
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Tippelt A, Nett M. Saccharomyces cerevisiae as host for the recombinant production of polyketides and nonribosomal peptides. Microb Cell Fact 2021; 20:161. [PMID: 34412657 PMCID: PMC8374128 DOI: 10.1186/s12934-021-01650-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 08/05/2021] [Indexed: 01/30/2023] Open
Abstract
As a robust, fast growing and genetically tractable organism, the budding yeast Saccharomyces cerevisiae is one of the most widely used hosts in biotechnology. Its applications range from the manufacturing of vaccines and hormones to bulk chemicals and biofuels. In recent years, major efforts have been undertaken to expand this portfolio to include structurally complex natural products, such as polyketides and nonribosomally synthesized peptides. These compounds often have useful pharmacological properties, which make them valuable drugs for the treatment of infectious diseases, cancer, or autoimmune disorders. In nature, polyketides and nonribosomal peptides are generated by consecutive condensation reactions of short chain acyl-CoAs or amino acids, respectively, with the substrates and reaction intermediates being bound to large, multidomain enzymes. For the reconstitution of these multistep catalytic processes, the enzymatic assembly lines need to be functionally expressed and the required substrates must be supplied in reasonable quantities. Furthermore, the production hosts need to be protected from the toxicity of the biosynthetic products. In this review, we will summarize and evaluate the status quo regarding the heterologous production of polyketides and nonribosomal peptides in S. cerevisiae. Based on a comprehensive literature analysis, prerequisites for a successful pathway reconstitution could be deduced, as well as recurring bottlenecks in this microbial host.
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Affiliation(s)
- Anna Tippelt
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany
| | - Markus Nett
- Department of Biochemical and Chemical Engineering, Laboratory of Technical Biology, TU Dortmund University, Emil-Figge-Strasse 66, 44227, Dortmund, Germany.
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40
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Mavrommati M, Daskalaki A, Papanikolaou S, Aggelis G. Adaptive laboratory evolution principles and applications in industrial biotechnology. Biotechnol Adv 2021; 54:107795. [PMID: 34246744 DOI: 10.1016/j.biotechadv.2021.107795] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 06/11/2021] [Accepted: 07/05/2021] [Indexed: 12/20/2022]
Abstract
Adaptive laboratory evolution (ALE) is an innovative approach for the generation of evolved microbial strains with desired characteristics, by implementing the rules of natural selection as presented in the Darwinian Theory, on the laboratory bench. New as it might be, it has already been used by several researchers for the amelioration of a variety of characteristics of widely used microorganisms in biotechnology. ALE is used as a tool for the deeper understanding of the genetic and/or metabolic pathways of evolution. Another important field targeted by ALE is the manufacturing of products of (high) added value, such as ethanol, butanol and lipids. In the current review, we discuss the basic principles and techniques of ALE, and then we focus on studies where it has been applied to bacteria, fungi and microalgae, aiming to improve their performance to biotechnological procedures and/or inspect the genetic background of evolution. We conclude that ALE is a promising and efficacious method that has already led to the acquisition of useful new microbiological strains in biotechnology and could possibly offer even more interesting results in the future.
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Affiliation(s)
- Maria Mavrommati
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece; Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - Alexandra Daskalaki
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece
| | - Seraphim Papanikolaou
- Laboratory of Food Microbiology and Biotechnology, Department of Food Science and Human Nutrition, Agricultural University of Athens, 75 Iera Odos, 11855 Athens, Greece
| | - George Aggelis
- Unit of Microbiology, Department of Biology, Division of Genetics, Cell Biology and Development, University of Patras, 26504 Patras, Greece.
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41
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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
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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: 36] [Impact Index Per Article: 12.0] [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.
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43
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Han J, Jiang L, Zhang L, Quinn RJ, Liu X, Feng Y. Peculiarities of meroterpenoids and their bioproduction. Appl Microbiol Biotechnol 2021; 105:3987-4003. [PMID: 33937926 DOI: 10.1007/s00253-021-11312-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/14/2021] [Accepted: 04/20/2021] [Indexed: 02/05/2023]
Abstract
Meroterpenoids are a class of terpenoid-containing hybrid natural products with impressive structural architectures and remarkable pharmacological activities. Remarkable advances in enzymology and synthetic biology have greatly contributed to the elucidation of the molecular basis for their biosynthesis. Here, we review structurally unique meroterpenoids catalyzed by novel enzymes and unusual enzymatic reactions over the period of last 5 years. We also discuss recent progress on the biomimetic synthesis of chrome meroterpenoids and synthetic biology-driven biomanufacturing of tropolone sesquiterpenoids, merochlorins, and plant-derived meroterpenoid cannabinoids. In particular, we focus on the novel enzymes involved in the biosynthesis of polyketide-terpenoids, nonribosomal peptide-terpenoids, terpenoid alkaloids, and meroterpenoid with unique structures. The biological activities of these meroterpenoids are also discussed. The information reviewed here might provide useful clues and lay the foundation for developing new meroterpenoid-derived drugs. KEY POINTS: • Meroterpenoids possess intriguing structural features and relevant biological activities. • Novel enzymes are involved in the biosynthesis of meroterpenoids with unique structures. • Biomimetic synthesis and synthetic biology enable the construction and manufacturing of complex meroterpenoids.
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Affiliation(s)
- Jianying Han
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia
| | - Lan Jiang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Lixin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Ronald J Quinn
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia
| | - Xueting Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, 200237, China.
| | - Yunjiang Feng
- Griffith Institute for Drug Discovery, Griffith University, QLD, Brisbane, 4111, Australia.
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44
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Xiberras J, Klein M, Prosch C, Malubhoy Z, Nevoigt E. Anaplerotic reactions active during growth of Saccharomyces cerevisiae on glycerol. FEMS Yeast Res 2021; 20:5672635. [PMID: 31821485 DOI: 10.1093/femsyr/foz086] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/09/2019] [Indexed: 02/01/2023] Open
Abstract
Anaplerotic reactions replenish TCA cycle intermediates during growth. In Saccharomyces cerevisiae, pyruvate carboxylase and the glyoxylate cycle have been experimentally identified to be the main anaplerotic routes during growth on glucose (C6) and ethanol (C2), respectively. The current study investigates the importance of the two isoenzymes of pyruvate carboxylase (PYC1 and PYC2) and one of the key enzymes of the glyoxylate cycle (ICL1) for growth on glycerol (C3) as a sole carbon source. As the wild-type strains of the CEN.PK family are unable to grow in pure synthetic glycerol medium, a reverse engineered derivative showing a maximum specific growth rate of 0.14 h-1 was used as the reference strain. While the deletion of PYC1 reduced the maximum specific growth rate by about 38%, the deletion of PYC2 had no significant impact, neither in the reference strain nor in the pyc1Δ mutant. The deletion of ICL1 only marginally reduced growth of the reference strain but further decreased the growth rate of the pyc1 deletion strain by 20%. Interestingly, the triple deletion (pyc1Δ pyc2Δ icl1Δ) did not show any growth. Therefore, both the pyruvate carboxylase and the glyoxylate cycle are involved in anaplerosis during growth on glycerol.
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Affiliation(s)
- Joeline Xiberras
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Mathias Klein
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Celina Prosch
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Zahabiya Malubhoy
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
| | - Elke Nevoigt
- Department of Life Sciences and Chemistry, Jacobs University Bremen gGmbH, Campus Ring 1, 28759 Bremen, Germany
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Sharma S, Ghoshal C, Arora A, Samar W, Nain L, Paul D. Strain Improvement of Native Saccharomyces cerevisiae LN ITCC 8246 Strain Through Protoplast Fusion To Enhance Its Xylose Uptake. Appl Biochem Biotechnol 2021; 193:2455-2469. [PMID: 33765267 DOI: 10.1007/s12010-021-03539-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 02/26/2021] [Indexed: 02/05/2023]
Abstract
Co-utilization of xylose and glucose and subsequent fermentation using Saccharomyces cerevisiae could enhance ethanol productivity. Directed engineering approaches have met with limited success due to interconnectivity of xylose metabolism with other intrinsic, hidden pathways. Therefore, random approaches like protoplast fusion were used to reprogram unidentified mechanisms. Saccharomyces cerevisiae LN, the best hexose fermenter, was fused with xylose fermenting Pichia stipitis NCIM 3498. Protoplasts prepared using glucanex were fused under electric impulse and fusants were selected using 10% ethanol and cycloheximide (50 ppm) markers. Two fusants, 1a.23 and 1a.30 showing fast growth on xylose and tolerance to 10% ethanol, were selected. Higher extracellular protein expression observed in fusants as compared to parents was corroborated by higher number of bands resolved by two-dimensional analysis. Overexpression of XYL1, XYL2, XKS, and XUT4 in fusants as compared to S. cerevisiae LN as observed by RT-PCR analysis was substantiated by higher specific activities of XR, XDH, and XKS enzymes in fusants. During lignocellulosic hydrolysate fermentation, fusants could utilize glucose faster than the parent P. stipitis NCIM 3498 and xylose consumption in fusants was higher than S. cerevisiae LN.
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Affiliation(s)
- Shalley Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Chandrika Ghoshal
- Division of Vegetable Science, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anju Arora
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Wara Samar
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Lata Nain
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Debarati Paul
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, 201303, India
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46
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Jayakody LN, Jin YS. In-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiae. Appl Microbiol Biotechnol 2021; 105:2675-2692. [PMID: 33743026 DOI: 10.1007/s00253-021-11213-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 02/17/2021] [Accepted: 02/28/2021] [Indexed: 11/25/2022]
Abstract
Aldehydes are ubiquitous electrophilic compounds that ferment microorganisms including Saccharomyces cerevisiae encounter during the fermentation processes to produce food, fuels, chemicals, and pharmaceuticals. Aldehydes pose severe toxicity to the growth and metabolism of the S. cerevisiae through a variety of toxic molecular mechanisms, predominantly via damaging macromolecules and hampering the production of targeted compounds. Compounds with aldehyde functional groups are far more toxic to S. cerevisiae than all other functional classes, and toxic potency depends on physicochemical characteristics of aldehydes. The yeast synthetic biology community established a design-build-test-learn framework to develop S. cerevisiae cell factories to valorize the sustainable and renewable biomass, including the lignin-derived substrates. However, thermochemically pretreated biomass-derived substrate streams contain diverse aldehydes (e.g., glycolaldehyde and furfural), and biological conversions routes of lignocellulosic compounds consist of toxic aldehyde intermediates (e.g., formaldehyde and methylglyoxal), and some of the high-value targeted products have aldehyde functional group (e.g., vanillin and benzaldehyde). Numerous studies comprehensively characterized both single and additive effects of aldehyde toxicity via systems biology investigations, and novel molecular approaches have been discovered to overcome the aldehyde toxicity. Based on those novel approaches, researchers successfully developed synthetic yeast cell factories to convert lignocellulosic substrates to valuable products, including aldehyde compounds. In this mini-review, we highlight the salient relationship of physicochemical characteristics and molecular toxicity of aldehydes, the molecular detoxification and macromolecules protection mechanisms of aldehydes, and the advances of engineering robust S. cerevisiae against complex mixtures of aldehyde inhibitors. KEY POINTS: • We reviewed structure-activity relationships of aldehyde toxicity on S. cerevisiae. • Two-tier protection mechanisms to alleviate aldehyde toxicity are presented. • We highlighted the strategies to overcome the synergistic toxicity of aldehydes.
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Affiliation(s)
- Lahiru N Jayakody
- School of Biological Sciences, Southern Illinois University Carbondale, Carbondale, IL, USA.
- Fermentation Science Institute, Southern Illinois University Carbondale, Carbondale, IL, USA.
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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47
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Fletcher E, Mercurio K, Walden EA, Baetz K. A yeast chemogenomic screen identifies pathways that modulate adipic acid toxicity. iScience 2021; 24:102327. [PMID: 33889823 PMCID: PMC8050732 DOI: 10.1016/j.isci.2021.102327] [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: 12/15/2020] [Revised: 02/19/2021] [Accepted: 03/15/2021] [Indexed: 11/18/2022] Open
Abstract
Adipic acid production by yeast fermentation is gaining attention as a renewable source of platform chemicals for making nylon products. However, adipic acid toxicity inhibits yeast growth and fermentation. Here, we performed a chemogenomic screen in Saccharomyces cerevisiae to understand the cellular basis of adipic acid toxicity. Our screen revealed that KGD1 (a key gene in the tricarboxylic acid cycle) deletion improved tolerance to adipic acid and its toxic precursor, catechol. Conversely, disrupting ergosterol biosynthesis as well as protein trafficking and vacuolar transport resulted in adipic acid hypersensitivity. Notably, we show that adipic acid disrupts the Membrane Compartment of Can1 (MCC) on the plasma membrane and impacts endocytosis. This was evidenced by the rapid internalization of Can1 for vacuolar degradation. As ergosterol is an essential component of the MCC and protein trafficking mechanisms are required for endocytosis, we highlight the importance of these cellular processes in modulating adipic acid toxicity. Deletion of the TCA cycle gene KGD1 improves tolerance to adipic acid and catechol Ergosterol and Pdr12 play non-overlapping roles protecting cell from adipic acid Adipic acid-induced plasma membrane localization of Pdr12 is independent of ergosterol Adipic acid disrupts the Membrane Compartment of Can1 (MCC) and induces endocytosis
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Affiliation(s)
- Eugene Fletcher
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Kevin Mercurio
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Elizabeth A. Walden
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
| | - Kristin Baetz
- Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology and Immunology, University of Ottawa, 451 Smyth Road, Ottawa, ON K1H 8M5, Canada
- Corresponding author
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48
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Anti-biofilm effect of the cell-free supernatant of probiotic Saccharomyces cerevisiae against Listeria monocytogenes. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107667] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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49
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Su Y, Shao W, Zhang A, Zhang W. Improving isobutanol tolerance and titers through EMS mutagenesis in Saccharomyces cerevisiae. FEMS Yeast Res 2021; 21:6147039. [PMID: 33620449 DOI: 10.1093/femsyr/foab012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 02/20/2021] [Indexed: 11/14/2022] Open
Abstract
Improving yeast tolerance toward isobutanol is a critical issue enabling high-titer industrial production. Here, we used EMS mutagenesis to screen Saccharomyces cerevisiae with greater tolerance toward isobutanol. By this method, we obtained EMS39 with high-viability in medium containing 16 g/L isobutanol. Then, we metabolically engineered isobutanol synthesis in EMS39. About 2μ plasmids carrying PGK1p-ILV2, PGK1p-ILV3 and TDH3p-cox4-ARO10 were used to over-express ILV2, ILV3 and ARO10 genes, respectively, in EMS39 and wild type W303-1A. And the resulting strains were designated as EMS39-20 and W303-1A-20. Our results showed that EMS39-20 increased isobutanol titers by 49.9% compared to W303-1A-20. Whole genome resequencing analysis of EMS39 showed that more than 59 genes had mutations in their open reading frames or regulatory regions. These 59 genes are enriched mainly into cell growth, basal transcription factors, cell integrity signaling, translation initiation and elongation, ribosome assembly and function, oxidative stress response, etc. Additionally, transcriptomic analysis of EMS39-20 was carried out. Finally, reverse engineering tests showed that overexpression of CWP2 and SRP4039 could improve tolerance of S.cerevisiae toward isobutanol. In conclusion, EMS mutagenesis could be used to increase yeast tolerance toward isobutanol. Our study supplied new insights into mechanisms of tolerance toward isobutanol and enhancing isobutanol production in S. cerevisiae.
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Affiliation(s)
- Yide Su
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Wenju Shao
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Aili Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
| | - Weiwei Zhang
- School of Chemical Engineering and Technology, Hebei University of Technology, No. 8 Guangrong Road, Hongqiao District, Tianjin 300130, PR China
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Chen LZ, Huang SL, Hou J, Guo XP, Wang FS, Sheng JZ. Cell-based and cell-free biocatalysis for the production of D-glucaric acid. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:203. [PMID: 33303009 PMCID: PMC7731778 DOI: 10.1186/s13068-020-01847-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 12/02/2020] [Indexed: 05/17/2023]
Abstract
D-Glucaric acid (GA) is a value-added chemical produced from biomass, and has potential applications as a versatile platform chemical, food additive, metal sequestering agent, and therapeutic agent. Marketed GA is currently produced chemically, but increasing demand is driving the search for eco-friendlier and more efficient production approaches. Cell-based production of GA represents an alternative strategy for GA production. A series of synthetic pathways for GA have been ported into Escherichia coli, Saccharomyces cerevisiae and Pichia pastoris, respectively, and these engineered cells show the ability to synthesize GA de novo. Optimization of the GA metabolic pathways in host cells has leapt forward, and the titer and yield have increased rapidly. Meanwhile, cell-free multi-enzyme catalysis, in which the desired pathway is constructed in vitro from enzymes and cofactors involved in GA biosynthesis, has also realized efficient GA bioconversion. This review presents an overview of studies of the development of cell-based GA production, followed by a brief discussion of potential applications of biosensors that respond to GA in these biosynthesis routes.
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Affiliation(s)
- Lu-Zhou Chen
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
| | - Si-Ling Huang
- Bloomage BioTechnology Corp., Ltd., Jinan, 250010, China
| | - Jin Hou
- The State Key Laboratory of Microbial Technology, Shandong University, Qingdao, 266237, China
| | - Xue-Ping Guo
- Bloomage BioTechnology Corp., Ltd., Jinan, 250010, China
| | - Feng-Shan Wang
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China
| | - Ju-Zheng Sheng
- Key Laboratory of Chemical Biology of Natural Products (Ministry of Education), School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, 250012, China.
- National Glycoengineering Research Center, Shandong University, Jinan, 250012, China.
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