1
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Choudhary N, Pucker B. Conserved amino acid residues and gene expression patterns associated with the substrate preferences of the competing enzymes FLS and DFR. PLoS One 2024; 19:e0305837. [PMID: 39196921 PMCID: PMC11356453 DOI: 10.1371/journal.pone.0305837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2024] [Accepted: 06/05/2024] [Indexed: 08/30/2024] Open
Abstract
BACKGROUND Flavonoids, an important class of specialized metabolites, are synthesized from phenylalanine and present in almost all plant species. Different branches of flavonoid biosynthesis lead to products like flavones, flavonols, anthocyanins, and proanthocyanidins. Dihydroflavonols form the branching point towards the production of non-colored flavonols via flavonol synthase (FLS) and colored anthocyanins via dihydroflavonol 4-reductase (DFR). Despite the wealth of publicly accessible data, there remains a gap in understanding the mechanisms that mitigate competition between FLS and DFR for the shared substrate, dihydroflavonols. RESULTS An angiosperm-wide comparison of FLS and DFR sequences revealed the amino acids at positions associated with the substrate specificity in both enzymes. A global analysis of the phylogenetic distribution of these amino acid residues revealed that monocots generally possess FLS with Y132 (FLSY) and DFR with N133 (DFRN). In contrast, dicots generally possess FLSH and DFRN, DFRD, and DFRA. DFRA, which restricts substrate preference to dihydrokaempferol, previously believed to be unique to strawberry species, is found to be more widespread in angiosperms and has evolved independently multiple times. Generally, angiosperm FLS appears to prefer dihydrokaempferol, whereas DFR appears to favor dihydroquercetin or dihydromyricetin. Moreover, in the FLS-DFR competition, the dominance of one over the other is observed, with typically only one gene being expressed at any given time. CONCLUSION This study illustrates how almost mutually exclusive gene expression and substrate-preference determining residues could mitigate competition between FLS and DFR, delineates the evolution of these enzymes, and provides insights into mechanisms directing the metabolic flux of the flavonoid biosynthesis, with potential implications for ornamental plants and molecular breeding strategies.
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Affiliation(s)
- Nancy Choudhary
- Institute of Plant Biology & BRICS, Plant Biotechnology and Bioinformatics, TU Braunschweig, Braunschweig, Germany
| | - Boas Pucker
- Institute of Plant Biology & BRICS, Plant Biotechnology and Bioinformatics, TU Braunschweig, Braunschweig, Germany
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2
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Ruan H, Gao L, Fang Z, Lei T, Xing D, Ding Y, Rashid A, Zhuang J, Zhang Q, Gu C, Qian W, Zhang N, Qian T, Li K, Xia T, Wang Y. A flavonoid metabolon: cytochrome b 5 enhances B-ring trihydroxylated flavan-3-ols synthesis in tea plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:1793-1814. [PMID: 38461478 DOI: 10.1111/tpj.16710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/02/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024]
Abstract
Flavan-3-ols are prominent phenolic compounds found abundantly in the young leaves of tea plants. The enzymes involved in flavan-3-ol biosynthesis in tea plants have been extensively investigated. However, the localization and associations of these numerous functional enzymes within cells have been largely neglected. In this study, we aimed to investigate the synthesis of flavan-3-ols in tea plants, particularly focusing on epigallocatechin gallate. Our analysis involving the DESI-MSI method to reveal a distinct distribution pattern of B-ring trihydroxylated flavonoids, primarily concentrated in the outer layer of buds. Subcellular localization showed that CsC4H, CsF3'H, and CsF3'5'H localizes endoplasmic reticulum. Protein-protein interaction studies demonstrated direct associations between CsC4H, CsF3'H, and cytoplasmic enzymes (CHS, CHI, F3H, DFR, FLS, and ANR), highlighting their interactions within the biosynthetic pathway. Notably, CsF3'5'H, the enzyme for B-ring trihydroxylation, did not directly interact with other enzymes. We identified cytochrome b5 isoform C serving as an essential redox partner, ensuring the proper functioning of CsF3'5'H. Our findings suggest the existence of distinct modules governing the synthesis of different B-ring hydroxylation compounds. This study provides valuable insights into the mechanisms underlying flavonoid diversity and efficient synthesis and enhances our understanding of the substantial accumulation of B-ring trihydroxylated flavan-3-ols in tea plants.
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Affiliation(s)
- Haixiang Ruan
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Zhou Fang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ting Lei
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Dawei Xing
- School of Biological and Environmental Engineering, Chaohu University, Chaohu, Anhui, 238024, China
| | - Yan Ding
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Arif Rashid
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang, Jiangsu, 212013, China
| | - Juhua Zhuang
- College of Tea Science, Guizhou University, Guiyang, Guizhou, 550025, China
| | - Qiang Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Chunyang Gu
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Wei Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Niuniu Zhang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Tao Qian
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Kongqing Li
- College of Humanities and Social Development, Nanjing Agriculture University, Nanjing, Jiangsu, 210095, China
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunsheng Wang
- School of Life Science, Anhui Agricultural University, Hefei, Anhui, 230036, China
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei, Anhui, 230036, China
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3
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Sugimoto K, Irani NG, Grotewold E, Howe GA. Catalytically impaired chalcone isomerase retains flavonoid biosynthetic capacity. PLANT PHYSIOLOGY 2024; 195:1143-1147. [PMID: 38386294 DOI: 10.1093/plphys/kiae096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 02/23/2024]
Affiliation(s)
- Koichi Sugimoto
- Tsukuba-Plant Innovation Center, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Niloufer G Irani
- Department of Biochemistry, University of Oxford, Oxford, OX1 3RB, UK
| | - Erich Grotewold
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
| | - Gregg A Howe
- Department of Biochemistry & Molecular Biology, Michigan State University, East Lansing, MI 48824, USA
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI 48824, USA
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4
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Lewis JA, Jacobo EP, Palmer N, Vermerris W, Sattler SE, Brozik JA, Sarath G, Kang C. Structural and Interactional Analysis of the Flavonoid Pathway Proteins: Chalcone Synthase, Chalcone Isomerase and Chalcone Isomerase-like Protein. Int J Mol Sci 2024; 25:5651. [PMID: 38891840 PMCID: PMC11172311 DOI: 10.3390/ijms25115651] [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: 04/04/2024] [Revised: 05/16/2024] [Accepted: 05/18/2024] [Indexed: 06/21/2024] Open
Abstract
Chalcone synthase (CHS) and chalcone isomerase (CHI) catalyze the first two committed steps of the flavonoid pathway that plays a pivotal role in the growth and reproduction of land plants, including UV protection, pigmentation, symbiotic nitrogen fixation, and pathogen resistance. Based on the obtained X-ray crystal structures of CHS, CHI, and chalcone isomerase-like protein (CHIL) from the same monocotyledon, Panicum virgatum, along with the results of the steady-state kinetics, spectroscopic/thermodynamic analyses, intermolecular interactions, and their effect on each catalytic step are proposed. In addition, PvCHI's unique activity for both naringenin chalcone and isoliquiritigenin was analyzed, and the observed hierarchical activity for those type-I and -II substrates was explained with the intrinsic characteristics of the enzyme and two substrates. The structure of PvCHS complexed with naringenin supports uncompetitive inhibition. PvCHS displays intrinsic catalytic promiscuity, evident from the formation of p-coumaroyltriacetic acid lactone (CTAL) in addition to naringenin chalcone. In the presence of PvCHIL, conversion of p-coumaroyl-CoA to naringenin through PvCHS and PvCHI displayed ~400-fold increased Vmax with reduced formation of CTAL by 70%. Supporting this model, molecular docking, ITC (Isothermal Titration Calorimetry), and FRET (Fluorescence Resonance Energy Transfer) indicated that both PvCHI and PvCHIL interact with PvCHS in a non-competitive manner, indicating the plausible allosteric effect of naringenin on CHS. Significantly, the presence of naringenin increased the affinity between PvCHS and PvCHIL, whereas naringenin chalcone decreased the affinity, indicating a plausible feedback mechanism to minimize spontaneous incorrect stereoisomers. These are the first findings from a three-body system from the same species, indicating the importance of the macromolecular assembly of CHS-CHI-CHIL in determining the amount and type of flavonoids produced in plant cells.
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Affiliation(s)
- Jacob A. Lewis
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (E.P.J.); (J.A.B.)
| | - Eric P. Jacobo
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (E.P.J.); (J.A.B.)
| | - Nathan Palmer
- Department of Agriculture—Agricultural Research Service, Wheat, Sorghum, and Forage Research Unit, Lincoln, NE 68583, USA; (N.P.); (S.E.S.); (G.S.)
| | - Wilfred Vermerris
- Department of Microbiology & Cell Science and UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA;
| | - Scott E. Sattler
- Department of Agriculture—Agricultural Research Service, Wheat, Sorghum, and Forage Research Unit, Lincoln, NE 68583, USA; (N.P.); (S.E.S.); (G.S.)
| | - James A Brozik
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (E.P.J.); (J.A.B.)
| | - Gautam Sarath
- Department of Agriculture—Agricultural Research Service, Wheat, Sorghum, and Forage Research Unit, Lincoln, NE 68583, USA; (N.P.); (S.E.S.); (G.S.)
| | - ChulHee Kang
- Department of Chemistry, Washington State University, Pullman, WA 99164, USA; (J.A.L.); (E.P.J.); (J.A.B.)
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5
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Albqmi M, Selim S, Bouqellah NA, Alnusaire TS, Almuhayawi MS, Al Jaouni SK, Hussein S, Warrad M, Al-Sanea MM, Abdelgawad MA, Mostafa EM, Aldilami M, Ahmed ES, AbdElgawad H. Improving plant adaptation to soil antimony contamination: the synergistic contribution of arbuscular mycorrhizal fungus and olive mill waste. BMC PLANT BIOLOGY 2024; 24:364. [PMID: 38702592 PMCID: PMC11069298 DOI: 10.1186/s12870-024-05044-1] [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: 02/06/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
BACKGROUND This study aimed to investigate the alterations in biochemical and physiological responses of oat plants exposed to antimony (Sb) contamination in soil. Specifically, we evaluated the effectiveness of an arbuscular mycorrhizal fungus (AMF) and olive mill waste (OMW) in mitigating the effects of Sb contamination. The soil was treated with a commercial strain of AMF (Rhizophagus irregularis) and OMW (4% w/w) under two different levels of Sb (0 and 1500 mg kg-1 soil). RESULTS The combined treatment (OMW + AMF) enhanced the photosynthetic rate (+ 40%) and chlorophyll a (+ 91%) and chlorophyll b (+ 50%) content under Sb condition, which in turn induced more biomass production (+ 67-78%) compared to the contaminated control plants. More photosynthesis in OMW + AMF-treated plants gives a route for phenylalanine amino acid synthesis (+ 69%), which is used as a precursor for the biosynthesis of secondary metabolites, including flavonoids (+ 110%), polyphenols (+ 26%), and anthocyanins (+ 63%) compared to control plants. More activation of phenylalanine ammonia-lyase (+ 38%) and chalcone synthase (+ 26%) enzymes in OMW + AMF-treated plants under Sb stress indicated the activation of phenylpropanoid pathways in antioxidant metabolites biosynthesis. There was also improved shifting of antioxidant enzyme activities in the ASC/GSH and catalytic pathways in plants in response to OMW + AMF and Sb contamination, remarkably reducing oxidative damage markers. CONCLUSIONS While individual applications of OMW and AMF also demonstrated some degree of plant tolerance induction, the combined presence of AMF with OMW supplementation significantly enhanced plant biomass production and adaptability to oxidative stress induced by soil Sb contamination.
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Affiliation(s)
- Mha Albqmi
- Department of Chemistry, College of Science, Jouf University, Sakaka, 72341, Saudi Arabia.
- Olive Research Center, Jouf University, Sakaka, Saudi Arabia.
| | - Samy Selim
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Sakaka, 72341, Saudi Arabia.
| | - Nahla Alsayd Bouqellah
- Science College, Biology Department, Taibah University, Almadina, Almunawwarah, 42317-8599, Saudi Arabia
| | - Taghreed S Alnusaire
- Department of Biology, College of Science, Jouf University, Sakaka, 72341, Saudi Arabia
| | - Mohammed S Almuhayawi
- Department of Clinical Microbiology and Immunology, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Soad K Al Jaouni
- Department of Hematology/Oncology, Yousef Abdulatif Jameel Scientific Chair of Prophetic Medicine Application, Faculty of Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Shaimaa Hussein
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka, Saudi Arabia
| | - Mona Warrad
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Jouf University, Al Qurayyat, Saudi Arabia
| | - Mohammad M Al-Sanea
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, 72341, Sakaka, Saudi Arabia
| | - Mohamed A Abdelgawad
- Department of Pharmaceutical Chemistry, College of Pharmacy, Jouf University, 72341, Sakaka, Saudi Arabia
| | - Ehab M Mostafa
- Department of Pharmacognosy, College of Pharmacy, Jouf University, 72341, Sakaka, Saudi Arabia
| | - Mohammad Aldilami
- Science College, Biology Department, Taibah University, Almadina, Almunawwarah, 42317-8599, Saudi Arabia
| | - Enas S Ahmed
- Biology Department, College of Sciences, Majmaah University, 11952, Zulfi, Saudi Arabia
- Botany and Microbiology Department, Faculty of Sciences, Beni Suef University, Beni Suef, Egypt
| | - Hamada AbdElgawad
- Botany and Microbiology Department, Faculty of Sciences, Beni Suef University, Beni Suef, Egypt
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6
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Dixon RA, Dickinson AJ. A century of studying plant secondary metabolism-From "what?" to "where, how, and why?". PLANT PHYSIOLOGY 2024; 195:48-66. [PMID: 38163637 PMCID: PMC11060662 DOI: 10.1093/plphys/kiad596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 08/15/2023] [Indexed: 01/03/2024]
Abstract
Over the past century, early advances in understanding the identity of the chemicals that collectively form a living plant have led scientists to deeper investigations exploring where these molecules localize, how they are made, and why they are synthesized in the first place. Many small molecules are specific to the plant kingdom and have been termed plant secondary metabolites, despite the fact that they can play primary and essential roles in plant structure, development, and response to the environment. The past 100 yr have witnessed elucidation of the structure, function, localization, and biosynthesis of selected plant secondary metabolites. Nevertheless, many mysteries remain about the vast diversity of chemicals produced by plants and their roles in plant biology. From early work characterizing unpurified plant extracts, to modern integration of 'omics technology to discover genes in metabolite biosynthesis and perception, research in plant (bio)chemistry has produced knowledge with substantial benefits for society, including human medicine and agricultural biotechnology. Here, we review the history of this work and offer suggestions for future areas of exploration. We also highlight some of the recently developed technologies that are leading to ongoing research advances.
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Affiliation(s)
- Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA
| | - Alexandra Jazz Dickinson
- Department of Cell and Developmental Biology, University of California at San Diego, La Jolla, CA 92093, USA
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7
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Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? FRONTIERS IN PLANT SCIENCE 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
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Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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8
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Yao L, Wu X, Jiang X, Shan M, Zhang Z, Li Y, Yang A, Li Y, Yang C. Subcellular compartmentalization in the biosynthesis and engineering of plant natural products. Biotechnol Adv 2023; 69:108258. [PMID: 37722606 DOI: 10.1016/j.biotechadv.2023.108258] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/07/2023] [Accepted: 09/11/2023] [Indexed: 09/20/2023]
Abstract
Plant natural products (PNPs) are specialized metabolites with diverse bioactivities. They are extensively used in the pharmaceutical, cosmeceutical and food industries. PNPs are synthesized in plant cells by enzymes that are distributed in different subcellular compartments with unique microenvironments, such as ions, co-factors and substrates. Plant metabolic engineering is an emerging and promising approach for the sustainable production of PNPs, for which the knowledge of the subcellular compartmentalization of their biosynthesis is instrumental. In this review we describe the state of the art on the role of subcellular compartments in the biosynthesis of major types of PNPs, including terpenoids, phenylpropanoids, alkaloids and glucosinolates, and highlight the efforts to target biosynthetic pathways to subcellular compartments in plants. In addition, we will discuss the challenges and strategies in the field of plant synthetic biology and subcellular engineering. We expect that newly developed methods and tools, together with the knowledge gained from the microbial chassis, will greatly advance plant metabolic engineering.
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Affiliation(s)
- Lu Yao
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xiuming Wu
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Xun Jiang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Zhuoxiang Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yiting Li
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Aiguo Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China
| | - Yu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Changqing Yang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, Shandong 266100, China.
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9
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Solis-Miranda J, Chodasiewicz M, Skirycz A, Fernie AR, Moschou PN, Bozhkov PV, Gutierrez-Beltran E. Stress-related biomolecular condensates in plants. THE PLANT CELL 2023; 35:3187-3204. [PMID: 37162152 PMCID: PMC10473214 DOI: 10.1093/plcell/koad127] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 04/07/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023]
Abstract
Biomolecular condensates are membraneless organelle-like structures that can concentrate molecules and often form through liquid-liquid phase separation. Biomolecular condensate assembly is tightly regulated by developmental and environmental cues. Although research on biomolecular condensates has intensified in the past 10 years, our current understanding of the molecular mechanisms and components underlying their formation remains in its infancy, especially in plants. However, recent studies have shown that the formation of biomolecular condensates may be central to plant acclimation to stress conditions. Here, we describe the mechanism, regulation, and properties of stress-related condensates in plants, focusing on stress granules and processing bodies, 2 of the most well-characterized biomolecular condensates. In this regard, we showcase the proteomes of stress granules and processing bodies in an attempt to suggest methods for elucidating the composition and function of biomolecular condensates. Finally, we discuss how biomolecular condensates modulate stress responses and how they might be used as targets for biotechnological efforts to improve stress tolerance.
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Affiliation(s)
- Jorge Solis-Miranda
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
| | - Monika Chodasiewicz
- Biological and Environmental Science and Engineering Division, Center for Desert Agriculture, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Panagiotis N Moschou
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
- Department of Biology, University of Crete, Heraklion 71409, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Heraklion 70013, Greece
| | - Peter V Bozhkov
- Department of Molecular Sciences, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, 75007 Uppsala, Sweden
| | - Emilio Gutierrez-Beltran
- Institutode Bioquimica Vegetal y Fotosintesis, Consejo Superior de Investigaciones Cientificas (CSIC)-Universidad de Sevilla, 41092 Sevilla, Spain
- Departamento de Bioquimica Vegetal y Biologia Molecular, Facultad de Biologia, Universidad de Sevilla, 41012 Sevilla, Spain
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10
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Dahmani I, Qin K, Zhang Y, Fernie AR. The formation and function of plant metabolons. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 114:1080-1092. [PMID: 36906885 DOI: 10.1111/tpj.16179] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/26/2023] [Accepted: 03/06/2023] [Indexed: 05/31/2023]
Abstract
Metabolons are temporary structural-functional complexes of sequential enzymes of a metabolic pathway that are distinct from stable multi-enzyme complexes. Here we provide a brief history of the study of enzyme-enzyme assemblies with a particular focus on those that mediate substrate channeling in plants. Large numbers of protein complexes have been proposed for both primary and secondary metabolic pathways in plants. However, to date only four substrate channels have been demonstrated. We provide an overview of current knowledge concerning these four metabolons and explain the methodologies that are currently being applied to unravel their functions. Although the assembly of metabolons has been documented to arise through diverse mechanisms, the physical interaction within the characterized plant metabolons all appear to be driven by interaction with structural elements of the cell. We therefore pose the question as to what methodologies could be brought to bear to enhance our knowledge of plant metabolons that assemble via different mechanisms? In addressing this question, we review recent findings in non-plant systems concerning liquid droplet phase separation and enzyme chemotaxis and propose strategies via which such metabolons could be identified in plants. We additionally discuss the possibilities that could be opened up by novel approaches based on: (i) subcellular-level mass spectral imaging, (ii) proteomics, and (iii) emergent methods in structural and computational biology.
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Affiliation(s)
- Ismail Dahmani
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Kezhen Qin
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Youjun Zhang
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant System Biology and Biotechnology, 4000, Plovdiv, Bulgaria
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11
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Yu K, Song Y, Lin J, Dixon RA. The complexities of proanthocyanidin biosynthesis and its regulation in plants. PLANT COMMUNICATIONS 2023; 4:100498. [PMID: 36435967 PMCID: PMC10030370 DOI: 10.1016/j.xplc.2022.100498] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/07/2022] [Accepted: 11/23/2022] [Indexed: 05/04/2023]
Abstract
Proanthocyanidins (PAs) are natural flavan-3-ol polymers that contribute protection to plants under biotic and abiotic stress, benefits to human health, and bitterness and astringency to food products. They are also potential targets for carbon sequestration for climate mitigation. In recent years, from model species to commercial crops, research has moved closer to elucidating the flux control and channeling, subunit biosynthesis and polymerization, transport mechanisms, and regulatory networks involved in plant PA metabolism. This review extends the conventional understanding with recent findings that provide new insights to address lingering questions and focus strategies for manipulating PA traits in plants.
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Affiliation(s)
- Keji Yu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China
| | - Yushuang Song
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Jinxing Lin
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing 100083, China; College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
| | - Richard A Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203, USA; Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, China.
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12
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Li X, Liao M, Huang J, Chen L, Huang H, Wu K, Pan Q, Zhang Z, Peng X. Dynamic and fluctuating generation of hydrogen peroxide via photorespiratory metabolic channeling in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1429-1446. [PMID: 36382906 DOI: 10.1111/tpj.16022] [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: 05/17/2022] [Revised: 11/02/2022] [Accepted: 11/05/2022] [Indexed: 06/16/2023]
Abstract
The homeostasis of hydrogen peroxide (H2 O2 ), a key regulator of basic biological processes, is a result of the cooperation between its generation and scavenging. However, the mechanistic basis of this balance is not fully understood. We previously proposed that the interaction between glycolate oxidase (GLO) and catalase (CAT) may serve as a molecular switch that modulates H2 O2 levels in plants. In this study, we demonstrate that the GLO-CAT complex in plants exists in different states, which are dynamically interchangeable in response to various stimuli, typically salicylic acid (SA), at the whole-plant level. More crucially, changes in the state of the complex were found to be closely linked to peroxisomal H2 O2 fluctuations, which were independent of the membrane-associated NADPH oxidase. Furthermore, evidence suggested that H2 O2 channeling occurred even in vitro when GLO and CAT worked cooperatively. These results demonstrate that dynamic changes in H2 O2 levels are physically created via photorespiratory metabolic channeling in plants, and that such H2 O2 fluctuations may serve as signals that are mechanistically involved in the known functions of photorespiratory H2 O2 . In addition, our study also revealed a new way for SA to communicate with H2 O2 in plants.
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Affiliation(s)
- Xiangyang Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Mengmeng Liao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Jiayu Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Linru Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Haiyin Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
| | - Kaixin Wu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Qing Pan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Zhisheng Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
| | - Xinxiang Peng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, China
- Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, South China Agricultural University, Guangzhou, China
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13
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Wiles D, Shanbhag BK, O'Brien M, Doblin MS, Bacic A, Beddoe T. Heterologous production of Cannabis sativa-derived specialised metabolites of medicinal significance - Insights into engineering strategies. PHYTOCHEMISTRY 2022; 203:113380. [PMID: 36049526 DOI: 10.1016/j.phytochem.2022.113380] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 08/08/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Cannabis sativa L. has been known for at least 2000 years as a source of important, medically significant specialised metabolites and several bio-active molecules have been enriched from multiple chemotypes. However, due to the many levels of complexity in both the commercial cultivation of cannabis and extraction of its specialised metabolites, several heterologous production approaches are being pursued in parallel. In this review, we outline the recent achievements in engineering strategies used for heterologous production of cannabinoids, terpenes and flavonoids along with their strength and weakness. We provide an overview of the specialised metabolism pathway in C. sativa and a comprehensive list of the specialised metabolites produced along with their medicinal significance. We highlight cannabinoid-like molecules produced by other species. We discuss the key biosynthetic enzymes and their heterologous production using various hosts such as microbial and eukaryotic systems. A brief discussion on complementary production strategies using co-culturing and cell-free systems is described. Various approaches to optimise specialised metabolite production through co-expression, enzyme engineering and pathway engineering are discussed. We derive insights from recent advances in metabolic engineering of hosts with improved precursor supply and suggest their application for the production of C. sativa speciality metabolites. We present a collation of non-conventional hosts with speciality traits that can improve the feasibility of commercial heterologous production of cannabis-based specialised metabolites. We provide a perspective of emerging research in synthetic biology, allied analytical techniques and plant heterologous platforms as focus areas for heterologous production of cannabis specialised metabolites in the future.
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Affiliation(s)
- Danielle Wiles
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Bhuvana K Shanbhag
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Martin O'Brien
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia
| | - Monika S Doblin
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Antony Bacic
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia; La Trobe Institute for Agriculture & Food, Department of Animal, Plant and Soil Science, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, Australia
| | - Travis Beddoe
- Department of Animal, Plant and Soil Sciences and AgriBio Centre for AgriBioscience, School of Agriculture, Biomedicine and Environment, La Trobe University, Bundoora, Victoria, 3083, Australia; Australian Research Council Research Hub for Medicinal Agriculture, AgriBio Centre for AgriBioscience, La Trobe University, Bundoora, VIC, 3086, Australia.
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14
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Yu K, Dixon RA, Duan C. A role for ascorbate conjugates of (+)-catechin in proanthocyanidin polymerization. Nat Commun 2022; 13:3425. [PMID: 35701431 PMCID: PMC9197940 DOI: 10.1038/s41467-022-31153-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 06/06/2022] [Indexed: 02/07/2023] Open
Abstract
Proanthocyanidins (PAs) are natural polymers of flavan-3-ols, commonly (+)-catechin and (-)-epicatechin. However, exactly how PA oligomerization proceeds is poorly understood. Here we show, both biochemically and genetically, that ascorbate (AsA) is an alternative "starter unit" to flavan-3-ol monomers for leucocyanidin-derived (+)-catechin subunit extension in the Arabidopsis thaliana anthocyanidin synthase (ans) mutant. These (catechin)n:ascorbate conjugates (AsA-[C]n) also accumulate throughout the phase of active PA biosynthesis in wild-type grape flowers, berry skins and seeds. In the presence of (-)-epicatechin, AsA-[C]n can further provide monomeric or oligomeric PA extension units for non-enzymatic polymerization in vitro, and their role in vivo is inferred from analysis of relative metabolite levels in both Arabidopsis and grape. Our findings advance the knowledge of (+)-catechin-type PA extension and indicate that PA oligomerization does not necessarily proceed by sequential addition of a single extension unit. AsA-[C]n defines a new type of PA intermediate which we term "sub-PAs".
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Affiliation(s)
- Keji Yu
- grid.22935.3f0000 0004 0530 8290Center for Viticulture and Enology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
| | - Richard A. Dixon
- grid.266869.50000 0001 1008 957XBioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton, TX 76203 USA
| | - Changqing Duan
- grid.22935.3f0000 0004 0530 8290Center for Viticulture and Enology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083 China ,grid.418524.e0000 0004 0369 6250Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing, 100083 China
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15
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Hildreth SB, Littleton ES, Clark LC, Puller GC, Kojima S, Winkel BSJ. Mutations that alter Arabidopsis flavonoid metabolism affect the circadian clock. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:932-945. [PMID: 35218268 PMCID: PMC9311810 DOI: 10.1111/tpj.15718] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/10/2022] [Accepted: 02/21/2022] [Indexed: 05/05/2023]
Abstract
Flavonoids are a well-known class of specialized metabolites that play key roles in plant development, reproduction, and survival. Flavonoids are also of considerable interest from the perspective of human health, as both phytonutrients and pharmaceuticals. RNA sequencing analysis of an Arabidopsis null allele for chalcone synthase (CHS), which catalyzes the first step in flavonoid metabolism, has uncovered evidence that these compounds influence the expression of genes associated with the plant circadian clock. Analysis of promoter-luciferase constructs further showed that the transcriptional activity of CCA1 and TOC1, two key clock genes, is altered in CHS-deficient seedlings across the day/night cycle. Similar findings for a mutant line lacking flavonoid 3'-hydroxylase (F3'H) activity, and thus able to synthesize mono- but not dihydroxylated B-ring flavonoids, suggests that the latter are at least partially responsible; this was further supported by the ability of quercetin to enhance CCA1 promoter activity in wild-type and CHS-deficient seedlings. The effects of flavonoids on circadian function were also reflected in photosynthetic activity, with chlorophyll cycling abolished in CHS- and F3'H-deficient plants. Remarkably, the same phenotype was exhibited by plants with artificially high flavonoid levels, indicating that neither the antioxidant potential nor the light-screening properties of flavonoids contribute to optimal clock function, as has recently also been demonstrated in animal systems. Collectively, the current experiments point to a previously unknown connection between flavonoids and circadian cycling in plants and open the way to better understanding of the molecular basis of flavonoid action.
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Affiliation(s)
- Sherry B. Hildreth
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVA24061USA
| | - Evan S. Littleton
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVA24061USA
| | - Leor C. Clark
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Present address:
Department of Global Health, Milken Institute School of Public HealthGeorge Washington UniversityWashingtonDC20052USA
| | - Gabrielle C. Puller
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Present address:
Laboratory of Molecular BiologyNational Cancer InstituteNational Institutes of HealthBethesdaMD20 892USA
| | - Shihoko Kojima
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVA24061USA
| | - Brenda S. J. Winkel
- Department of Biological SciencesVirginia TechBlacksburgVA24061USA
- Fralin Life Sciences InstituteVirginia TechBlacksburgVA24061USA
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16
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Lin CY, Sun Y, Song J, Chen HC, Shi R, Yang C, Liu J, Tunlaya-Anukit S, Liu B, Loziuk PL, Williams CM, Muddiman DC, Lin YCJ, Sederoff RR, Wang JP, Chiang VL. Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa. FRONTIERS IN PLANT SCIENCE 2021; 12:727932. [PMID: 34691108 PMCID: PMC8527181 DOI: 10.3389/fpls.2021.727932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. In Populus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation of PtrHCTs reduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenic P. trichocarpa. The Ptr4CL/PtrHCT interactions were then validated in vivo using biomolecular fluorescence complementation (BiFC) and protein pull-down assays in P. trichocarpa SDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
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Affiliation(s)
- Chien-Yuan Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Jina Song
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - Hsi-Chuan Chen
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Rui Shi
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Chenmin Yang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jie Liu
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Sermsawat Tunlaya-Anukit
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Baoguang Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- Department of Forestry, Beihua University, Jilin, China
| | - Philip L. Loziuk
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Cranos M. Williams
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, United States
| | - David C. Muddiman
- W.M. Keck FTMS Laboratory, Department of Chemistry, North Carolina State University, Raleigh, NC, United States
| | - Ying-Chung Jimmy Lin
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Jack P. Wang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Vincent L. Chiang
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
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17
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Zhang Y, Fernie AR. Metabolons, enzyme-enzyme assemblies that mediate substrate channeling, and their roles in plant metabolism. PLANT COMMUNICATIONS 2021; 2:100081. [PMID: 33511342 PMCID: PMC7816073 DOI: 10.1016/j.xplc.2020.100081] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 05/05/2023]
Abstract
Metabolons are transient multi-protein complexes of sequential enzymes that mediate substrate channeling. They differ from multi-enzyme complexes in that they are dynamic, rather than permanent, and as such have considerably lower dissociation constants. Despite the fact that a huge number of metabolons have been suggested to exist in plants, most of these claims are erroneous as only a handful of these have been proven to channel metabolites. We believe that physical protein-protein interactions between consecutive enzymes of a pathway should rather be called enzyme-enzyme assemblies. In this review, we describe how metabolons are generally assembled by transient interactions and held together by both structural elements and non-covalent interactions. Experimental evidence for their existence comes from protein-protein interaction studies, which indicate that the enzymes physically interact, and direct substrate channeling measurements, which indicate that they functionally interact. Unfortunately, advances in cell biology and proteomics have far outstripped those in classical enzymology and flux measurements, rendering most reports reliant purely on interactome studies. Recent developments in co-fractionation mass spectrometry will likely further exacerbate this bias. Given this, only dynamic enzyme-enzyme assemblies in which both physical and functional interactions have been demonstrated should be termed metabolons. We discuss the level of evidence for the manifold plant pathways that have been postulated to contain metabolons and then list examples in both primary and secondary metabolism for which strong evidence has been provided to support these claims. In doing so, we pay particular attention to experimental and mathematical approaches to study metabolons as well as complexities that arise in attempting to follow them. Finally, we discuss perspectives for improving our understanding of these fascinating but enigmatic interactions.
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Affiliation(s)
- Youjun Zhang
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
| | - Alisdair R. Fernie
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
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18
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Zhang Y, Sampathkumar A, Kerber SML, Swart C, Hille C, Seerangan K, Graf A, Sweetlove L, Fernie AR. A moonlighting role for enzymes of glycolysis in the co-localization of mitochondria and chloroplasts. Nat Commun 2020; 11:4509. [PMID: 32908151 PMCID: PMC7481185 DOI: 10.1038/s41467-020-18234-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 08/11/2020] [Indexed: 12/15/2022] Open
Abstract
Glycolysis is one of the primordial pathways of metabolism, playing a pivotal role in energy metabolism and biosynthesis. Glycolytic enzymes are known to form transient multi-enzyme assemblies. Here we examine the wider protein-protein interactions of plant glycolytic enzymes and reveal a moonlighting role for specific glycolytic enzymes in mediating the co-localization of mitochondria and chloroplasts. Knockout mutation of phosphoglycerate mutase or enolase resulted in a significantly reduced association of the two organelles. We provide evidence that phosphoglycerate mutase and enolase form a substrate-channelling metabolon which is part of a larger complex of proteins including pyruvate kinase. These results alongside a range of genetic complementation experiments are discussed in the context of our current understanding of chloroplast-mitochondrial interactions within photosynthetic eukaryotes.
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Affiliation(s)
- Youjun Zhang
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
| | - Arun Sampathkumar
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sandra Mae-Lin Kerber
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Corné Swart
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Carsten Hille
- Department of Physical Chemistry, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476, Potsdam-Golm, Germany
- Technical University of Applied Sciences Wildau, Hochschulring 1, 15745, Wildau, Germany
| | - Kumar Seerangan
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Alexander Graf
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Lee Sweetlove
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Alisdair R Fernie
- Max-Planck-Institut für Molekulare Pflanzenphysiologie, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
- Center of Plant Systems Biology and Biotechnology, 4000, Plovdiv, Bulgaria.
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19
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García-Calderón M, Pérez-Delgado CM, Palove-Balang P, Betti M, Márquez AJ. Flavonoids and Isoflavonoids Biosynthesis in the Model Legume Lotus japonicus; Connections to Nitrogen Metabolism and Photorespiration. PLANTS 2020; 9:plants9060774. [PMID: 32575698 PMCID: PMC7357106 DOI: 10.3390/plants9060774] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
Phenylpropanoid metabolism represents an important metabolic pathway from which originates a wide number of secondary metabolites derived from phenylalanine or tyrosine, such as flavonoids and isoflavonoids, crucial molecules in plants implicated in a large number of biological processes. Therefore, various types of interconnection exist between different aspects of nitrogen metabolism and the biosynthesis of these compounds. For legumes, flavonoids and isoflavonoids are postulated to play pivotal roles in adaptation to their biological environments, both as defensive compounds (phytoalexins) and as chemical signals in symbiotic nitrogen fixation with rhizobia. In this paper, we summarize the recent progress made in the characterization of flavonoid and isoflavonoid biosynthetic pathways in the model legume Lotus japonicus (Regel) Larsen under different abiotic stress situations, such as drought, the impairment of photorespiration and UV-B irradiation. Emphasis is placed on results obtained using photorespiratory mutants deficient in glutamine synthetase. The results provide different types of evidence showing that an enhancement of isoflavonoid compared to standard flavonol metabolism frequently occurs in Lotus under abiotic stress conditions. The advance produced in the analysis of isoflavonoid regulatory proteins by the use of co-expression networks, particularly MYB transcription factors, is also described. The results obtained in Lotus japonicus plants can be also extrapolated to other cultivated legume species, such as soybean, of extraordinary agronomic importance with a high impact in feeding, oil production and human health.
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Affiliation(s)
- Margarita García-Calderón
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Carmen M. Pérez-Delgado
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Peter Palove-Balang
- Institute of Biology and Ecology, Faculty of Science, P.J. Šafárik University in Košice, Mánesova 23, SK-04001 Košice, Slovakia;
| | - Marco Betti
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
| | - Antonio J. Márquez
- Departamento de Bioquímica Vegetal y Biología Molecular, Facultad de Química, Universidad de Sevilla, Calle Profesor García González, 1, 41012-Sevilla, Spain; (M.G.-C.); (C.M.P.-D.); (M.B.)
- Correspondence: ; Tel.: +34-954557145
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20
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Gomez-Cano L, Gomez-Cano F, Dillon FM, Alers-Velazquez R, Doseff AI, Grotewold E, Gray J. Discovery of modules involved in the biosynthesis and regulation of maize phenolic compounds. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 291:110364. [PMID: 31928683 DOI: 10.1016/j.plantsci.2019.110364] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 11/25/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Phenolic compounds are among the most diverse and widespread of specialized plant compounds and underly many important agronomic traits. Our comprehensive analysis of the maize genome unraveled new aspects of the genes involved in phenylpropanoid, monolignol, and flavonoid production in this important crop. Remarkably, just 19 genes accounted for 70 % of the overall mRNA accumulation of these genes across 95 tissues, indicating that these are the main contributors to the flux of phenolic metabolites. Eighty genes with intermediate to low expression play minor and more specialized roles. Remaining genes are likely undergoing loss of function or are expressed in limited cell types. Phylogenetic and expression analyses revealed which members of gene families governing metabolic entry and branch points exhibit duplication, subfunctionalization, or loss of function. Co-expression analysis applied to genes in sequential biosynthetic steps revealed that certain isoforms are highly co-expressed and are candidates for metabolic complexes that ensure metabolite delivery to correct cellular compartments. Co-expression of biosynthesis genes with transcription factors discovered connections that provided candidate components for regulatory modules governing this pathway. Our study provides a comprehensive analysis of maize phenylpropanoid related genes, identifies major pathway contributors, and novel candidate enzymatic and regulatory modules of the metabolic network.
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Affiliation(s)
- Lina Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Fabio Gomez-Cano
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - Francisco M Dillon
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - Andrea I Doseff
- Department of Physiology, Department of Pharmacology and Toxicology, Michigan State University, East Lansing, MI, 48824, USA
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, USA
| | - John Gray
- Department of Biological Sciences, University of Toledo, Toledo, OH, 43606, USA.
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21
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Abstract
Protein-protein interactions (PPI) are essential for a plethora of biological processes. These interactions can be visualized and quantified with spatial resolution using Förster resonance energy transfer (FRET) measured by fluorescence lifetime imaging microscopy (FLIM) technology. Currently, FRET-FLIM is routinely used in cell biology, and it has become a powerful tool to map protein interactions in native environments. However, implementing this technology in living multicellular organism remains challenging, especially when dealing with developing plant embryos where tissues are confined in multiple cell layers preventing direct imaging. In this chapter, we describe a step-by-step protocol for studying PPI using FRET-FLIM of the two transcription factors SCARECROW and SHORTROOT in Arabidopsis embryos. We provide a detailed description from embryo isolation to data analysis and representation.
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22
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Ni R, Zhu TT, Zhang XS, Wang PY, Sun CJ, Qiao YN, Lou HX, Cheng AX. Identification and evolutionary analysis of chalcone isomerase-fold proteins in ferns. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:290-304. [PMID: 31557291 PMCID: PMC6913697 DOI: 10.1093/jxb/erz425] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 09/12/2019] [Indexed: 05/07/2023]
Abstract
The distribution of type I and II chalcone isomerases (CHIs) in plants is highly family specific. We have previously reported that ancient land plants, such as the liverworts and Selaginella moellendorffii, harbor type II CHIs. To better understand the function and evolution of CHI-fold proteins, transcriptomic data obtained from 52 pteridophyte species were subjected to sequence alignment and phylogenetic analysis. The residues determining type I/II CHI identity in the pteridophyte CHIs were identical to those of type I CHIs. The enzymatic characterization of a sample of 24 CHIs, representing all the key pteridophyte lineages, demonstrated that 19 of them were type I enzymes and that five exhibited some type II activity due to an amino acid mutation. Two pteridophyte chalcone synthases (CHSs) were also characterized, and a type IV CHI (CHIL) was demonstrated to interact physically with CHSs and CHI, and to increase CHS activity by decreasing derailment products, thus enhancing flavonoid production. These findings suggest that the emergence of type I CHIs may have coincided with the divergence of the pteridophytes. This study deepens our understanding of the molecular mechanism of CHIL as an enhancer in the flavonoid biosynthesis pathway.
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Affiliation(s)
- Rong Ni
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ting-Ting Zhu
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Xiao-Shuang Zhang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Piao-Yi Wang
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Chun-Jing Sun
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ya-Nan Qiao
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Hong-Xiang Lou
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
| | - Ai-Xia Cheng
- Key Laboratory of Chemical Biology of Natural Products, Ministry of Education, School of Pharmaceutical Sciences, Shandong University, Jinan, China
- Correspondence:
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23
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Teunissen AJP, Paffen TFE, Filot IAW, Lanting MD, van der Haas RJC, de Greef TFA, Meijer EW. Supramolecular interactions between catalytic species allow rational control over reaction kinetics. Chem Sci 2019; 10:9115-9124. [PMID: 31827754 PMCID: PMC6889839 DOI: 10.1039/c9sc02357g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 11/21/2022] Open
Abstract
The adaptivity of biological reaction networks largely arises through non-covalent regulation of catalysts' activity. Such type of catalyst control is still nascent in synthetic chemical networks and thereby hampers their ability to display life-like behavior. Here, we report a bio-inspired system in which non-covalent interactions between two complementary phase-transfer catalysts are used to regulate reaction kinetics. While one catalyst gives bimolecular kinetics, the second displays autoinductive feedback, resulting in sigmoidal kinetics. When both catalysts are combined, the interactions between them allow rational control over the shape of the kinetic curves. Computational models are used to gain insight into the structure, interplay, and activity of each catalytic species, and the scope of the system is examined by optimizing the linearity of the kinetic curves. Combined, our findings highlight the effectiveness of regulating reaction kinetics using non-covalent catalyst interactions, but also emphasize the risk for unforeseen catalytic contributions in complex systems and the necessity to combine detailed experiments with kinetic modelling.
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Affiliation(s)
- Abraham J P Teunissen
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Laboratory of Macromolecular and Organic Chemistry , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Tim F E Paffen
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Laboratory of Macromolecular and Organic Chemistry , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Ivo A W Filot
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Schuit Institute for Catalysis , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Menno D Lanting
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Laboratory of Macromolecular and Organic Chemistry , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Roy J C van der Haas
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Laboratory of Macromolecular and Organic Chemistry , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - Tom F A de Greef
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Computational Biology , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
| | - E W Meijer
- Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands . ; .,Laboratory of Macromolecular and Organic Chemistry , Eindhoven University of Technology , P.O. Box 513 , 5600 MB Eindhoven , The Netherlands
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24
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Burke JR, La Clair JJ, Philippe RN, Pabis A, Corbella M, Jez JM, Cortina GA, Kaltenbach M, Bowman ME, Louie GV, Woods KB, Nelson AT, Tawfik DS, Kamerlin SC, Noel JP. Bifunctional Substrate Activation via an Arginine Residue Drives Catalysis in Chalcone Isomerases. ACS Catal 2019. [DOI: 10.1021/acscatal.9b01926] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Jason R. Burke
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - James J. La Clair
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Ryan N. Philippe
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Anna Pabis
- Department of Cell and Molecular Biology, Uppsala University, BMC Box 596, S-751 24 Uppsala, Sweden
| | - Marina Corbella
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph M. Jez
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - George A. Cortina
- Department of Molecular Physiology and Biomedical Engineering, University of Virginia, Charlottesville, Virginia 22903, United States
| | - Miriam Kaltenbach
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Marianne E. Bowman
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Gordon V. Louie
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Katherine B. Woods
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
| | - Andrew T. Nelson
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Dan S. Tawfik
- Department of Biomolecular Sciences, The Weizmann Institute of Science, Rehovot 76100, Israel
| | - Shina C.L. Kamerlin
- Department of Chemistry−BMC, Uppsala University, BMC Box 576, S-751 23 Uppsala, Sweden
| | - Joseph P. Noel
- Howard Hughes Medical Institute, Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, United States
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25
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Solopova A, van Tilburg AY, Foito A, Allwood JW, Stewart D, Kulakauskas S, Kuipers OP. Engineering Lactococcus lactis for the production of unusual anthocyanins using tea as substrate. Metab Eng 2019; 54:160-169. [PMID: 30978503 DOI: 10.1016/j.ymben.2019.04.002] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 11/30/2022]
Abstract
Plant material rich in anthocyanins has been historically used in traditional medicines, but only recently have the specific pharmacological properties of these compounds been the target of extensive studies. In addition to their potential to modulate the development of various diseases, coloured anthocyanins are valuable natural alternatives commonly used to replace synthetic colourants in food industry. Exploitation of microbial hosts as cell factories is an attractive alternative to extraction of anthocyanins and other flavonoids from plant sources or chemical synthesis. In this study, we present the lactic acid bacterium Lactococcus lactis as an ideal host for the production of high-value plant-derived bioactive anthocyanins using green tea as substrate. Besides the anticipated red-purple compounds cyanidin and delphinidin, orange and yellow pyranoanthocyanidins with unexpected methylation patterns were produced from green tea by engineered L. lactis strains. The pyranoanthocyanins are currently attracting significant interest as one of the most important classes of anthocyanin derivatives and are mainly formed during the aging of wine, contributing to both colour and sensory experience.
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Affiliation(s)
- Ana Solopova
- Molecular Genetics, University of Groningen, Groningen, Netherlands.
| | | | - Alexandre Foito
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Dundee, UK.
| | - J William Allwood
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Dundee, UK.
| | - Derek Stewart
- Environmental and Biochemical Sciences Group, The James Hutton Institute, Dundee, UK; School of Engineering and Physical Sciences, Institute of Mechanical, Process and Energy Engineering, Heriot-Watt University, Edinburgh, UK.
| | - Saulius Kulakauskas
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France.
| | - Oscar P Kuipers
- Molecular Genetics, University of Groningen, Groningen, Netherlands.
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26
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Eichenberger M, Hansson A, Fischer D, Dürr L, Naesby M. De novo biosynthesis of anthocyanins in Saccharomyces cerevisiae. FEMS Yeast Res 2019; 18:4975775. [PMID: 29771352 DOI: 10.1093/femsyr/foy046] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 04/16/2018] [Indexed: 12/19/2022] Open
Abstract
Anthocyanins (ACNs) are plant secondary metabolites responsible for most of the red, purple and blue colors of flowers, fruits and vegetables. They are increasingly used in the food and beverage industry as natural alternative to artificial colorants. Production of these compounds by fermentation of microorganisms would provide an attractive alternative. In this study, Saccharomyces cerevisiae was engineered for de novo production of the three basic anthocyanins, as well as the three main trans-flavan-3-ols. Enzymes from different plant sources were screened and efficient variants found for most steps of the biosynthetic pathway. However, the anthocyanidin synthase was identified as a major obstacle to efficient production. In yeast, this enzyme converts the majority of its natural substrates leucoanthocyanidins into the off-pathway flavonols. Nonetheless, de novo biosynthesis of ACNs was shown for the first time in yeast and for the first time in a single microorganism. It provides a framework for optimizing the activity of anthocyanidin synthase and represents an important step towards sustainable industrial production of these highly relevant molecules in yeast.
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Affiliation(s)
- Michael Eichenberger
- Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland.,Department of Biology, Technical University Darmstadt, Schnittspahnstrasse 10, 64287 Darmstadt, Germany
| | - Anders Hansson
- Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
| | - David Fischer
- Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
| | - Lara Dürr
- Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
| | - Michael Naesby
- Evolva SA, Duggingerstrasse 23, 4153 Reinach, Switzerland
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27
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Schäfer P, Helm S, Köhler D, Agne B, Baginsky S. Consequences of impaired 1-MDa TIC complex assembly for the abundance and composition of chloroplast high-molecular mass protein complexes. PLoS One 2019; 14:e0213364. [PMID: 30865669 PMCID: PMC6415892 DOI: 10.1371/journal.pone.0213364] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 02/20/2019] [Indexed: 12/28/2022] Open
Abstract
We report a systematic analysis of chloroplast high-molecular mass protein complexes using a combination of native gel electrophoresis and absolute protein quantification by MSE. With this experimental setup, we characterized the effect of the tic56-3 mutation in the 1-MDa inner envelope translocase (TIC) on the assembly of the chloroplast proteome. We show that the tic56-3 mutation results in a reduction of the 1-MDa TIC complex to approximately 10% of wildtype levels. Hierarchical clustering confirmed the association of malate dehydrogenase (MDH) with an envelope-associated FtsH/FtsHi complex and suggested the association of a glycine-rich protein with the 1-MDa TIC complex. Depletion of this complex leads to a reduction of chloroplast ATPase to approx. 75% of wildtype levels, while the abundance of the FtsH/FtsHi complex is increased to approx. 140% of wildtype. The accumulation of the major photosynthetic complexes is not affected by the mutation, suggesting that tic56-3 plants can sustain a functional photosynthetic machinery despite a significant reduction of the 1-MDa TIC complex. Together our analysis expands recent efforts to catalogue the native molecular masses of chloroplast proteins and provides information on the consequences of impaired accumulation of the 1-MDa TIC translocase for chloroplast proteome assembly.
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Affiliation(s)
- Peter Schäfer
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Stefan Helm
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Daniel Köhler
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Birgit Agne
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
| | - Sacha Baginsky
- Institute of Biochemistry and Biotechnology, Martin-Luther-University Halle-Wittenberg, Biozentrum, Halle (Saale), Germany
- * E-mail:
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28
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Nakayama T, Takahashi S, Waki T. Formation of Flavonoid Metabolons: Functional Significance of Protein-Protein Interactions and Impact on Flavonoid Chemodiversity. FRONTIERS IN PLANT SCIENCE 2019; 10:821. [PMID: 31338097 PMCID: PMC6629762 DOI: 10.3389/fpls.2019.00821] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Accepted: 06/07/2019] [Indexed: 05/21/2023]
Abstract
Flavonoids are a class of plant specialized metabolites with more than 6,900 known structures and play important roles in plant survival and reproduction. These metabolites are derived from p-coumaroyl-CoA via the sequential actions of a variety of flavonoid enzymes, which have been proposed to form weakly bound, ordered protein complexes termed flavonoid metabolons. This review discusses the impacts of the formation of flavonoid metabolons on the chemodiversity of flavonoids. Specific protein-protein interactions in the metabolons of Arabidopsis thaliana and other plant species have been studied for two decades. In many cases, metabolons are associated with the ER membrane, with ER-bound cytochromes P450 hypothesized to serve as nuclei for metabolon formation. Indeed, cytochromes P450 have been found to be components of flavonoid metabolons in rice, snapdragon, torenia, and soybean. Recent studies illustrate the importance of specific interactions for the efficient production and temporal/spatial distribution of flavonoids. For example, in diverse plant species, catalytically inactive type-IV chalcone isomerase-like protein serves as an enhancer of flavonoid production via its involvement in flavonoid metabolons. In soybean roots, a specific isozyme of chalcone reductase (CHR) interacts with 2-hydroxyisoflavanone synthase, to which chalcone synthase (CHS) can also bind, providing a mechanism to prevent the loss of the unstable CHR substrate during its transfer from CHS to CHR. Thus, diversification in chemical structures and temporal/spatial distribution patterns of flavonoids in plants is likely to be mediated by the formation of specific flavonoid metabolons via specific protein-protein interactions.
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29
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Winkel BSJ. Charting blackwater rivers. NATURE PLANTS 2018; 4:987-988. [PMID: 30478362 DOI: 10.1038/s41477-018-0314-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Brenda S J Winkel
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA.
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30
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Watkinson JI, Bowerman PA, Crosby KC, Hildreth SB, Helm RF, Winkel BSJ. Identification of MOS9 as an interaction partner for chalcone synthase in the nucleus. PeerJ 2018; 6:e5598. [PMID: 30258711 PMCID: PMC6151112 DOI: 10.7717/peerj.5598] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Accepted: 08/17/2018] [Indexed: 01/12/2023] Open
Abstract
Plant flavonoid metabolism has served as a platform for understanding a range of fundamental biological phenomena, including providing some of the early insights into the subcellular organization of metabolism. Evidence assembled over the past three decades points to the organization of the component enzymes as a membrane-associated complex centered on the entry-point enzyme, chalcone synthase (CHS), with flux into branch pathways controlled by competitive protein interactions. Flavonoid enzymes have also been found in the nucleus in a variety of plant species, raising the possibility of alternative, or moonlighting functions for these proteins in this compartment. Here, we present evidence that CHS interacts with MOS9, a nuclear-localized protein that has been linked to epigenetic control of R genes that mediate effector-triggered immunity. Overexpression of MOS9 results in a reduction of CHS transcript levels and a metabolite profile that substantially intersects with the effects of a null mutation in CHS. These results suggest that the MOS9-CHS interaction may point to a previously-unknown mechanism for controlling the expression of the highly dynamic flavonoid pathway.
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Affiliation(s)
- Jonathan I Watkinson
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Peter A Bowerman
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,BASF Plant Science LP, Research Triangle Park, NC, USA
| | - Kevin C Crosby
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO, USA
| | - Sherry B Hildreth
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA.,Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Richard F Helm
- Department of Biochemistry, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
| | - Brenda S J Winkel
- Department of Biological Sciences, Virginia Polytechnic Institute and State University (Virginia Tech), Blacksburg, VA, USA
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31
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Fujino N, Tenma N, Waki T, Ito K, Komatsuzaki Y, Sugiyama K, Yamazaki T, Yoshida S, Hatayama M, Yamashita S, Tanaka Y, Motohashi R, Denessiouk K, Takahashi S, Nakayama T. Physical interactions among flavonoid enzymes in snapdragon and torenia reveal the diversity in the flavonoid metabolon organization of different plant species. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 94:372-392. [PMID: 29421843 DOI: 10.1111/tpj.13864] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 01/04/2018] [Accepted: 01/31/2018] [Indexed: 05/02/2023]
Abstract
Flavonoid metabolons (weakly-bound multi-enzyme complexes of flavonoid enzymes) are believed to occur in diverse plant species. However, how flavonoid enzymes are organized to form a metabolon is unknown for most plant species. We analyzed the physical interaction partnerships of the flavonoid enzymes from two lamiales plants (snapdragon and torenia) that produce flavones and anthocyanins. In snapdragon, protein-protein interaction assays using yeast and plant systems revealed the following binary interactions: flavone synthase II (FNSII)/chalcone synthase (CHS); FNSII/chalcone isomerase (CHI); FNSII/dihydroflavonol 4-reductase (DFR); CHS/CHI; CHI/DFR; and flavonoid 3'-hydroxylase/CHI. These results along with the subcellular localizations and membrane associations of snapdragon flavonoid enzymes suggested that FNSII serves as a component of the flavonoid metabolon tethered to the endoplasmic reticulum (ER). The observed interaction partnerships and temporal gene expression patterns of flavonoid enzymes in red snapdragon petal cells suggested the flower stage-dependent formation of the flavonoid metabolon, which accounted for the sequential flavone and anthocyanin accumulation patterns therein. We also identified interactions between FNSII and other flavonoid enzymes in torenia, in which the co-suppression of FNSII expression was previously reported to diminish petal anthocyanin contents. The observed physical interactions among flavonoid enzymes of these plant species provided further evidence supporting the long-suspected organization of flavonoid metabolons as enzyme complexes tethered to the ER via cytochrome P450, and illustrated how flavonoid metabolons mediate flower coloration. Moreover, the observed interaction partnerships were distinct from those previously identified in other plant species (Arabidopsis thaliana and soybean), suggesting that the organization of flavonoid metabolons may differ among plant species.
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Affiliation(s)
- Naoto Fujino
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Natsuki Tenma
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Toshiyuki Waki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Keisuke Ito
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Yuki Komatsuzaki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Keigo Sugiyama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Tatsuya Yamazaki
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Saori Yoshida
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Masayoshi Hatayama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Satoshi Yamashita
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Yoshikazu Tanaka
- Suntory World Research Center, Suntory Holdings Ltd., Soraku-gun, Kyoto, 619-0284, Japan
| | - Reiko Motohashi
- Department of Biological and Environmental Science, Faculty of Agriculture, Shizuoka University, Shizuoka, 422-8529, Japan
| | | | - Seiji Takahashi
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
| | - Toru Nakayama
- Graduate School of Engineering, Tohoku University, Aza Aoba, Aramaki, Aoba 6-6-11, Sendai, Miyagi, 980-8579, Japan
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Biała W, Jasiński M. The Phenylpropanoid Case - It Is Transport That Matters. FRONTIERS IN PLANT SCIENCE 2018; 9:1610. [PMID: 30443262 PMCID: PMC6221964 DOI: 10.3389/fpls.2018.01610] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 10/17/2018] [Indexed: 05/19/2023]
Abstract
Phenylpropanoids fulfill numerous physiological functions, essential for plant growth and development, as well as plant-environment interactions. Over the last few decades, many studies have shown that exquisite regulatory mechanisms at multiple levels control the phenylpropanoid metabolic pathway. Deciphering this pathway not only provides a greater, basic understanding of plant specialized metabolism, but also enhances our ability to rationally design plant metabolic pathways for future applications. Despite the identification of the participating enzymes of this complex, biosynthetic machinery, we still lack a complete picture of other genes, enzymes, and metabolites essential for regulation and compartmentation/distribution of phenylpropanoids. Compartmentation, as well as distribution, are critical for the fate/functioning of those molecules, and their effective biosynthesis. At the cellular level, we have narrowed down our understanding of these processes to organelles. Furthermore, various, overlapping, but not exclusive scenarios of phenylpropanoid distribution within the cell have also been described. The cross-membrane dynamics, but also intercellular communication of different branches from phenylpropanoid biosynthesis have become an exciting research frontier in plant science. The intra- and intercellular channeling of intermediates by various transport mechanisms and notably membrane transporters could be a meaningful tool that ensures, inter alia, efficient metabolite production.
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Affiliation(s)
- Wanda Biała
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
| | - Michał Jasiński
- Department of Plant Molecular Physiology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Poznań, Poland
- *Correspondence: Michał Jasiński,
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Bassard JE, Halkier BA. How to prove the existence of metabolons? PHYTOCHEMISTRY REVIEWS : PROCEEDINGS OF THE PHYTOCHEMICAL SOCIETY OF EUROPE 2018; 17:211-227. [PMID: 29755303 PMCID: PMC5932110 DOI: 10.1007/s11101-017-9509-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 04/19/2017] [Indexed: 05/21/2023]
Abstract
Sequential enzymes in biosynthetic pathways are organized in metabolons. It is challenging to provide experimental evidence for the existence of metabolons as biosynthetic pathways are composed of highly dynamic protein-protein interactions. Many different methods are being applied, each with strengths and weaknesses. We will present and evaluate several techniques that have been applied in providing evidence for the orchestration of the biosynthetic pathways of cyanogenic glucosides and glucosinolates in metabolons. These evolutionarily related pathways have ER-localized cytochromes P450 that are proposed to function as anchoring site for assembly of the enzymes into metabolons. Additionally, we have included commonly used techniques, even though they have not been used (yet) on these two pathways. In the review, special attention will be given to less-exploited fluorescence-based methods such as FCS and FLIM. Ultimately, understanding the orchestration of biosynthetic pathways may contribute to successful engineering in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity”, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Barbara Ann Halkier
- DynaMo Center, Department of Plant and Environmental Sciences, University of Copenhagen, Copenhagen, Denmark
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Long Y, Stahl Y, Weidtkamp-Peters S, Smet W, Du Y, Gadella TWJ, Goedhart J, Scheres B, Blilou I. Optimizing FRET-FLIM Labeling Conditions to Detect Nuclear Protein Interactions at Native Expression Levels in Living Arabidopsis Roots. FRONTIERS IN PLANT SCIENCE 2018; 9:639. [PMID: 29868092 PMCID: PMC5962846 DOI: 10.3389/fpls.2018.00639] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 04/25/2018] [Indexed: 05/21/2023]
Abstract
Protein complex formation has been extensively studied using Förster resonance energy transfer (FRET) measured by Fluorescence Lifetime Imaging Microscopy (FLIM). However, implementing this technology to detect protein interactions in living multicellular organism at single-cell resolution and under native condition is still difficult to achieve. Here we describe the optimization of the labeling conditions to detect FRET-FLIM in living plants. This study exemplifies optimization procedure involving the identification of the optimal position for the labels either at the N or C terminal region and the selection of the bright and suitable, fluorescent proteins as donor and acceptor labels for the FRET study. With an effective optimization strategy, we were able to detect the interaction between the stem cell regulators SHORT-ROOT and SCARECROW at endogenous expression levels in the root pole of living Arabidopsis embryos and developing lateral roots by FRET-FLIM. Using this approach we show that the spatial profile of interaction between two transcription factors can be highly modulated in reoccurring and structurally resembling organs, thus providing new information on the dynamic redistribution of nuclear protein complex configurations in different developmental stages. In principle, our optimization procedure for transcription factor complexes is applicable to any biological system.
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Affiliation(s)
- Yuchen Long
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yvonne Stahl
- Institute for Developmental Genetics, Heinrich Heine University, Düsseldorf, Germany
| | | | - Wouter Smet
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Yujuan Du
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Theodorus W. J. Gadella
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Joachim Goedhart
- Section of Molecular Cytology, van Leeuwenhoek Centre for Advanced Microscopy, Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - Ben Scheres
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
| | - Ikram Blilou
- Plant Developmental Biology, Wageningen University and Research Centre, Wageningen, Netherlands
- Plant Cell and Developmental Biology, King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering (BESE), Thuwal, Saudi Arabia
- *Correspondence: Ikram Blilou
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Yao H, Li C, Zhao H, Zhao J, Chen H, Bu T, Anhu W, Wu Q. Deep sequencing of the transcriptome reveals distinct flavonoid metabolism features of black tartary buckwheat ( Fagopyrum tataricum Garetn.). PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2017; 124:49-60. [DOI: 10.1016/j.pbiomolbio.2016.11.003] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 11/05/2016] [Indexed: 10/20/2022]
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Abstract
Purpose of Review We provide an overview of the current knowledge on cytochrome P450-mediated metabolism organized as metabolons and factors that facilitate their stabilization. Essential parameters will be discussed including those that are commonly disregarded using the dhurrin metabolon from Sorghum bicolor as a case study. Recent Findings Sessile plants control their metabolism to prioritize their resources between growth and development, or defense. This requires fine-tuned complex dynamic regulation of the metabolic networks involved. Within the recent years, numerous studies point to the formation of dynamic metabolons playing a major role in controlling the metabolic fluxes within such networks. Summary We propose that P450s and their partners interact and associate dynamically with POR, which acts as a charging station possibly in concert with Cytb5. Solvent environment, lipid composition, and non-catalytic proteins guide metabolon formation and thereby activity, which have important implications for synthetic biology approaches aiming to produce high-value specialized metabolites in heterologous hosts.
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Affiliation(s)
- Jean-Etienne Bassard
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
| | - Birger Lindberg Møller
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Carlsberg Research Laboratory, Gamle Carlsberg Vej 10, DK-1799 Copenhagen V, Denmark
| | - Tomas Laursen
- Plant Biochemistry Laboratory, Center for Synthetic Biology, VILLUM Research Center “Plant Plasticity,” Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg C, Copenhagen Denmark
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA 94608 USA
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Lei R, Jiang H, Hu F, Yan J, Zhu S. Chlorophyll fluorescence lifetime imaging provides new insight into the chlorosis induced by plant virus infection. PLANT CELL REPORTS 2017; 36:327-341. [PMID: 27904946 DOI: 10.1007/s00299-016-2083-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 11/15/2016] [Indexed: 06/06/2023]
Abstract
KEY MESSAGE Leaf chlorosis induced by plant virus infection has a short fluorescence lifetime, which reflects damaged photosynthetic complexes and degraded chloroplasts. Plant viruses often induce chlorosis and necrosis, which are intimately related to photosynthetic functions. Chlorophyll fluorescence lifetime measurement is a valuable noninvasive tool for analyzing photosynthetic processes and is a sensitive indicator of the environment surrounding the fluorescent molecules. In this study, our central goal was to explore the effect of viral infection on photosynthesis by employing chlorophyll fluorescence lifetime imaging (FLIM), steady-state fluorescence, non-photochemical quenching (NPQ), transmission electron microscopy (TEM), and pigment analysis. The data indicated that the chlorophyll fluorescence lifetime of chlorotic leaves was significantly shorter than that of healthy control leaves, and the fitted short lifetime component of chlorophyll fluorescence of chlorotic leaves was dominant. This dominant short lifetime component may result from damage to the structure of thylakoid, which was confirmed by TEM. The NPQ value of chlorotic leaves was slightly higher than that of healthy green leaves, which can be explained by increased neoxanthin, lutein and violaxanthin content relative to chlorophyll a. The difference in NPQ is slight, but FLIM can provide simple and direct characterization of PSII structure and photosynthetic function. Therefore, this technique shows great potential as a simple and rapid method for studying mechanisms of plant virus infection.
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Affiliation(s)
- Rong Lei
- Institute of Plant Quarantine of China, Chinese Academy of Inspection and Quarantine, Beijing, 100762, China
| | - Hongshan Jiang
- Institute of Plant Quarantine of China, Chinese Academy of Inspection and Quarantine, Beijing, 100762, China
| | - Fan Hu
- Institute of Plant Quarantine of China, Chinese Academy of Inspection and Quarantine, Beijing, 100762, China
| | - Jin Yan
- Institute of Plant Quarantine of China, Chinese Academy of Inspection and Quarantine, Beijing, 100762, China
| | - Shuifang Zhu
- Institute of Plant Quarantine of China, Chinese Academy of Inspection and Quarantine, Beijing, 100762, China.
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Villalobos-González L, Peña-Neira A, Ibáñez F, Pastenes C. Long-term effects of abscisic acid (ABA) on the grape berry phenylpropanoid pathway: Gene expression and metabolite content. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2016; 105:213-223. [PMID: 27116369 DOI: 10.1016/j.plaphy.2016.04.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2016] [Revised: 04/05/2016] [Accepted: 04/07/2016] [Indexed: 05/09/2023]
Abstract
ABA has been proposed as the main signal triggering the onset of the ripening process in grapes, and modulating the secondary metabolism in grape berry skins. To determine the effect of ABA on secondary metabolism in berries, clusters of Carménère were sprayed with 0 μLL(-1) ABA; 50 μLL(-1) ABA and 100 μLL(-1) ABA during pre-véraison, and the gene expression of the transcription factors and enzymes of the phenylpropanoid pathway were assessed from véraison to 70 days after véraison (DAV). Additionally, flavonols, tannins and anthocyanins were assessed from véraison until harvest (110 DAV). ABA accelerated sugar and anthocyanin accumulation at véraison. The grape transcript abundance of VvDFR, VvANS, VvUFGT and VvMybA1, all peaking around véraison mimicked the concentration of ABA throughout the season. The highest anthocyanin concentration occurred 35 DAV for all treatments, but higher pigment concentrations were observed in ABA-treated berries at véraison and from 60 to 70 DAV to harvest. VvPAL was also increased by treatment at the higher concentration of ABA from véraison to 40 DAV. Regarding flavanol synthesis, VvLAR2 and VvMyb4A decreased from véraison until 40 DAV and then increased again until 70 DAV. Compared to the control, both ABA treatments resulted in a less-than-proportional reduction of the expression of both genes compared to the control and, after 40 DAV, in a more-than-proportional increase compared to the control, suggesting a long-term effect of the pre-véraison ABA spray on the berries. A concomitant increase in flavanols was observed in berries after 40 DAV, and this occurred at a higher extent in berries treated with the highest ABA concentration.
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Affiliation(s)
| | - Alvaro Peña-Neira
- Facultad de Ciencias Agronómicas, Universidad de Chile, Casilla, 1004, Santiago, Chile
| | - Freddy Ibáñez
- Facultad de Ciencias Agronómicas, Universidad de Chile, Casilla, 1004, Santiago, Chile
| | - Claudio Pastenes
- Facultad de Ciencias Agronómicas, Universidad de Chile, Casilla, 1004, Santiago, Chile.
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Diharce J, Golebiowski J, Fiorucci S, Antonczak S. Fine-tuning of microsolvation and hydrogen bond interaction regulates substrate channelling in the course of flavonoid biosynthesis. Phys Chem Chem Phys 2016; 18:10337-45. [PMID: 27027108 DOI: 10.1039/c5cp05059f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the course of metabolite formation, some multienzymatic edifices, the so-called metabolon, are formed and lead to a more efficient production of these natural compounds. One of the major features of these enzyme complexes is the facilitation of direct transfer of the metabolite between enzyme active sites by substrate channelling. Biophysical insights into substrate channelling remain scarce because the transient nature of these macromolecular complexes prevents the observation of high resolution structures. Here, using molecular modelling, we describe the substrate channelling of a flavonoid compound between DFR (dihydroflavonol-4-reductase) and LAR (leucoanthocyanidin reductase). The simulation presents crucial details concerning the kinetic, thermodynamic, and structural aspects of this diffusion. The formation of the DFR-LAR complex leads to the opening of the DFR active site giving rise to a facilitated diffusion, in about 1 μs, of the DFR product towards LAR cavity. The theoretically observed substrate channelling is supported experimentally by the fact that this metabolite, i.e. the product of the DFR enzyme, is not stable in the media. Moreover, along this path, the influence of the solvent is crucial. The metabolite remains close to the surface of the complex avoiding full solvation. In addition, when the dynamic behaviour of the system leads to a loss of interaction between the metabolite and the enzymes, water molecules through bridging H-bonds prevent the former from escaping to the bulk.
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Affiliation(s)
- Julien Diharce
- Institut de Chimie de Nice, UMR-CNRS 7272, Faculté des Sciences, Université de Nice-Sophia Antipolis, 28 Avenue Valrose, 06108 Nice Cedex 2, France.
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Waki T, Yoo D, Fujino N, Mameda R, Denessiouk K, Yamashita S, Motohashi R, Akashi T, Aoki T, Ayabe SI, Takahashi S, Nakayama T. Identification of protein-protein interactions of isoflavonoid biosynthetic enzymes with 2-hydroxyisoflavanone synthase in soybean (Glycine max (L.) Merr.). Biochem Biophys Res Commun 2016; 469:546-51. [PMID: 26694697 DOI: 10.1016/j.bbrc.2015.12.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2015] [Accepted: 12/10/2015] [Indexed: 12/19/2022]
Abstract
Metabolic enzymes, including those involved in flavonoid biosynthesis, are proposed to form weakly bound, ordered protein complexes, called "metabolons". Some hypothetical models of flavonoid biosynthetic metabolons have been proposed, in which metabolic enzymes are believed to anchor to the cytoplasmic surface of the endoplasmic reticulum (ER) via ER-bound cytochrome P450 isozymes (P450s). However, no convincing evidence for the interaction of flavonoid biosynthetic enzymes with P450s has been reported previously. Here, we analyzed binary protein-protein interactions of 2-hydroxyisoflavanone synthase 1 (GmIFS1), a P450 (CYP93C), with cytoplasmic enzymes involved in isoflavone biosynthesis in soybean. We identified binary interactions between GmIFS1 and chalcone synthase 1 (GmCHS1) and between GmIFS1 and chalcone isomerases (GmCHIs) by using a split-ubiquitin membrane yeast two-hybrid system. These binary interactions were confirmed in planta by means of bimolecular fluorescence complementation (BiFC) using tobacco leaf cells. In these BiFC analyses, fluorescence signals that arose from the interaction of these cytoplasmic enzymes with GmIFS1 generated sharp, network-like intracellular patterns, which was very similar to the ER-localized fluorescence patterns of GmIFS1 labeled with a fluorescent protein. These observations provide strong evidence that, in planta, interaction of GmCHS1 and GmCHIs with GmIFS1 takes place on ER on which GmIFS1 is located, and also provide important clues to understand how enzymes and proteins form metabolons to establish efficient metabolic flux of (iso)flavonoid biosynthesis.
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Affiliation(s)
- Toshiyuki Waki
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - DongChan Yoo
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Naoto Fujino
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Ryo Mameda
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Konstantin Denessiouk
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan; Faculty of Science and Engineering, Åbo Akademi University, Turku, Finland
| | - Satoshi Yamashita
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Reiko Motohashi
- Department of Biological and Environmental Science, Faculty of Agriculture, Shizuoka University, Shizuoka 422-8529, Japan
| | - Tomoyoshi Akashi
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Toshio Aoki
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Shin-ichi Ayabe
- Department of Applied Biological Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Seiji Takahashi
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan
| | - Toru Nakayama
- Department of Biomolecular Engineering, Graduate School of Engineering, Tohoku University, Sendai, Miyagi 980-8579, Japan.
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Bashandy H, Pietiäinen M, Carvalho E, Lim KJ, Elomaa P, Martens S, Teeri TH. Anthocyanin biosynthesis in gerbera cultivar 'Estelle' and its acyanic sport 'Ivory'. PLANTA 2015; 242:601-11. [PMID: 26093654 DOI: 10.1007/s00425-015-2349-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Accepted: 06/07/2015] [Indexed: 05/22/2023]
Abstract
Identification of distinct allelic versions for dihydroflavonol 4-reductase in gerbera cultivars reveals that gerbera DFR enzymes have strong substrate preference in vivo that is not reflected to the activity in vitro. Flavonoids in the model ornamental plant Gerbera hybrida consist of flavones, flavonols and anthocyanins. Anthocyanins accumulate in the adaxial epidermis of petals and give the different cultivars their characteristic red and violet colour. Both pelargonidin and cyanidin derivatives are found in gerbera, but none of the cultivars contain delphinidin. 'Ivory', a cultivar with white petals, is a sport of the pelargonidin-containing pink cultivar 'Estelle', i.e. it originates from an acyanic branch of 'Estelle'. In this work, four different alleles encoding dihydroflavonol 4-reductase (DFR) were identified in gerbera cultivars. We found that, in contrast to 'Estelle' with the functional allele GDFR1-2, 'Ivory' carries a mutation in this gene that results in an inactive enzyme. Interestingly, 'Ivory' also expresses a second, nonmutated allele (GDFR1-3) in petal epidermi, leading to extractable DFR activity but not to anthocyanin biosynthesis. The second allele encodes a protein identical in amino acid sequence to the DFR of the cyanidin-containing variety 'President'. Pelargonidin-containing cultivars do not react to the flavonoid 3'-hydroxylase inhibitor tetcyclacis, but cyanidin-containing cultivars lose their colour, instead of starting to synthesise pelargonidins, indicating the specificity of GDFR1-3 for the cyanidin pathway. This explains why petals of 'Ivory' are white, even when it has lost only one of the two enzymatically functional DFR forms, and shows that anthocyanin biosynthesis in gerbera is under more complex regulation than earlier thought.
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Affiliation(s)
- Hany Bashandy
- Department of Agricultural Sciences, Viikki Plant Science Centre, University of Helsinki, P.O. Box 27, 00014, Helsinki, Finland
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Investigating protein-protein interactions in the plant endomembrane system using multiphoton-induced FRET-FLIM. Methods Mol Biol 2015; 1209:81-95. [PMID: 25117276 DOI: 10.1007/978-1-4939-1420-3_6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Real-time noninvasive fluorescence-based protein assays enable a direct access to study interactions in their natural environment and hence overcome the limitations of other methods that rely on invasive cell disruption techniques. The determination of Förster resonance energy transfer (FRET) by means of fluorescence lifetime imaging microscopy (FLIM) is currently the most advanced method to observe protein-protein interactions at nanometer resolution inside single living cells and in real-time. In the FRET-FLIM approach, the information gained using steady-state FRET between interacting proteins is considerably improved by monitoring changes in the excited-state lifetime of the donor fluorophore where its quenching in the presence of the acceptor is evidence for a direct physical interaction. The combination of confocal laser scanning microscopy with the sensitive advanced technique of time-correlated single photon counting allows the mapping of the spatial distribution of fluorescence lifetimes inside living cells on a pixel-by-pixel basis that is the same as the fluorescence image. Moreover, the use of multiphoton excitation particularly for plant cells provides further advantages such as reduced phototoxicity and photobleaching. In this protocol, we briefly describe the instrumentation and experimental design to study protein interactions within the plant endomembrane system, with a focus on the imaging of plant cells expressing fluorescent proteins and acquisition and analysis of fluorescence lifetime resolved data.
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Trantas EA, Koffas MAG, Xu P, Ververidis F. When plants produce not enough or at all: metabolic engineering of flavonoids in microbial hosts. FRONTIERS IN PLANT SCIENCE 2015; 6:7. [PMID: 25688249 PMCID: PMC4310283 DOI: 10.3389/fpls.2015.00007] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2014] [Accepted: 01/06/2015] [Indexed: 05/30/2023]
Abstract
As a result of the discovery that flavonoids are directly or indirectly connected to health, flavonoid metabolism and its fascinating molecules that are natural products in plants, have attracted the attention of both the industry and researchers involved in plant science, nutrition, bio/chemistry, chemical bioengineering, pharmacy, medicine, etc. Subsequently, in the past few years, flavonoids became a top story in the pharmaceutical industry, which is continually seeking novel ways to produce safe and efficient drugs. Microbial cell cultures can act as workhorse bio-factories by offering their metabolic machinery for the purpose of optimizing the conditions and increasing the productivity of a selective flavonoid. Furthermore, metabolic engineering methodology is used to reinforce what nature does best by correcting the inadequacies and dead-ends of a metabolic pathway. Combinatorial biosynthesis techniques led to the discovery of novel ways of producing natural and even unnatural plant flavonoids, while, in addition, metabolic engineering provided the industry with the opportunity to invest in synthetic biology in order to overcome the currently existing restricted diversification and productivity issues in synthetic chemistry protocols. In this review, is presented an update on the rationalized approaches to the production of natural or unnatural flavonoids through biotechnology, analyzing the significance of combinatorial biosynthesis of agricultural/pharmaceutical compounds produced in heterologous organisms. Also mentioned are strategies and achievements that have so far thrived in the area of synthetic biology, with an emphasis on metabolic engineering targeting the cellular optimization of microorganisms and plants that produce flavonoids, while stressing the advances in flux dynamic control and optimization. Finally, the involvement of the rapidly increasing numbers of assembled genomes that contribute to the gene- or pathway-mining in order to identify the gene(s) responsible for producing species-specific secondary metabolites is also considered herein.
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Affiliation(s)
- Emmanouil A. Trantas
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological and Educational Institute of CreteHeraklion, Greece
| | - Mattheos A. G. Koffas
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic InstituteTroy, NY, USA
| | - Peng Xu
- Department of Chemical Engineering, Massachusetts Institute of Technology CambridgeMA, USA
| | - Filippos Ververidis
- Plant Biochemistry and Biotechnology Laboratory, Department of Agriculture, School of Agriculture and Food Technology, Technological and Educational Institute of CreteHeraklion, Greece
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Laursen T, Møller BL, Bassard JE. Plasticity of specialized metabolism as mediated by dynamic metabolons. TRENDS IN PLANT SCIENCE 2015; 20:20-32. [PMID: 25435320 DOI: 10.1016/j.tplants.2014.11.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 10/24/2014] [Accepted: 11/07/2014] [Indexed: 05/02/2023]
Abstract
The formation of specialized metabolites enables plants to respond to biotic and abiotic stresses, but requires the sequential action of multiple enzymes. To facilitate swift production and to avoid leakage of potentially toxic and labile intermediates, many of the biosynthetic pathways are thought to organize in multienzyme clusters termed metabolons. Dynamic assembly and disassembly enable the plant to rapidly switch the product profile and thereby prioritize its resources. The lifetime of metabolons is largely unknown mainly due to technological limitations. This review focuses on the factors that facilitate and stimulate the dynamic assembly of metabolons, including microenvironments, noncatalytic proteins, and allosteric regulation. Understanding how plants organize carbon fluxes within their metabolic grids would enable targeted bioengineering of high-value specialized metabolites.
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Affiliation(s)
- Tomas Laursen
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
| | - Birger Lindberg Møller
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark; Carlsberg Laboratory, 10 Gamle Carlsberg Vej, DK-1799 Copenhagen V, Denmark.
| | - Jean-Etienne Bassard
- VILLUM Research Center for Plant Plasticity, Center for Synthetic Biology 'bioSYNergy', and Plant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of Copenhagen, 40 Thorvaldsensvej, DK-1871 Frederiksberg C, Copenhagen, Denmark
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Singleton C, Howard TP, Smirnoff N. Synthetic metabolons for metabolic engineering. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:1947-1954. [PMID: 24591054 DOI: 10.1093/jxb/eru050] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
It has been proposed that enzymes can associate into complexes (metabolons) that increase the efficiency of metabolic pathways by channelling substrates between enzymes. Metabolons may increase flux by increasing the local concentration of intermediates, decreasing the concentration of enzymes needed to maintain a given flux, directing the products of a pathway to a specific subcellular location or minimizing the escape of reactive intermediates. Metabolons can be formed by relatively loose non-covalent protein-protein interaction, anchorage to membranes, and (in bacteria) by encapsulation of enzymes in protein-coated microcompartments. Evidence that non-coated metabolons are effective at channelling substrates is scarce and difficult to obtain. In plants there is strong evidence that small proportions of glycolytic enzymes are associated with the outside of mitochondria and are effective in substrate channelling. More recently, synthetic metabolons, in which enzymes are scaffolded to synthetic proteins or nucleic acids, have been expressed in microorganisms and these provide evidence that scaffolded enzymes are more effective than free enzymes for metabolic engineering. This provides experimental evidence that metabolons may have a general advantage and opens the way to improving the outcome of metabolic engineering in plants by including synthetic metabolons in the toolbox.
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Affiliation(s)
- Chloe Singleton
- Biosciences, College of Environmental and Life Sciences, University of Exeter, Geoffrey Pope Building, Stocker Road, Exeter EX4 4QD, UK
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Müller SM, Galliardt H, Schneider J, Barisas BG, Seidel T. Quantification of Förster resonance energy transfer by monitoring sensitized emission in living plant cells. FRONTIERS IN PLANT SCIENCE 2013; 4:413. [PMID: 24194740 PMCID: PMC3810607 DOI: 10.3389/fpls.2013.00413] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Accepted: 09/29/2013] [Indexed: 05/20/2023]
Abstract
Förster resonance energy transfer (FRET) describes excitation energy exchange between two adjacent molecules typically in distances ranging from 2 to 10 nm. The process depends on dipole-dipole coupling of the molecules and its probability of occurrence cannot be proven directly. Mostly, fluorescence is employed for quantification as it represents a concurring process of relaxation of the excited singlet state S1 so that the probability of fluorescence decreases as the probability of FRET increases. This reflects closer proximity of the molecules or an orientation of donor and acceptor transition dipoles that facilitates FRET. Monitoring sensitized emission by 3-Filter-FRET allows for fast image acquisition and is suitable for quantifying FRET in dynamic systems such as living cells. In recent years, several calibration protocols were established to overcome to previous difficulties in measuring FRET-efficiencies. Thus, we can now obtain by 3-filter FRET FRET-efficiencies that are comparable to results from sophisticated fluorescence lifetime measurements. With the discovery of fluorescent proteins and their improvement toward spectral variants and usability in plant cells, the tool box for in vivo FRET-analyses in plant cells was provided and FRET became applicable for the in vivo detection of protein-protein interactions and for monitoring conformational dynamics. The latter opened the door toward a multitude of FRET-sensors such as the widely applied Ca(2+)-sensor Cameleon. Recently, FRET-couples of two fluorescent proteins were supplemented by additional fluorescent proteins toward FRET-cascades in order to monitor more complex arrangements. Novel FRET-couples involving switchable fluorescent proteins promise to increase the utility of FRET through combination with photoactivation-based super-resolution microscopy.
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Affiliation(s)
- Sara M. Müller
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
| | - Helena Galliardt
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
| | - Jessica Schneider
- Bioinformatic Resource Facility, Center for Biotechnology, Bielefeld UniversityBielefeld, Germany
| | - B. George Barisas
- Chemistry Department, Colorado State UniversityFort Collins, CO, USA
| | - Thorsten Seidel
- Dynamic Cell Imaging, Faculty of Biology, Bielefeld UniversityBielefeld, Germany
- *Correspondence: Thorsten Seidel, Dynamic Cell Imaging, Faculty of Biology, Bielefeld University, Universitätsstraße 25, 33501 Bielefeld, Germany e-mail:
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Jaakola L. New insights into the regulation of anthocyanin biosynthesis in fruits. TRENDS IN PLANT SCIENCE 2013; 18:477-83. [PMID: 23870661 DOI: 10.1016/j.tplants.2013.06.003] [Citation(s) in RCA: 608] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2013] [Revised: 06/04/2013] [Accepted: 06/17/2013] [Indexed: 05/18/2023]
Abstract
Anthocyanins are important health-promoting pigments that make a major contribution to the quality of fruits. The biosynthetic pathway leading to anthocyanins is well known and the key regulatory genes controlling the pathway have been isolated in many species. Recently, a considerable amount of new information has been gathered on the developmental and environmental regulation of anthocyanin biosynthesis in fruits, specifically the impact of regulation through light. New discoveries have begun to reveal links between the developmental regulatory network and the specific regulators of anthocyanin biosynthesis during fruit ripening. In this opinion article, a simplified model for the different regulatory networks involved with anthocyanin production in fruit is proposed.
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Affiliation(s)
- Laura Jaakola
- Climate Laboratory, Department of Arctic and Marine Biology, University of Tromsø, Norway.
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Groenenboom M, Gomez-Roldan V, Stigter H, Astola L, van Daelen R, Beekwilder J, Bovy A, Hall R, Molenaar J. The flavonoid pathway in tomato seedlings: transcript abundance and the modeling of metabolite dynamics. PLoS One 2013; 8:e68960. [PMID: 23922672 PMCID: PMC3724892 DOI: 10.1371/journal.pone.0068960] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Accepted: 06/07/2013] [Indexed: 01/28/2023] Open
Abstract
Flavonoids are secondary metabolites present in all terrestrial plants. The flavonoid pathway has been extensively studied, and many of the involved genes and metabolites have been described in the literature. Despite this extensive knowledge, the functioning of the pathway in vivo is still poorly understood. Here, we study the flavonoid pathway using both experiments and mathematical models. We measured flavonoid metabolite dynamics in two tissues, hypocotyls and cotyledons, during tomato seedling development. Interestingly, the same backbone of interactions leads to very different accumulation patterns in the different tissues. Initially, we developed a mathematical model with constant enzyme concentrations that described the metabolic networks separately in both tissues. This model was unable to fit the measured flavonoid dynamics in the hypocotyls, even if we allowed unrealistic parameter values. This suggested us to investigate the effect of transcript abundance on flavonoid accumulation. We found that the expression of candidate flavonoid genes varies considerably with time. Variation in transcript abundance results in enzymatic variation, which could have a large effect on metabolite accumulation. Candidate transcript abundance was included in the mathematical model as representative for enzyme concentration. We fitted the resulting model to the flavonoid dynamics in the cotyledons, and tested it by applying it to the data from hypocotyls. When transcript abundance is included, we are indeed able to explain flavonoid dynamics in both tissues. Importantly, this is possible under the biologically relevant restriction that the enzymatic properties estimated by the model are conserved between the tissues.
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Affiliation(s)
- Marian Groenenboom
- Biometris, Wageningen University and Research Center, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands
| | - Victoria Gomez-Roldan
- Plant Research International, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands
| | - Hans Stigter
- Biometris, Wageningen University and Research Center, Wageningen, The Netherlands
| | - Laura Astola
- Biometris, Wageningen University and Research Center, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands
| | | | | | - Arnaud Bovy
- Plant Research International, Wageningen, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Robert Hall
- Plant Research International, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands
- Centre for BioSystems Genomics (CBSG), Wageningen, The Netherlands
| | - Jaap Molenaar
- Biometris, Wageningen University and Research Center, Wageningen, The Netherlands
- Netherlands Consortium for Systems Biology (NCSB), Amsterdam, The Netherlands
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Lallemand B, Erhardt M, Heitz T, Legrand M. Sporopollenin biosynthetic enzymes interact and constitute a metabolon localized to the endoplasmic reticulum of tapetum cells. PLANT PHYSIOLOGY 2013; 162:616-25. [PMID: 23632852 PMCID: PMC3668057 DOI: 10.1104/pp.112.213124] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 04/19/2013] [Indexed: 05/17/2023]
Abstract
The sporopollenin polymer is the major constituent of exine, the outer pollen wall. Recently fatty acid derivatives have been shown to be the precursors of sporopollenin building units. ACYL-COA SYNTHETASE, POLYKETIDE SYNTHASE A (PKSA) and PKSB, TETRAKETIDE α-PYRONE REDUCTASE1 (TKPR1) and TKPR2 have been demonstrated to be involved in sporopollenin biosynthesis in Arabidopsis (Arabidopsis thaliana). Here all these sporopollenin biosynthetic enzymes but TKPR2 have been immunolocalized to endoplasmic reticulum of anther tapetal cells. Pull-down experiments demonstrated that tagged recombinant proteins interacted to form complexes whose constituents were characterized by immunoblotting. In vivo protein interactions were evidenced by yeast (Saccharomyces cerevisiae) two-hybrid analysis and by fluorescence lifetime imaging microscopy/Förster resonance energy transfer studies in transgenic Nicotiana benthamiana, which were used to test the possibility that the enzymes interact to form a biosynthetic metabolon. Various pairs of proteins fused to two distinct fluorochromes were coexpressed in N. benthamiana leaf tissues and fluorescence lifetime imaging microscopy/Förster resonance energy transfer measurements demonstrated that proteins interacted pairwise in planta. Taken together, these results suggest the existence of a sporopollenin metabolon.
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Affiliation(s)
- Benjamin Lallemand
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France
| | - Mathieu Erhardt
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France
| | - Thierry Heitz
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France
| | - Michel Legrand
- Institut de Biologie Moléculaire des Plantes, Unité Propre de Recherche 2357 du Centre National de la Recherche Scientifique, Université de Strasbourg, 67084 Strasbourg cedex, France
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Schoberer J, Liebminger E, Botchway SW, Strasser R, Hawes C. Time-resolved fluorescence imaging reveals differential interactions of N-glycan processing enzymes across the Golgi stack in planta. PLANT PHYSIOLOGY 2013; 161:1737-54. [PMID: 23400704 PMCID: PMC3613452 DOI: 10.1104/pp.112.210757] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 02/10/2013] [Indexed: 05/18/2023]
Abstract
N-Glycan processing is one of the most important cellular protein modifications in plants and as such is essential for plant development and defense mechanisms. The accuracy of Golgi-located processing steps is governed by the strict intra-Golgi localization of sequentially acting glycosidases and glycosyltransferases. Their differential distribution goes hand in hand with the compartmentalization of the Golgi stack into cis-, medial-, and trans-cisternae, which separate early from late processing steps. The mechanisms that direct differential enzyme concentration are still unknown, but the formation of multienzyme complexes is considered a feasible Golgi protein localization strategy. In this study, we used two-photon excitation-Förster resonance energy transfer-fluorescence lifetime imaging microscopy to determine the interaction of N-glycan processing enzymes with differential intra-Golgi locations. Following the coexpression of fluorescent protein-tagged amino-terminal Golgi-targeting sequences (cytoplasmic-transmembrane-stem [CTS] region) of enzyme pairs in leaves of tobacco (Nicotiana spp.), we observed that all tested cis- and medial-Golgi enzymes, namely Arabidopsis (Arabidopsis thaliana) Golgi α-mannosidase I, Nicotiana tabacum β1,2-N-acetylglucosaminyltransferase I, Arabidopsis Golgi α-mannosidase II (GMII), and Arabidopsis β1,2-xylosyltransferase, form homodimers and heterodimers, whereas among the late-acting enzymes Arabidopsis β1,3-galactosyltransferase1 (GALT1), Arabidopsis α1,4-fucosyltransferase, and Rattus norvegicus α2,6-sialyltransferase (a nonplant Golgi marker), only GALT1 and medial-Golgi GMII were found to form a heterodimer. Furthermore, the efficiency of energy transfer indicating the formation of interactions decreased considerably in a cis-to-trans fashion. The comparative fluorescence lifetime imaging of several full-length cis- and medial-Golgi enzymes and their respective catalytic domain-deleted CTS clones further suggested that the formation of protein-protein interactions can occur through their amino-terminal CTS region.
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Affiliation(s)
| | - Eva Liebminger
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria (J.S., E.L., R.S.)
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom (J.S., C.H.); and
- Research Complex at Harwell, Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell-Oxford, Didcot OX11 0QX, United Kingdom (S.W.B.)
| | - Stanley W. Botchway
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria (J.S., E.L., R.S.)
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom (J.S., C.H.); and
- Research Complex at Harwell, Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell-Oxford, Didcot OX11 0QX, United Kingdom (S.W.B.)
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria (J.S., E.L., R.S.)
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom (J.S., C.H.); and
- Research Complex at Harwell, Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell-Oxford, Didcot OX11 0QX, United Kingdom (S.W.B.)
| | - Chris Hawes
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria (J.S., E.L., R.S.)
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom (J.S., C.H.); and
- Research Complex at Harwell, Central Laser Facility, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell-Oxford, Didcot OX11 0QX, United Kingdom (S.W.B.)
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