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Stogios PJ, Liston SD, Semper C, Quade B, Michalska K, Evdokimova E, Ram S, Otwinowski Z, Borek D, Cowen LE, Savchenko A. Molecular analysis and essentiality of Aro1 shikimate biosynthesis multi-enzyme in Candida albicans. Life Sci Alliance 2022; 5:e202101358. [PMID: 35512834 PMCID: PMC9074039 DOI: 10.26508/lsa.202101358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2021] [Revised: 04/10/2022] [Accepted: 04/13/2022] [Indexed: 11/24/2022] Open
Abstract
In the human fungal pathogen Candida albicans, ARO1 encodes an essential multi-enzyme that catalyses consecutive steps in the shikimate pathway for biosynthesis of chorismate, a precursor to folate and the aromatic amino acids. We obtained the first molecular image of C. albicans Aro1 that reveals the architecture of all five enzymatic domains and their arrangement in the context of the full-length protein. Aro1 forms a flexible dimer allowing relative autonomy of enzymatic function of the individual domains. Our activity and in cellulo data suggest that only four of Aro1's enzymatic domains are functional and essential for viability of C. albicans, whereas the 3-dehydroquinate dehydratase (DHQase) domain is inactive because of active site substitutions. We further demonstrate that in C. albicans, the type II DHQase Dqd1 can compensate for the inactive DHQase domain of Aro1, suggesting an unrecognized essential role for this enzyme in shikimate biosynthesis. In contrast, in Candida glabrata and Candida parapsilosis, which do not encode a Dqd1 homolog, Aro1 DHQase domains are enzymatically active, highlighting diversity across Candida species.
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Affiliation(s)
- Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Sean D Liston
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Cameron Semper
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Bradley Quade
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Karolina Michalska
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Argonne, IL, USA
| | - Elena Evdokimova
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
| | - Shane Ram
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
| | - Zbyszek Otwinowski
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Dominika Borek
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Leah E Cowen
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, Canada
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Optimization of the l-tyrosine metabolic pathway in Saccharomyces cerevisiae by analyzing p-coumaric acid production. 3 Biotech 2020; 10:258. [PMID: 32550099 DOI: 10.1007/s13205-020-02223-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 04/24/2020] [Indexed: 10/24/2022] Open
Abstract
In this study, we applied a series of genetic modifications to wild-type S. cerevisiae strain BY4741 to address the bottlenecks in the l-tyrosine pathway. A tyrosine ammonia-lyase (TAL) gene from Rhodobacter capsulatus, which can catalyze conversion of l-tyrosine into p-coumaric acid, was overexpressed to facilitate the analysis of l-tyrosine and test the strain's capability to synthesize heterologous derivatives. First, we enhanced the supply of precursors by overexpressing transaldolase gene TAL1, enolase II gene ENO2, and pentafunctional enzyme gene ARO1 resulting in a 1.55-fold increase in p-coumaric acid production. Second, feedback inhibition of 3-deoxy-d-arabino-heptulosonate-7-phosphate synthase and chorismate mutase was relieved by overexpressing the mutated feedback-resistant ARO4 K229L and ARO7 G141S , and a 3.61-fold improvement of p-coumaric acid production was obtained. Finally, formation of byproducts was decreased by deleting pyruvate decarboxylase gene PDC5 and phenylpyruvate decarboxylase gene ARO10, and p-coumaric acid production was increased 2.52-fold. The best producer-when TAL1, ENO2, ARO1, ARO4 K229L , ARO7 G141S , and TAL were overexpressed, and PDC5 and ARO10 were deleted-increased p-coumaric acid production by 14.08-fold (from 1.4 to 19.71 mg L-1). Our study provided a valuable insight into the optimization of l-tyrosine metabolic pathway.
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Zhang J, Pierick AT, van Rossum HM, Maleki Seifar R, Ras C, Daran JM, Heijnen JJ, Aljoscha Wahl S. Determination of the Cytosolic NADPH/NADP Ratio in Saccharomyces cerevisiae using Shikimate Dehydrogenase as Sensor Reaction. Sci Rep 2015; 5:12846. [PMID: 26243542 PMCID: PMC4525286 DOI: 10.1038/srep12846] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/14/2015] [Indexed: 12/04/2022] Open
Abstract
Eukaryotic metabolism is organised in complex networks of enzyme catalysed reactions which are distributed over different organelles. To quantify the compartmentalised reactions, quantitative measurements of relevant physiological variables in different compartments are needed, especially of cofactors. NADP(H) are critical components in cellular redox metabolism. Currently, available metabolite measurement methods allow whole cell measurements. Here a metabolite sensor based on a fast equilibrium reaction is introduced to monitor the cytosolic NADPH/NADP ratio in Saccharomyces cerevisiae: NADP + shikimate ⇄ NADPH + H(+) + dehydroshikimate. The cytosolic NADPH/NADP ratio was determined by measuring the shikimate and dehydroshikimate concentrations (by GC-MS/MS). The cytosolic NADPH/NADP ratio was determined under batch and chemostat (aerobic, glucose-limited, D = 0.1 h(-1)) conditions, to be 22.0 ± 2.6 and 15.6 ± 0.6, respectively. These ratios were much higher than the whole cell NADPH/NADP ratio (1.05 ± 0.08). In response to a glucose pulse, the cytosolic NADPH/NADP ratio first increased very rapidly and restored the steady state ratio after 3 minutes. In contrast to this dynamic observation, the whole cell NADPH/NADP ratio remained nearly constant. The novel cytosol NADPH/NADP measurements provide new insights into the thermodynamic driving forces for NADP(H)-dependent reactions, like amino acid synthesis, product pathways like fatty acid production or the mevalonate pathway.
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Affiliation(s)
- Jinrui Zhang
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Angela ten Pierick
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Harmen M. van Rossum
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Reza Maleki Seifar
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Cor Ras
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Jean-Marc Daran
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - Joseph J. Heijnen
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
| | - S. Aljoscha Wahl
- Department of Biotechnology, Delft University of Technology, Delft, 2628BC, The Netherlands
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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] [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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Mittelstädt G, Negron L, Schofield LR, Marsh K, Parker EJ. Biochemical and structural characterisation of dehydroquinate synthase from the New Zealand kiwifruit Actinidia chinensis. Arch Biochem Biophys 2013; 537:185-91. [PMID: 23916589 DOI: 10.1016/j.abb.2013.07.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2013] [Revised: 07/17/2013] [Accepted: 07/18/2013] [Indexed: 11/25/2022]
Abstract
One of the novel aspects of kiwifruit is the presence of a high level of quinic acid which contributes to the flavour of the fruit. Quinic acid metabolism intersects with the shikimate pathway, which is responsible for the de novo biosynthesis of primary and secondary aromatic metabolites. The gene encoding the enzyme which catalyses the second step of the shikimate pathway, dehydroquinate synthase (DHQS), from the New Zealand kiwifruit Actinidia chinensis was identified, cloned and expressed. A. chinensis DHQS was activated by divalent metal ions, and was found to require NAD(+) for catalysis. The protein was crystallised and the structure was solved, revealing a homodimeric protein. Each monomer has a NAD(+) binding site nestled between the distinct N- and C-terminal domains. In contrast to other microbial DHQSs, which show an open conformation in the absence of active site ligands, A. chinensis DHQS adopts a closed conformation. This is the first report of the structure of a DHQS from a plant source.
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Affiliation(s)
- Gerd Mittelstädt
- Biomolecular Interaction Centre and Department of Chemistry, University of Canterbury, PO Box 4800, Christchurch 8140, New Zealand
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Lin WY, Chang JY, Hish CH, Pan TM. Proteome response of Monascus pilosus during rice starch limitation with suppression of monascorubramine production. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2007; 55:9226-9234. [PMID: 17924709 DOI: 10.1021/jf071109u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
For centuries, red mold rice has been made by fermentation of cooked rice with Monascus species. However, the influence of different carbon sources on the metabolism of Monascus cells remains unclear. We compared the proteome response of Monascus pilosus to replacement of the rice starch fraction with lactose during cultivation, using two-dimensional gel electrophoresis, matrix-assisted laser desorption-ionization time-of-flight/time-of-flight mass spectrometry, and tandem mass spectrometry to identify the proteins expressed. The results showed that cell growth and monascorubramine pigment formation of M. pilosus were sensitive to rice starch limitation during cultivation. A total of 12 proteins were identified with statistically altered expression in the cells cultivated with lactose. These deregulated proteins were involved in glycolysis, TCA cycle, energy generation, protein folding, and peptide biosynthesis. The possible metabolic flux shifts induced by rice starch limitation were discussed. The results suggested that the suppression of monascorubramine formation could be related to the necessary energy-requiring adaptations executed in response to carbon depletion during rice starch limitation.
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Affiliation(s)
- Wun-Yuan Lin
- Department of Food Science, Nutrition and Nutraceutical Biotechnology, Shih Chien University, Taiwan, Republic of China
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Abstract
A search of the genomic sequences of the thermophilic microorganisms Aquifex aeolicus, Archaeoglobus fulgidus, Methanobacterium thermoautotrophicum, and Methanococcus jannaschii for the first seven enzymes (aroG, B, D, E, K, A, and C ) involved in the shikimic acid biosynthetic pathway reveal two key enzymes are missing. The first enzyme in the pathway, 3-deoxy-d-arabino-heptulosonic acid 7-phosphate synthase (aroG) and the second enzyme in the pathway, 5-dehydroquinic acid synthase (aroB) are "missing." The remaining five genes for the shikimate pathway in these organism are present and are similar to the corresponding Escherichia coli genes. The genomic sequences of the thermophiles Pyrococcus abyssi and Thermotoga maritima contain the aroG and aroB genes. Several fungi such as Aspergillus fumigatus, Aspergillus nidulans, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Pneumocystis carinii f. sp. carinii, and Neurospora crassa contain the gene aroM, a pentafunctional enzyme whose overall activity is equivalent to the combined catalytic activities of proteins expressed by aroB, D, E, K, and A genes. Two of these fungi also lack an aroG gene. A discussion of potential reasons for these missing enzymes is presented.
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Affiliation(s)
- Ronald W Woodard
- Department of Medicinal Chemistry and Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1065, USA.
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