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Masudi WL, Titilawo Y, Keshinro TA, Cowan AK. Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds. ENVIRONMENTAL TECHNOLOGY 2024; 45:4003-4016. [PMID: 37469005 DOI: 10.1080/09593330.2023.2238928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH 4 + , PO 4 3 - , and K + . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH 4 + , seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.
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Affiliation(s)
- Wiya L Masudi
- Institute for Environmental Biotechnology, Rhodes University (EBRU), Makhanda, South Africa
| | - Yinka Titilawo
- Institute for Environmental Biotechnology, Rhodes University (EBRU), Makhanda, South Africa
| | - Taobat A Keshinro
- Institute for Environmental Biotechnology, Rhodes University (EBRU), Makhanda, South Africa
| | - A Keith Cowan
- Institute for Environmental Biotechnology, Rhodes University (EBRU), Makhanda, South Africa
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2
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Bai Y, Liu X, Baldwin IT. Using Synthetic Biology to Understand the Function of Plant Specialized Metabolites. ANNUAL REVIEW OF PLANT BIOLOGY 2024; 75:629-653. [PMID: 38424065 DOI: 10.1146/annurev-arplant-060223-013842] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/02/2024]
Abstract
Plant specialized metabolites (PSMs) are variably distributed across taxa, tissues, and ecological contexts; this variability has inspired many theories about PSM function, which, to date, remain poorly tested because predictions have outpaced the available data. Advances in mass spectrometry-based metabolomics have enabled unbiased PSM profiling, and molecular biology techniques have produced PSM-free plants; the combination of these methods has accelerated our understanding of the complex ecological roles that PSMs play in plants. Synthetic biology techniques and workflows are producing high-value, structurally complex PSMs in quantities and purities sufficient for both medicinal and functional studies. These workflows enable the reengineering of PSM transport, externalization, structural diversity, and production in novel taxa, facilitating rigorous tests of long-standing theoretical predictions about why plants produce so many different PSMs in particular tissues and ecological contexts. Plants use their chemical prowess to solve ecological challenges, and synthetic biology workflows are accelerating our understanding of these evolved functions.
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Affiliation(s)
- Yuechen Bai
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China; ,
| | - Xinyu Liu
- State Key Laboratory of Genetic Engineering, Shanghai Engineering Research Center of Industrial Microorganisms, Department of Biochemistry, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, China; ,
| | - Ian T Baldwin
- Max Planck Institute for Chemical Ecology, Jena, Germany;
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3
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Homma M, Wakabayashi T, Moriwaki Y, Shiotani N, Shigeta T, Isobe K, Okazawa A, Ohta D, Terada T, Shimizu K, Mizutani M, Takikawa H, Sugimoto Y. Insights into stereoselective ring formation in canonical strigolactone: Identification of a dirigent domain-containing enzyme catalyzing orobanchol synthesis. Proc Natl Acad Sci U S A 2024; 121:e2313683121. [PMID: 38905237 PMCID: PMC11214005 DOI: 10.1073/pnas.2313683121] [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: 08/14/2023] [Accepted: 04/30/2024] [Indexed: 06/23/2024] Open
Abstract
Strigolactones (SLs) are plant apocarotenoids with diverse roles and structures. Canonical SLs, widespread and characterized by structural variations in their tricyclic lactone (ABC-ring), are classified into two types based on C-ring configurations. The steric C-ring configuration emerges during the BC-ring closure, downstream of the biosynthetic intermediate, carlactonoic acid (CLA). Most plants produce either type of canonical SLs stereoselectively, e.g., tomato (Solanum lycopersicum) yields orobanchol with an α-oriented C-ring. The mechanisms driving SL structural diversification are partially understood, with limited insight into functional implications. Furthermore, the exact molecular mechanism for the stereoselective BC-ring closure reaction is yet to be known. We identified an enzyme, the stereoselective BC-ring-forming factor (SRF), from the dirigent protein (DIR) family, specifically the DIR-f subfamily, whose biochemical function had not been characterized, making it a key enzyme in stereoselective canonical SL biosynthesis with the α-oriented C-ring. We first confirm the precise catalytic function of the tomato cytochrome P450 SlCYP722C, previously shown to be involved in orobanchol biosynthesis [T. Wakabayashi et al., Sci. Adv. 5, eaax9067 (2019)], to convert CLA to 18-oxocarlactonoic acid. We then show that SRF catalyzes the stereoselective BC-ring closure reaction of 18-oxocarlactonoic acid, forming orobanchol. Our methodology combines experimental and computational techniques, including SRF structure prediction and conducting molecular dynamics simulations, suggesting a catalytic mechanism based on the conrotatory 4π-electrocyclic reaction for the stereoselective BC-ring formation in orobanchol. This study sheds light on the molecular basis of how plants produce SLs with specific stereochemistry in a controlled manner.
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Affiliation(s)
- Masato Homma
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Takatoshi Wakabayashi
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Yoshitaka Moriwaki
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Nanami Shiotani
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Takumi Shigeta
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Kazuki Isobe
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
| | - Atsushi Okazawa
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Daisaku Ohta
- Department of Applied Life Sciences, Graduate School of Life and Environmental Sciences, Osaka Prefecture University, Sakai599-8531, Japan
- Department of Agricultural Biology, Graduate School of Agriculture, Osaka Metropolitan University, Sakai599-8531, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Kentaro Shimizu
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
- Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Tokyo113-8657, Japan
| | - Masaharu Mizutani
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
| | - Hirosato Takikawa
- Department of Applied Biological Chemistry, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo113-8657, Japan
| | - Yukihiro Sugimoto
- Department of Agrobioscience, Graduate School of Agricultural Science, Kobe University, Kobe657-8501, Japan
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Daignan-Fornier S, Keita A, Boyer FD. Chemistry of Strigolactones, Key Players in Plant Communication. Chembiochem 2024; 25:e202400133. [PMID: 38607659 DOI: 10.1002/cbic.202400133] [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: 02/12/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/13/2024]
Abstract
Today, the use of artificial pesticides is questionable and the adaptation to global warming is a necessity. The promotion of favorable natural interactions in the rhizosphere offers interesting perspectives for changing the type of agriculture. Strigolactones (SLs), the latest class of phytohormones to be discovered, are also chemical mediators in the rhizosphere. We present in this review the diversity of natural SLs, their analogs, mimics, and probes essential for the biological studies of this class of compounds. Their biosynthesis and access by organic synthesis are highlighted especially concerning noncanonical SLs, the more recently discovered natural SLs. Organic synthesis of analogs, stable isotope-labeled standards, mimics, and probes are also reviewed here. In the last part, the knowledge about the SL perception is described as well as the different inhibitors of SL receptors that have been developed.
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Affiliation(s)
- Suzanne Daignan-Fornier
- Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, CNRS, 91198, Gif-sur-Yvette, France
| | - Antoinette Keita
- Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, CNRS, 91198, Gif-sur-Yvette, France
| | - François-Didier Boyer
- Institut de Chimie des Substances Naturelles, UPR 2301, Université Paris-Saclay, CNRS, 91198, Gif-sur-Yvette, France
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Nomura T, Seto Y, Kyozuka J. Unveiling the complexity of strigolactones: exploring structural diversity, biosynthesis pathways, and signaling mechanisms. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1134-1147. [PMID: 37877933 DOI: 10.1093/jxb/erad412] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/20/2023] [Indexed: 10/26/2023]
Abstract
Strigolactone is the collective name for compounds containing a butenolide as a part of their structure, first discovered as compounds that induce seed germination of root parasitic plants. They were later found to be rhizosphere signaling molecules that induce hyphal branching of arbuscular mycorrhizal fungi, and, finally, they emerged as a class of plant hormones. Strigolactones are found in root exudates, where they display a great variability in their chemical structure. Their structure varies among plant species, and multiple strigolactones can exist in one species. Over 30 strigolactones have been identified, yet the chemical structure of the strigolactone that functions as an endogenous hormone and is found in the above-ground parts of plants remains unknown. We discuss our current knowledge of the synthetic pathways of diverse strigolactones and their regulation, as well as recent progress in identifying strigolactones as plant hormones. Strigolactone is perceived by the DWARF14 (D14), receptor, an α/β hydrolase which originated by gene duplication of KARRIKIN INSENSITIVE 2 (KAI2). D14 and KAI2 signaling pathways are partially overlapping paralogous pathways. Progress in understanding the signaling mechanisms mediated by two α/β hydrolase receptors as well as remaining challenges in the field of strigolactone research are reviewed.
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Affiliation(s)
- Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Yoshiya Seto
- School of Agriculture, Meiji University, Kawasaki, Japan
| | - Junko Kyozuka
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
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6
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Bureau JA, Oliva ME, Dong Y, Ignea C. Engineering yeast for the production of plant terpenoids using synthetic biology approaches. Nat Prod Rep 2023; 40:1822-1848. [PMID: 37523210 DOI: 10.1039/d3np00005b] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023]
Abstract
Covering: 2011-2022The low amounts of terpenoids produced in plants and the difficulty in synthesizing these complex structures have stimulated the production of terpenoid compounds in microbial hosts by metabolic engineering and synthetic biology approaches. Advances in engineering yeast for terpenoid production will be covered in this review focusing on four directions: (1) manipulation of host metabolism, (2) rewiring and reconstructing metabolic pathways, (3) engineering the catalytic activity, substrate selectivity and product specificity of biosynthetic enzymes, and (4) localizing terpenoid production via enzymatic fusions and scaffolds, or subcellular compartmentalization.
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Affiliation(s)
| | | | - Yueming Dong
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
| | - Codruta Ignea
- Department of Bioengineering, McGill University, Montreal, QC, H3A 0C3, Canada.
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7
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Qi Z, Tong X, Zhang Y, Jia S, Fang X, Zhao L. Carotenoid Cleavage Dioxygenase 1 and Its Application for the Production of C13-Apocarotenoids in Microbial Cell Factories: A Review. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19240-19254. [PMID: 38047615 DOI: 10.1021/acs.jafc.3c06459] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
C13-apocarotenoids are naturally derived from the C9-C10 (C9'-C10') double-bond cleavage of carotenoids by carotenoid cleavage dioxygenases (CCDs). As high-value flavors and fragrances in the food and cosmetic industries, the sustainable production of C13-apocarotenoids is emerging in microbial cell factories by the carotenoid cleavage dioxygenase 1 (CCD1) subfamily. However, the commercialization of microbial-based C13-apocarotenoids is still limited by the poor performance of CCD1, which severely constrains its conversion efficiency from precursor carotenoids. This review focuses on the classification of CCDs and their cleavage modes for carotenoids to generate corresponding apocarotenoids. We then emphatically discuss the advances for C13-apocarotenoid biosynthesis in microbial cell factories with various strategies, including optimization of CCD1 expression, improvement of CCD1's catalytic activity and substrate specificity, strengthening of substrate channeling, and development of oleaginous microbial hosts, which have been verified to increase the conversion rate from carotenoids. Lastly, the current challenges and future directions will be discussed to enhance CCDs' application for C13-apocarotenoids biomanufacturing.
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Affiliation(s)
- Zhipeng Qi
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Xinyi Tong
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Yangyang Zhang
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Shutong Jia
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
| | - Xianying Fang
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China
| | - Linguo Zhao
- Jiangsu Co-Innovation Center of Efficient Processing and Utilization of Forest Resources, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- College of Chemical Engineering, Nanjing Forestry University, 159 Long Pan Road, Nanjing 210037, China
- Jiangsu Province Key Lab for the Chemistry & Utilization of Agricultural and Forest, Nanjing 210037, China
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8
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Yoda A, Xie X, Yoneyama K, Miura K, McErlean CSP, Nomura T. A Stereoselective Strigolactone Biosynthesis Catalyzed by a 2-Oxoglutarate-Dependent Dioxygenase in Sorghum. PLANT & CELL PHYSIOLOGY 2023; 64:1034-1045. [PMID: 37307421 PMCID: PMC10504574 DOI: 10.1093/pcp/pcad060] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 06/06/2023] [Accepted: 06/10/2023] [Indexed: 06/14/2023]
Abstract
Seeds of root parasitic plants, Striga, Orobanche and Phelipanche spp., are induced to germinate by strigolactones (SLs) exudated from host roots. In Striga-resistant cultivars of Sorghum bicolor, the loss-of-function of the Low Germination Stimulant 1 (LGS1) gene changes the major SL from 5-deoxystrigol (5DS) to orobanchol, which has an opposite C-ring stereochemistry. The biosynthetic pathway of 5DS catalyzed by LGS1 has not been fully elucidated. Since other unknown regulators, in addition to LGS1 encoding a sulfotransferase, appear to be necessary for the stereoselective biosynthesis of 5DS, we examined Sobic.005G213500 (Sb3500), encoding a 2-oxoglutarate-dependent dioxygenase, as a candidate regulator, which is co-expressed with LGS1 and located 5'-upstream of LGS1 in the sorghum genome. When LGS1 was expressed with known SL biosynthetic enzyme genes including the cytochrome P450 SbMAX1a in Nicotiana benthamiana leaves, 5DS and its diastereomer 4-deoxyorobanchol (4DO) were produced in approximately equal amounts, while the production of 5DS was significantly larger than that of 4DO when Sb3500 was also co-expressed. We also confirmed the stereoselective 5DS production in an in vitro feeding experiment using synthetic chemicals with recombinant proteins expressed in Escherichia coli and yeast. This finding demonstrates that Sb3500 is a stereoselective regulator in the conversion of the SL precursor carlactone to 5DS, catalyzed by LGS1 and SbMAX1a, providing a detailed understanding of how different SLs are produced to combat parasitic weed infestations.
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Affiliation(s)
- Akiyoshi Yoda
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
| | - Xiaonan Xie
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
| | - Kaori Yoneyama
- Graduate School of Agriculture, Ehime University, Matsuyama, Ehime, 790-8566 Japan
- Research and Development Bureau, Saitama University, Saitama-shi, Saitama, 338-8570 Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572 Japan
| | | | - Takahito Nomura
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Tochigi, 321-8505 Japan
- United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Fuchu, Tokyo, 183-8509 Japan
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Pan R, Yang X, Qiu M, Jiang W, Zhang W, Jiang Y, Xin F, Jiang M. Construction of Coculture System Containing Escherichia coli with Different Microbial Species for Biochemical Production. ACS Synth Biol 2023; 12:2208-2216. [PMID: 37506399 DOI: 10.1021/acssynbio.3c00329] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2023]
Abstract
Microbial synthesis of target chemicals usually involves multienzymatic reactions in vivo, especially for compounds with a long metabolic pathway. However, when various genes are introduced into one single strain, it leads to a heavy metabolic burden. In contrast, the microbial coculture system can allocate metabolic pathways into different hosts, which will relieve the metabolic burdens. Escherichia coli is the most used chassis to synthesize biofuels and chemicals owing to its well-known genetics, high transformation efficiency, and easy cultivation. Accordingly, cocultures containing the cooperative E. coli with other microbial species have received great attention. In this review, the individual applications and boundedness of different combinations will be summarized. Additionally, the strategies for the self-regulation of population composition, which can help enhance the stability of a coculture system, will also be discussed. Finally, perspectives for the cocultures will be proposed.
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Affiliation(s)
- Runze Pan
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Xinyi Yang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Min Qiu
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wankui Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Wenming Zhang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Yujia Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
| | - Fengxue Xin
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
| | - Min Jiang
- State Key Laboratory of Materials-Oriented Chemical Engineering, College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, Nanjing, 211800, P. R. China
- Jiangsu Academy of Chemical Inherent Safety, Nanjing, 211800, P. R. China
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10
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Li Z, Gao X, Li M, Yan Q, Zhang N, Yu B, Zhang B, Zhang S, Helal MH, Abu Ali OA, Nassan MA, Qyyum MA, Asif S, Bokhari A. Steroid hormone-inducible biosensor based on EGFP-tagged and environmental application. ENVIRONMENTAL RESEARCH 2022; 215:114303. [PMID: 36116500 DOI: 10.1016/j.envres.2022.114303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/04/2022] [Accepted: 09/06/2022] [Indexed: 06/15/2023]
Abstract
Steroid hormones as a class of emerging organic pollutant and high concern, due to their potential risks for human and environmental. Accurate analytical methods of steroid hormones are necessary in quantifying and monitoring. Biosensor is a promising technique. In this study, though part of 3α-HSD DNA to construct a regulatory plasmid and with the EGFP reporter gene to generate a reporter plasmid. Separately transformed into Escherichia coli strain BL21 and extracted the cell lysates as novel biosensor reagents. Analyzed the total amounts of steroid hormones in water, sediment, and soil samples using biosensor reagents, and compared these results with those obtained by HPLC. In summary, detection method using an EGFP reporter that can detect trace amounts of steroid hormones to reached fg/L. The optimal reaction time range and temperature were 30 min and 30 °C, respectively, while the most suitable organic solvent for the steroid hormone was 100% ethanol, up to 96-well plate format. This method is very suitable for high-throughput detection of environmental steroid hormone pollutants.
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Affiliation(s)
- Zhonghe Li
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China.
| | - Xingai Gao
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Ming Li
- Jilin Jianzhu University, Changchun, 130118, China
| | - Qiuliang Yan
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Nan Zhang
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Boyang Yu
- Jilin Academy of Agricultural Sciences, Changchun, 130033, China
| | - Bimi Zhang
- Economic Management Institute of Jilin Province, Changchun, 130012, China
| | - Shuying Zhang
- Animal Disease Prevention and Control Center of Jilin Province, China.
| | - Mohamed H Helal
- Department of Chemistry, Faculty of Arts and Science, Northern Border University, Rafha, 91911, PO 840, Saudi Arabia.
| | - Ola A Abu Ali
- Department of Chemistry, College of Science, Taif University, P.O.Box 11099, Taif, 21944, Saudi Arabia
| | - Mohamed A Nassan
- Department of Clinical Laboratory Sciences, Turabah University College, Taif University, P.O. Box 11099, Taif, 21944, Saudi Arabia
| | - Muhammad Abdul Qyyum
- Department of Petroleum & Chemical Engineering, Sultan Qaboos University, Muscat, Oman
| | - Saira Asif
- Sustainable Process Integration Laboratory, SPIL, NETME Centra, Faculty of Mechanical Engineering, Brno University of Technology, VUT Brno, Technická 2896/2, 616 00, Brno, Czech Republic
| | - Awais Bokhari
- Sustainable Process Integration Laboratory, SPIL, NETME Centra, Faculty of Mechanical Engineering, Brno University of Technology, VUT Brno, Technická 2896/2, 616 00, Brno, Czech Republic; Department of Chemical Engineering, COMSATS University Islamabad (CUI), Lahore Campus, 54000, Punjab, Lahore, Pakistan
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11
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Panda S, Zhou K. Engineering microbes to overproduce natural products as agrochemicals. Synth Syst Biotechnol 2022; 8:79-85. [PMID: 36514486 PMCID: PMC9731846 DOI: 10.1016/j.synbio.2022.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/12/2022] [Accepted: 11/20/2022] [Indexed: 11/29/2022] Open
Abstract
Current agricultural practices heavily rely on the excessive application of synthetic pesticides and fertilizers to meet the food demands of the increasing global population. This practice has several drawbacks including its negative impact on the environment and human health. Recently, the use of natural products has gained interest as alternatives to these synthetic agrochemicals due to their selective working mechanisms and biodegradability. In order to efficiently produce these natural agrochemicals, engineering microorganisms is emerging as an increasingly viable approach, and it is anticipated that it will have a significant market share in the near future. This approach manipulates the metabolism of microbes to manufacture the desired natural compounds from low-cost starting materials. This review discusses recent examples of this approach. The produced natural products can serve as biopesticides or plant growth regulators for the sustainable improvement of plant growth and disease control. The challenges in further developing these strategies are also discussed.
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12
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Wen S, Tu Z, Wei L, Li H. Liriodendron chinense LcMAX1 regulates primary root growth and shoot branching in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 190:1-10. [PMID: 36084353 DOI: 10.1016/j.plaphy.2022.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 08/10/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Strigolactones (SLs) play prominent roles in regulating shoot branching and root architecture in model plants. However, their roles in non-model (particularly woody) plants remain unclear. Liriodendron chinense is a timber tree species widely planted in southern China. The outturn percentage and wood quality of L. chinense are greatly affected by the branching characteristics of its shoot, and the rooting ability of the cuttings is key for its vegetative propagation. Here, we isolated and analyzed the function of the MORE AXILLARY GROWTH 1 (LcMAX1) gene, which is involved in L. chinense SL biosynthesis. RT-qPCR showed that LcMAX1 was highly expressed in the roots and axillary buds. LcMAX1 was located in the endoplasmic reticulum (ER) and nucleus. LcMAX1 ectopic expression promoted primary root growth, whereas there were no phenotypic differences in shoot branching between transgenic and wild-type (WT) A. thaliana plants. LcMAX1 overexpression in the max1 mutant restored them to the WT A. thaliana phenotypes. Additionally, AtPIN1, AtPIN2, and AtBRC1 expressions were significantly upregulated in transgenic A. thaliana and the max1 mutant. It was therefore speculated that LcMAX1 promotes primary root growth by regulating expression of auxin transport-related genes in A. thaliana, and LcMAX1 inhibits shoot branching by upregulating expression of AtBRC1 in the max1 mutant. Altogether, these results demonstrated that the root development and shoot branching functions of LcMAX1 were similar to those of AtMAX1. Our findings provide a foundation for obtaining further insights into root and branch development in L. chinense.
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Affiliation(s)
- Shaoying Wen
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
| | - Zhonghua Tu
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
| | - Lingming Wei
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
| | - Huogen Li
- Key Laboratory of Forest Genetics & Biotechnology of Ministry of Education, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China; Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, Jiangsu, 210037, China.
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13
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Yata A, Nosaki S, Yoda A, Nomura T, Miura K. Production and stably maintenance of strigolactone by transient expression of biosynthetic enzymes in Nicotiana benthamiana. FRONTIERS IN PLANT SCIENCE 2022; 13:1027004. [PMID: 36388605 PMCID: PMC9650523 DOI: 10.3389/fpls.2022.1027004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Strigolactones (SLs) are phytohormones that play an essential role in plant-microbe interactions. The instability of SLs makes it challenging to use them for application to agriculture. In this study, we successfully produced a large amount of the 4-deoxyorobanchol (4DO), one of SLs, in the leaves of Nicotiana benthamiana, using a transient expression system to express SL biosynthetic enzymes. Using this system, the yield of 4DO was 2.1 ± 0.3 μg/gFM (fresh mass). Treatment of leaves at 80°C for 16 h killed Agrobacterium and approximately half amount of 4DO was left in the leaves (1.0 μg/gFM (calculated based on the original FM) ± 0.3). Interestingly, incubation of dried leaves at room temperature for 1 month maintained an almost equal amount of 4DO (0.9 ± 0.2 μg/gFM) in the leaves. These results suggest that high accumulation of 4DO with stability for long periods can be achieved in plant leaves.
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Affiliation(s)
- Akira Yata
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Shohei Nosaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
| | - Akiyoshi Yoda
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Takahito Nomura
- Department of Biological Production Science, United Graduate School of Agricultural Science, Tokyo University of Agriculture and Technology, Tokyo, Japan
- Center for Bioscience Research and Education, Utsunomiya University, Utsunomiya, Japan
| | - Kenji Miura
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Tsukuba-Plant Innovation Research Center (T-PIRC), University of Tsukuba, Tsukuba, Japan
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14
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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. THE NEW PHYTOLOGIST 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] [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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15
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Ding Q, Li Z, Guo L, Song W, Wu J, Chen X, Liu L, Gao C. Engineering Escherichia coli asymmetry distribution-based synthetic consortium for shikimate production. Biotechnol Bioeng 2022; 119:3230-3240. [PMID: 35982023 DOI: 10.1002/bit.28211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 08/11/2022] [Accepted: 08/16/2022] [Indexed: 11/09/2022]
Abstract
Microbial consortia constitute a promising tool for achieving high-value chemical bio-production. However, customizing the consortium ratio remains challenging. Herein, an asymmetry distribution-based synthetic consortium (ADSC) was developed to switch cell phenotypes using shikimate synthesis for proof of concept. First, the cell pole-organizing protein PopZ was screened as a mediator of asymmetric protein distribution in Escherichia coli. The ADSC was then constructed to incorporate PopZ-mediated asymmetry distribution and a TetR-based transcription repression switch to achieve the dynamical control of microbial population ratio. Finally, the ADSC was used to decouple cell growth from shikimate synthesis by effectively coordinating the ratio of growing cells and production cells at the consortium level, thereby increasing shikimate titer to 30.1 g/L in the 7.5-L bioreactor with a minimal medium. This titer was further improved to 82.5 g/L when using rich medium fermentation. Our results illustrate a novel approach to control consortium structure through ADSC-mediated regulation, highlighting its potential as an efficient strategy for controlling metabolic state in microbes. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Qiang Ding
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China.,School of Life Sciences, Anhui University, Hefei, 230601, China
| | - Zhendong Li
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liang Guo
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Wei Song
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Jing Wu
- School of Life Sciences and Health Engineering, Jiangnan University, Wuxi, 214122, China
| | - Xiulai Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Liming Liu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
| | - Cong Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, China.,International Joint Laboratory on Food Safety, Jiangnan University, Wuxi, 214122, China
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16
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Jin K, Xia H, Liu Y, Li J, Du G, Lv X, Liu L. Compartmentalization and transporter engineering strategies for terpenoid synthesis. Microb Cell Fact 2022; 21:92. [PMID: 35599322 PMCID: PMC9125818 DOI: 10.1186/s12934-022-01819-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/12/2022] [Indexed: 12/18/2022] Open
Abstract
Microbial cell factories for terpenoid synthesis form a less expensive and more environment-friendly approach than chemical synthesis and extraction, and are thus being regarded as mainstream research recently. Organelle compartmentalization for terpenoid synthesis has received much attention from researchers owing to the diverse physiochemical characteristics of organelles. In this review, we first systematically summarized various compartmentalization strategies utilized in terpenoid production, mainly plant terpenoids, which can provide catalytic reactions with sufficient intermediates and a suitable environment, while bypassing competing metabolic pathways. In addition, because of the limited storage capacity of cells, strategies used for the expansion of specific organelle membranes were discussed. Next, transporter engineering strategies to overcome the cytotoxic effects of terpenoid accumulation were analyzed. Finally, we discussed the future perspectives of compartmentalization and transporter engineering strategies, with the hope of providing theoretical guidance for designing and constructing cell factories for the purpose of terpenoid production.
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Affiliation(s)
- Ke Jin
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Hongzhi Xia
- Richen Bioengineering Co., Ltd, Nantong, 226000, China
| | - Yanfeng Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Jianghua Li
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Guocheng Du
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China
| | - Xueqin Lv
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
| | - Long Liu
- Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, Jiangnan University, Wuxi, 214122, China.
- Science Center for Future Foods, Jiangnan University, Wuxi, 214122, China.
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17
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Liu X, Li L, Zhao GR. Systems Metabolic Engineering of Escherichia coli Coculture for De Novo Production of Genistein. ACS Synth Biol 2022; 11:1746-1757. [PMID: 35507680 DOI: 10.1021/acssynbio.1c00590] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Genistein is a plant-derived isoflavone possessing various bioactivities to prevent aging, carcinogenesis, and neurodegenerative and inflammation diseases. As a typical complex flavonoid, its microbial production from sugar remains to be completed. Here, we use systems metabolic engineering stategies to design and develop a three-strain commensalistic Escherichia coli coculture that for the first time realized the de novo production of genistein. First, we reconstituted the naringenin module by screening and incorporating chalcone isomerase-like protein, an auxiliary component to rectify the chalcone synthase promiscuity. Furthermore, we devised and constructed the genistein module by N-terminal modifications of plant P450 enzyme 2-hydroxyisoflavanone synthase and cytochrome P450 enzyme reductase. When naringenin-producing strain was cocultivated with p-coumaric acid-overproducing strain (a phenylalanine-auxotroph), two-strain coculture worked as commensalism through a unidirectional nutrient flow, which favored the efficient production of naringenin with a titer of 206.5 mg/L from glucose. A three-strain commensalistic coculture was subsequently engineered, which produced the highest titer to date of 60.8 mg/L genistein from a glucose and glycerol mixture. The commensalistic coculture is a flexible and versatile platform for the production of flavonoids, indicating a promising future for production of complex natural products in engineered E. coli.
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Affiliation(s)
- Xue Liu
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Lingling Li
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
| | - Guang-Rong Zhao
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Yaguan Road 135, Jinnan District, Tianjin 300350, China
- Georgia Tech Shenzhen Institute, Tianjin University, Dashi Road 1, Nanshan District, Shenzhen 518055, China
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18
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Patel JR, Oh J, Wang S, Crawford JM, Isaacs FJ. Cross-kingdom expression of synthetic genetic elements promotes discovery of metabolites in the human microbiome. Cell 2022; 185:1487-1505.e14. [PMID: 35366417 PMCID: PMC10619838 DOI: 10.1016/j.cell.2022.03.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 02/04/2022] [Accepted: 03/07/2022] [Indexed: 12/12/2022]
Abstract
Small molecules encoded by biosynthetic pathways mediate cross-species interactions and harbor untapped potential, which has provided valuable compounds for medicine and biotechnology. Since studying biosynthetic gene clusters in their native context is often difficult, alternative efforts rely on heterologous expression, which is limited by host-specific metabolic capacity and regulation. Here, we describe a computational-experimental technology to redesign genes and their regulatory regions with hybrid elements for cross-species expression in Gram-negative and -positive bacteria and eukaryotes, decoupling biosynthetic capacity from host-range constraints to activate silenced pathways. These synthetic genetic elements enabled the discovery of a class of microbiome-derived nucleotide metabolites-tyrocitabines-from Lactobacillus iners. Tyrocitabines feature a remarkable orthoester-phosphate, inhibit translational activity, and invoke unexpected biosynthetic machinery, including a class of "Amadori synthases" and "abortive" tRNA synthetases. Our approach establishes a general strategy for the redesign, expression, mobilization, and characterization of genetic elements in diverse organisms and communities.
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Affiliation(s)
- Jaymin R Patel
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA; Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA
| | - Joonseok Oh
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA
| | - Shenqi Wang
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA
| | - Jason M Crawford
- Institute of Biomolecular Design and Discovery, Yale University, West Haven, CT, USA; Department of Chemistry, Yale University, New Haven, CT, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT, USA.
| | - Farren J Isaacs
- Department of Molecular, Cellular, & Developmental Biology, Yale University, New Haven, CT, USA; Systems Biology Institute, Yale University, West Haven, CT, USA; Department of Biomedical Engineering, Yale University, New Haven, CT, USA.
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19
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Ma X, Liang H, Pan Q, Prather KLJ, Sinskey AJ, Stephanopoulos G, Zhou K. Optimization of the Isopentenol Utilization Pathway for Isoprenoid Synthesis in Escherichia coli. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:3512-3520. [PMID: 35286075 DOI: 10.1021/acs.jafc.2c00014] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Engineering microbes to produce isoprenoids can be limited by the competition between product formation and cell growth because biomass and isoprenoids are naturally derived from central metabolism. Recently, a two-step synthetic pathway was developed to partially decouple isoprenoid formation from central carbon metabolism. The pathway used exogenously added isopentenols as substrates. In the present study, we systematically optimized this isopentenol utilization pathway in Escherichia coli by comparing enzyme variants from different species, tuning enzyme expression levels, and using a two-stage process. Under the optimal conditions found in this study, ∼300 mg/L lycopene was synthesized from 2 g/L isopentenol in 24 h. The strain could be easily modified to synthesize two other isoprenoid molecules efficiently (248 mg/L β-carotene or 364 mg/L R-(-)-linalool produced from 2 g/L isopentenol). This study lays a solid foundation for producing agri-food isoprenoids at high titer/productivity from cost-effective feedstocks.
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Affiliation(s)
- Xiaoqiang Ma
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hong Liang
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Qiuchi Pan
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
| | - Kristala L J Prather
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony J Sinskey
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Gregory Stephanopoulos
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Kang Zhou
- Disruptive & Sustainable Technologies for Agricultural Precision (DiSTAP), Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Chemical and Biomolecular Engineering, National University of Singapore, Singapore 117585, Singapore
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20
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Wakabayashi T, Ueno K, Sugimoto Y. Structure Elucidation and Biosynthesis of Orobanchol. FRONTIERS IN PLANT SCIENCE 2022; 13:835160. [PMID: 35222492 PMCID: PMC8863659 DOI: 10.3389/fpls.2022.835160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Strigolactones (SLs), a class of phytohormones that regulate diverse developmental processes, were initially characterized as host-derived germination stimulants for seeds belonging to the genera Striga, Orobanche, and Phelipanche. Orobanchol (1), which is detected in the root exudates of several plants and recognized as a prevalent SL, was first isolated from the root exudates of red clover as a germination stimulant for Orobanche minor in 1998. However, the structure of this stimulant proposed at that time was disputable considering its predicted germination-inducing activity for Striga gesnerioides. The genuine structure of orobanchol was elucidated following a decade-long controversy, which ultimately facilitated the understanding of the importance of SL stereochemistry in Striga seed germination. Recently, studies focusing on clarifying the biosynthesis pathway of orobanchol are being conducted. Cytochrome P450 monooxygenases are involved in orobanchol biosynthesis downstream of carlactonoic acid (CLA) via two pathways: either through 4-deoxyorobanchol or direct conversion from CLA. Substantial progress in the identification of more SL structures and clarification of their biosynthetic mechanisms will further contribute in the comprehension of their structural diversity's functional importance and agricultural applications. Herein, we have reviewed the history leading to the discovery of the genuine structure of orobanchol and the current understanding of its biosynthetic mechanisms.
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Affiliation(s)
| | - Kotomi Ueno
- Faculty of Agriculture, Tottori University, Tottori, Japan
| | - Yukihiro Sugimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
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21
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Xu S, Wu S, Li Y. Investigating Plant Biosynthetic Pathways Using Heterologous Gene Expression: Yeast as a Heterologous Host. Methods Mol Biol 2022; 2489:369-393. [PMID: 35524060 DOI: 10.1007/978-1-0716-2273-5_19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Plant natural products (PNPs) are valuable resources for the development of pharmaceuticals and agrochemicals, yet the biosynthesis and metabolism of PNPs are largely unknown. Heterologous pathway reconstitution is a heavily adopted strategy in secondary metabolism characterization. Yeast systems have been broadly utilized in the heterologous production of PNPs and have been considered as a promising platform to investigate plant biosynthetic pathways. Here, we describe the reconstitution and verification of the upstream part of brassinolide biosynthesis in S. cerevisiae using this method.
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Affiliation(s)
- Shanhui Xu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Sheng Wu
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | - Yanran Li
- Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
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22
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Zhou K. Engineering microbes to synthesize functionalized biopolymers. J Mater Chem B 2022; 10:7132-7135. [DOI: 10.1039/d2tb01063a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Engineering metabolism of microbes has allowed simultaneous co-production of functional small molecules and biopolymers. This Perspective briefly introduced its working principles and summarized my views on how this approach could...
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23
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Wu S, Li Y. A Unique Sulfotransferase-Involving Strigolactone Biosynthetic Route in Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:793459. [PMID: 34970291 PMCID: PMC8713700 DOI: 10.3389/fpls.2021.793459] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 11/08/2021] [Indexed: 05/17/2023]
Abstract
LOW GERMINATION STIMULANT 1 (LGS1) plays an important role in strigolactones (SLs) biosynthesis and Striga resistance in sorghum, but the catalytic function remains unclear. Using the recently developed SL-producing microbial consortia, we examined the activities of sorghum MORE AXILLARY GROWTH1 (MAX1) analogs and LGS1. Surprisingly, SbMAX1a (cytochrome P450 711A enzyme in sorghum) synthesized 18-hydroxy-carlactonoic acid (18-hydroxy-CLA) directly from carlactone (CL) through four-step oxidations. The further oxidated product orobanchol (OB) was also detected in the microbial consortium. Further addition of LGS1 led to the synthesis of both 5-deoxystrigol (5DS) and 4-deoxyorobanchol (4DO). Further biochemical characterization found that LGS1 functions after SbMAX1a by converting 18-hydroxy-CLA to 5DS and 4DO possibly through a sulfonation-mediated pathway. The unique functions of SbMAX1 and LGS1 imply a previously unknown synthetic route toward SLs.
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