1
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Pyne ME, Gold ND, Martin VJJ. Pathway elucidation and microbial synthesis of proaporphine and bis-benzylisoquinoline alkaloids from sacred lotus (Nelumbo nucifera). Metab Eng 2023; 77:162-173. [PMID: 37004909 DOI: 10.1016/j.ymben.2023.03.010] [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] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 03/07/2023] [Accepted: 03/25/2023] [Indexed: 04/03/2023]
Abstract
Sacred lotus (Nelumbo nucifera) has been utilized as a food, medicine, and spiritual symbol for nearly 3000 years. The medicinal properties of lotus are largely attributed to its unique profile of benzylisoquinoline alkaloids (BIAs), which includes potential anti-cancer, anti-malarial and anti-arrhythmic compounds. BIA biosynthesis in sacred lotus differs markedly from that of opium poppy and other members of the Ranunculales, most notably in an abundance of BIAs possessing the (R)-stereochemical configuration and the absence of reticuline, a major branchpoint intermediate in most BIA producers. Owing to these unique metabolic features and the pharmacological potential of lotus, we set out to elucidate the BIA biosynthesis network in N. nucifera. Here we show that lotus CYP80G (NnCYP80G) and a superior ortholog from Peruvian nutmeg (Laurelia sempervirens; LsCYP80G) stereospecifically convert (R)-N-methylcoclaurine to the proaporphine alkaloid glaziovine, which is subsequently methylated to pronuciferine, the presumed precursor to nuciferine. While sacred lotus employs a dedicated (R)-route to aporphine alkaloids from (R)-norcoclaurine, we implemented an artificial stereochemical inversion approach to flip the stereochemistry of the core BIA pathway. Exploiting the unique substrate specificity of dehydroreticuline synthase from common poppy (Papaver rhoeas) and pairing it with dehydroreticuline reductase enabled de novo synthesis of (R)-N-methylcoclaurine from (S)-norcoclaurine and its subsequent conversion to pronuciferine. We leveraged our stereochemical inversion approach to also elucidate the role of NnCYP80A in sacred lotus metabolism, which we show catalyzes the stereospecific formation of the bis-BIA nelumboferine. Screening our collection of 66 plant O-methyltransferases enabled conversion of nelumboferine to liensinine, a potential anti-cancer bis-BIA from sacred lotus. Our work highlights the unique benzylisoquinoline metabolism of N. nucifera and enables the targeted overproduction of potential lotus pharmaceuticals using engineered microbial systems.
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Affiliation(s)
- Michael E Pyne
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
| | - Nicholas D Gold
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada; Concordia Genome Foundry, Concordia University, Montréal, Québec, Canada
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Québec, Canada; Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada.
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2
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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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3
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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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4
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Gold ND, Fossati E, Hansen CC, DiFalco M, Douchin V, Martin VJJ. A Combinatorial Approach To Study Cytochrome P450 Enzymes for De Novo Production of Steviol Glucosides in Baker's Yeast. ACS Synth Biol 2018; 7:2918-2929. [PMID: 30474973 DOI: 10.1021/acssynbio.8b00470] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Biosynthesis of steviol glycosides in planta proceeds via two cytochrome P450 enzymes (CYPs): kaurene oxidase (KO) and kaurenoic acid hydroxylase (KAH). KO and KAH function in succession with the support of a NADPH-dependent cytochrome P450 reductase (CPR) to convert kaurene to steviol. This work describes a platform for recombinant production of steviol glucosides (SGs) in Saccharomyces cerevisiae, demonstrating the full reconstituted pathway from the simple sugar glucose to the SG precursor steviol. With a focus on optimization of the KO-KAH activities, combinations of functional homologues were tested in batch growth. Among the CYPs, novel KO75 (CYP701) and novel KAH82 (CYP72) outperformed their respective functional homologues from Stevia rebaudiana, SrKO (CYP701A5) and SrKAH (CYP81), in assays where substrate was supplemented to culture broth. With kaurene produced from glucose in the cell, SrCPR1 from S. rebaudiana supported highest turnover for KO-KAH combinations, besting two other CPRs isolated from S. rebaudiana, the Arabidopsis thaliana ATR2, and a new class I CPR12. Some coexpressions of ATR2 with a second CPR were found to diminish KAH activity, showing that coexpression of CPRs can lead to competition for CYPs with possibly adverse effects on catalysis.
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Affiliation(s)
- Nicholas D. Gold
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Elena Fossati
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Cecilie Cetti Hansen
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Plant Biochemistry Laboratory, Department of Plant and Environmental Science, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
- Center for Synthetic Biology, University of Copenhagen, DK-1871 Frederiksberg C, Denmark
| | - Marcos DiFalco
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | | | - Vincent J. J. Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec H4B 1R6, Canada
- Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
- Department of Biology, Centre for Structural and Functional Genomic, Concordia University, Montréal, Québec H4B 1R6, Canada
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Zhan Y, Marchand CH, Maes A, Mauries A, Sun Y, Dhaliwal JS, Uniacke J, Arragain S, Jiang H, Gold ND, Martin VJJ, Lemaire SD, Zerges W. Pyrenoid functions revealed by proteomics in Chlamydomonas reinhardtii. PLoS One 2018; 13:e0185039. [PMID: 29481573 PMCID: PMC5826530 DOI: 10.1371/journal.pone.0185039] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 01/29/2018] [Indexed: 01/19/2023] Open
Abstract
Organelles are intracellular compartments which are themselves compartmentalized. Biogenic and metabolic processes are localized to specialized domains or microcompartments to enhance their efficiency and suppress deleterious side reactions. An example of intra-organellar compartmentalization is the pyrenoid in the chloroplasts of algae and hornworts. This microcompartment enhances the photosynthetic CO2-fixing activity of the Calvin-Benson cycle enzyme Rubisco, suppresses an energetically wasteful oxygenase activity of Rubisco, and mitigates limiting CO2 availability in aquatic environments. Hence, the pyrenoid is functionally analogous to the carboxysomes in cyanobacteria. However, a comprehensive analysis of pyrenoid functions based on its protein composition is lacking. Here we report a proteomic characterization of the pyrenoid in the green alga Chlamydomonas reinhardtii. Pyrenoid-enriched fractions were analyzed by quantitative mass spectrometry. Contaminant proteins were identified by parallel analyses of pyrenoid-deficient mutants. This pyrenoid proteome contains 190 proteins, many of which function in processes that are known or proposed to occur in pyrenoids: e.g. the carbon concentrating mechanism, starch metabolism or RNA metabolism and translation. Using radioisotope pulse labeling experiments, we show that pyrenoid-associated ribosomes could be engaged in the localized synthesis of the large subunit of Rubisco. New pyrenoid functions are supported by proteins in tetrapyrrole and chlorophyll synthesis, carotenoid metabolism or amino acid metabolism. Hence, our results support the long-standing hypothesis that the pyrenoid is a hub for metabolism. The 81 proteins of unknown function reveal candidates for new participants in these processes. Our results provide biochemical evidence of pyrenoid functions and a resource for future research on pyrenoids and their use to enhance agricultural plant productivity. Data are available via ProteomeXchange with identifier PXD004509.
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Affiliation(s)
- Yu Zhan
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Christophe H. Marchand
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, Paris, France
| | - Alexandre Maes
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, Paris, France
| | - Adeline Mauries
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, Paris, France
| | - Yi Sun
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - James S. Dhaliwal
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - James Uniacke
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Simon Arragain
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Heng Jiang
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Nicholas D. Gold
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Vincent J. J. Martin
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, UMR8226, CNRS, Sorbonne Universités, UPMC Univ Paris 06, 13 rue Pierre et Marie Curie, Paris, France
- * E-mail: (SDL); (WZ)
| | - William Zerges
- Department of Biology & Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada
- * E-mail: (SDL); (WZ)
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Campbell A, Bauchart P, Gold ND, Zhu Y, De Luca V, Martin VJJ. Engineering of a Nepetalactol-Producing Platform Strain of Saccharomyces cerevisiae for the Production of Plant Seco-Iridoids. ACS Synth Biol 2016; 5:405-14. [PMID: 26981892 DOI: 10.1021/acssynbio.5b00289] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [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: 12/23/2022]
Abstract
The monoterpene indole alkaloids (MIAs) are a valuable family of chemicals that include the anticancer drugs vinblastine and vincristine. These compounds are of global significance-appearing on the World Health Organization's list of model essential medicines-but remain exorbitantly priced due to low in planta levels. Chemical synthesis and genetic manipulation of MIA producing plants such as Catharanthus roseus have so far failed to find a solution to this problem. Synthetic biology holds a potential answer, by building the pathway into more tractable organisms such as Saccharomyces cerevisiae. Recent work has taken the first steps in this direction by producing small amounts of the intermediate strictosidine in yeast. In order to help improve on these titers, we aimed to optimize the early biosynthetic steps of the MIA pathway to the metabolite nepetalactol. We combined a number of strategies to create a base strain producing 11.4 mg/L of the precursor geraniol. We also show production of the critical intermediate 10-hydroxygeraniol and demonstrate nepetalactol production in vitro. Lastly we demonstrate that activity of the iridoid synthase toward the intermediates geraniol and 10-hydroxygeraniol results in the synthesis of the nonproductive intermediates citronellol and 10-hydroxycitronellol. This discovery has serious implications for the reconstruction of the MIA in heterologous organisms.
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Affiliation(s)
- Alex Campbell
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Philippe Bauchart
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Nicholas D. Gold
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Yun Zhu
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
| | - Vincenzo De Luca
- Department
of Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, Ontario L2S 3A1, Canada
| | - Vincent J. J. Martin
- Department
of Biology, Centre for Structural and Functional Genomics, Concordia University, Montréal, Québec H4B 1R6, Canada
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Gold ND, Gowen CM, Lussier FX, Cautha SC, Mahadevan R, Martin VJJ. Metabolic engineering of a tyrosine-overproducing yeast platform using targeted metabolomics. Microb Cell Fact 2015; 14:73. [PMID: 26016674 PMCID: PMC4458059 DOI: 10.1186/s12934-015-0252-2] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [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: 12/09/2014] [Accepted: 05/06/2015] [Indexed: 11/30/2022] Open
Abstract
Background L-tyrosine is a common precursor for a wide range of valuable secondary metabolites, including benzylisoquinoline alkaloids (BIAs) and many polyketides. An industrially tractable yeast strain optimized for production of L-tyrosine could serve as a platform for the development of BIA and polyketide cell factories. This study applied a targeted metabolomics approach to evaluate metabolic engineering strategies to increase the availability of intracellular L-tyrosine in the yeast Saccharomyces cerevisiae CEN.PK. Our engineering strategies combined localized pathway engineering with global engineering of central metabolism, facilitated by genome-scale steady-state modelling. Results Addition of a tyrosine feedback resistant version of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase Aro4 from S. cerevisiae was combined with overexpression of either a tyrosine feedback resistant yeast chorismate mutase Aro7, the native pentafunctional arom protein Aro1, native prephenate dehydrogenase Tyr1 or cyclohexadienyl dehydrogenase TyrC from Zymomonas mobilis. Loss of aromatic carbon was limited by eliminating phenylpyruvate decarboxylase Aro10. The TAL gene from Rhodobacter sphaeroides was used to produce coumarate as a simple test case of a heterologous by-product of tyrosine. Additionally, multiple strategies for engineering global metabolism to promote tyrosine production were evaluated using metabolic modelling. The T21E mutant of pyruvate kinase Cdc19 was hypothesized to slow the conversion of phosphoenolpyruvate to pyruvate and accumulate the former as precursor to the shikimate pathway. The ZWF1 gene coding for glucose-6-phosphate dehydrogenase was deleted to create an NADPH deficiency designed to force the cell to couple its growth to tyrosine production via overexpressed NADP+-dependent prephenate dehydrogenase Tyr1. Our engineered Zwf1− strain expressing TYRC ARO4FBR and grown in the presence of methionine achieved an intracellular L-tyrosine accumulation up to 520 μmol/g DCW or 192 mM in the cytosol, but sustained flux through this pathway was found to depend on the complete elimination of feedback inhibition and degradation pathways. Conclusions Our targeted metabolomics approach confirmed a likely regulatory site at DAHP synthase and identified another possible cofactor limitation at prephenate dehydrogenase. Additionally, the genome-scale metabolic model identified design strategies that have the potential to improve availability of erythrose 4-phosphate for DAHP synthase and cofactor availability for prephenate dehydrogenase. We evaluated these strategies and provide recommendations for further improvement of aromatic amino acid biosynthesis in S. cerevisiae. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0252-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nicholas D Gold
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
| | - Christopher M Gowen
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
| | - Francois-Xavier Lussier
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
| | - Sarat C Cautha
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada.
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON, M5S 3E5, Canada. .,Institute of Biomaterials and Biomedical Engineering, University of Toronto, 164 College Street, Toronto, ON, M5S 3G9, Canada.
| | - Vincent J J Martin
- Department of Biology and Centre for Structural and Functional Genomics, Concordia University, 7141 Sherbrooke West, Montreal, QC, H4B 1R6, Canada.
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Cautha SC, Gowen CM, Lussier FX, Gold ND, Martin VJ, Mahadevan R. Model-driven design of a Saccharomyces cerevisiae platform strain with improved tyrosine production capabilities. ACTA ACUST UNITED AC 2013. [DOI: 10.3182/20131216-3-in-2044.00066] [Citation(s) in RCA: 4] [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] [Indexed: 11/23/2022]
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Wilde C, Gold ND, Bawa N, Tambor JHM, Mougharbel L, Storms R, Martin VJJ. Expression of a library of fungal β-glucosidases in Saccharomyces cerevisiae for the development of a biomass fermenting strain. Appl Microbiol Biotechnol 2012; 95:647-59. [DOI: 10.1007/s00253-011-3788-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Revised: 11/21/2011] [Accepted: 11/23/2011] [Indexed: 10/14/2022]
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Rogowski K, van Dijk J, Magiera MM, Bosc C, Deloulme JC, Bosson A, Peris L, Gold ND, Lacroix B, Bosch Grau M, Bec N, Larroque C, Desagher S, Holzer M, Andrieux A, Moutin MJ, Janke C. A family of protein-deglutamylating enzymes associated with neurodegeneration. Cell 2010; 143:564-78. [PMID: 21074048 DOI: 10.1016/j.cell.2010.10.014] [Citation(s) in RCA: 232] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Revised: 08/13/2010] [Accepted: 10/05/2010] [Indexed: 12/11/2022]
Abstract
Polyglutamylation is a posttranslational modification that generates glutamate side chains on tubulins and other proteins. Although this modification has been shown to be reversible, little is known about the enzymes catalyzing deglutamylation. Here we describe the enzymatic mechanism of protein deglutamylation by members of the cytosolic carboxypeptidase (CCP) family. Three enzymes (CCP1, CCP4, and CCP6) catalyze the shortening of polyglutamate chains and a fourth (CCP5) specifically removes the branching point glutamates. In addition, CCP1, CCP4, and CCP6 also remove gene-encoded glutamates from the carboxyl termini of proteins. Accordingly, we show that these enzymes convert detyrosinated tubulin into Δ2-tubulin and also modify other substrates, including myosin light chain kinase 1. We further analyze Purkinje cell degeneration (pcd) mice that lack functional CCP1 and show that microtubule hyperglutamylation is directly linked to neurodegeneration. Taken together, our results reveal that controlling the length of the polyglutamate side chains on tubulin is critical for neuronal survival.
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Affiliation(s)
- Krzysztof Rogowski
- CRBM, Université Montpellier 2 and 1, CNRS UMR 5237, Montpellier 34293, France.
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Lacroix B, van Dijk J, Gold ND, Guizetti J, Aldrian-Herrada G, Rogowski K, Gerlich DW, Janke C. Tubulin polyglutamylation stimulates spastin-mediated microtubule severing. ACTA ACUST UNITED AC 2010; 189:945-54. [PMID: 20530212 PMCID: PMC2886356 DOI: 10.1083/jcb.201001024] [Citation(s) in RCA: 208] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microtubules with long polyglutamylated C-terminal tails are more prone to severing by spastin, establishing the importance of tubulin posttranslational modifications. Posttranslational glutamylation of tubulin is present on selected subsets of microtubules in cells. Although the modification is expected to contribute to the spatial and temporal organization of the cytoskeleton, hardly anything is known about its functional relevance. Here we demonstrate that glutamylation, and in particular the generation of long glutamate side chains, promotes the severing of microtubules. In human cells, the generation of long side chains induces spastin-dependent microtubule disassembly and, consistently, only microtubules modified by long glutamate side chains are efficiently severed by spastin in vitro. Our study reveals a novel control mechanism for microtubule mass and stability, which is of fundamental importance to cellular physiology and might have implications for diseases related to microtubule severing.
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Affiliation(s)
- Benjamin Lacroix
- Centre de Recherche de Biochimie Macromoléculaire, Université Montpellier 2 and 1, Centre National de la Recherche Scientifique UMR 5237, Montpellier, France
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Abstract
The rapid expansion of structural information for protein ligand-binding sites is potentially an important source of information in structure-based drug design and in understanding ligand cross-reactivity and toxicity. We have developed SitesBase, a comprehensive database of ligand-binding sites extracted automatically from the Macromolecular Structure Database. SitesBase is an easily accessible database which is simple to use and holds pre-calculated information about structural similarities between known ligand-binding sites. These similarities are presented to the wider community enabling binding-site comparisons for therapeutically interesting protein families, such as the proteases and for new proteins to enable the discovery of interesting new structure-function relationships. The database is available from http://www.modelling.leeds.ac.uk/sb/.
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Affiliation(s)
- N D Gold
- Institute of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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13
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Abstract
A metabolic isotope-labeling strategy was used in conjunction with nano-liquid chromatography-electrospray ionization mass spectrometry peptide sequencing to assess quantitative alterations in the expression patterns of subunits within cellulosomes of the cellulolytic bacterium Clostridium thermocellum, grown on either cellulose or cellobiose. In total, 41 cellulosomal proteins were detected, including 36 type I dockerin-containing proteins, which count among them all but three of the known docking components and 16 new subunits. All differential expression data were normalized to the scaffoldin CipA such that protein per cellulosome was compared for growth between the two substrates. Proteins that exhibited higher expression in cellulosomes from cellulose-grown cells than in cellobiose-grown cells were the cell surface anchor protein OlpB, exoglucanases CelS and CelK, and the glycoside hydrolase family 9 (GH9) endoglucanase CelJ. Conversely, lower expression in cellulosomes from cells grown on cellulose than on cellobiose was observed for the GH8 endoglucanase CelA; GH5 endoglucanases CelB, CelE, CelG; and hemicellulases XynA, XynC, XynZ, and XghA. GH9 cellulases were the most abundant group of enzymes per CipA when cells were grown on cellulose, while hemicellulases were the most abundant group on cellobiose. The results support the existing theory that expression of scaffoldin-related proteins is coordinately regulated by a catabolite repression type of mechanism, as well as the prior observation that xylanase expression is subject to a growth rate-independent type of regulation. However, concerning transcriptional control of cellulases, which had also been previously shown to be subject to catabolite repression, a novel distinction was observed with respect to endoglucanases.
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Affiliation(s)
- Nicholas D Gold
- Department of Biology, Concordia University, Montréal, Québec, Canada H4B 1R6
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Zhou JM, Gold ND, Martin VJJ, Wollenweber E, Ibrahim RK. Sequential O-methylation of tricetin by a single gene product in wheat. Biochim Biophys Acta Gen Subj 2006; 1760:1115-24. [PMID: 16730127 DOI: 10.1016/j.bbagen.2006.02.008] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Revised: 02/08/2006] [Accepted: 02/09/2006] [Indexed: 10/24/2022]
Abstract
Flavonoid compounds are ubiquitous in nature. They constitute an important part of the human diet and act as active principles of many medicinal plants. Their O-methylation increases their lipophilicity and hence, their compartmentation and functional diversity. We have isolated and characterized a full-length flavonoid O-methyltransferase cDNA (TaOMT2) from a wheat leaf cDNA library. The recombinant TaOMT2 protein was purified to near homogeneity and tested for its substrate preference against a number of phenolic compounds. Enzyme assays and kinetic analyses indicate that TaOMT2 exhibits a pronounced preference for the flavone, tricetin and gives rise to three methylated enzyme reaction products that were identified by TLC, HPLC and ESI-MS/MS as its mono-, di- and trimethyl ether derivatives. The sequential order of tricetin methylation by TaOMT2 is envisaged to proceed via its 3'-mono--->3',5'-di--->3',4',5'-trimethyl ether derivatives. To our knowledge, this is the first report of a gene product that catalyzes three sequential O-methylations of a flavonoid substrate.
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Affiliation(s)
- Jian-Min Zhou
- Plant Biochemistry Laboratory, Concordia University, Montréal, Quebec, Canada H4B 1R6
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Abstract
Many current methods for protein analysis depend on the detection of similarity in either the primary sequence, or the overall tertiary structure (the Calpha atoms of the protein backbone). These common sequences or structures may imply similar functional characteristics or active properties. Active sites and ligand binding sites usually occur on or near the surface of the protein; so similarly shaped surface regions could imply similar functions. We investigate various methods for describing the shape properties of protein surfaces and for comparing them. Our current work uses algorithms from computer vision to describe the protein surfaces, and methods from graph theory to compare the surface regions. Early results indicate that we can successfully match a family of related ligand binding sites, and find their similarly shaped surface regions. This method of surface analysis could be extended to help identify unknown surface regions for possible ligand binding or active sites.
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Affiliation(s)
- S J Pickering
- School of Biochemistry and Molecular Biology, University of Leeds, Leeds LS2 9JT, UK
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