1
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Loan TD, Vickers CE, Ayliffe M, Luo M. β-Dicarbonyls Facilitate Engineered Microbial Bromoform Biosynthesis. ACS Synth Biol 2024. [PMID: 38525720 DOI: 10.1021/acssynbio.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/26/2024]
Abstract
Ruminant livestock produce around 24% of global anthropogenic methane emissions. Methanogenesis in the animal rumen is significantly inhibited by bromoform, which is abundant in seaweeds of the genus Asparagopsis. This has prompted the development of livestock feed additives based on Asparagopsis to mitigate methane emissions, although this approach alone is unlikely to satisfy global demand. Here we engineer a non-native biosynthesis pathway to produce bromoform in vivo with yeast as an alternative biological source that may enable sustainable, scalable production of bromoform by fermentation. β-dicarbonyl compounds with low pKa values were identified as essential substrates for bromoform production and enabled bromoform synthesis in engineered Saccharomyces cerevisiae expressing a vanadate-dependent haloperoxidase gene. In addition to providing a potential route to the sustainable biological production of bromoform at scale, this work advances the development of novel microbial biosynthetic pathways for halogenation.
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Affiliation(s)
- Thomas D Loan
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Michael Ayliffe
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
| | - Ming Luo
- CSIRO Agriculture and Food, Box 1700, Clunies Ross Street, Canberra 2601, Australia
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2
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Peng B, Weintraub SJ, Lu Z, Evans S, Shen Q, McDonnell L, Plan M, Collier T, Cheah LC, Ji L, Howard CB, Anderson W, Trau M, Dumsday G, Bredeweg EL, Young EM, Speight R, Vickers CE. Integration of Yeast Episomal/Integrative Plasmid Causes Genotypic and Phenotypic Diversity and Improved Sesquiterpene Production in Metabolically Engineered Saccharomyces cerevisiae. ACS Synth Biol 2024; 13:141-156. [PMID: 38084917 DOI: 10.1021/acssynbio.3c00363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2024]
Abstract
The variability in phenotypic outcomes among biological replicates in engineered microbial factories presents a captivating mystery. Establishing the association between phenotypic variability and genetic drivers is important to solve this intricate puzzle. We applied a previously developed auxin-inducible depletion of hexokinase 2 as a metabolic engineering strategy for improved nerolidol production in Saccharomyces cerevisiae, and biological replicates exhibit a dichotomy in nerolidol production of either 3.5 or 2.5 g L-1 nerolidol. Harnessing Oxford Nanopore's long-read genomic sequencing, we reveal a potential genetic cause─the chromosome integration of a 2μ sequence-based yeast episomal plasmid, encoding the expression cassettes for nerolidol synthetic enzymes. This finding was reinforced through chromosome integration revalidation, engineering nerolidol and valencene production strains, and generating a diverse pool of yeast clones, each uniquely fingerprinted by gene copy numbers, plasmid integrations, other genomic rearrangements, protein expression levels, growth rate, and target product productivities. Τhe best clone in two strains produced 3.5 g L-1 nerolidol and ∼0.96 g L-1 valencene. Comparable genotypic and phenotypic variations were also generated through the integration of a yeast integrative plasmid lacking 2μ sequences. Our work shows that multiple factors, including plasmid integration status, subchromosomal location, gene copy number, sesquiterpene synthase expression level, and genome rearrangement, together play a complicated determinant role on the productivities of sesquiterpene product. Integration of yeast episomal/integrative plasmids may be used as a versatile method for increasing the diversity and optimizing the efficiency of yeast cell factories, thereby uncovering metabolic control mechanisms.
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Affiliation(s)
- Bingyin Peng
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Sarah J Weintraub
- Bioinformatics and Computational Biology, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States of America
| | - Zeyu Lu
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Samuel Evans
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Qianyi Shen
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, Brisbane, QLD4072, Australia
| | - Liam McDonnell
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Collier
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Li Chen Cheah
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lei Ji
- Shandong Provincial Key Laboratory of Applied Microbiology, Ecology Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250103, PR China
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Will Anderson
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, Brisbane, QLD4072, Australia
| | | | - Erin L Bredeweg
- Functional and Systems Biology Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Eric M Young
- Department of Chemical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Robert Speight
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
- Advanced Engineering Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Sydney, NSW 2109, Australia
- Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD 4000, Australia
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3
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Guo Z, Smutok O, Ayva CE, Walden P, Parker J, Whitfield J, Vickers CE, Ungerer JPJ, Katz E, Alexandrov K. Development of epistatic YES and AND protein logic gates and their assembly into signalling cascades. Nat Nanotechnol 2023; 18:1327-1334. [PMID: 37500780 DOI: 10.1038/s41565-023-01450-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 06/09/2023] [Indexed: 07/29/2023]
Abstract
The construction and assembly of artificial allosteric protein switches into information and energy processing networks connected to both biological and non-biological systems is a central goal of synthetic biology and bionanotechnology. However, designing protein switches with the desired input, output and performance parameters is challenging. Here we use a range of reporter proteins to demonstrate that their chimeras with duplicated receptor domains produce YES gate protein switches with large (up to 9,000-fold) dynamic ranges and fast (minutes) response rates. In such switches, the epistatic interactions between largely independent synthetic allosteric sites result in an OFF state with minimal background noise. We used YES gate protein switches based on β-lactamase to develop quantitative biosensors of therapeutic drugs and protein biomarkers. Furthermore, we demonstrated the reconfiguration of YES gate switches into AND gate switches controlled by two different inputs, and their assembly into signalling networks regulated at multiple nodes.
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Affiliation(s)
- Zhong Guo
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Oleh Smutok
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Cagla Ergun Ayva
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Patricia Walden
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jake Parker
- Yakka Bio, Canberra, New South Wales, Australia
| | - Jason Whitfield
- UNSW Founders, University of New South Wales, Sydney, New South Wales, Australia
| | - Claudia E Vickers
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland, Australia
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Jacobus P J Ungerer
- Department of Chemical Pathology, Pathology Queensland, Brisbane, Queensland, Australia
- Faculty of Health and Behavioural Sciences, University of Queensland, Brisbane, Queensland, Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, Potsdam, NY, USA
| | - Kirill Alexandrov
- ARC Centre of Excellence in Synthetic Biology, Brisbane, Queensland, Australia.
- Centre for Agriculture and the Bioeconomy, Queensland University of Technology, Brisbane, Queensland, Australia.
- School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland, Australia.
- CSIRO-QUT Synthetic Biology Alliance, Brisbane, Queensland, Australia.
- Centre for Genomics and Personalised Health, Queensland University of Technology, Brisbane, Queensland, Australia.
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4
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Cheah LC, Liu L, Plan MR, Peng B, Lu Z, Schenk G, Vickers CE, Sainsbury F. Product Profiles of Promiscuous Enzymes Can be Altered by Controlling In Vivo Spatial Organization. Adv Sci (Weinh) 2023; 10:e2303415. [PMID: 37750486 PMCID: PMC10646250 DOI: 10.1002/advs.202303415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 07/31/2023] [Indexed: 09/27/2023]
Abstract
Enzyme spatial organization is an evolved mechanism for facilitating multi-step biocatalysis and can play an important role in the regulation of promiscuous enzymes. The latter function suggests that artificial spatial organization can be an untapped avenue for controlling the specificity of bioengineered metabolic pathways. A promiscuous terpene synthase (nerolidol synthase) is co-localized and spatially organized with the preceding enzyme (farnesyl diphosphate synthase) in a heterologous production pathway, via translational protein fusion and/or co-encapsulation in a self-assembling protein cage. Spatial organization enhances nerolidol production by ≈11- to ≈62-fold relative to unorganized enzymes. More interestingly, striking differences in the ratio of end products (nerolidol and linalool) are observed with each spatial organization approach. This demonstrates that artificial spatial organization approaches can be harnessed to modulate the product profiles of promiscuous enzymes in engineered pathways in vivo. This extends the application of spatial organization beyond situations where multiple enzymes compete for a single substrate to cases where there is competition among multiple substrates for a single enzyme.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Present address:
Australian Centre for Disease Preparedness5 Portarlington RdEast GeelongVIC3219Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Manuel R. Plan
- Metabolomics Australia (Queensland Node)The University of QueenslandSt LuciaQLD4072Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQLD4072Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQLD4000Australia
- School of Biological and Environmental ScienceQueensland University of TechnologyBrisbaneQLD4000Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQLD4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Dutton ParkSt LuciaQLD4102Australia
- Centre for Cell Factories and BiopolymersGriffith Institute for Drug DiscoveryGriffith UniversityNathanQLD4111Australia
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5
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Cheah LC, Liu L, Stark T, Plan MR, Peng B, Lu Z, Schenk G, Sainsbury F, Vickers CE. Metabolic flux enhancement from the translational fusion of terpene synthases is linked to terpene synthase accumulation. Metab Eng 2023; 77:143-151. [PMID: 36990382 DOI: 10.1016/j.ymben.2023.03.012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/13/2023] [Accepted: 03/26/2023] [Indexed: 03/30/2023]
Abstract
The end-to-end fusion of enzymes that catalyse successive steps in a reaction pathway is a metabolic engineering strategy that has been successfully applied in a variety of pathways and is particularly common in terpene bioproduction. Despite its popularity, limited work has been done to interrogate the mechanism of metabolic enhancement from enzyme fusion. We observed a remarkable >110-fold improvement in nerolidol production upon translational fusion of nerolidol synthase (a sesquiterpene synthase) to farnesyl diphosphate synthase. This delivered a titre increase from 29.6 mg/L up to 4.2 g/L nerolidol in a single engineering step. Whole-cell proteomic analysis revealed that nerolidol synthase levels in the fusion strains were greatly elevated compared to the non-fusion control. Similarly, the fusion of nerolidol synthase to non-catalytic domains also produced comparable increases in titre, which coincided with improved enzyme expression. When farnesyl diphosphate synthase was fused to other terpene synthases, we observed more modest improvements in terpene titre (1.9- and 3.8-fold), corresponding with increases of a similar magnitude in terpene synthase levels. Our data demonstrate that increased in vivo enzyme levels - resulting from improved expression and/or improved protein stability - is a major driver of catalytic enhancement from enzyme fusion.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia
| | - Lian Liu
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Terra Stark
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Manuel R Plan
- Metabolomics Australia (Queensland Node), The University of Queensland, QLD, 4072, Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, 4072, Australia; CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Dutton Park, QLD, 4102, Australia; ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia; School of Biological and Environmental Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia; Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, 4111, Australia.
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6
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Alexandrov K, Vickers CE. In vivo protein-based biosensors: seeing metabolism in real time: (Trends in Biotechnology, 41:1 p:19-26, 2023). Trends Biotechnol 2023; 41:257. [PMID: 36581483 DOI: 10.1016/j.tibtech.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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7
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Satta A, Esquirol L, Ebert BE, Newman J, Peat TS, Plan M, Schenk G, Vickers CE. Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase. FEBS J 2022; 289:6672-6693. [PMID: 35704353 PMCID: PMC9796789 DOI: 10.1111/febs.16556] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/03/2022] [Accepted: 06/14/2022] [Indexed: 01/07/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short-chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC 7942 and Synechocystis sp. PCC 6803. Each species has a single putative SPT (SeCrtE and SyCrtE, respectively). Sequence analysis identified these as type-II geranylgeranyl pyrophosphate synthases (GGPPSs) with high homology to GGPPSs found in the plastids of green plants and other photosynthetic organisms. In vitro analysis demonstrated that SyCrtE is multifunctional, producing geranylgeranyl pyrophosphate (GGPP; C20 ) primarily but also significant amounts of farnesyl pyrophosphate (FPP, C15 ) and geranyl pyrophosphate (GPP, C10 ); whereas SeCrtE appears to produce only GGPP. The crystal structures were solved to 2.02 and 1.37 Å, respectively, and the superposition of the structures against the GGPPS of Synechococcus elongatus sp. PCC 7002 yield a root mean square deviation of 0.8 Å (SeCrtE) and 1.1 Å (SyCrtE). We also discovered that SeCrtE is co-encoded in an operon with a functional GGPP phosphatase, suggesting metabolic pairing of these two activities and a putative function in tocopherol biosynthesis. This work sheds light on the activity of SPTs and terpenoid synthesis in cyanobacteria. Understanding native prenyl phosphate metabolism is an important step in developing approaches to engineering the production of different chain-length terpenoids in cyanobacteria.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Janet Newman
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Thomas S. Peat
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Manuel Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaAustralia,Sustainable Minerals InstituteThe University of QueenslandSt. LuciaAustralia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia,Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia,ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneAustralia
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8
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Vinde MH, Cao D, Chesterfield RJ, Yoneyama K, Gumulya Y, Thomson RES, Matila T, Ebert BE, Beveridge CA, Vickers CE, Gillam EMJ. Ancestral sequence reconstruction of the CYP711 family reveals functional divergence in strigolactone biosynthetic enzymes associated with gene duplication events in monocot grasses. New Phytol 2022; 235:1900-1912. [PMID: 35644901 PMCID: PMC9544836 DOI: 10.1111/nph.18285] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
The strigolactone (SL) class of phytohormones shows broad chemical diversity, the functional importance of which remains to be fully elucidated, along with the enzymes responsible for the diversification of the SL structure. Here we explore the functional evolution of the highly conserved CYP711A P450 family, members of which catalyze several key monooxygenation reactions in the strigolactone pathway. Ancestral sequence reconstruction was utilized to infer ancestral CYP711A sequences based on a comprehensive set of extant CYP711 sequences. Eleven ancestral enzymes, corresponding to key points in the CYP711A phylogenetic tree, were resurrected and their activity was characterized towards the native substrate carlactone and the pure enantiomers of the synthetic strigolactone analogue, GR24. The ancestral and extant CYP711As tested accepted GR24 as a substrate and catalyzed several diversifying oxidation reactions on the structure. Evidence was obtained for functional divergence in the CYP711A family. The monocot group 3 ancestor, arising from gene duplication events within monocot grasses, showed both increased catalytic activity towards GR24 and high stereoselectivity towards the GR24 isomer resembling strigol-type SLs. These results are consistent with a role for CYP711As in strigolactone diversification in early land plants, which may have extended to the diversification of strigol-type SLs.
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Affiliation(s)
- Marcos H. Vinde
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
- CSIRO Synthetic Biology Future Science PlatformCSIRO Land & Water, EcoSciences PrecinctDutton ParkBrisbaneQld4012Australia
| | - Da Cao
- School of Biological Sciences, ARC Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQld4072Australia
| | - Rebecca J. Chesterfield
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
- CSIRO Synthetic Biology Future Science PlatformCSIRO Land & Water, EcoSciences PrecinctDutton ParkBrisbaneQld4012Australia
| | - Kaori Yoneyama
- Graduate School of AgricultureEhime UniversityEhime790‐8566Japan
- Japan Science and Technology AgencyPRESTOSaitama332‐0012Japan
| | - Yosephine Gumulya
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Raine E. S. Thomson
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Tebogo Matila
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt LuciaQld4072Australia
| | - Christine A. Beveridge
- School of Biological Sciences, ARC Centre of Excellence for Plant Success in Nature and AgricultureThe University of QueenslandSt LuciaQld4072Australia
| | - Claudia E. Vickers
- Japan Science and Technology AgencyPRESTOSaitama332‐0012Japan
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
- Griffith Institute for Drug DesignGriffith UniversityNathanBrisbaneQld4111Australia
| | - Elizabeth M. J. Gillam
- School of Chemistry and Molecular BiosciencesThe University of QueenslandSt LuciaQld4072Australia
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9
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Esquirol L, McNeale D, Douglas T, Vickers CE, Sainsbury F. Rapid Assembly and Prototyping of Biocatalytic Virus-like Particle Nanoreactors. ACS Synth Biol 2022; 11:2709-2718. [PMID: 35880829 DOI: 10.1021/acssynbio.2c00117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein cages are attractive as molecular scaffolds for the fundamental study of enzymes and metabolons and for the creation of biocatalytic nanoreactors for in vitro and in vivo use. Virus-like particles (VLPs) such as those derived from the P22 bacteriophage capsid protein make versatile self-assembling protein cages and can be used to encapsulate a broad range of protein cargos. In vivo encapsulation of enzymes within VLPs requires fusion to the coat protein or a scaffold protein. However, the expression level, stability, and activity of cargo proteins can vary upon fusion. Moreover, it has been shown that molecular crowding of enzymes inside VLPs can affect their catalytic properties. Consequently, testing of numerous parameters is required for production of the most efficient nanoreactor for a given cargo enzyme. Here, we present a set of acceptor vectors that provide a quick and efficient way to build, test, and optimize cargo loading inside P22 VLPs. We prototyped the system using a yellow fluorescent protein and then applied it to mevalonate kinases (MKs), a key enzyme class in the industrially important terpene (isoprenoid) synthesis pathway. Different MKs required considerably different approaches to deliver maximal encapsulation as well as optimal kinetic parameters, demonstrating the value of being able to rapidly access a variety of encapsulation strategies. The vector system described here provides an approach to optimize cargo enzyme behavior in bespoke P22 nanoreactors. This will facilitate industrial applications as well as basic research on nanoreactor-cargo behavior.
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Affiliation(s)
- Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Donna McNeale
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia
| | - Trevor Douglas
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Claudia E Vickers
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane 4000 Australia
| | - Frank Sainsbury
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia.,Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland 4102, Australia
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10
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Peng B, Esquirol L, Lu Z, Shen Q, Cheah LC, Howard CB, Scott C, Trau M, Dumsday G, Vickers CE. An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae. Nat Commun 2022; 13:2895. [PMID: 35610221 PMCID: PMC9130285 DOI: 10.1038/s41467-022-30529-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 05/05/2022] [Indexed: 11/09/2022] Open
Abstract
Bottlenecks in metabolic pathways due to insufficient gene expression levels remain a significant problem for industrial bioproduction using microbial cell factories. Increasing gene dosage can overcome these bottlenecks, but current approaches suffer from numerous drawbacks. Here, we describe HapAmp, a method that uses haploinsufficiency as evolutionary force to drive in vivo gene amplification. HapAmp enables efficient, titratable, and stable integration of heterologous gene copies, delivering up to 47 copies onto the yeast genome. The method is exemplified in metabolic engineering to significantly improve production of the sesquiterpene nerolidol, the monoterpene limonene, and the tetraterpene lycopene. Limonene titre is improved by 20-fold in a single engineering step, delivering ∼1 g L-1 in the flask cultivation. We also show a significant increase in heterologous protein production in yeast. HapAmp is an efficient approach to unlock metabolic bottlenecks rapidly for development of microbial cell factories.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia. .,CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia.
| | - Lygie Esquirol
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Qianyi Shen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia.,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia
| | - Christopher B Howard
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Colin Scott
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia.,Biocatalysis and Synthetic Biology Team, CSIRO Land and Water, Black Mountain Science and Innovation Park, Canberra, ACT, 2061, Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, 4072, Australia.,School of Chemistry and Molecular Biosciences (SCMB), The University of Queensland, Brisbane, QLD, 4072, Australia
| | | | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, 2601, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Centre of Agriculture and the Bioeconomy, School of Biology and Environmental Science, Faculty of Science, Queensland University of Technology, Brisbane, QLD, 4000, Australia. .,Griffith Institute for Drug Discovery, Griffith University, Brisbane, QLD, 4111, Australia.
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11
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Vickers CE, Freemont PS. Pandemic preparedness: synthetic biology and publicly funded biofoundries can rapidly accelerate response time. Nat Commun 2022; 13:453. [PMID: 35064129 PMCID: PMC8783017 DOI: 10.1038/s41467-022-28103-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 01/06/2022] [Indexed: 12/26/2022] Open
Abstract
Synthetic biology has played a key role in responding to the current pandemic. Biofoundries are critical synthetic biology infrastructure which should be available to all nations as a part of their independent bioengineering, biosecurity, and countermeasure response systems.
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Affiliation(s)
- Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land & Water, EcoSciences Precinct, Dutton Park, 4012, Australia. .,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, 4000, Australia. .,Griffith Institute for Drug Design, Griffith University, Nathan, 4111, Australia.
| | - Paul S Freemont
- Section of Structural and Synthetic Biology, Department of Infectious Disease, Imperial College London, Sir Alexander Fleming Building, South Kensington Campus, South Kensington, London, SW7 2AZ, UK.,UK Dementia Research Institute Care Research and Technology Centre, Imperial College London, Hammersmith Campus, Du Cane Road, London, W12 0NN, UK.,UK Innovation and Knowledge Centre for Synthetic Biology (SynbiCITE) and the London Biofoundry, Imperial College Translation & Innovation Hub, White City Campus 80 Wood Lane, London, W12 0BZ, UK
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12
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Cheah LC, Stark T, Adamson LSR, Abidin RS, Lau YH, Sainsbury F, Vickers CE. Artificial Self-assembling Nanocompartment for Organizing Metabolic Pathways in Yeast. ACS Synth Biol 2021; 10:3251-3263. [PMID: 34591448 PMCID: PMC8689640 DOI: 10.1021/acssynbio.1c00045] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Metabolic pathways are commonly organized by sequestration into discrete cellular compartments. Compartments prevent unfavorable interactions with other pathways and provide local environments conducive to the activity of encapsulated enzymes. Such compartments are also useful synthetic biology tools for examining enzyme/pathway behavior and for metabolic engineering. Here, we expand the intracellular compartmentalization toolbox for budding yeast (Saccharomyces cerevisiae) with Murine polyomavirus virus-like particles (MPyV VLPs). The MPyV system has two components: VP1 which self-assembles into the compartment shell and a short anchor, VP2C, which mediates cargo protein encapsulation via binding to the inner surface of the VP1 shell. Destabilized green fluorescent protein (GFP) fused to VP2C was specifically sorted into VLPs and thereby protected from host-mediated degradation. An engineered VP1 variant displayed improved cargo capture properties and differential subcellular localization compared to wild-type VP1. To demonstrate their ability to function as a metabolic compartment, MPyV VLPs were used to encapsulate myo-inositol oxygenase (MIOX), an unstable and rate-limiting enzyme in d-glucaric acid biosynthesis. Strains with encapsulated MIOX produced ∼20% more d-glucaric acid compared to controls expressing "free" MIOX─despite accumulating dramatically less expressed protein─and also grew to higher cell densities. This is the first demonstration in yeast of an artificial biocatalytic compartment that can participate in a metabolic pathway and establishes the MPyV platform as a promising synthetic biology tool for yeast engineering.
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Affiliation(s)
- Li Chen Cheah
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
| | - Terra Stark
- Metabolomics Australia (Queensland Node), The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Lachlan S. R. Adamson
- School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Rufika S. Abidin
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, New South Wales 2006, Australia
| | - Frank Sainsbury
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), 41 Boggo Road, Dutton Park, Queensland 4102, Australia
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, Queensland 4111, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane City, Queensland 4000, Australia
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13
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Hayat IF, Plan M, Ebert BE, Dumsday G, Vickers CE, Peng B. Auxin-mediated induction of GAL promoters by conditional degradation of Mig1p improves sesquiterpene production in Saccharomyces cerevisiae with engineered acetyl-CoA synthesis. Microb Biotechnol 2021; 14:2627-2642. [PMID: 34499421 PMCID: PMC8601163 DOI: 10.1111/1751-7915.13880] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 06/19/2021] [Accepted: 06/19/2021] [Indexed: 11/30/2022] Open
Abstract
The yeast Saccharomyces cerevisiae uses the pyruvate dehydrogenase-bypass for acetyl-CoA biosynthesis. This relatively inefficient pathway limits production potential for acetyl-CoA-derived biochemical due to carbon loss and the cost of two high-energy phosphate bonds per molecule of acetyl-CoA. Here, we attempted to improve acetyl-CoA production efficiency by introducing heterologous acetylating aldehyde dehydrogenase and phosphoketolase pathways for acetyl-CoA synthesis to enhance production of the sesquiterpene trans-nerolidol. In addition, we introduced auxin-mediated degradation of the glucose-dependent repressor Mig1p to allow induced expression of GAL promoters on glucose so that production potential on glucose could be examined. The novel genes that we used to reconstruct the heterologous acetyl-CoA pathways did not sufficiently complement the loss of endogenous acetyl-CoA pathways, indicating that superior heterologous enzymes are necessary to establish fully functional synthetic acetyl-CoA pathways and properly explore their potential for nerolidol synthesis. Notwithstanding this, nerolidol production was improved twofold to a titre of ˜ 900 mg l-1 in flask cultivation using a combination of heterologous acetyl-CoA pathways and Mig1p degradation. Conditional Mig1p depletion is presented as a valuable strategy to improve the productivities in the strains engineered with GAL promoters-controlled pathways when growing on glucose.
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Affiliation(s)
- Irfan Farabi Hayat
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- School of Chemistry and Molecular Biosciences (SCMB)the University of QueenslandBrisbaneQld4072Australia
| | - Manuel Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN)the University of QueenslandBrisbaneQld4072Australia
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organisation (CSIRO)Black MountainCanberraACT2601Australia
- ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneQld4000Australia
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14
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Raman K, Sinha H, Vickers CE, Nikel PI. Synthetic biology beyond borders. Microb Biotechnol 2021; 14:2254-2256. [PMID: 34792854 PMCID: PMC8601182 DOI: 10.1111/1751-7915.13966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 10/22/2021] [Indexed: 11/26/2022] Open
Affiliation(s)
- Karthik Raman
- Department of BiotechnologyCentre for Integrative Biology and Systems Medicine (IBSE)Indian Institute of Technology MadrasChennaiIndia
| | - Himanshu Sinha
- Department of BiotechnologyCentre for Integrative Biology and Systems Medicine (IBSE)Indian Institute of Technology MadrasChennaiIndia
| | - Claudia E. Vickers
- CSIRO Future Science Platform in Synthetic BiologyCommonwealth Scientific and Industrial Research Organization (CSIRO)Dutton ParkAustralia
| | - Pablo I. Nikel
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkKongens LyngbyDenmark
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15
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Bollella P, Edwardraja S, Guo Z, Vickers CE, Whitfield J, Walden P, Melman A, Alexandrov K, Katz E. Connecting Artificial Proteolytic and Electrochemical Signaling Systems with Caged Messenger Peptides. ACS Sens 2021; 6:3596-3603. [PMID: 34637274 DOI: 10.1021/acssensors.1c00845] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Enzymatic polypeptide proteolysis is a widespread and powerful biological control mechanism. Over the last few years, substantial progress has been made in creating artificial proteolytic systems where an input of choice modulates the protease activity and thereby the activity of its substrates. However, all proteolytic systems developed so far have relied on the direct proteolytic cleavage of their effectors. Here, we propose a new concept where protease biosensors with a tunable input uncage a signaling peptide, which can then transmit a signal to an allosteric protein reporter. We demonstrate that both the cage and the regulatory domain of the reporter can be constructed from the same peptide-binding domain, such as calmodulin. To demonstrate this concept, we constructed a proteolytic rapamycin biosensor and demonstrated its quantitative actuation on fluorescent, luminescent, and electrochemical reporters. Using the latter, we constructed sensitive bioelectrodes that detect the messenger peptide release and quantitatively convert the recognition event into electric current. We discuss the application of such systems for the construction of in vitro sensory arrays and in vivo signaling circuits.
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Affiliation(s)
- Paolo Bollella
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
- Department of Chemistry, University of Bari A. Moro, Via E. Orabona 4, Bari 70125, Italy
| | - Selvakumar Edwardraja
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GP.O. Box 2583, Brisbane, Queensland 4001, Australia
| | - Jason Whitfield
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Patricia Walden
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Artem Melman
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Centre for Genomics and Personalised Health, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Evgeny Katz
- Department of Chemistry and Biomolecular Science, Clarkson University, 8 Clarkson Avenue, Potsdam, New York 13699, United States
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16
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Lu Z, Peng B, Ebert BE, Dumsday G, Vickers CE. Auxin-mediated protein depletion for metabolic engineering in terpene-producing yeast. Nat Commun 2021; 12:1051. [PMID: 33594068 PMCID: PMC7886869 DOI: 10.1038/s41467-021-21313-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/15/2021] [Indexed: 12/12/2022] Open
Abstract
In metabolic engineering, loss-of-function experiments are used to understand and optimise metabolism. A conditional gene inactivation tool is required when gene deletion is lethal or detrimental to growth. Here, we exploit auxin-inducible protein degradation as a metabolic engineering approach in yeast. We demonstrate its effectiveness using terpenoid production. First, we target an essential prenyl-pyrophosphate metabolism protein, farnesyl pyrophosphate synthase (Erg20p). Degradation successfully redirects metabolic flux toward monoterpene (C10) production. Second, depleting hexokinase-2, a key protein in glucose signalling transduction, lifts glucose repression and boosts production of sesquiterpene (C15) nerolidol to 3.5 g L-1 in flask cultivation. Third, depleting acetyl-CoA carboxylase (Acc1p), another essential protein, delivers growth arrest without diminishing production capacity in nerolidol-producing yeast, providing a strategy to decouple growth and production. These studies demonstrate auxin-mediated protein degradation as an advanced tool for metabolic engineering. It also has potential for broader metabolic perturbation studies to better understand metabolism.
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Affiliation(s)
- Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia
- School of Chemistry and Molecular Biosciences (SCMB), the University of Queensland, Brisbane, QLD, Australia
| | - Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia.
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia.
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia
| | | | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), the University of Queensland, Brisbane, QLD, Australia.
- CSIRO Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
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17
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Holowko MB, Frow EK, Reid JC, Rourke M, Vickers CE. Building a biofoundry. Synth Biol (Oxf) 2020; 6:ysaa026. [PMID: 33817343 DOI: 10.1093/synbio/ysaa026] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 10/26/2020] [Accepted: 11/12/2020] [Indexed: 01/21/2023] Open
Abstract
A biofoundry provides automation and analytics infrastructure to support the engineering of biological systems. It allows scientists to perform synthetic biology and aligned experimentation on a high-throughput scale, massively increasing the solution space that can be examined for any given problem or question. However, establishing a biofoundry is a challenging undertaking, with numerous technical and operational considerations that must be addressed. Using collated learnings, here we outline several considerations that should be addressed prior to and during establishment. These include drivers for establishment, institutional models, funding and revenue models, personnel, hardware and software, data management, interoperability, client engagement and biosecurity issues. The high cost of establishment and operation means that developing a long-term business model for biofoundry sustainability in the context of funding frameworks, actual and potential client base, and costing structure is critical. Moreover, since biofoundries are leading a conceptual shift in experimental design for bioengineering, sustained outreach and engagement with the research community are needed to grow the client base. Recognition of the significant, long-term financial investment required and an understanding of the complexities of operationalization is critical for a sustainable biofoundry venture. To ensure state-of-the-art technology is integrated into planning, extensive engagement with existing facilities and community groups, such as the Global Biofoundries Alliance, is recommended.
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Affiliation(s)
- Maciej B Holowko
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land and Water, Brisbane, QLD 4102, Australia
| | - Emma K Frow
- School for the Future of Innovation in Society and School of Biological & Health Systems Engineering, Arizona State University, Tempe, AZ 85287, USA
| | - Janet C Reid
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land and Water, Brisbane, QLD 4102, Australia
| | - Michelle Rourke
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land and Water, Brisbane, QLD 4102, Australia.,Law Futures Centre, Griffith Law School, Griffith University, Nathan, QLD 4111, Australia
| | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, CSIRO Land and Water, Brisbane, QLD 4102, Australia.,ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD 4001, Australia
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18
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Chesterfield RJ, Vickers CE, Beveridge CA. Translation of Strigolactones from Plant Hormone to Agriculture: Achievements, Future Perspectives, and Challenges. Trends Plant Sci 2020; 25:1087-1106. [PMID: 32660772 DOI: 10.1016/j.tplants.2020.06.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/04/2020] [Accepted: 06/10/2020] [Indexed: 05/21/2023]
Abstract
Strigolactones (SLs) control plant development, enhance symbioses, and act as germination stimulants for some of the most destructive species of parasitic weeds, making SLs a potential tool to improve crop productivity and resilience. Field trials demonstrate the potential use of SLs as agrochemicals or genetic targets in breeding programs, with applications in improving drought tolerance, increasing yields, and controlling parasitic weeds. However, for effective translation of SLs into agriculture, understanding and exploiting SL diversity and the development of economically viable sources of SL analogs will be critical. Here we review how manipulation of SL signaling can be used when developing new tools and crop varieties to address some critical challenges, such as nutrient acquisition, resource allocation, stress tolerance, and plant-parasite interactions.
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Affiliation(s)
- Rebecca J Chesterfield
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; Synthetic Biology Future Science Platform, CSIRO, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia; Synthetic Biology Future Science Platform, CSIRO, Australia.
| | - Christine A Beveridge
- School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
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19
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Chesterfield RJ, Whitfield JH, Pouvreau B, Cao D, Alexandrov K, Beveridge CA, Vickers CE. Rational Design of Novel Fluorescent Enzyme Biosensors for Direct Detection of Strigolactones. ACS Synth Biol 2020; 9:2107-2118. [PMID: 32786922 DOI: 10.1021/acssynbio.0c00192] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Strigolactones are plant hormones and rhizosphere signaling molecules with key roles in plant development, mycorrhizal fungal symbioses, and plant parasitism. Currently, sensitive, specific, and high-throughput methods of detecting strigolactones are limited. Here, we developed genetically encoded fluorescent strigolactone biosensors based on the strigolactone receptors DAD2 from Petunia hybrida, and HTL7 from Striga hermonthica. The biosensors were constructed via domain insertion of circularly permuted GFP. The biosensors exhibited loss of cpGFP fluorescence in vitro upon treatment with the strigolactones 5-deoxystrigol and orobanchol, or the strigolactone analogue rac-GR24, and the ShHTL7 biosensor also responded to a specific antagonist. To overcome biosensor sensitivity to changes in expression level and protein degradation, an additional strigolactone-insensitive fluorophore, LSSmOrange, was included as an internal normalization control. Other plant hormones and karrikins resulted in no fluorescence change, demonstrating that the biosensors report on compounds that specifically bind the SL receptors. The DAD2 biosensor likewise responded to strigolactones in an in vivo protoplast system, and retained strigolactone hydrolysis activity. These biosensors have applications in high-throughput screening for agrochemical compounds, and may also have utility in understanding strigolactone mediated signaling in plants.
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Affiliation(s)
- Rebecca J. Chesterfield
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Synthetic Biology Future Science Platform, CSIRO, Black Mountain, ACT 2601, Australia
| | - Jason H. Whitfield
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Synthetic Biology Future Science Platform, CSIRO, Dutton Park, QLD 4001, Australia
| | - Benjamin Pouvreau
- Synthetic Biology Future Science Platform, CSIRO, Black Mountain, ACT 2601, Australia
| | - Da Cao
- School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Kirill Alexandrov
- Synthetic Biology Future Science Platform, CSIRO, Dutton Park, QLD 4001, Australia
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, QLD 4001, Australia
| | - Christine A. Beveridge
- School of Biological Sciences, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
- Synthetic Biology Future Science Platform, CSIRO, Dutton Park, QLD 4001, Australia
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20
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Edwardraja S, Guo Z, Whitfield J, Lantadilla IR, Johnston WA, Walden P, Vickers CE, Alexandrov K. Caged Activators of Artificial Allosteric Protein Biosensors. ACS Synth Biol 2020; 9:1306-1314. [PMID: 32339455 DOI: 10.1021/acssynbio.9b00500] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The ability of proteins to interconvert unrelated biochemical inputs and outputs underlays most energy and information processing in biology. A common conversion mechanism involves a conformational change of a protein receptor in response to a ligand binding or a covalent modification, leading to allosteric activity modulation of the effector domain. Designing such systems rationally is a central goal of synthetic biology and protein engineering. A two-component sensory system based on the scaffolding of modules in the presence of an analyte is one of the most generalizable biosensor architectures. An inherent problem of such systems is dependence of the response on the absolute and relative concentrations of the components. Here we use the example of two-component sensory systems based on calmodulin-operated synthetic switches to analyze and address this issue. We constructed "caged" versions of the activating domain thereby creating a thermodynamic barrier for spontaneous activation of the system. We demonstrate that the caged biosensor architectures could operate at concentrations spanning 3 orders of magnitude and are applicable to electrochemical, luminescent, and fluorescent two-component biosensors. We analyzed the activation kinetics of the caged biosensors and determined that the core allosteric switch is likely to be the rate limiting component of the system. These findings provide guidance for predictable engineering of robust sensory systems with inputs and outputs of choice.
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Affiliation(s)
- Selvakumar Edwardraja
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Zhong Guo
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Jason Whitfield
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | | | - Wayne A. Johnston
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Patricia Walden
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Kirill Alexandrov
- CSIRO-QUT Synthetic Biology Alliance, ARC Centre of Excellence in Synthetic Biology, Centre for Agriculture and the Bioeconomy, Institute of Health and Biomedical Innovation, Institute for Future Environments, School of Biology and Environmental Science, Queensland University of Technology, Brisbane, Queensland 4001, Australia
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21
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Fabris M, George J, Kuzhiumparambil U, Lawson CA, Jaramillo-Madrid AC, Abbriano RM, Vickers CE, Ralph P. Extrachromosomal Genetic Engineering of the Marine Diatom Phaeodactylum tricornutum Enables the Heterologous Production of Monoterpenoids. ACS Synth Biol 2020; 9:598-612. [PMID: 32032487 DOI: 10.1021/acssynbio.9b00455] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Geraniol is a commercially relevant plant-derived monoterpenoid that is a main component of rose essential oil and used as insect repellent. Geraniol is also a key intermediate compound in the biosynthesis of the monoterpenoid indole alkaloids (MIAs), a group of over 2000 compounds that include high-value pharmaceuticals. As plants naturally produce extremely small amounts of these molecules and their chemical synthesis is complex, industrially sourcing these compounds is costly and inefficient. Hence, microbial hosts suitable to produce MIA precursors through synthetic biology and metabolic engineering are currently being sought. Here, we evaluated the suitability of a eukaryotic microalga, the marine diatom Phaeodactylum tricornutum, for the heterologous production of monoterpenoids. Profiling of endogenous metabolism revealed that P. tricornutum, unlike other microbes employed for industrial production of terpenoids, accumulates free pools of the precursor geranyl diphosphate. To evaluate the potential for larger synthetic biology applications, we engineered P. tricornutum through extrachromosomal, episome-based expression, for the heterologous biosynthesis of the MIA intermediate geraniol. By profiling the production of geraniol resulting from various genetic and cultivation arrangements, P. tricornutum reached the maximum geraniol titer of 0.309 mg/L in phototrophic conditions. This work provides (i) a detailed analysis of P. tricornutum endogenous terpenoid metabolism, (ii) a successful demonstration of extrachromosomal expression for metabolic pathway engineering with potential gene-stacking applications, and (iii) a convincing proof-of-concept of the suitability of P. tricornutum as a novel production platform for heterologous monoterpenoids, with potential for complex pathway engineering aimed at the heterologous production of MIAs.
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Affiliation(s)
- Michele Fabris
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
| | - Jestin George
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Caitlin A. Lawson
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | | | - Raffaela M. Abbriano
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Peter Ralph
- Climate Change Cluster, University of Technology, 15 Broadway, Ultimo, NSW 2007, Australia
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22
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Bongers M, Perez-Gil J, Hodson MP, Schrübbers L, Wulff T, Sommer MO, Nielsen LK, Vickers CE. Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production. eLife 2020; 9:48685. [PMID: 32163032 PMCID: PMC7067565 DOI: 10.7554/elife.48685] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 02/16/2020] [Indexed: 12/12/2022] Open
Abstract
Volatile isoprenoids produced by plants are emitted in vast quantities into the atmosphere, with substantial effects on global carbon cycling. Yet, the molecular mechanisms regulating the balance between volatile and non-volatile isoprenoid production remain unknown. Isoprenoids are synthesised via sequential condensation of isopentenyl pyrophosphate (IPP) to dimethylallyl pyrophosphate (DMAPP), with volatile isoprenoids containing fewer isopentenyl subunits. The DMAPP:IPP ratio could affect the balance between volatile and non-volatile isoprenoids, but the plastidic DMAPP:IPP ratio is generally believed to be similar across different species. Here we demonstrate that the ratio of DMAPP:IPP produced by hydroxymethylbutenyl diphosphate reductase (HDR/IspH), the final step of the plastidic isoprenoid production pathway, is not fixed. Instead, this ratio varies greatly across HDRs from phylogenetically distinct plants, correlating with isoprenoid production patterns. Our findings suggest that adaptation of HDR plays a previously unrecognised role in determining in vivo carbon availability for isoprenoid emissions, directly shaping global biosphere-atmosphere interactions.
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Affiliation(s)
- Mareike Bongers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Jordi Perez-Gil
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona, Spain
| | - Mark P Hodson
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,Metabolomics Australia, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,School of Pharmacy, The University of Queensland, Brisbane, Australia
| | - Lars Schrübbers
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Morten Oa Sommer
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark
| | - Lars K Nielsen
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Lyngby, Denmark.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, Australia
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23
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Wurtzel ET, Vickers CE, Hanson AD, Millar AH, Cooper M, Voss-Fels KP, Nikel PI, Erb TJ. Revolutionizing agriculture with synthetic biology. Nat Plants 2019; 5:1207-1210. [PMID: 31740769 DOI: 10.1038/s41477-019-0539-0] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 09/27/2019] [Indexed: 05/26/2023]
Abstract
Synthetic biology is here to stay and will transform agriculture if given the chance. The huge challenges facing food, fuel and chemical production make it vital to give synthetic biology that chance-notwithstanding the shifts in mindset, training and infrastructure investment this demands. Here, we assess opportunities for agricultural synthetic biology and ways to remove barriers to their realization.
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Affiliation(s)
- Eleanore T Wurtzel
- Department of Biological Sciences, Lehman College, City University of New York, New York, NY, USA.
- Graduate School and University Center-CUNY, New York, NY, USA.
| | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, Canberra, Australia.
- Australian Institute for Bioengineering & Nanotechnology, University of Queensland, Brisbane, Queensland, Australia.
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA.
| | - A Harvey Millar
- ARC Centre of Excellence in Plant Energy Biology, School of Molecular Sciences, University of Western Australia, Crawley, Western Australia, Australia
| | - Mark Cooper
- Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St. Lucia, Queensland, Australia
| | - Kai P Voss-Fels
- Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St. Lucia, Queensland, Australia
| | - Pablo I Nikel
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kgs Lyngby, Denmark
| | - Tobias J Erb
- Max-Planck-Institute for Terrestrial Microbiology, Department of Biochemistry & Synthetic Metabolism, Marburg, Germany
- LOEWE Center for Synthetic Microbiology, Marburg, Germany
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24
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Vavitsas K, Crozet P, Vinde MH, Davies F, Lemaire SD, Vickers CE. The Synthetic Biology Toolkit for Photosynthetic Microorganisms. Plant Physiol 2019; 181:14-27. [PMID: 31262955 PMCID: PMC6716251 DOI: 10.1104/pp.19.00345] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/09/2019] [Indexed: 05/10/2023]
Abstract
Photosynthetic microorganisms offer novel characteristics as synthetic biology chassis, and the toolbox of components and techniques for cyanobacteria and algae is rapidly increasing.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Marcos Hamborg Vinde
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Fiona Davies
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
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25
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Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Feuvre RL, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, Keasling JD, Kitney RI, Kondo A, Liu C, Martin VJJ, Menolascina F, Ogino C, Patron NJ, Pavan M, Poh CL, Pretorius IS, Rosser SJ, Scrutton NS, Storch M, Tekotte H, Travnik E, Vickers CE, Yew WS, Yuan Y, Zhao H, Freemont PS. Author Correction: Building a global alliance of biofoundries. Nat Commun 2019; 10:3132. [PMID: 31296848 PMCID: PMC6624256 DOI: 10.1038/s41467-019-10862-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Affiliation(s)
| | - Mark Caddick
- GeneMill, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Yizhi Cai
- SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Jose A Carrasco
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Matthew Wook Chang
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Natalie C Curach
- Bioplatforms Australia, Research Park Drive, Macquarie University, Macquarie Park, NSW, 2109, Australia
| | - David J Bell
- London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 WoodLane, London, W12 0BZ, UK
| | - Rosalind Le Feuvre
- SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Douglas C Friedman
- Engineering Biology Research Consortium (EBRC), Emeryville, CA, 94608, USA
| | - Xiongfei Fu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Nicholas D Gold
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Montreal, QC, H4B 1R6, Canada
| | - Markus J Herrgård
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Maciej B Holowko
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia.,Department of Molecular Sciences, Macquarie University, Macquarie, NSW, 2109, Australia
| | - James R Johnson
- GeneMill, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Richard A Johnson
- Global Helix LLC, BioBricks Foundation, and Engineering Biology Research Consortium (EBRC), Emeryville, CA 94608, USA
| | | | - Richard I Kitney
- London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 WoodLane, London, W12 0BZ, UK
| | - Akihiko Kondo
- Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, 657-8501, Japan
| | - Chenli Liu
- Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People's Republic of China
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Montreal, QC, H4B 1R6, Canada
| | - Filippo Menolascina
- UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF, UK
| | - Chiaki Ogino
- Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, 657-8501, Japan
| | - Nicola J Patron
- Earlham Institute, Norwich Research Park, Norfolk, NR4 7UZ, UK
| | - Marilene Pavan
- DAMP Lab, Biological Design Center, Boston University, Boston, MA, 02215, USA
| | - Chueh Loo Poh
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | | | - Susan J Rosser
- UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF, UK
| | - Nigel S Scrutton
- SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL, UK
| | - Marko Storch
- London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 WoodLane, London, W12 0BZ, UK
| | - Hille Tekotte
- UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF, UK
| | - Evelyn Travnik
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800, Kongens Lyngby, Denmark
| | - Claudia E Vickers
- CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601, Australia.,Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Wen Shan Yew
- NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456, Singapore
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology (MOE), TianjinUniversity, Tianjin, People's Republic of China
| | - Huimin Zhao
- Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB), University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Paul S Freemont
- London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 WoodLane, London, W12 0BZ, UK.
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26
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Hillson N, Caddick M, Cai Y, Carrasco JA, Chang MW, Curach NC, Bell DJ, Le Feuvre R, Friedman DC, Fu X, Gold ND, Herrgård MJ, Holowko MB, Johnson JR, Johnson RA, Keasling JD, Kitney RI, Kondo A, Liu C, Martin VJJ, Menolascina F, Ogino C, Patron NJ, Pavan M, Poh CL, Pretorius IS, Rosser SJ, Scrutton NS, Storch M, Tekotte H, Travnik E, Vickers CE, Yew WS, Yuan Y, Zhao H, Freemont PS. Building a global alliance of biofoundries. Nat Commun 2019; 10:2040. [PMID: 31068573 PMCID: PMC6506534 DOI: 10.1038/s41467-019-10079-2] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 04/15/2019] [Indexed: 02/08/2023] Open
Abstract
Biofoundries provide an integrated infrastructure to enable the rapid design, construction, and testing of genetically reprogrammed organisms for biotechnology applications and research. Many biofoundries are being built and a Global Biofoundry Alliance has recently been established to coordinate activities worldwide.
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Affiliation(s)
| | - Mark Caddick
- 0000 0004 1936 8470grid.10025.36GeneMill, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Yizhi Cai
- 0000000121662407grid.5379.8SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL UK
| | | | - Matthew Wook Chang
- 0000 0001 2180 6431grid.4280.eNUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456 Singapore
| | - Natalie C. Curach
- 0000 0001 2158 5405grid.1004.5Bioplatforms Australia, Research Park Drive, Macquarie University, Macquarie Park, NSW 2109 Australia
| | - David J. Bell
- 0000 0001 2113 8111grid.7445.2London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ UK
| | - Rosalind Le Feuvre
- 0000000121662407grid.5379.8SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL UK
| | | | - Xiongfei Fu
- 0000000119573309grid.9227.eShenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People’s Republic of China
| | - Nicholas D. Gold
- 0000 0004 1936 8630grid.410319.eCentre for Applied Synthetic Biology, Concordia University, Montreal, Montreal, QC H4B 1R6 Canada
| | - Markus J. Herrgård
- 0000 0001 2181 8870grid.5170.3The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Maciej B. Holowko
- grid.1016.6CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601 Australia ,0000 0000 9320 7537grid.1003.2Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia ,0000 0001 2158 5405grid.1004.5Department of Molecular Sciences, Macquarie University, Macquarie, NSW 2109 Australia
| | - James R. Johnson
- 0000 0004 1936 8470grid.10025.36GeneMill, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB UK
| | - Richard A. Johnson
- grid.487833.3Global Helix LLC, BioBricks Foundation, and Engineering Biology Research Consortium (EBRC), Emeryville, CA 94608 USA
| | | | - Richard I. Kitney
- 0000 0001 2113 8111grid.7445.2London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ UK
| | - Akihiko Kondo
- 0000 0001 1092 3077grid.31432.37Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, 657-8501 Japan
| | - Chenli Liu
- 0000000119573309grid.9227.eShenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, People’s Republic of China
| | - Vincent J. J. Martin
- 0000 0004 1936 8630grid.410319.eCentre for Applied Synthetic Biology, Concordia University, Montreal, Montreal, QC H4B 1R6 Canada
| | - Filippo Menolascina
- 0000 0004 1936 7988grid.4305.2UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF UK
| | - Chiaki Ogino
- 0000 0001 1092 3077grid.31432.37Graduate School of Science, Technology, and Innovation, Kobe University, Kobe, 657-8501 Japan
| | | | - Marilene Pavan
- 0000 0004 1936 7558grid.189504.1DAMP Lab, Biological Design Center, Boston University, Boston, MA 02215 USA
| | - Chueh Loo Poh
- 0000 0001 2180 6431grid.4280.eNUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456 Singapore
| | - Isak S. Pretorius
- 0000 0001 2158 5405grid.1004.5Macquarie University, North Ryde, NSW 2109 Australia
| | - Susan J. Rosser
- 0000 0004 1936 7988grid.4305.2UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF UK
| | - Nigel S. Scrutton
- 0000000121662407grid.5379.8SYNBIOCHEM, Manchester Institute of Biotechnology and School of Chemistry, University of Manchester, Manchester, M13 9PL UK
| | - Marko Storch
- 0000 0001 2113 8111grid.7445.2London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ UK
| | - Hille Tekotte
- 0000 0004 1936 7988grid.4305.2UK Centre for Mammalian Synthetic Biology SynthSys, School of Biological Sciences, University of Edinburgh, Edinburgh, EH93FF UK
| | - Evelyn Travnik
- 0000 0001 2181 8870grid.5170.3The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Claudia E. Vickers
- grid.1016.6CSIRO Synthetic Biology Future Science Platform, Canberra, ACT 2601 Australia ,0000 0000 9320 7537grid.1003.2Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072 Australia
| | - Wen Shan Yew
- 0000 0001 2180 6431grid.4280.eNUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117456 Singapore
| | - Yingjin Yuan
- 0000 0004 1761 2484grid.33763.32Frontier Science Center for Synthetic Biology (MOE), Tianjin University, Tianjin, People’s Republic of China
| | - Huimin Zhao
- 0000 0004 1936 9991grid.35403.31Illinois Biological Foundry for Advanced Biomanufacturing (iBioFAB), University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Paul S. Freemont
- 0000 0001 2113 8111grid.7445.2London DNA Foundry, Imperial College Translation & Innovation Hub, White City Campus, 80 Wood Lane, London, W12 0BZ UK
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27
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de Souza VF, Niinemets Ü, Rasulov B, Vickers CE, Duvoisin Júnior S, Araújo WL, Gonçalves JFDC. Alternative Carbon Sources for Isoprene Emission. Trends Plant Sci 2018; 23:1081-1101. [PMID: 30472998 PMCID: PMC6354897 DOI: 10.1016/j.tplants.2018.09.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 09/03/2018] [Accepted: 09/25/2018] [Indexed: 05/07/2023]
Abstract
Isoprene and other plastidial isoprenoids are produced primarily from recently assimilated photosynthates via the 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. However, when environmental conditions limit photosynthesis, a fraction of carbon for MEP pathway can come from extrachloroplastic sources. The flow of extrachloroplastic carbon depends on the species and on leaf developmental and environmental conditions. The exchange of common phosphorylated intermediates between the MEP pathway and other metabolic pathways can occur via plastidic phosphate translocators. C1 and C2 carbon intermediates can contribute to chloroplastic metabolism, including photosynthesis and isoprenoid synthesis. Integration of these metabolic processes provide an example of metabolic flexibility, and results in the synthesis of primary metabolites for plant growth and secondary metabolites for plant defense, allowing effective use of environmental resources under multiple stresses.
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Affiliation(s)
- Vinícius Fernandes de Souza
- Laboratory of Plant Physiology and Biochemistry, National Institute for Amazonian Research (INPA), Manaus, AM 69011-970, Brazil; University of Amazonas State, Manaus, AM 69050-010, Brazil
| | - Ülo Niinemets
- Department of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu 51006, Estonia; Estonian Academy of Sciences, 10130 Tallinn, Estonia
| | - Bahtijor Rasulov
- Department of Crop Science and Plant Biology, Estonian University of Life Sciences, Tartu 51006, Estonia; Institute of Technology, University of Tartu, Tartu, Estonia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, St Lucia, QLD 4072, Australia; Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, EcoSciences Precinct, Brisbane, QLD 4001, Australia
| | | | - Wagner L Araújo
- Max-Planck Partner Group at the Departamento de Biologia Vegetal, Universidade Federal de Viçosa, 36570-900 Viçosa, MG, Brazil
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Pollier J, Vancaester E, Kuzhiumparambil U, Vickers CE, Vandepoele K, Goossens A, Fabris M. A widespread alternative squalene epoxidase participates in eukaryote steroid biosynthesis. Nat Microbiol 2018; 4:226-233. [DOI: 10.1038/s41564-018-0305-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Accepted: 10/24/2018] [Indexed: 11/09/2022]
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Vavitsas K, Fabris M, Vickers CE. Terpenoid Metabolic Engineering in Photosynthetic Microorganisms. Genes (Basel) 2018; 9:E520. [PMID: 30360565 PMCID: PMC6266707 DOI: 10.3390/genes9110520] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 12/13/2022] Open
Abstract
Terpenoids are a group of natural products that have a variety of roles, both essential and non-essential, in metabolism and in biotic and abiotic interactions, as well as commercial applications such as pharmaceuticals, food additives, and chemical feedstocks. Economic viability for commercial applications is commonly not achievable by using natural source organisms or chemical synthesis. Engineered bio-production in suitable heterologous hosts is often required to achieve commercial viability. However, our poor understanding of regulatory mechanisms and other biochemical processes makes obtaining efficient conversion yields from feedstocks challenging. Moreover, production from carbon dioxide via photosynthesis would significantly increase the environmental and potentially the economic credentials of these processes by disintermediating biomass feedstocks. In this paper, we briefly review terpenoid metabolism, outline some recent advances in terpenoid metabolic engineering, and discuss why photosynthetic unicellular organisms-such as algae and cyanobacteria-might be preferred production platforms for the expression of some of the more challenging terpenoid pathways.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Michele Fabris
- Climate Change Cluster, University of Technology Sydney, 15 Broadway, Ultimo, NSW 2007, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
- CSIRO Synthetic Biology Future Science Platform, GPO Box 2583, Brisbane, QLD 4001, Australia.
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Peng B, Nielsen LK, Kampranis SC, Vickers CE. Engineered protein degradation of farnesyl pyrophosphate synthase is an effective regulatory mechanism to increase monoterpene production in Saccharomyces cerevisiae. Metab Eng 2018; 47:83-93. [DOI: 10.1016/j.ymben.2018.02.005] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Revised: 02/02/2018] [Accepted: 02/14/2018] [Indexed: 10/18/2022]
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Schulz BL, Phung TK, Bruschi M, Janusz A, Stewart J, Meehan J, Healy P, Nouwens AS, Fox GP, Vickers CE. Process Proteomics of Beer Reveals a Dynamic Proteome with Extensive Modifications. J Proteome Res 2018; 17:1647-1653. [PMID: 29457908 DOI: 10.1021/acs.jproteome.7b00907] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Modern beer production is a complex industrial process. However, some of its biochemical details remain unclear. Using mass spectrometry proteomics, we have performed a global untargeted analysis of the proteins present across time during nanoscale beer production. Samples included sweet wort produced by a high temperature infusion mash, hopped wort, and bright beer. This analysis identified over 200 unique proteins from barley and yeast, emphasizing the complexity of the process and product. We then used data independent SWATH-MS to quantitatively compare the relative abundance of these proteins throughout the process. This identified large and significant changes in the proteome at each process step. These changes described enrichment of proteins by their biophysical properties, and identified the appearance of dominant yeast proteins during fermentation. Altered levels of malt modification also quantitatively changed the proteomes throughout the process. Detailed inspection of the proteomic data revealed that many proteins were modified by protease digestion, glycation, or oxidation during the processing steps. This work demonstrates the opportunities offered by modern mass spectrometry proteomics in understanding the ancient process of beer production.
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Affiliation(s)
- Benjamin L Schulz
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,ARC Training Centre for Biopharmaceutical Innovation, Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Michele Bruschi
- Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | | | - Jeff Stewart
- Lion , Sydney , New South Wales 2127 , Australia
| | - John Meehan
- Lion , Brisbane , Queensland 4064 , Australia
| | - Peter Healy
- Lion , Brisbane , Queensland 4064 , Australia
| | - Amanda S Nouwens
- School of Chemistry and Molecular Biosciences , The University of Queensland , Brisbane , Queensland 4072 , Australia.,Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Glen P Fox
- Queensland Alliance for Agriculture and Food Innovation , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Claudia E Vickers
- Australian Institute of Bioengineering and Nanotechnology , The University of Queensland , Brisbane , Queensland 4072 , Australia
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Peng B, Wood RJ, Nielsen LK, Vickers CE. An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae. ACS Synth Biol 2018; 7:748-751. [PMID: 29301066 DOI: 10.1021/acssynbio.7b00355] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The GAL promoters are applied in metabolic engineering and synthetic biology to control gene expression in the budding yeast Saccharomyces cerevisiae. In gal80Δ background strains, they show diauxie-inducible expression, a feature beneficial in metabolic pathway optimization. However, only a limited number of GAL promoters have been characterized and are available for engineering purposes. Multiple uses of the same promoters can result in genetic instability in engineered strains due to homologous recombination. Here, 11 GAL1/2 promoters from other Saccharomyces species were isolated and characterized in S. cerevisiae. They exhibited diauxie-inducible expression patterns with low strength in exponential growth phase and induction in the ethanol growth phase. These promoters represent an expansion to the collection of GAL promoters available for genetic engineering in S. cerevisiae, including an increased diversity of expression levels. This provides the capacity for increased numbers of genetic manipulations with a lower risk of genetic instability.
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Affiliation(s)
- Bingyin Peng
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Rebecca J. Wood
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
| | - Lars K. Nielsen
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- Novo
Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kemitorvet, 2800 Kgs.
Lyngby, Denmark
| | - Claudia E. Vickers
- Australian
Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD 4072, Australia
- CSIRO
Future Science Platform in Synthetic Biology, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Black Mountain, ACT 2601, Australia
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Alonso‐Gutierrez J, Koma D, Hu Q, Yang Y, Chan LJG, Petzold CJ, Adams PD, Vickers CE, Nielsen LK, Keasling JD, Lee TS. Toward industrial production of isoprenoids in
Escherichia coli
: Lessons learned from CRISPR‐Cas9 based optimization of a chromosomally integrated mevalonate pathway. Biotechnol Bioeng 2018; 115:1000-1013. [DOI: 10.1002/bit.26530] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Revised: 12/18/2017] [Accepted: 12/22/2017] [Indexed: 01/13/2023]
Affiliation(s)
- Jorge Alonso‐Gutierrez
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Daisuke Koma
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- Osaka Municipal Technical Research InstituteOsakaJapan
| | - Qijun Hu
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Yuchen Yang
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Leanne J. G. Chan
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Christopher J. Petzold
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Paul D. Adams
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Molecular Biophysics and Integrated Bioimaging DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Jay D. Keasling
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
- The Novo Nordisk Foundation Center for BiosustainabilityTechnical University of DenmarkHorsholmDenmark
- Department of Chemical and Biomolecular EngineeringUniversity of CaliforniaBerkeleyCalifornia
- Department of BioengineeringUniversity of CaliforniaBerkeleyCalifornia
| | - Taek S. Lee
- Joint BioEnergy Institute (JBEI)EmeryvilleCalifornia
- Biological Systems and Engineering DivisionLawrence Berkeley National LaboratoryBerkeleyCalifornia
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Affiliation(s)
- Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
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Gagoski D, Shi Z, Nielsen LK, Vickers CE, Mahler S, Speight R, Johnston WA, Alexandrov K. Cell-free pipeline for discovery of thermotolerant xylanases and endo -1,4-β-glucanases. J Biotechnol 2017; 259:191-198. [DOI: 10.1016/j.jbiotec.2017.07.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Revised: 07/04/2017] [Accepted: 07/12/2017] [Indexed: 11/29/2022]
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Peng B, Plan MR, Carpenter A, Nielsen LK, Vickers CE. Coupling gene regulatory patterns to bioprocess conditions to optimize synthetic metabolic modules for improved sesquiterpene production in yeast. Biotechnol Biofuels 2017; 10:43. [PMID: 28239415 PMCID: PMC5320780 DOI: 10.1186/s13068-017-0728-x] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/09/2017] [Indexed: 05/23/2023]
Abstract
BACKGROUND Assembly of heterologous metabolic pathways is commonly required to generate microbial cell factories for industrial production of both commodity chemicals (including biofuels) and high-value chemicals. Promoter-mediated transcriptional regulation coordinates the expression of the individual components of these heterologous pathways. Expression patterns vary during culture as conditions change, and this can influence yeast physiology and productivity in both positive and negative ways. Well-characterized strategies are required for matching transcriptional regulation with desired output across changing culture conditions. RESULTS Here, constitutive and inducible regulatory mechanisms were examined to optimize synthetic isoprenoid metabolic pathway modules for production of trans-nerolidol, an acyclic sesquiterpene alcohol, in yeast. The choice of regulatory system significantly affected physiological features (growth and productivity) over batch cultivation. Use of constitutive promoters resulted in poor growth during the exponential phase. Delaying expression of the assembled metabolic modules using the copper-inducible CUP1 promoter resulted in a 1.6-fold increase in the exponential-phase growth rate and a twofold increase in productivity in the post-exponential phase. However, repeated use of the CUP1 promoter in multiple expression cassettes resulted in genetic instability. A diauxie-inducible expression system, based on an engineered GAL regulatory circuit and a set of four different GAL promoters, was characterized and employed to assemble nerolidol synthetic metabolic modules. Nerolidol production was further improved by 60% to 392 mg L-1 using this approach. Various carbon source systems were investigated in batch/fed-batch cultivation to regulate induction through the GAL system; final nerolidol titres of 4-5.5 g L-1 were achieved, depending on the conditions. CONCLUSION Direct comparison of different transcriptional regulatory mechanisms clearly demonstrated that coupling the output strength to the fermentation stage is important to optimize the growth fitness and overall productivities of engineered cells in industrially relevant processes. Applying different well-characterized promoters with the same induction behaviour mitigates against the risks of homologous sequence-mediated genetic instability. Using these approaches, we significantly improved sesquiterpene production in yeast.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Manuel R. Plan
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
- Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Alexander Carpenter
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072 Australia
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Peng B, Plan MR, Chrysanthopoulos P, Hodson MP, Nielsen LK, Vickers CE. A squalene synthase protein degradation method for improved sesquiterpene production in Saccharomyces cerevisiae. Metab Eng 2017; 39:209-219. [DOI: 10.1016/j.ymben.2016.12.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 11/17/2016] [Accepted: 12/07/2016] [Indexed: 10/20/2022]
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Williams TC, Peng B, Vickers CE, Nielsen LK. The Saccharomyces cerevisiae pheromone-response is a metabolically active stationary phase for bio-production. Metab Eng Commun 2016; 3:142-152. [PMID: 29468120 PMCID: PMC5779721 DOI: 10.1016/j.meteno.2016.05.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Revised: 05/02/2016] [Accepted: 05/10/2016] [Indexed: 11/04/2022] Open
Abstract
The growth characteristics and underlying metabolism of microbial production hosts are critical to the productivity of metabolically engineered pathways. Production in parallel with growth often leads to biomass/bio-product competition for carbon. The growth arrest phenotype associated with the Saccharomyces cerevisiae pheromone-response is potentially an attractive production phase because it offers the possibility of decoupling production from population growth. However, little is known about the metabolic phenotype associated with the pheromone-response, which has not been tested for suitability as a production phase. Analysis of extracellular metabolite fluxes, available transcriptomic data, and heterologous compound production (para-hydroxybenzoic acid) demonstrate that a highly active and distinct metabolism underlies the pheromone-response. These results indicate that the pheromone-response is a suitable production phase, and that it may be useful for informing synthetic biology design principles for engineering productive stationary phase phenotypes.
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Affiliation(s)
| | | | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD 4072, Australia
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Shi Z, Vickers CE. Molecular Cloning Designer Simulator (MCDS): All-in-one molecular cloning and genetic engineering design, simulation and management software for complex synthetic biology and metabolic engineering projects. Metab Eng Commun 2016; 3:173-186. [PMID: 29468123 PMCID: PMC5779711 DOI: 10.1016/j.meteno.2016.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2015] [Revised: 03/30/2016] [Accepted: 05/10/2016] [Indexed: 01/15/2023] Open
Abstract
Molecular Cloning Designer Simulator (MCDS) is a powerful new all-in-one cloning and genetic engineering design, simulation and management software platform developed for complex synthetic biology and metabolic engineering projects. In addition to standard functions, it has a number of features that are either unique, or are not found in combination in any one software package: (1) it has a novel interactive flow-chart user interface for complex multi-step processes, allowing an integrated overview of the whole project; (2) it can perform a user-defined workflow of cloning steps in a single execution of the software; (3) it can handle multiple types of genetic recombineering, a technique that is rapidly replacing classical cloning for many applications; (4) it includes experimental information to conveniently guide wet lab work; and (5) it can store results and comments to allow the tracking and management of the whole project in one platform. MCDS is freely available from https://mcds.codeplex.com. MCDS is an all-in-one in silico design, simulation and management platform. MCDS supports the design, simulation management of most cloning and recombineering technologies. MCDS has a novel interactive flowchart that allows simpler and more precise transactions. MCDS enables complete information integrity and consistency by keeping all details in one file.
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Affiliation(s)
- Zhenyu Shi
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering & Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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Bongers M, Chrysanthopoulos PK, Behrendorff JBYH, Hodson MP, Vickers CE, Nielsen LK. Systems analysis of methylerythritol-phosphate pathway flux in E. coli: insights into the role of oxidative stress and the validity of lycopene as an isoprenoid reporter metabolite. Microb Cell Fact 2015; 14:193. [PMID: 26610700 PMCID: PMC4662018 DOI: 10.1186/s12934-015-0381-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 11/11/2015] [Indexed: 12/13/2022] Open
Abstract
Background High-throughput screening methods assume that the output measured is representative of changes in metabolic flux toward the desired product and is not affected by secondary phenotypes. However, metabolic engineering can result in unintended phenotypes that may go unnoticed in initial screening. The red pigment lycopene, a carotenoid with antioxidant properties, has been used as a reporter of isoprenoid pathway flux in metabolic engineering for over a decade. Lycopene production is known to vary between wild-type Escherichia coli hosts, but the reasons behind this variation have never been fully elucidated. Results In an examination of six E. coli strains we observed that strains also differ in their capacity for increased lycopene production in response to metabolic engineering. A combination of genetic complementation, quantitative SWATH proteomics, and biochemical analysis in closely-related strains was used to examine the mechanistic reasons for variation in lycopene accumulation. This study revealed that rpoS, a gene previously identified in lycopene production association studies, exerts its effect on lycopene accumulation not through modulation of pathway flux, but through alteration of cellular oxidative status. Specifically, absence of rpoS results in increased accumulation of reactive oxygen species during late log and stationary phases. This change in cellular redox has no effect on isoprenoid pathway flux, despite the presence of oxygen-sensitive iron-sulphur cluster enzymes and the heavy redox requirements of the methylerythritol phosphate pathway. Instead, decreased cellular lycopene in the ΔrpoS strain is caused by degradation of lycopene in the presence of excess reactive oxygen species. Conclusions Our results demonstrate that lycopene is not a reliable indicator of isoprenoid pathway flux in the presence of oxidative stress, and suggest that caution should be exercised when using lycopene as a screening tool in genome-wide metabolic engineering studies. More extensive use of systems biology for strain analysis will help elucidate such unpredictable side-effects in metabolic engineering projects. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0381-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mareike Bongers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Panagiotis K Chrysanthopoulos
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - James B Y H Behrendorff
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Mark P Hodson
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia. .,Metabolomics Australia (Queensland Node), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Peng B, Williams TC, Henry M, Nielsen LK, Vickers CE. Controlling heterologous gene expression in yeast cell factories on different carbon substrates and across the diauxic shift: a comparison of yeast promoter activities. Microb Cell Fact 2015; 14:91. [PMID: 26112740 PMCID: PMC4480987 DOI: 10.1186/s12934-015-0278-5] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 06/01/2015] [Indexed: 11/10/2022] Open
Abstract
Background Predictable control of gene expression is necessary for the rational design and optimization of cell factories. In the yeast Saccharomyces cerevisiae, the promoter is one of the most important tools available for controlling gene expression. However, the complex expression patterns of yeast promoters have not been fully characterised and compared on different carbon sources (glucose, sucrose, galactose and ethanol) and across the diauxic shift in glucose batch cultivation. These conditions are of importance to yeast cell factory design because they are commonly used and encountered in industrial processes. Here, the activities of a series of “constitutive” and inducible promoters were characterised in single cells throughout the fermentation using green fluorescent protein (GFP) as a reporter. Results The “constitutive” promoters, including glycolytic promoters, transcription elongation factor promoters and ribosomal promoters, differed in their response patterns to different carbon sources; however, in glucose batch cultivation, expression driven by these promoters decreased sharply as glucose was depleted and cells moved towards the diauxic shift. Promoters induced at low-glucose levels (PHXT7, PSSA1 and PADH2) varied in induction strength on non-glucose carbon sources (sucrose, galactose and ethanol); in contrast to the “constitutive” promoters, GFP expression increased as glucose decreased and cells moved towards the diauxic shift. While lower than several “constitutive” promoters during the exponential phase, expression from the SSA1 promoter was higher in the post-diauxic phase than the commonly-used TEF1 promoter. The galactose-inducible GAL1 promoter provided the highest GFP expression on galactose, and the copper-inducible CUP1 promoter provided the highest induced GFP expression following the diauxic shift. Conclusions The data provides a foundation for predictable and optimised control of gene expression levels on different carbon sources and throughout batch fermentation, including during and after the diauxic shift. This information can be applied for designing expression approaches to improve yields, rates and titres in yeast cell factories. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0278-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Bingyin Peng
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Thomas C Williams
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Williams TC, Espinosa MI, Nielsen LK, Vickers CE. Dynamic regulation of gene expression using sucrose responsive promoters and RNA interference in Saccharomyces cerevisiae. Microb Cell Fact 2015; 14:43. [PMID: 25886317 PMCID: PMC4427958 DOI: 10.1186/s12934-015-0223-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 03/06/2015] [Indexed: 11/24/2022] Open
Abstract
Background Engineering dynamic, environmentally- and temporally-responsive control of gene expression is one of the principle objectives in the field of synthetic biology. Dynamic regulation is desirable because many engineered functions conflict with endogenous processes which have evolved to facilitate growth and survival, and minimising conflict between growth and production phases can improve product titres in microbial cell factories. There are a limited number of mechanisms that enable dynamic regulation in yeast, and fewer still that are appropriate for application in an industrial setting. Results To address this problem we have identified promoters that are repressed during growth on glucose, and activated during growth on sucrose. Catabolite repression and preferential glucose utilisation allows active growth on glucose before switching to production on sucrose. Using sucrose as an activator of gene expression circumvents the need for expensive inducer compounds and enables gene expression to be triggered during growth on a fermentable, high energy-yield carbon source. The ability to fine-tune the timing and population density at which gene expression is activated from the SUC2 promoter was demonstrated by varying the ratio of glucose to sucrose in the growth medium. Finally, we demonstrated that the system could also be used to repress gene expression (a process also required for many engineering projects). We used the glucose/sucrose system to control a heterologous RNA interference module and dynamically repress the expression of a constitutively regulated GFP gene. Conclusions The low noise levels and high dynamic range of the SUC2 promoter make it a promising option for implementing dynamic regulation in yeast. The capacity to repress gene expression using RNA interference makes the system highly versatile, with great potential for metabolic engineering applications. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0223-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas C Williams
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Monica I Espinosa
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Lars K Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, 4072, Australia.
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Jardine K, Chambers J, Alves EG, Teixeira A, Garcia S, Holm J, Higuchi N, Manzi A, Abrell L, Fuentes JD, Nielsen LK, Torn MS, Vickers CE. Dynamic balancing of isoprene carbon sources reflects photosynthetic and photorespiratory responses to temperature stress. Plant Physiol 2014; 166:2051-64. [PMID: 25318937 PMCID: PMC4256868 DOI: 10.1104/pp.114.247494] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The volatile gas isoprene is emitted in teragrams per annum quantities from the terrestrial biosphere and exerts a large effect on atmospheric chemistry. Isoprene is made primarily from recently fixed photosynthate; however, alternate carbon sources play an important role, particularly when photosynthate is limiting. We examined the relative contribution of these alternate carbon sources under changes in light and temperature, the two environmental conditions that have the strongest influence over isoprene emission. Using a novel real-time analytical approach that allowed us to examine dynamic changes in carbon sources, we observed that relative contributions do not change as a function of light intensity. We found that the classical uncoupling of isoprene emission from net photosynthesis at elevated leaf temperatures is associated with an increased contribution of alternate carbon. We also observed a rapid compensatory response where alternate carbon sources compensated for transient decreases in recently fixed carbon during thermal ramping, thereby maintaining overall increases in isoprene production rates at high temperatures. Photorespiration is known to contribute to the decline in net photosynthesis at high leaf temperatures. A reduction in the temperature at which the contribution of alternate carbon sources increased was observed under photorespiratory conditions, while photosynthetic conditions increased this temperature. Feeding [2-(13)C]glycine (a photorespiratory intermediate) stimulated emissions of [(13)C1-5]isoprene and (13)CO2, supporting the possibility that photorespiration can provide an alternate source of carbon for isoprene synthesis. Our observations have important implications for establishing improved mechanistic predictions of isoprene emissions and primary carbon metabolism, particularly under the predicted increases in future global temperatures.
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Affiliation(s)
- Kolby Jardine
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Jeffrey Chambers
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Eliane G Alves
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Andrea Teixeira
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Sabrina Garcia
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Jennifer Holm
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Niro Higuchi
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Antonio Manzi
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Leif Abrell
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Jose D Fuentes
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Lars K Nielsen
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Margaret S Torn
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
| | - Claudia E Vickers
- Climate Science Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720 (K.J., J.C., J.H., M.S.T.);National Institute for Amazon Research, Manaus, Amazonas 69080-971, Brazil (E.G.A., A.T., S.G., N.H., A.M.);Departments of Chemistry and Biochemistry and Soil, Water, and Environmental Science, University of Arizona, Tucson, Arizona 85721 (L.A.);Department of Meteorology, College of Earth and Mineral Sciences, Pennsylvania State University, University Park, Pennsylvania 16802 (J.D.F.); andAustralian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, St. Lucia, Queensland 4072, Australia (L.K.N., C.E.V.)
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Arifin Y, Archer C, Lim S, Quek LE, Sugiarto H, Marcellin E, Vickers CE, Krömer JO, Nielsen LK. Escherichia coli W shows fast, highly oxidative sucrose metabolism and low acetate formation. Appl Microbiol Biotechnol 2014; 98:9033-44. [DOI: 10.1007/s00253-014-5956-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Revised: 07/07/2014] [Accepted: 07/08/2014] [Indexed: 10/24/2022]
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Vickers CE, Bongers M, Liu Q, Delatte T, Bouwmeester H. Metabolic engineering of volatile isoprenoids in plants and microbes. Plant Cell Environ 2014; 37:1753-75. [PMID: 24588680 DOI: 10.1111/pce.12316] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2014] [Revised: 02/18/2014] [Accepted: 02/18/2014] [Indexed: 05/09/2023]
Abstract
The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids.
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Affiliation(s)
- Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland, 4072, Australia
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Steen JA, Bohlke N, Vickers CE, Nielsen LK. The trehalose phosphotransferase system (PTS) in E. coli W can transport low levels of sucrose that are sufficient to facilitate induction of the csc sucrose catabolism operon. PLoS One 2014; 9:e88688. [PMID: 24586369 PMCID: PMC3938415 DOI: 10.1371/journal.pone.0088688] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Accepted: 01/09/2014] [Indexed: 11/24/2022] Open
Abstract
Plasticity in substrate acceptance is a well-characterised phenomenon for disaccharide transporters. Sucrose, a non-reducing disaccharide, is usually metabolised via either the permease-mediated chromosomally-encoded sucrose catabolism (csc) regulon or the sucrose phosphotransferase system (PTS). E. coli W is a fast-growing strain which efficiently utilises sucrose at concentrations above 1% via the csc regulon. To examine if sucrose could be metabolised via other routes, a library of transposon mutants was generated and screened on 0.2% sucrose. One mutant identified from this library had an insertion in the repressor for the regulon controlling catabolism of the disaccharide trehalose (treR). A series of mutants was constructed to elucidate the mechanism of sucrose utilization in the treR insertion strain. Analysis of these mutants provided evidence that deletion of TreR enables uptake of sucrose via TreB, an enzyme II protein required for PTS-mediated uptake of trehalose. Once inside the cell, this sucrose is not processed by the TreC hydrolase, nor is it sufficient for growth of the strain. QRT-PCR analysis showed that levels of cscA (invertase) transcript increased in the WΔtreR mutant relative to the wild-type strain when grown under low sucrose conditions. This result suggests that the intracellular sucrose provided by TreB can facilitate de-repression of the csc regulon, leading to increased gene expression, sucrose uptake and sucrose utilization in the treR mutant.
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Affiliation(s)
- Jennifer A. Steen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Nina Bohlke
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
| | - Claudia E. Vickers
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
- * E-mail:
| | - Lars K. Nielsen
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, Queensland, Australia
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Ryan AC, Hewitt CN, Possell M, Vickers CE, Purnell A, Mullineaux PM, Davies WJ, Dodd IC. Isoprene emission protects photosynthesis but reduces plant productivity during drought in transgenic tobacco (Nicotiana tabacum) plants. New Phytol 2014; 201:205-216. [PMID: 24102245 DOI: 10.1111/nph.12477] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/30/2013] [Indexed: 05/26/2023]
Abstract
Isoprene protects the photosynthetic apparatus of isoprene-emitting plants from oxidative stress. The role of isoprene in the response of plants to drought is less clear. Water was withheld from transgenic isoprene-emitting and non-emitting tobacco (Nicotiana tabacum) plants, to examine: the response of isoprene emission to plant water deficit; a possible relationship between concentrations of the drought-induced phytohormone abscisic acid (ABA) and isoprene; and whether isoprene affected foliar reactive oxygen species (ROS) and lipid peroxidation levels. Isoprene emission did not affect whole-plant water use, foliar ABA concentration or leaf water potential under water deficit. Compared with well-watered controls, droughted non-emitting plants significantly increased ROS content (31-46%) and lipid peroxidation (30-47%), concomitant with decreased operating and maximum efficiencies of photosystem II photochemistry and lower leaf and whole-plant water use efficiency (WUE). Droughted isoprene-emitting plants showed no increase in ROS content or lipid peroxidation relative to well-watered controls, despite isoprene emission decreasing before leaf wilting. Although isoprene emission protected the photosynthetic apparatus and enhanced leaf and whole-plant WUE, non-emitting plants had 8-24% more biomass under drought, implying that isoprene emission incurred a yield penalty.
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Affiliation(s)
- Annette C Ryan
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - C Nicholas Hewitt
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Malcolm Possell
- Faculty of Agriculture and Environment, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Anna Purnell
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | | | - William J Davies
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
| | - Ian C Dodd
- Lancaster Environment Centre, Lancaster University, Lancaster, LA1 4YQ, UK
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Behrendorff JB, Vickers CE, Chrysanthopoulos P, Nielsen LK. 2,2-Diphenyl-1-picrylhydrazyl as a screening tool for recombinant monoterpene biosynthesis. Microb Cell Fact 2013; 12:76. [PMID: 23968454 PMCID: PMC3847554 DOI: 10.1186/1475-2859-12-76] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2012] [Accepted: 08/15/2013] [Indexed: 12/03/2022] Open
Abstract
Background Monoterpenes are a class of natural C10 compounds with a range of potential applications including use as fuel additives, fragrances, and chemical feedstocks. Biosynthesis of monoterpenes in heterologous systems is yet to reach commercially-viable levels, and therefore is the subject of strain engineering and fermentation optimization studies. Detection of monoterpenes typically relies on gas chromatography/mass spectrometry; this represents a significant analytical bottleneck which limits the potential to analyse combinatorial sets of conditions. To address this, we developed a high-throughput method for pre-screening monoterpene biosynthesis. Results An optimised DPPH assay was developed for detecting monoterpenes from two-phase microbial cultures using dodecane as the extraction solvent. The assay was useful for reproducible qualitative ranking of monoterpene concentrations, and detected standard preparations of myrcene and γ-terpinene dissolved in dodecane at concentrations as low as 10 and 15 μM, respectively, and limonene as low as 200 μM. The assay could not be used quantitatively due to technical difficulties in capturing the initial reaction rate in a multi-well plate and the presence of minor DPPH-reactive contaminants. Initially, limonene biosynthesis in Saccharomyces cerevisiae was tested using two different limonene synthase enzymes and three medium compositions. The assay indicated that limonene biosynthesis was enhanced in a supplemented YP medium and that the Citrus limon limonene synthase (CLLS) was more effective than the Mentha spicata limonene synthase (MSLS). GC-MS analysis revealed that the DPPH assay had correctly identified the best limonene synthase (CLLS) and culture medium (supplemented YP medium). Because only traces of limonene were detected in SD medium, we subsequently identified medium components that improved limonene production and developed a defined medium based on these findings. The best limonene titres obtained were 1.48 ± 0.22 mg limonene per L in supplemented YP medium and 0.9 ± 0.15 mg limonene per L in a pH-adjusted supplemented SD medium. Conclusions The DPPH assay is useful for detecting biosynthesis of limonene. Although the assay cannot be used quantitatively, it proved successful in ranking limonene production conditions qualitatively and thus is suitable as a first-tier screen. The DPPH assay will likely be applicable in detecting biosynthesis of several other monoterpenes and for screening libraries of monoterpene-producing strains.
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Affiliation(s)
- James Byh Behrendorff
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia QLD 4072, Australia.
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Sabri S, Steen JA, Bongers M, Nielsen LK, Vickers CE. Knock-in/Knock-out (KIKO) vectors for rapid integration of large DNA sequences, including whole metabolic pathways, onto the Escherichia coli chromosome at well-characterised loci. Microb Cell Fact 2013; 12:60. [PMID: 23799955 PMCID: PMC3706339 DOI: 10.1186/1475-2859-12-60] [Citation(s) in RCA: 70] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 05/23/2013] [Indexed: 11/21/2022] Open
Abstract
Background Metabolic engineering projects often require integration of multiple genes in order to control the desired phenotype. However, this often requires iterative rounds of engineering because many current insertion approaches are limited by the size of the DNA that can be transferred onto the chromosome. Consequently, construction of highly engineered strains is very time-consuming. A lack of well-characterised insertion loci is also problematic. Results A series of knock-in/knock-out (KIKO) vectors was constructed for integration of large DNA sequences onto the E. coli chromosome at well-defined loci. The KIKO plasmids target three nonessential genes/operons as insertion sites: arsB (an arsenite transporter); lacZ (β-galactosidase); and rbsA-rbsR (a ribose metabolism operon). Two homologous ‘arms’ target each insertion locus; insertion is mediated by λ Red recombinase through these arms. Between the arms is a multiple cloning site for the introduction of exogenous sequences and an antibiotic resistance marker (either chloramphenicol or kanamycin) for selection of positive recombinants. The resistance marker can subsequently be removed by flippase-mediated recombination. The insertion cassette is flanked by hairpin loops to isolate it from the effects of external transcription at the integration locus. To characterize each target locus, a xylanase reporter gene (xynA) was integrated onto the chromosomes of E. coli strains W and K-12 using the KIKO vectors. Expression levels varied between loci, with the arsB locus consistently showing the highest level of expression. To demonstrate the simultaneous use of all three loci in one strain, xynA, green fluorescent protein (gfp) and a sucrose catabolic operon (cscAKB) were introduced into lacZ, arsB and rbsAR respectively, and shown to be functional. Conclusions The KIKO plasmids are a useful tool for efficient integration of large DNA fragments (including multiple genes and pathways) into E. coli. Chromosomal insertion provides stable expression without the need for continuous antibiotic selection. Three non-essential loci have been characterised as insertion loci; combinatorial insertion at all three loci can be performed in one strain. The largest insertion at a single site described here was 5.4 kb; we have used this method in other studies to insert a total of 7.3 kb at one locus and 11.3 kb across two loci. These vectors are particularly useful for integration of multigene cassettes for metabolic engineering applications.
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Affiliation(s)
- Suriana Sabri
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia
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