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Du Z, Bhat WW, Poliner E, Johnson S, Bertucci C, Farre E, Hamberger B. Engineering Nannochloropsis oceanica for the production of diterpenoid compounds. MLIFE 2023; 2:428-437. [PMID: 38818264 PMCID: PMC10989085 DOI: 10.1002/mlf2.12097] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Revised: 08/24/2023] [Accepted: 10/04/2023] [Indexed: 06/01/2024]
Abstract
Photosynthetic microalgae like Nannochloropsis hold enormous potential as sustainable, light-driven biofactories for the production of high-value natural products such as terpenoids. Nannochloropsis oceanica is distinguished as a particularly robust host with extensive genomic and transgenic resources available. Its capacity to grow in wastewater, brackish, and sea waters, coupled with advances in microalgal metabolic engineering, genome editing, and synthetic biology, provides an excellent opportunity. In the present work, we demonstrate how N. oceanica can be engineered to produce the diterpene casbene-an important intermediate in the biosynthesis of pharmacologically relevant macrocyclic diterpenoids. Casbene accumulated after stably expressing and targeting the casbene synthase from Daphne genkwa (DgTPS1) to the algal chloroplast. The engineered strains yielded production titers of up to 0.12 mg g-1 total dry cell weight (DCW) casbene. Heterologous overexpression and chloroplast targeting of two upstream rate-limiting enzymes in the 2-C-methyl- d-erythritol 4-phosphate pathway, Coleus forskohlii 1-deoxy- d-xylulose-5-phosphate synthase and geranylgeranyl diphosphate synthase genes, further enhanced the yield of casbene to a titer up to 1.80 mg g-1 DCW. The results presented here form a basis for further development and production of complex plant diterpenoids in microalgae.
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Affiliation(s)
- Zhi‐Yan Du
- Department of Molecular Biosciences and BioengineeringUniversity of Hawaii at ManoaHonoluluHawaiiUSA
| | - Wajid W. Bhat
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eric Poliner
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Sean Johnson
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
- Present address:
New England Biolabs Inc.240 County RoadIpswich01938MAUSA
| | - Conor Bertucci
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Eva Farre
- Department of Plant BiologyMichigan State UniversityEast LansingMichiganUSA
| | - Bjoern Hamberger
- Department of Biochemistry and Molecular BiologyMichigan State UniversityEast LansingMichiganUSA
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2
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Giehl A, dos Santos AA, Cadamuro RD, Tadioto V, Guterres IZ, Prá Zuchi ID, Minussi GDA, Fongaro G, Silva IT, Alves SL. Biochemical and Biotechnological Insights into Fungus-Plant Interactions for Enhanced Sustainable Agricultural and Industrial Processes. PLANTS (BASEL, SWITZERLAND) 2023; 12:2688. [PMID: 37514302 PMCID: PMC10385130 DOI: 10.3390/plants12142688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/07/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]
Abstract
The literature is full of studies reporting environmental and health issues related to using traditional pesticides in food production and storage. Fortunately, alternatives have arisen in the last few decades, showing that organic agriculture is possible and economically feasible. And in this scenario, fungi may be helpful. In the natural environment, when associated with plants, these microorganisms offer plant-growth-promoting molecules, facilitate plant nutrient uptake, and antagonize phytopathogens. It is true that fungi can also be phytopathogenic, but even they can benefit agriculture in some way-since pathogenicity is species-specific, these fungi are shown to be useful against weeds (as bioherbicides). Finally, plant-associated yeasts and molds are natural biofactories, and the metabolites they produce while dwelling in leaves, flowers, roots, or the rhizosphere have the potential to be employed in different industrial activities. By addressing all these subjects, this manuscript comprehensively reviews the biotechnological uses of plant-associated fungi and, in addition, aims to sensitize academics, researchers, and investors to new alternatives for healthier and more environmentally friendly production processes.
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Affiliation(s)
- Anderson Giehl
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Angela Alves dos Santos
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
| | - Rafael Dorighello Cadamuro
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Viviani Tadioto
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Iara Zanella Guterres
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Isabella Dai Prá Zuchi
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Gabriel do Amaral Minussi
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Environment and Sustainable Technologies, Federal University of Fronteira Sul, Cerro Largo 97900-000, RS, Brazil
| | - Gislaine Fongaro
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Izabella Thais Silva
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Pharmacy, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
| | - Sergio Luiz Alves
- Laboratory of Yeast Biochemistry, Federal University of Fronteira Sul, Chapecó 89815-899, SC, Brazil
- Graduate Program in Biotechnology and Biosciences, Federal University of Santa Catarina, Florianópolis 88040-900, SC, Brazil
- Graduate Program in Environment and Sustainable Technologies, Federal University of Fronteira Sul, Cerro Largo 97900-000, RS, Brazil
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3
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de Freitas BB, Overmans S, Medina JS, Hong PY, Lauersen KJ. Biomass generation and heterologous isoprenoid milking from engineered microalgae grown in anaerobic membrane bioreactor effluent. WATER RESEARCH 2023; 229:119486. [PMID: 36535088 DOI: 10.1016/j.watres.2022.119486] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 06/17/2023]
Abstract
Wastewater (WW) treatment in anaerobic membrane bioreactors (AnMBR) is considered more sustainable than in aerobic reactors. However, outputs from AnMBR are a mixed methane and carbon dioxide gas stream as well as ammonium- (N) and phosphate- (P) containing waters. Using AnMBR outputs as inputs for photoautotrophic algal cultivation can strip the CO2 while removing N and P from effluent which feed algal biomass generation. Recent advances in algal engineering have generated strains that produce high-value side products concomitant with biomass, although only shown in heavily domesticated, lab-adapted strains. Here, it was investigated whether engineered Chlamydomonas reinhardtii could be grown directly in AnMBR effluent with CO2 concentrations found in AnMBR off-gas. The strain was found to proliferate over bacteria in the non-sterile effluent, consume N and P to levels that meet general discharge or reuse limits, and tolerate cultivation in modelled (extreme) outdoor environmental conditions prevalent along the central Red Sea coast. In addition to ∼2.4 g CDW L-1 biomass production in 96 h, a high-value heterologous sesquiterpene co-product could be obtained from 'milking' up to 837 µg L-1 culture in 96 h. This is the first demonstration of a combined bio-process that employs a heavily engineered algal strain to enhance the product generation potentials from AnMBR effluent treatment. This study shows it is possible to convert waste into value through use of engineered algae while also improving wastewater treatment economics through co-product generation.
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Affiliation(s)
- Bárbara Bastos de Freitas
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Sebastian Overmans
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Julie Sanchez Medina
- Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Pei-Ying Hong
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia; Water Desalination and Reuse Center, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia.
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Hoqani UA, León R, Purton S. Over-expression of a cyanobacterial gene for 1-deoxy-d-xylulose-5-phosphate synthase in the chloroplast of Chlamydomonas reinhardtii perturbs chlorophyll: carotenoid ratios. JOURNAL OF KING SAUD UNIVERSITY. SCIENCE 2022; 34:None. [PMID: 35923766 PMCID: PMC9329130 DOI: 10.1016/j.jksus.2022.102141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 05/25/2022] [Accepted: 05/28/2022] [Indexed: 06/15/2023]
Abstract
Terpenoids are a diverse class of naturally occurring compounds consisting of more than 50,000 structurally different molecules and are found in all living organisms. Many terpenoid compounds, in particular those isolated from plants, have applications in various commercial sectors including medicine, agriculture and cosmetics. However, these high value terpenoids are produced in relatively small quantities in their natural hosts and their chemical synthesis for large scale production is costly and complicated. Therefore, there is much focus on producing these compounds in novel biological hosts using metabolic engineering technologies. As a photosynthetic system, the unicellular green alga C. reinhardtii is of particular interest as the most well-studied model alga with well-established molecular tools for genetic manipulation. However, the direct manipulation of terpenoid biosynthetic pathways in C. reinhardtii necessitates a thorough understanding of the basic terpenoid metabolism. To gain a better understanding of the methylerythritol phosphate (MEP) pathway that leads to terpenoid biosynthesis in the chloroplast of C. reinhardtii, hence this study has investigated the effect of over-expressing 1-deoxy-d-xylulose-5-phosphate synthase (DXS) on plastidic downstream terpenoids. We produced marker-free chloroplast transformants of C. reinhardtii lines that express an additional cyanobacterial gene for DXS. The analysis of terpenoid content for the transgenic line demonstrates that overexpressing DXS resulted in a two-fold decrease in the chlorophyll levels while carotenoid levels showed variable changes: zeaxanthin and antherxanthin levels increased several-fold, lutein levels dropped to approximately half, but β-carotene and violaxanthin did not show a significant change.
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Affiliation(s)
- Umaima Al Hoqani
- Applied Biology Section, Applied Sciences Department, Higher College of Technology, University of Technology and Applied Sciences, Al-Khuwair 133, Oman
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
| | - Rosa León
- Lab Bioquímica y Biología Molecular, Dpto Química, Facultad de Ciencias Experimentales, Universidad de Huelva, Avda Fuerzas Armadas s/n, 21007 Huelva, Spain
| | - Saul Purton
- Algal Research Group, Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, United Kingdom
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5
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Paramasivan K, Abdulla A, Gupta N, Mutturi S. In silico target-based strain engineering of Saccharomyces cerevisiae for terpene precursor improvement. Integr Biol (Camb) 2022; 14:25-36. [DOI: 10.1093/intbio/zyac003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 11/13/2022]
Abstract
Abstract
Systems-based metabolic engineering enables cells to enhance product formation by predicting gene knockout and overexpression targets using modeling tools. FOCuS, a novel metaheuristic tool, was used to predict flux improvement targets in terpenoid pathway using the genome-scale model of Saccharomyces cerevisiae, iMM904. Some of the key knockout target predicted includes LYS1, GAP1, AAT1, AAT2, TH17, KGD-m, MET14, PDC1 and ACO1. It was also observed that the knockout reactions belonged either to fatty acid biosynthesis, amino acid synthesis pathways or nucleotide biosynthesis pathways. Similarly, overexpression targets such as PFK1, FBA1, ZWF1, TDH1, PYC1, ALD6, TPI1, PDX1 and ENO1 were established using three different existing gene amplification algorithms. Most of the overexpression targets belonged to glycolytic and pentose phosphate pathways. Each of these targets had plausible role for improving flux toward sterol pathway and were seemingly not artifacts. Moreover, an in vitro study as validation was carried with overexpression of ALD6 and TPI1. It was found that there was an increase in squalene synthesis by 2.23- and 4.24- folds, respectively, when compared with control. In general, the rationale for predicting these in silico targets was attributed to either increasing the acetyl-CoA precursor pool or regeneration of NADPH, which increase the sterol pathway flux.
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Affiliation(s)
- Kalaivani Paramasivan
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
- Department of Bioengineering, University of Illinois, Urbana-Champaign, IL, USA
| | - Aneesha Abdulla
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
| | - Nabarupa Gupta
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, India
| | - Sarma Mutturi
- Microbiology and Fermentation Technology Department, CSIR-Central Food Technological Research Institute, Mysuru, India
- Academy of Scientific and Innovative Research, Ghaziabad, Uttar Pradesh, India
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6
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Li Y, Li J, Diao M, Peng L, Huang S, Xie N. Characterization of a Group of UDP-Glycosyltransferases Involved in the Biosynthesis of Triterpenoid Saponins of Panax notoginseng. ACS Synth Biol 2022; 11:770-779. [PMID: 35107265 DOI: 10.1021/acssynbio.1c00469] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
UDP-glycosyltransferase (UGT)-mediated glycosylation is a common modification in triterpene saponins, which exhibit a wide range of bioactivities and important pharmacological effects. However, few UGTs involved in saponin biosynthesis have been identified, limiting the biosynthesis of saponins. In this study, an efficient heterologous expression system was established for evaluating the UGT-mediated glycosylation process of triterpene saponins. Six UGTs (UGTPn17, UGTPn42, UGTPn35, UGTPn87, UGTPn19, and UGTPn12) from Panax notoginseng were predicted and found to be responsible for efficient and direct enzymatic biotransformation of 21 triterpenoid saponins via 26 various glycosylation reactions. Among them, UGTPn87 exhibited promiscuous sugar-donor specificity of UDP-glucose (UDP-Glc) and UDP-xylose (UDP-Xyl) by catalyzing the elongation of the second sugar chain at the C3 or/and C20 sites of protopanaxadiol-type saponins with a UDP-Glc or UDP-Xyl donor, as well as at the C20 site of protopanaxadiol-type saponins with a UDP-Glc donor. Two new saponins, Fd-Xyl and Fe-Xyl, were generated by catalyzing the C3-O-Glc xylosylations of notoginsenoside Fd and notoginsenoside Fe when incubated with UGTPn87. Moreover, the complete biosynthetic pathways of 17 saponins were elucidated, among which notoginsenoside L, vinaginsenoside R16, gypenoside LXXV, and gypenoside XVII were revealed in Panax for the first time. A yeast cell factory was constructed with a yield of Rh2 at 354.69 mg/L and a glycosylation ratio of 60.40% in flasks. Our results reveal the biosynthetic pathway of a group of saponins in P. notoginseng and provide a theoretical basis for producing rare and valuable saponins, promoting their industrial application in medicine and functional foods.
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Affiliation(s)
- Yanting Li
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, China
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Jianxiu Li
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Mengxue Diao
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Longyun Peng
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
| | - Shihai Huang
- College of Life Science and Technology, Guangxi University, 100 Daxue Road, Nanning 530004, China
| | - Nengzhong Xie
- State Key Laboratory of Non-Food Biomass and Enzyme Technology, National Engineering Research Center for Non-Food Biorefinery, Guangxi Biomass Engineering Technology Research Center, Guangxi Academy of Sciences, 98 Daling Road, Nanning 530007, China
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Ahmed MS, Lauersen KJ, Ikram S, Li C. Efflux Transporters' Engineering and Their Application in Microbial Production of Heterologous Metabolites. ACS Synth Biol 2021; 10:646-669. [PMID: 33751883 DOI: 10.1021/acssynbio.0c00507] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Metabolic engineering of microbial hosts for the production of heterologous metabolites and biochemicals is an enabling technology to generate meaningful quantities of desired products that may be otherwise difficult to produce by traditional means. Heterologous metabolite production can be restricted by the accumulation of toxic products within the cell. Efflux transport proteins (transporters) provide a potential solution to facilitate the export of these products, mitigate toxic effects, and enhance production. Recent investigations using knockout lines, heterologous expression, and expression profiling of transporters have revealed candidates that can enhance the export of heterologous metabolites from microbial cell systems. Transporter engineering efforts have revealed that some exhibit flexible substrate specificity and may have broader application potentials. In this Review, the major superfamilies of efflux transporters, their mechanistic modes of action, selection of appropriate efflux transporters for desired compounds, and potential transporter engineering strategies are described for potential applications in enhancing engineered microbial metabolite production. Future studies in substrate recognition, heterologous expression, and combinatorial engineering of efflux transporters will assist efforts to enhance heterologous metabolite production in microbial hosts.
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Affiliation(s)
- Muhammad Saad Ahmed
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- Department of Biological Sciences, National University of Medical Sciences (NUMS), Abid Majeed Road, The Mall, Rawalpindi 46000, Pakistan
| | - Kyle J. Lauersen
- Biological and Environmental Sciences and Engineering Division (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Kingdom of Saudi Arabia
| | - Sana Ikram
- Beijing Higher Institution Engineering Research Center for Food Additives and Ingredients, Beijing Technology & Business University (BTBU), Beijing 100048, P. R. China
| | - Chun Li
- Institute for Synthetic Biosystem/Department of Biochemical Engineering, School of Chemistry and Chemical Engineering, Beijing Institute of Technology (BIT), Beijing 100081, P. R. China
- SynBio Research Platform, Collaborative Innovation Center of Chemical Science and Engineering, Key Laboratory of Systems Bioengineering, Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300350, P. R. China
- Key Laboratory for Industrial Biocatalysis, Ministry of Education, Department of Chemical Engineering, Tsinghua University, Beijing 100084, P. R. China
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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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9
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Microbial production of limonene and its derivatives: Achievements and perspectives. Biotechnol Adv 2020; 44:107628. [DOI: 10.1016/j.biotechadv.2020.107628] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/14/2022]
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10
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Troost K, Loeschcke A, Hilgers F, Özgür AY, Weber TM, Santiago-Schübel B, Svensson V, Hage-Hülsmann J, Habash SS, Grundler FMW, Schleker ASS, Jaeger KE, Drepper T. Engineered Rhodobacter capsulatus as a Phototrophic Platform Organism for the Synthesis of Plant Sesquiterpenoids. Front Microbiol 2019; 10:1998. [PMID: 31555236 PMCID: PMC6742980 DOI: 10.3389/fmicb.2019.01998] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 08/15/2019] [Indexed: 12/11/2022] Open
Abstract
Sesquiterpenoids are a large class of natural compounds offering manifold properties valuable for food, cosmetics, agriculture, and pharma industry. Production in microorganisms is a sustainable approach to provide sesquiterpenoids for research and industrial use independent of their natural sources. This requires the functional transfer of the respective biocatalytic pathways in an adequate host microorganism offering a sufficient supply of precursors that is ideally adjusted to the individual demand of the recombinant biosynthesis route. The phototrophic purple bacterium Rhodobacter capsulatus offers unique physiological properties that are favorable for biosynthesis of hydrophobic terpenes. Under phototrophic conditions, it develops a large intracytoplasmic membrane suitable for hosting membrane-bound enzymes and metabolites of respective biosynthetic pathways. In addition, Rhodobacter harbors an intrinsic carotenoid biosynthesis that can be engineered toward the production of foreign terpenes. Here, we evaluate R. capsulatus as host for the production of plant sesquiterpenoids under phototrophic conditions using patchoulol and valencene as a proof of concept. The heterologous expression of patchoulol synthase PcPS from Pogostemon cablin as well as the valencene synthases CsVS from Citrus sinensis and CnVS from Callitropsis nootkatensis led to the production of the respective sesquiterpenoids in R. capsulatus. To analyze, if gradually adjustable formation of the key precursor farnesylpyrophosphate (FPP) is beneficial for sesquiterpene synthesis under phototrophic conditions, the intrinsic 1-deoxy-D-xylulose 5-phosphate (DXP) pathway genes as well as the heterologous mevalonate pathway genes were modularly expressed in various combinations. To this end, different plasmids and chromosomally integrated expression tools were developed harboring the strong and tightly controlled Pnif promoter for heterologous gene expression. Notably, comparative studies identified a distinct combination of precursor biosynthetic genes as best-performing setup for each of the tested sesquiterpene synthases. In summary, we could demonstrate that R. capsulatus is a promising alternative platform organism that is suited for sustainable sesquiterpenoid formation under phototrophic cultivation conditions. A modular engineering of R. capsulatus strains via tailored co-expression of FPP biosynthetic genes further allowed adaptation of sesquiterpene precursor formation to its catalytic conversion by different plant terpene synthases.
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Affiliation(s)
- Katrin Troost
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Anita Loeschcke
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Fabienne Hilgers
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Armagan Yakup Özgür
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Tim Moritz Weber
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Beatrix Santiago-Schübel
- Central Institute for Engineering, Electronics and Analytics ZEA-3, Analytics, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Vera Svensson
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Jennifer Hage-Hülsmann
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Samer S Habash
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Florian M W Grundler
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - A Sylvia S Schleker
- INRES-Molecular Phytomedicine, Rhenish Friedrich-Wilhelm University of Bonn, Bonn, Germany
| | - Karl-Erich Jaeger
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany.,Institute of Bio- and Geosciences IBG-1, Biotechnology, Forschungszentrum Jülich GmbH, Jülich, Germany
| | - Thomas Drepper
- Institute of Molecular Enzyme Technology, Heinrich Heine University Düsseldorf, Düsseldorf, Germany, Forschungszentrum Jülich GmbH, Jülich, Germany
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11
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Arhar S, Natter K. Common aspects in the engineering of yeasts for fatty acid- and isoprene-based products. Biochim Biophys Acta Mol Cell Biol Lipids 2019; 1864:158513. [PMID: 31465888 DOI: 10.1016/j.bbalip.2019.08.009] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Revised: 06/26/2019] [Accepted: 08/20/2019] [Indexed: 11/18/2022]
Abstract
The biosynthetic pathways for most lipophilic metabolites share several common principles. These substances are built almost exclusively from acetyl-CoA as the donor for the carbon scaffold and NADPH is required for the reductive steps during biosynthesis. Due to their hydrophobicity, the end products are sequestered into the same cellular compartment, the lipid droplet. In this review, we will summarize the efforts in the metabolic engineering of yeasts for the production of two major hydrophobic substance classes, fatty acid-based lipids and isoprenoids, with regard to these common aspects. We will compare and discuss the results of genetic engineering strategies to construct strains with enhanced synthesis of the precursor acetyl-CoA and with modified redox metabolism for improved NADPH supply. We will also discuss the role of the lipid droplet in the storage of the hydrophobic product and review the strategies to either optimize this organelle for higher capacity or to achieve excretion of the product into the medium.
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Affiliation(s)
- Simon Arhar
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria
| | - Klaus Natter
- Institute of Molecular Biosciences, NAWI Graz, University of Graz, Humboldtstrasse 50/II, 8010 Graz, Austria.
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12
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Ma B, Liu M, Li ZH, Tao X, Wei DZ, Wang FQ. Significantly Enhanced Production of Patchoulol in Metabolically Engineered Saccharomyces cerevisiae. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2019; 67:8590-8598. [PMID: 31287301 DOI: 10.1021/acs.jafc.9b03456] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Patchoulol, a natural sesquiterpene compound, is widely used in perfumes and cosmetics. Several strategies were adopted to enhance patchoulol production in Saccharomyces cerevisiae: (i) farnesyl pyrophosphate (FPP) synthase and patchoulol synthase were fused to increase the utilization of FPP precursor; (ii) expression of the limiting genes of the mevalonate pathway was enhanced; (iii) squalene synthase was weakened by a glucose-inducible promoter of HXT1 (promoter for hexose transporter) to reduce metabolic flux from FPP to ergosterol; and (iv) farnesol biosynthesis was inhibited to decrease the consumption of FPP. Glucose was used to balance the trade-off between the competitive squalene and patchoulol pathways. The patchoulol production was 59.2 ± 0.7 mg/L in a shaken flask with a final production of 466.8 ± 12.3 mg/L (20.5 ± 0.5 mg/g dry cell weight) combined with fermentation optimization, which was 7.8-fold higher than the reported maximum production. The work significantly promoted the industrialization process of patchoulol production using biobased microbial platforms.
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Affiliation(s)
- Bin Ma
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Min Liu
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Zhen-Hai Li
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
| | - Xinyi Tao
- 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
| | - Feng-Qing Wang
- State key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology , East China University of Science and Technology , Shanghai 200237 , China
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13
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Paramasivan K, Kumar HN P, Mutturi S. Systems-based Saccharomyces cerevisiae strain design for improved squalene synthesis. Biochem Eng J 2019. [DOI: 10.1016/j.bej.2019.04.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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14
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Lauersen KJ. Eukaryotic microalgae as hosts for light-driven heterologous isoprenoid production. PLANTA 2019; 249:155-180. [PMID: 30467629 DOI: 10.1007/s00425-018-3048-x] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 11/14/2018] [Indexed: 05/21/2023]
Abstract
Eukaryotic microalgae hold incredible metabolic potential for the sustainable production of heterologous isoprenoid products. Recent advances in algal engineering have enabled the demonstration of prominent examples of heterologous isoprenoid production. Isoprenoids, also known as terpenes or terpenoids, are the largest class of natural chemicals, with a vast diversity of structures and biological roles. Some have high-value in human-use applications, although may be found in their native contexts in low abundance or be difficult to extract and purify. Heterologous production of isoprenoid compounds in heterotrophic microbial hosts such as bacteria or yeasts has been an active area of research for some time and is now a mature technology. Eukaryotic microalgae represent sustainable alternatives to these hosts for biotechnological production processes as their cultivation can be driven by light and freely available CO2 as a carbon source. Their photosynthetic lifestyles require metabolic architectures structured towards the generation of associated isoprenoids (carotenoids, phytol) which participate in photon capture, energy dissipation, and electron transfer. Eukaryotic microalgae should, therefore, contain inherently high capacities for the generation of heterologous isoprenoid products. Although engineering strategies in eukaryotic microalgae have lagged behind the more genetically tractable bacteria and yeasts, recent advances in algal engineering concepts have demonstrated prominent examples of light-driven heterologous isoprenoid production from these photosynthetic hosts. This work seeks to provide practical insights into the choice of eukaryotic microalgae as biotechnological chassis. Recent reports of advances in algal engineering for heterologous isoprenoid production are highlighted as encouraging examples that promote their expanded use as sustainable green-cell factories. Current state of the art, limitations, and future challenges are also discussed.
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Affiliation(s)
- Kyle J Lauersen
- Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Universitätsstrasse 27, 33615, Bielefeld, Germany.
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15
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Castillo S, Patil KR, Jouhten P. Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019; 58:111-133. [PMID: 30911891 DOI: 10.1007/978-3-030-13035-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Understanding genotype-phenotype dependency is a universal aim for all life sciences. While the complete genotype-phenotype relations remain challenging to resolve, metabolic phenotypes are moving within the reach through genome-scale metabolic model simulations. Genome-scale metabolic models are available for commonly investigated yeasts, such as model eukaryote and domesticated fermentation species Saccharomyces cerevisiae, and automatic reconstruction methods facilitate obtaining models for any sequenced species. The models allow for investigating genotype-phenotype relations through simulations simultaneously considering the effects of nutrient availability, and redox and energy homeostasis in cells. Genome-scale models also offer frameworks for omics data integration to help to uncover how the translation of genotypes to the apparent phenotypes is regulated at different levels. In this chapter, we provide an overview of the yeast genome-scale metabolic models and the simulation approaches for using these models to interrogate genotype-phenotype relations. We review the methodological approaches according to the underlying biological reasoning in order to inspire formulating novel questions and applications that the genome-scale metabolic models could contribute to. Finally, we discuss current challenges and opportunities in the genome-scale metabolic model simulations.
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Affiliation(s)
- Sandra Castillo
- VTT Technical Research Centre of Finland Ltd., Tietotie 2, 02044, Espoo, Finland
| | - Kiran Raosaheb Patil
- European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Paula Jouhten
- VTT Technical Research Centre of Finland Ltd., Tietotie 2, 02044, Espoo, Finland.
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16
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Huang YY, Jian XX, Lv YB, Nian KQ, Gao Q, Chen J, Wei LJ, Hua Q. Enhanced squalene biosynthesis in Yarrowia lipolytica based on metabolically engineered acetyl-CoA metabolism. J Biotechnol 2018; 281:106-114. [PMID: 29986837 DOI: 10.1016/j.jbiotec.2018.07.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 06/28/2018] [Accepted: 07/01/2018] [Indexed: 12/13/2022]
Abstract
As a bioactive triterpenoid, squalene is widely used in the food industry, cosmetics, and pharmacology. Squalene's major commercial sources are the liver oil of deep-sea sharks and plant oils. In this study, we focused on the enhancement of squalene biosynthesis in Yarrowia lipolytica, with particular attention to the engineering of acetyl-CoA metabolism based on genome-scale metabolic reaction network analysis. Although the overexpression of the rate-limiting endogenous ylHMG1 (3-hydroxy-3-methylglutaryl-CoA reductase gene) could improve squalene synthesis by 3.2-fold over that by the control strain, the availability of the key intracellular precursor, acetyl-CoA, was found to play a more significant role in elevating squalene production. Analysis of metabolic networks with the newly constructed genome-scale metabolic model of Y. lipolytica iYL_2.0 showed that the acetyl-CoA pool size could be increased by redirecting carbon flux of pyruvate dehydrogenation towards the ligation of acetate and CoA or the cleavage of citrate to form oxaloacetate and acetyl-CoA. The overexpression of either acetyl-CoA synthetase gene from Salmonella enterica (acs*) or the endogenous ATP citrate lyase gene (ylACL1) resulted in a more than 50% increase in the cytosolic acetyl-CoA level. Moreover, iterative chromosomal integration of the ylHMG1, asc*, and ylACL1 genes resulted in a significant improvement in squalene production (16.4-fold increase in squalene content over that in the control strain). We also found that supplementation with 10 mM citrate in a flask culture further enhanced squalene production to 10 mg/g DCW. The information obtained in this study demonstrates that rationally engineering acetyl-CoA metabolism to ensure the supply of this key metabolic precursor is an efficient strategy for the enhancement of squalene biosynthesis.
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Affiliation(s)
- Yu-Ying Huang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Xing-Xing Jian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Yu-Bei Lv
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Ke-Qing Nian
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Qi Gao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Jun Chen
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China
| | - Liu-Jing Wei
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China.
| | - Qiang Hua
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, PR China; Shanghai Collaborative Innovation Center for Biomanufacturing Technology, 130 Meilong Road, Shanghai, 200237, PR China
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17
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Patchoulol Production with Metabolically Engineered Corynebacterium glutamicum. Genes (Basel) 2018; 9:genes9040219. [PMID: 29673223 PMCID: PMC5924561 DOI: 10.3390/genes9040219] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/25/2022] Open
Abstract
Patchoulol is a sesquiterpene alcohol and an important natural product for the perfume industry. Corynebacterium glutamicum is the prominent host for the fermentative production of amino acids with an average annual production volume of ~6 million tons. Due to its robustness and well established large-scale fermentation, C. glutamicum has been engineered for the production of a number of value-added compounds including terpenoids. Both C40 and C50 carotenoids, including the industrially relevant astaxanthin, and short-chain terpenes such as the sesquiterpene valencene can be produced with this organism. In this study, systematic metabolic engineering enabled construction of a patchoulol producing C. glutamicum strain by applying the following strategies: (i) construction of a farnesyl pyrophosphate-producing platform strain by combining genomic deletions with heterologous expression of ispA from Escherichia coli; (ii) prevention of carotenoid-like byproduct formation; (iii) overproduction of limiting enzymes from the 2-c-methyl-d-erythritol 4-phosphate (MEP)-pathway to increase precursor supply; and (iv) heterologous expression of the plant patchoulol synthase gene PcPS from Pogostemon cablin. Additionally, a proof of principle liter-scale fermentation with a two-phase organic overlay-culture medium system for terpenoid capture was performed. To the best of our knowledge, the patchoulol titers demonstrated here are the highest reported to date with up to 60 mg L−1 and volumetric productivities of up to 18 mg L−1 d−1.
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18
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Averesch NJH, Martínez VS, Nielsen LK, Krömer JO. Toward Synthetic Biology Strategies for Adipic Acid Production: An in Silico Tool for Combined Thermodynamics and Stoichiometric Analysis of Metabolic Networks. ACS Synth Biol 2018; 7:490-509. [PMID: 29237121 DOI: 10.1021/acssynbio.7b00304] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adipic acid, a nylon-6,6 precursor, has recently gained popularity in synthetic biology. Here, 16 different production routes to adipic acid were evaluated using a novel tool for network-embedded thermodynamic analysis of elementary flux modes. The tool distinguishes between thermodynamically feasible and infeasible modes under determined metabolite concentrations, allowing the thermodynamic feasibility of theoretical yields to be assessed. Further, patterns that always caused infeasible flux distributions were identified, which will aid the development of tailored strain design. A review of cellular efflux mechanisms revealed that significant accumulation of extracellular product is only possible if coupled with ATP hydrolysis. A stoichiometric analysis demonstrated that the maximum theoretical product carbon yield heavily depends on the metabolic route, ranging from 32 to 99% on glucose and/or palmitate in Escherichia coli and Saccharomyces cerevisiae metabolic models. Equally important, metabolite concentrations appeared to be thermodynamically restricted in several pathways. Consequently, the number of thermodynamically feasible flux distributions was reduced, in some cases even rendering whole pathways infeasible, highlighting the importance of pathway choice. Only routes based on the shikimate pathway were thermodynamically favorable over a large concentration and pH range. The low pH capability of S. cerevisiae shifted the thermodynamic equilibrium of some pathways toward product formation. One identified infeasible-pattern revealed that the reversibility of the mitochondrial malate dehydrogenase contradicted the current state of knowledge, which imposes a major restriction on the metabolism of S. cerevisiae. Finally, the evaluation of industrially relevant constraints revealed that two shikimate pathway-based routes in E. coli were the most robust.
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Affiliation(s)
- Nils J. H. Averesch
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Universities Space Research Association at NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Verónica S. Martínez
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- ARC
Training Centre for Biopharmaceutical Innovation (CBI), Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
| | - Lars K. Nielsen
- Systems
and Synthetic Biology Group, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Brisbane 4072, Australia
- DTU
BIOSUSTAIN, Novo Nordisk Foundation Center for Biosustainability, Danmarks Tekniske Universitet, Kemitorvet, 2800 Kongens Lyngby, Denmark
| | - Jens O. Krömer
- Centre
for Microbial Electrochemical Systems (CEMES), Advanced Water Management
Centre (AWMC), The University of Queensland, Brisbane 4072, Australia
- Department
for Solar Materials, Helmholtz Centre of Environmental Research−UFZ, 04318 Leipzig, Germany
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20
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Schwarzhans JP, Luttermann T, Geier M, Kalinowski J, Friehs K. Towards systems metabolic engineering in Pichia pastoris. Biotechnol Adv 2017; 35:681-710. [DOI: 10.1016/j.biotechadv.2017.07.009] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Revised: 07/20/2017] [Accepted: 07/24/2017] [Indexed: 12/30/2022]
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21
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Vickers CE, Williams TC, Peng B, Cherry J. Recent advances in synthetic biology for engineering isoprenoid production in yeast. Curr Opin Chem Biol 2017. [DOI: 10.1016/j.cbpa.2017.05.017] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Lopes H, Rocha I. Genome-scale modeling of yeast: chronology, applications and critical perspectives. FEMS Yeast Res 2017; 17:3950252. [PMID: 28899034 PMCID: PMC5812505 DOI: 10.1093/femsyr/fox050] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/07/2017] [Indexed: 01/21/2023] Open
Abstract
Over the last 15 years, several genome-scale metabolic models (GSMMs) were developed for different yeast species, aiding both the elucidation of new biological processes and the shift toward a bio-based economy, through the design of in silico inspired cell factories. Here, an historical perspective of the GSMMs built over time for several yeast species is presented and the main inheritance patterns among the metabolic reconstructions are highlighted. We additionally provide a critical perspective on the overall genome-scale modeling procedure, underlining incomplete model validation and evaluation approaches and the quest for the integration of regulatory and kinetic information into yeast GSMMs. A summary of experimentally validated model-based metabolic engineering applications of yeast species is further emphasized, while the main challenges and future perspectives for the field are finally addressed.
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Affiliation(s)
- Helder Lopes
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
| | - Isabel Rocha
- CEB - Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
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Lauersen KJ, Baier T, Wichmann J, Wördenweber R, Mussgnug JH, Hübner W, Huser T, Kruse O. Efficient phototrophic production of a high-value sesquiterpenoid from the eukaryotic microalga Chlamydomonas reinhardtii. Metab Eng 2016; 38:331-343. [DOI: 10.1016/j.ymben.2016.07.013] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 06/17/2016] [Accepted: 07/26/2016] [Indexed: 02/07/2023]
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