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Bradley JM, Bunsick M, Ly G, Aquino B, Wang FZ, Holbrook-Smith D, Suginoo S, Bradizza D, Kato N, As'sadiq O, Marsh N, Osada H, Boyer FD, McErlean CSP, Tsuchiya Y, Subramaniam R, Bonetta D, McCourt P, Lumba S. Modulation of fungal phosphate homeostasis by the plant hormone strigolactone. Mol Cell 2024; 84:4031-4047.e11. [PMID: 39357514 DOI: 10.1016/j.molcel.2024.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Revised: 07/12/2024] [Accepted: 09/05/2024] [Indexed: 10/04/2024]
Abstract
Inter-kingdom communication through small molecules is essential to the coexistence of organisms in an ecosystem. In soil communities, the plant root is a nexus of interactions for a remarkable number of fungi and is a source of small-molecule plant hormones that shape fungal compositions. Although hormone signaling pathways are established in plants, how fungi perceive and respond to molecules is unclear because many plant-associated fungi are recalcitrant to experimentation. Here, we develop an approach using the model fungus, Saccharomyces cerevisiae, to elucidate mechanisms of fungal response to plant hormones. Two plant hormones, strigolactone and methyl jasmonate, produce unique transcript profiles in yeast, affecting phosphate and sugar metabolism, respectively. Genetic analysis in combination with structural studies suggests that SLs require the high-affinity transporter Pho84 to modulate phosphate homeostasis. The ability to study small-molecule plant hormones in a tractable genetic system should have utility in understanding fungal-plant interactions.
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Affiliation(s)
- James M Bradley
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Michael Bunsick
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - George Ly
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Bruno Aquino
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Flora Zhiqi Wang
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | | | - Shingo Suginoo
- Department of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa, Nagoya 464-8601, Japan
| | - Dylan Bradizza
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Naoki Kato
- RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Omar As'sadiq
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Nina Marsh
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada
| | - Hiroyuki Osada
- RIKEN Center for Sustainable Research Science, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - François-Didier Boyer
- Université Paris-Saclay, CNRS, Institut de Chimie des Substances Naturelles, UPR 2301, 91198 Gif-sur-Yvette, France
| | | | - Yuichiro Tsuchiya
- Institute of Transformative Bio-Molecules, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | | | - Dario Bonetta
- Ontario Tech University, 2000 Simcoe St. N, Oshawa, ON L1G 0C5, Canada
| | - Peter McCourt
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
| | - Shelley Lumba
- Department of Cell & Systems Biology, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks Street, Toronto, ON M5S 3B2, Canada.
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Pham C, Nasr MA, Skarina T, Di Leo R, Kwan DH, Martin VJJ, Stogios PJ, Mahadevan R, Savchenko A. Functional and structural characterization of an IclR family transcription factor for the development of dicarboxylic acid biosensors. FEBS J 2024; 291:3481-3498. [PMID: 38696354 DOI: 10.1111/febs.17149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 03/15/2024] [Accepted: 04/17/2024] [Indexed: 05/04/2024]
Abstract
Prokaryotic transcription factors (TFs) regulate gene expression in response to small molecules, thus representing promising candidates as versatile small molecule-detecting biosensors valuable for synthetic biology applications. The engineering of such biosensors requires thorough in vitro and in vivo characterization of TF ligand response as well as detailed molecular structure information. In this work, we functionally and structurally characterize the Pca regulon regulatory protein (PcaR) transcription factor belonging to the IclR transcription factor family. Here, we present in vitro functional analysis of the ligand profile of PcaR and the construction of genetic circuits for the characterization of PcaR as an in vivo biosensor in the model eukaryote Saccharomyces cerevisiae. We report the crystal structures of PcaR in the apo state and in complex with one of its ligands, succinate, which suggests the mechanism of dicarboxylic acid recognition by this transcription factor. This work contributes key structural and functional insights enabling the engineering of PcaR for dicarboxylic acid biosensors, in addition to providing more insights into the IclR family of regulators.
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Affiliation(s)
- Chester Pham
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
| | - Tatiana Skarina
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Rosa Di Leo
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
- PROTEO, Quebec Network for Research on Protein Function, Structure, and Engineering, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montreal, Canada
- Department of Biology, Concordia University, Montreal, Canada
| | - Peter J Stogios
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
| | - Radhakrishnan Mahadevan
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- The Institute of Biomedical Engineering, University of Toronto, Canada
| | - Alexei Savchenko
- Department of Chemical Engineering and Applied Chemistry, University of Toronto, Canada
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Canada
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Abstract
A fundamental challenge of metabolic engineering involves assembling and screening vast combinations of orthologous enzymes across a multistep biochemical pathway. Current pathway assembly workflows involve combining genetic parts ex vivo and assembling one pathway configuration per tube or well. Here, we present CRAPS, Chromosomal-Repair-Assisted Pathway Shuffling, an in vivo pathway engineering technique that enables the self-assembly of one pathway configuration per cell. CRAPS leverages the yeast chromosomal repair pathway and utilizes a pool of inactive, chromosomally integrated orthologous gene variants corresponding to a target multistep pathway. Supplying gRNAs to the CRAPS host activates the expression of one gene variant per pathway step, resulting in a unique pathway configuration in each cell. We deployed CRAPS to build more than 1000 theoretical combinations of a four-step carotenoid biosynthesis network. Sampling the CRAPS pathway space yielded strains with distinct color phenotypes and carotenoid product profiles. We anticipate that CRAPS will expedite strain engineering campaigns by enabling the generation and sampling of vast biochemical spaces.
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Affiliation(s)
- Christien B Dykstra
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
| | - Michael E Pyne
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
| | - Vincent J J Martin
- Department of Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Quebec, Canada H4B 1R6
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Nasr MA, Martin VJJ, Kwan DH. Divergent directed evolution of a TetR-type repressor towards aromatic molecules. Nucleic Acids Res 2023; 51:7675-7690. [PMID: 37377432 PMCID: PMC10415137 DOI: 10.1093/nar/gkad503] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 05/18/2023] [Accepted: 06/25/2023] [Indexed: 06/29/2023] Open
Abstract
Reprogramming cellular behaviour is one of the hallmarks of synthetic biology. To this end, prokaryotic allosteric transcription factors (aTF) have been repurposed as versatile tools for processing small molecule signals into cellular responses. Expanding the toolbox of aTFs that recognize new inducer molecules is of considerable interest in many applications. Here, we first establish a resorcinol responsive aTF-based biosensor in Escherichia coli using the TetR-family repressor RolR from Corynebacterium glutamicum. We then perform an iterative walk along the fitness landscape of RolR to identify new inducer specificities, namely catechol, methyl catechol, caffeic acid, protocatechuate, L-DOPA, and the tumour biomarker homovanillic acid. Finally, we demonstrate the versatility of these engineered aTFs by transplanting them into the model eukaryote Saccharomyces cerevisiae. This work provides a framework for efficient aTF engineering to expand ligand specificity towards novel molecules on laboratory timescales, which, more broadly, is invaluable across a wide range of applications such as protein and metabolic engineering, as well as point-of-care diagnostics.
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Affiliation(s)
- Mohamed A Nasr
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
| | - Vincent J J Martin
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
| | - David H Kwan
- Centre for Applied Synthetic Biology, Concordia University, Montréal, Québec, Canada
- Department of Biology, Concordia University, Montréal, Québec, Canada
- Department of Chemistry and Biochemistry, Concordia University, Montréal, Québec, Canada
- PROTEO, Québec Network for Research on Protein Function, Structure, and Engineering, Québec City, Québec, Canada
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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: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [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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