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Tat VT, Lee YJ. Spatio-Temporal Study of Galactolipid Biosynthesis in Duckweed Using Mass Spectrometry Imaging and in vivo Isotope Labeling. PLANT & CELL PHYSIOLOGY 2024; 65:986-998. [PMID: 38590126 DOI: 10.1093/pcp/pcae032] [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: 01/09/2024] [Revised: 03/19/2024] [Accepted: 03/26/2024] [Indexed: 04/10/2024]
Abstract
Isotope labeling coupled with mass spectrometry imaging (MSI) presents a potent strategy for elucidating the dynamics of metabolism at cellular resolution, yet its application to plant systems is scarce. It has the potential to reveal the spatio-temporal dynamics of lipid biosynthesis during plant development. In this study, we explore its application to galactolipid biosynthesis of an aquatic plant, Lemna minor, with D2O labeling. Specifically, matrix-assisted laser desorption/ionization-MSI data of two major galactolipids in L. minor, monogalactosyldiacylglycerol and digalactosyldiacylglycerol, were studied after growing in 50% D2O media over a 15-day time period. When they were partially labeled after 5 d, three distinct binomial isotopologue distributions were observed corresponding to the labeling of partial structural moieties: galactose only, galactose and a fatty acyl chain and the entire molecule. The temporal change in the relative abundance of these distributions follows the expected linear pathway of galactolipid biosynthesis. Notably, their mass spectrometry images revealed the localization of each isotopologue group to the old parent frond, the intermediate tissues and the newly grown daughter fronds. Besides, two additional labeling experiments, (i) 13CO2 labeling and (ii) backward labeling of completely 50% D2O-labeled L. minor in H2O media, confirm the observations in forward labeling. Furthermore, these experiments unveiled hidden isotopologue distributions indicative of membrane lipid restructuring. This study suggests the potential of isotope labeling using MSI to provide spatio-temporal details in lipid biosynthesis in plant development.
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Affiliation(s)
- Vy T Tat
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011, USA
| | - Young Jin Lee
- Department of Chemistry, Iowa State University, 2415 Osborn Drive, Ames, IA 50011, USA
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2
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Rao X, Barros J. Modeling lignin biosynthesis: a pathway to renewable chemicals. TRENDS IN PLANT SCIENCE 2024; 29:546-559. [PMID: 37802691 DOI: 10.1016/j.tplants.2023.09.011] [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: 05/31/2023] [Revised: 09/01/2023] [Accepted: 09/18/2023] [Indexed: 10/08/2023]
Abstract
Plant biomass contains lignin that can be converted into high-value-added chemicals, fuels, and materials. The precise genetic manipulation of lignin content and composition in plant cells offers substantial environmental and economic benefits. However, the intricate regulatory mechanisms governing lignin formation challenge the development of crops with specific lignin profiles. Mathematical models and computational simulations have recently been employed to gain fundamental understanding of the metabolism of lignin and related phenolic compounds. This review article discusses the strategies used for modeling plant metabolic networks, focusing on the application of mathematical modeling for flux network analysis in monolignol biosynthesis. Furthermore, we highlight how current challenges might be overcome to optimize the use of metabolic modeling approaches for developing lignin-engineered plants.
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Affiliation(s)
- Xiaolan Rao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China.
| | - Jaime Barros
- Division of Plant Sciences and Interdisciplinary Plant Group, University of Missouri, Columbia, MO 65211, USA.
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3
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Wen F, Chen S, Wang Y, Wu Q, Yan J, Pei J, Zhou T. The synthesis of Paris saponin VII mainly occurs in leaves and is promoted by light intensity. FRONTIERS IN PLANT SCIENCE 2023; 14:1199215. [PMID: 37575916 PMCID: PMC10420111 DOI: 10.3389/fpls.2023.1199215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/10/2023] [Indexed: 08/15/2023]
Abstract
Unraveling the specific organs and tissues involved in saponin synthesis, as well as the light regulatory mechanisms, is crucial for improving the quality of artificially cultivated medicinal materials of Paris plants. Paris saponin VII (PS VII), a high-value active ingredient, is found in almost all organs of Paris plant species. In this study, we focused on Paris polyphylla var. yunnanensis (Franch.) Hand. - Mzt. (PPY) and found that PS VII synthesis predominantly occurs in leaves and is increased by high light intensity. This intriguing discovery has unveiled the potential for manipulating non-traditional medicinal organ leaves to improve the quality of medicinal organ rhizomes. The analysis of the impact of organ differences on saponin concentration in P. polyphylla var. chinensis (Franch.) Hara (PPC), P. fargesii Franch. (PF), and PPY revealed consistency among the three Paris species and was mainly dominated by PS VII. Notably, the leaves and stems exhibited much higher proportions of PS VII than other organs, accounting for 80-90% of the four main saponins. Among the three Paris species, PPY had the highest concentration of PS VII and was selected for subsequent experiments. Further investigations on saponin subcellular localization, temporal variation, and stem wound fluid composition demonstrated that PS VII is synthesized in mesophyll cells, released into the intercellular space through exocytosis, and then transported to the rhizome via vascular tissue. These findings confirm the significant role of leaves in PS VII synthesis. Additionally, a 13C-glucose feeding to trace PS VII biosynthesis revealed that only PS VII in the leaves exhibited incorporation of the labeled carbon, despite conducting 13C-glucose feeding in leaves, stems, rhizomes, and roots. Thus, the leaves are indeed the primary organ for PS VII synthesis in PPY. Furthermore, compared with plants under 100 μmol m-2 s-1, plants under 400 μmol m-2 s-1 exhibited a higher PS VII concentration, particularly in the upper epidermal cells of the leaves. We propose that high light intensity promotes PS VII synthesis in leaves through three mechanisms: (1) increased availability of substrates for saponin synthesis; (2) protection of leaves from high light damage through enhanced saponin synthesis; and (3) enhanced compartmentalization of saponins within the leaves, which in turn feedback regulates saponin synthesis.
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Affiliation(s)
- Feiyan Wen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Siyu Chen
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Yue Wang
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Qinghua Wu
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jie Yan
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Jin Pei
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Tao Zhou
- State Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
- College of Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
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4
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Chandrakanth NN, Zhang C, Freeman J, de Souza WR, Bartley LE, Mitchell RA. Modification of plant cell walls with hydroxycinnamic acids by BAHD acyltransferases. FRONTIERS IN PLANT SCIENCE 2023; 13:1088879. [PMID: 36733587 PMCID: PMC9887202 DOI: 10.3389/fpls.2022.1088879] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 12/28/2022] [Indexed: 06/18/2023]
Abstract
In the last decade it has become clear that enzymes in the "BAHD" family of acyl-CoA transferases play important roles in the addition of phenolic acids to form ester-linked moieties on cell wall polymers. We focus here on the addition of two such phenolics-the hydroxycinnamates, ferulate and p-coumarate-to two cell wall polymers, glucuronoarabinoxylan and to lignin. The resulting ester-linked feruloyl and p-coumaroyl moities are key features of the cell walls of grasses and other commelinid monocots. The capacity of ferulate to participate in radical oxidative coupling means that its addition to glucuronoarabinoxylan or to lignin has profound implications for the properties of the cell wall - allowing respectively oxidative crosslinking to glucuronoarabinoxylan chains or introducing ester bonds into lignin polymers. A subclade of ~10 BAHD genes in grasses is now known to (1) contain genes strongly implicated in addition of p-coumarate or ferulate to glucuronoarabinoxylan (2) encode enzymes that add p-coumarate or ferulate to lignin precursors. Here, we review the evidence for functions of these genes and the biotechnological applications of manipulating them, discuss our understanding of mechanisms involved, and highlight outstanding questions for future research.
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Affiliation(s)
| | - Chengcheng Zhang
- Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, United States
| | - Jackie Freeman
- Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
| | | | - Laura E. Bartley
- Institute of Biological Chemistry, Washington State University, Pullman, WA, United States
| | - Rowan A.C. Mitchell
- Plant Sciences, Rothamsted Research, West Common, Harpenden, Hertfordshire, United Kingdom
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5
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Wang P, Guo L, Morgan J, Dudareva N, Chapple C. Transcript and metabolite network perturbations in lignin biosynthetic mutants of Arabidopsis. PLANT PHYSIOLOGY 2022; 190:2828-2846. [PMID: 35880844 PMCID: PMC9706439 DOI: 10.1093/plphys/kiac344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 06/24/2022] [Indexed: 06/01/2023]
Abstract
Lignin, one of the most abundant polymers in plants, is derived from the phenylpropanoid pathway, which also gives rise to an array of metabolites that are essential for plant fitness. Genetic engineering of lignification can cause drastic changes in transcription and metabolite accumulation with or without an accompanying development phenotype. To understand the impact of lignin perturbation, we analyzed transcriptome and metabolite data from the rapidly lignifying stem tissue in 13 selected phenylpropanoid mutants and wild-type Arabidopsis (Arabidopsis thaliana). Our dataset contains 20,974 expressed genes, of which over 26% had altered transcript levels in at least one mutant, and 18 targeted metabolites, all of which displayed altered accumulation in at least one mutant. We found that lignin biosynthesis and phenylalanine supply via the shikimate pathway are tightly co-regulated at the transcriptional level. The hierarchical clustering analysis of differentially expressed genes (DEGs) grouped the 13 mutants into 5 subgroups with similar profiles of mis-regulated genes. Functional analysis of the DEGs in these mutants and correlation between gene expression and metabolite accumulation revealed system-wide effects on transcripts involved in multiple biological processes.
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Affiliation(s)
- Peng Wang
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Longyun Guo
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - John Morgan
- Davidson School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
| | - Natalia Dudareva
- Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Center for Plant Biology, Purdue University, West Lafayette, Indiana 47907, USA
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6
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Hann EC, Overa S, Harland-Dunaway M, Narvaez AF, Le DN, Orozco-Cárdenas ML, Jiao F, Jinkerson RE. A hybrid inorganic-biological artificial photosynthesis system for energy-efficient food production. NATURE FOOD 2022; 3:461-471. [PMID: 37118051 DOI: 10.1038/s43016-022-00530-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/09/2022] [Indexed: 04/30/2023]
Abstract
Artificial photosynthesis systems are proposed as an efficient alternative route to capture CO2 to produce additional food for growing global demand. Here a two-step CO2 electrolyser system was developed to produce a highly concentrated acetate stream with a 57% carbon selectivity (CO2 to acetate), allowing its direct use for the heterotrophic cultivation of yeast, mushroom-producing fungus and a photosynthetic green alga, in the dark without inputs from biological photosynthesis. An evaluation of nine crop plants found that carbon from exogenously supplied acetate incorporates into biomass through major metabolic pathways. Coupling this approach to existing photovoltaic systems could increase solar-to-food energy conversion efficiency by about fourfold over biological photosynthesis, reducing the solar footprint required. This technology allows for a reimagination of how food can be produced in controlled environments.
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Affiliation(s)
- Elizabeth C Hann
- Center for Industrial Biotechnology, Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Sean Overa
- Center for Catalytic Science and Technology, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA
| | - Marcus Harland-Dunaway
- Center for Industrial Biotechnology, Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Andrés F Narvaez
- Center for Industrial Biotechnology, Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
- Plant Transformation Research Center, University of California, Riverside, CA, USA
| | - Dang N Le
- Center for Industrial Biotechnology, Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA
| | | | - Feng Jiao
- Center for Catalytic Science and Technology, Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, DE, USA.
| | - Robert E Jinkerson
- Center for Industrial Biotechnology, Department of Chemical and Environmental Engineering, University of California, Riverside, CA, USA.
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, CA, USA.
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7
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Tag you're it: Application of stable isotope labeling and LC-MS to identify the precursors of specialized metabolites in plants. Methods Enzymol 2022; 676:279-303. [DOI: 10.1016/bs.mie.2022.07.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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8
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Wang H, Guo H, Wang N, Huo YX. Toward the Heterologous Biosynthesis of Plant Natural Products: Gene Discovery and Characterization. ACS Synth Biol 2021; 10:2784-2795. [PMID: 34757715 DOI: 10.1021/acssynbio.1c00315] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Plant natural products (PNPs) represent a vast and diverse group of natural products, which have wide applications such as emulsifiers in cosmetics, sweeteners in foods, and active ingredients in medicines. Large-scale production of certain PNPs (e.g., artemisinin, taxol) has been implemented by reconstruction of biosynthetic pathways in heterologous hosts. However, unknown biosynthetic pathways greatly restrict wide applications of heterologous production of PNPs of interest. With the rapid development of sequencing and multiomics analysis technologies, huge amounts of omics data, i.e., genomics, transcriptomics, and proteomics, have been deposited in public databases, which is a precious resource for identification of the unknown biosynthetic pathway of PNPs. Herein, we have enumerated the approaches which have been widely used to screen candidate genes involved in the biosynthesis of PNPs of interest. We also discuss recent developments in the characterization of putative genes and elucidation of the complete biosynthetic pathway in heterologous hosts.
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Affiliation(s)
- Huiyan Wang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Hao Guo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Ning Wang
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
| | - Yi-Xin Huo
- School of Life Science, Beijing Institute of Technology, No. 5 South Zhongguancun Street, 100081 Beijing, China
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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9
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Simpson JP, Wunderlich C, Li X, Svedin E, Dilkes B, Chapple C. Metabolic source isotopic pair labeling and genome-wide association are complementary tools for the identification of metabolite-gene associations in plants. THE PLANT CELL 2021; 33:492-510. [PMID: 33955498 PMCID: PMC8136897 DOI: 10.1093/plcell/koaa046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 12/21/2020] [Indexed: 05/02/2023]
Abstract
The optimal extraction of information from untargeted metabolomics analyses is a continuing challenge. Here, we describe an approach that combines stable isotope labeling, liquid chromatography- mass spectrometry (LC-MS), and a computational pipeline to automatically identify metabolites produced from a selected metabolic precursor. We identified the subset of the soluble metabolome generated from phenylalanine (Phe) in Arabidopsis thaliana, which we refer to as the Phe-derived metabolome (FDM) In addition to identifying Phe-derived metabolites present in a single wild-type reference accession, the FDM was established in nine enzymatic and regulatory mutants in the phenylpropanoid pathway. To identify genes associated with variation in Phe-derived metabolites in Arabidopsis, MS features collected by untargeted metabolite profiling of an Arabidopsis diversity panel were retrospectively annotated to the FDM and natural genetic variants responsible for differences in accumulation of FDM features were identified by genome-wide association. Large differences in Phe-derived metabolite accumulation and presence/absence variation of abundant metabolites were observed in the nine mutants as well as between accessions from the diversity panel. Many Phe-derived metabolites that accumulated in mutants also accumulated in non-Col-0 accessions and was associated to genes with known or suspected functions in the phenylpropanoid pathway as well as genes with no known functions. Overall, we show that cataloguing a biochemical pathway's products through isotopic labeling across genetic variants can substantially contribute to the identification of metabolites and genes associated with their biosynthesis.
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Affiliation(s)
| | | | - Xu Li
- Plants for Human Health Institute, North Carolina State University, Kannapolis, NC 28081, USA
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC 27695, USA
| | | | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Center for Plant Biology, West Lafayette, IN 47907, USA
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN 47907, USA
- Purdue University Center for Plant Biology, West Lafayette, IN 47907, USA
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10
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Zhang Y, Gao B, Valdiviez L, Zhu C, Gallagher T, Whiteson K, Fiehn O. Comparing Stable Isotope Enrichment by Gas Chromatography with Time-of-Flight, Quadrupole Time-of-Flight, and Quadrupole Mass Spectrometry. Anal Chem 2021; 93:2174-2182. [PMID: 33434014 PMCID: PMC10782559 DOI: 10.1021/acs.analchem.0c04013] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Stable isotope tracers are applied for in vivo and in vitro studies to reveal the activity of enzymes and intracellular metabolic pathways. Most often, such tracers are used with gas chromatography coupled to mass spectrometry (GC-MS) owing to its ease of operation and reproducible mass spectral databases. Differences in isotope tracer performance of the classic GC-quadrupole MS instrument and newer time-of-flight instruments are not well studied. Here, we used three commercially available instruments for the analysis of identical samples from a stable isotope labeling study that used [U-13C6] d-glucose to investigate the metabolism of the bacterium Rothia mucilaginosa with respect to 29 amino acids and hydroxyl acids involved in primary metabolism. The prokaryote R. mucilaginosa belongs to the family of Micrococcaceae and is present and metabolically active in the airways and sputum of cystic fibrosis patients. Overall, all three GC-MS instruments (low-resolution GC-SQ MS, low-resolution GC-TOF MS, and high-resolution GC-QTOF MS) can be used to perform stable isotope tracing studies for glycolytic intermediates, tricarboxylic acid (TCA) metabolites, and amino acids, yielding similar biological results, with high-resolution GC-QTOF MS offering additional capabilities to identify the chemical structures of unknown compounds that might show significant isotope enrichments in biological studies.
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Affiliation(s)
- Ying Zhang
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
- Department of Chemistry, University of California, Davis, 95616, CA, USA
| | - Bei Gao
- Department of Medicine, University of California, San Diego, San Diego, 92093, CA, USA
- School of Marine Sciences, Nanjing University of Information Science and Technology, Nanjing, 210044, China
| | - Luis Valdiviez
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
| | - Chao Zhu
- College of Medicine & Nursing, Dezhou University, De Zhou, Shandong, 253023, China
| | - Tara Gallagher
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Katrine Whiteson
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Oliver Fiehn
- West Coast Metabolomics Center, University of California, Davis, 95616, CA, USA
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11
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Simpson JP, Olson J, Dilkes B, Chapple C. Identification of the Tyrosine- and Phenylalanine-Derived Soluble Metabolomes of Sorghum. FRONTIERS IN PLANT SCIENCE 2021; 12:714164. [PMID: 34594350 PMCID: PMC8476951 DOI: 10.3389/fpls.2021.714164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 07/23/2021] [Indexed: 05/16/2023]
Abstract
The synthesis of small organic molecules, known as specialized or secondary metabolites, is one mechanism by which plants resist and tolerate biotic and abiotic stress. Many specialized metabolites are derived from the aromatic amino acids phenylalanine (Phe) and tyrosine (Tyr). In addition, the improved characterization of compounds derived from these amino acids could inform strategies for developing crops with greater resilience and improved traits for the biorefinery. Sorghum and other grasses possess phenylalanine ammonia-lyase (PAL) enzymes that generate cinnamic acid from Phe and bifunctional phenylalanine/tyrosine ammonia-lyase (PTAL) enzymes that generate cinnamic acid and p-coumaric acid from Phe and Tyr, respectively. Cinnamic acid can, in turn, be converted into p-coumaric acid by cinnamate 4-hydroxylase. Thus, Phe and Tyr are both precursors of common downstream products. Not all derivatives of Phe and Tyr are shared, however, and each can act as a precursor for unique metabolites. In this study, 13C isotopic-labeled precursors and the recently developed Precursor of Origin Determination in Untargeted Metabolomics (PODIUM) mass spectrometry (MS) analytical pipeline were used to identify over 600 MS features derived from Phe and Tyr in sorghum. These features comprised 20% of the MS signal collected by reverse-phase chromatography and detected through negative-ionization. Ninety percent of the labeled mass features were derived from both Phe and Tyr, although the proportional contribution of each precursor varied. In addition, the relative incorporation of Phe and Tyr varied between metabolites and tissues, suggesting the existence of multiple pools of p-coumaric acid that are fed by the two amino acids. Furthermore, Phe incorporation was greater for many known hydroxycinnamate esters and flavonoid glycosides. In contrast, mass features derived exclusively from Tyr were the most abundant in every tissue. The Phe- and Tyr-derived metabolite library was also utilized to retrospectively annotate soluble MS features in two brown midrib mutants (bmr6 and bmr12) identifying several MS features that change significantly in each mutant.
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Affiliation(s)
- Jeffrey P. Simpson
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Jacob Olson
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
| | - Brian Dilkes
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Plant Biology, West Lafayette, IN, United States
- *Correspondence: Brian Dilkes
| | - Clint Chapple
- Department of Biochemistry, Purdue University, West Lafayette, IN, United States
- Purdue University Center for Plant Biology, West Lafayette, IN, United States
- Clint Chapple
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12
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Tivendale ND, Hanson AD, Henry CS, Hegeman AD, Millar AH. Enzymes as Parts in Need of Replacement - and How to Extend Their Working Life. TRENDS IN PLANT SCIENCE 2020; 25:661-669. [PMID: 32526171 DOI: 10.1016/j.tplants.2020.02.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 02/11/2020] [Accepted: 02/14/2020] [Indexed: 06/11/2023]
Abstract
Enzymes catalyze reactions in vivo at different rates and each enzyme molecule has a lifetime limit before it is degraded and replaced to enable catalysis to continue. Considering these rates together as a unitless ratio of catalytic cycles until replacement (CCR) provides a new quantitative tool to assess the replacement schedule of and energy investment into enzymes as they relate to function. Here, we outline the challenges of determining CCRs and new approaches to overcome them and then assess the CCRs of selected enzymes in bacteria and plants to reveal a range of seven orders of magnitude for this ratio. Modifying CCRs in plants holds promise to lower cellular costs, to tailor enzymes for particular environments, and to breed enzyme improvements for crop productivity.
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Affiliation(s)
- Nathan D Tivendale
- ARC Centre for Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, M316, Perth, WA 6009, Australia
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, PO Box 110690, Gainesville, FL 32611-0690, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA; Computation Institute, The University of Chicago, Chicago, IL 60637, USA
| | - Adrian D Hegeman
- Department of Horticultural Science, Department of Plant and Microbial Biology, and The Microbial and Plant Genomics Institute, University of Minnesota, 1970 Folwell Avenue, Saint Paul, MN 55108-6007, USA
| | - A Harvey Millar
- ARC Centre for Excellence in Plant Energy Biology, School of Molecular Sciences, The University of Western Australia, M316, Perth, WA 6009, Australia.
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13
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Jacobowitz JR, Weng JK. Exploring Uncharted Territories of Plant Specialized Metabolism in the Postgenomic Era. ANNUAL REVIEW OF PLANT BIOLOGY 2020; 71:631-658. [PMID: 32176525 DOI: 10.1146/annurev-arplant-081519-035634] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
For millennia, humans have used plants for food, raw materials, and medicines, but only within the past two centuries have we begun to connect particular plant metabolites with specific properties and utilities. Since the utility of classical molecular genetics beyond model species is limited, the vast specialized metabolic systems present in the Earth's flora remain largely unstudied. With an explosion in genomics resources and a rapidly expanding toolbox over the past decade, exploration of plant specialized metabolism in nonmodel species is becoming more feasible than ever before. We review the state-of-the-art tools that have enabled this rapid progress. We present recent examples of de novo biosynthetic pathway discovery that employ various innovative approaches. We also draw attention to the higher-order organization of plant specialized metabolism at subcellular, cellular, tissue, interorgan, and interspecies levels, which will have important implications for the future design of comprehensive metabolic engineering strategies.
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Affiliation(s)
- Joseph R Jacobowitz
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Jing-Ke Weng
- Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA;
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Allen DK, Young JD. Tracing metabolic flux through time and space with isotope labeling experiments. Curr Opin Biotechnol 2019; 64:92-100. [PMID: 31864070 PMCID: PMC7302994 DOI: 10.1016/j.copbio.2019.11.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 11/02/2019] [Accepted: 11/04/2019] [Indexed: 12/11/2022]
Abstract
Metabolism is dynamic and must function in context-specific ways to adjust to changes in the surrounding cellular and ecological environment. When isotopic tracers are used, metabolite flow (i.e. metabolic flux) can be quantified through biochemical networks to assess metabolic pathway operation. The cellular activities considered across multiple tissues and organs result in the observed phenotype and can be analyzed to discover emergent, whole-system properties of biology and elucidate misconceptions about network operation. However, temporal and spatial challenges remain significant hurdles and require novel approaches and creative solutions. We survey current investigations in higher plant and animal systems focused on dynamic isotope labeling experiments, spatially resolved measurement strategies, and observations from re-analysis of our own studies that suggest prospects for future work. Related discoveries will be necessary to push the frontier of our understanding of metabolism to suggest novel solutions to cure disease and feed a growing future world population.
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Affiliation(s)
- Doug K Allen
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, 975 North Warson Road, St. Louis, MO 63132, United States; Donald Danforth Plant Science Center, 975 North Warson Road, St. Louis, MO 63132, United States.
| | - Jamey D Young
- Department of Chemical & Biomolecular Engineering, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States; Department of Molecular Physiology & Biophysics, Vanderbilt University, PMB 351604, 2301 Vanderbilt Place, Nashville, TN 37235, United States.
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15
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Dixon RA, Barros J. Lignin biosynthesis: old roads revisited and new roads explored. Open Biol 2019; 9:190215. [PMID: 31795915 PMCID: PMC6936255 DOI: 10.1098/rsob.190215] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 10/30/2019] [Indexed: 12/31/2022] Open
Abstract
Lignin is a major component of secondarily thickened plant cell walls and is considered to be the second most abundant biopolymer on the planet. At one point believed to be the product of a highly controlled polymerization procedure involving just three potential monomeric components (monolignols), it is becoming increasingly clear that the composition of lignin is quite flexible. Furthermore, the biosynthetic pathways to the major monolignols also appear to exhibit flexibility, particularly as regards the early reactions leading to the formation of caffeic acid from coumaric acid. The operation of parallel pathways to caffeic acid occurring at the level of shikimate esters or free acids may help provide robustness to the pathway under different physiological conditions. Several features of the pathway also appear to link monolignol biosynthesis to both generation and detoxification of hydrogen peroxide, one of the oxidants responsible for creating monolignol radicals for polymerization in the apoplast. Monolignol transport to the apoplast is not well understood. It may involve passive diffusion, although this may be targeted to sites of lignin initiation/polymerization by ordered complexes of both biosynthetic enzymes on the cytosolic side of the plasma membrane and structural anchoring of proteins for monolignol oxidation and polymerization on the apoplastic side. We present several hypothetical models to illustrate these ideas and stimulate further research. These are based primarily on studies in model systems, which may or may not reflect the major lignification process in forest trees.
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Affiliation(s)
- Richard A. Dixon
- Hagler Institute for Advanced Studies and Department of Biological Sciences, Texas A&M University, College Station, TX, USA
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
| | - Jaime Barros
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, 1155 Union Circle #311428, Denton, TX 76203-5017, USA
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16
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Wang S, Alseekh S, Fernie AR, Luo J. The Structure and Function of Major Plant Metabolite Modifications. MOLECULAR PLANT 2019; 12:899-919. [PMID: 31200079 DOI: 10.1016/j.molp.2019.06.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 05/27/2019] [Accepted: 06/04/2019] [Indexed: 05/23/2023]
Abstract
Plants produce a myriad of structurally and functionally diverse metabolites that play many different roles in plant growth and development and in plant response to continually changing environmental conditions as well as abiotic and biotic stresses. This metabolic diversity is, to a large extent, due to chemical modification of the basic skeletons of metabolites. Here, we review the major known plant metabolite modifications and summarize the progress that has been achieved and the challenges we are facing in the field. We focus on discussing both technical and functional aspects in studying the influences that various modifications have on biosynthesis, degradation, transport, and storage of metabolites, as well as their bioactivity and toxicity. Finally, we discuss some emerging insights into the evolution of metabolic pathways and metabolite functionality.
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Affiliation(s)
- Shouchuang Wang
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China
| | - Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria
| | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm 14476, Germany; Centre of Plant Systems Biology and Biotechnology, Plovdiv 4000, Bulgaria.
| | - Jie Luo
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou 572208, China; National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
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17
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4-Coumarate 3-hydroxylase in the lignin biosynthesis pathway is a cytosolic ascorbate peroxidase. Nat Commun 2019; 10:1994. [PMID: 31040279 PMCID: PMC6491607 DOI: 10.1038/s41467-019-10082-7] [Citation(s) in RCA: 125] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 04/15/2019] [Indexed: 12/04/2022] Open
Abstract
Lignin biosynthesis is evolutionarily conserved among higher plants and features a critical 3-hydroxylation reaction involving phenolic esters. However, increasing evidence questions the involvement of a single pathway to lignin formation in vascular plants. Here we describe an enzyme catalyzing the direct 3-hydroxylation of 4-coumarate to caffeate in lignin biosynthesis as a bifunctional peroxidase that oxidizes both ascorbate and 4-coumarate at comparable rates. A combination of biochemical and genetic evidence in the model plants Brachypodium distachyon and Arabidopsis thaliana supports a role for this coumarate 3-hydroxylase (C3H) in the early steps of lignin biosynthesis. The subsequent efficient O-methylation of caffeate to ferulate in grasses is substantiated by in vivo biochemical assays. Our results identify C3H as the only non-membrane bound hydroxylase in the lignin pathway and revise the currently accepted models of lignin biosynthesis, suggesting new gene targets to improve forage and bioenergy crops. Lignin biosynthesis in higher plants relies upon a 3-hydroxylation reaction that can occur via shikimate esters of 4-coumarate. Here, Barros et al. define an alternative biosynthetic pathway via cytosolic ascorbate peroxidase that can catalyze direct 3-hydroxylation of 4-coumarate.
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18
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Perez de Souza L, Scossa F, Proost S, Bitocchi E, Papa R, Tohge T, Fernie AR. Multi-tissue integration of transcriptomic and specialized metabolite profiling provides tools for assessing the common bean (Phaseolus vulgaris) metabolome. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:1132-1153. [PMID: 30480348 PMCID: PMC6850281 DOI: 10.1111/tpj.14178] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 11/15/2018] [Accepted: 11/23/2018] [Indexed: 05/02/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an important legume species with a rich natural diversity of landraces that originated from the wild forms following multiple independent domestication events. After the publication of its genome, several resources for this relevant crop have been made available. A comprehensive characterization of specialized metabolism in P. vulgaris, however, is still lacking. In this study, we used a metabolomics approach based on liquid chromatography-mass spectrometry to dissect the chemical composition at a tissue-specific level in several accessions of common bean belonging to different gene pools. Using a combination of literature search, mass spectral interpretation, 13 C-labeling, and correlation analyses, we were able to assign chemical classes and/or putative structures for approximately 39% of all measured metabolites. Additionally, we integrated this information with transcriptomics data and phylogenetic inference from multiple legume species to reconstruct the possible metabolic pathways and identify sets of candidate genes involved in the biosynthesis of specialized metabolites. A particular focus was given to flavonoids, triterpenoid saponins and hydroxycinnamates, as they represent metabolites involved in important ecological interactions and they are also associated with several health-promoting benefits when integrated into the human diet. The data are presented here in the form of an accessible resource that we hope will set grounds for further studies on specialized metabolism in legumes.
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Affiliation(s)
| | - Federico Scossa
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Consiglio per la ricerca in agricoltura e l′analisi dell′economia agrariaCREA‐OFAVia di Fioranello 5200134RomeItaly
| | - Sebastian Proost
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental SciencesUniversità Politecnica delle Marche60131AnconaItaly
| | - Takayuki Tohge
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
- Graduate School of Biological SciencesNara Institute of Science and TechnologyIkoma, Nara630‐0192Japan
| | - Alisdair R. Fernie
- Max‐Planck‐Institute of Molecular Plant PhysiologyAm Müehlenberg 1Potsdam‐Golm14476Germany
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Borland K, Diesend J, Ito-Kureha T, Heissmeyer V, Hammann C, Buck AH, Michalakis S, Kellner S. Production and Application of Stable Isotope-Labeled Internal Standards for RNA Modification Analysis. Genes (Basel) 2019; 10:E26. [PMID: 30621251 PMCID: PMC6356711 DOI: 10.3390/genes10010026] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/17/2018] [Accepted: 12/26/2018] [Indexed: 12/04/2022] Open
Abstract
Post-transcriptional RNA modifications have been found to be present in a wide variety of organisms and in different types of RNA. Nucleoside modifications are interesting due to their already known roles in translation fidelity, enzyme recognition, disease progression, and RNA stability. In addition, the abundance of modified nucleosides fluctuates based on growth phase, external stress, or possibly other factors not yet explored. With modifications ever changing, a method to determine absolute quantities for multiple nucleoside modifications is required. Here, we report metabolic isotope labeling to produce isotopically labeled internal standards in bacteria and yeast. These can be used for the quantification of 26 different modified nucleosides. We explain in detail how these internal standards are produced and show their mass spectrometric characterization. We apply our internal standards and quantify the modification content of transfer RNA (tRNA) from bacteria and various eukaryotes. We can show that the origin of the internal standard has no impact on the quantification result. Furthermore, we use our internal standard for the quantification of modified nucleosides in mouse tissue messenger RNA (mRNA), where we find different modification profiles in liver and brain tissue.
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Affiliation(s)
- Kayla Borland
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Jan Diesend
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Taku Ito-Kureha
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
| | - Vigo Heissmeyer
- Institute for Immunology at the Biomedical Center, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany.
- Helmholtz Zentrum München, Research Unit Molecular Immune Regulation, Marchioninistr. 25, 81377 Munich, Germany.
| | - Christian Hammann
- Department of Life Sciences and Chemistry, Jacobs University Bremen GmbH, Campus Ring 1, 28759 Bremen, Germany.
| | - Amy H Buck
- Institute of Immunology & Infection and Centre for Immunity, Infection & Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FL, UK.
| | - Stylianos Michalakis
- Center for Integrated Protein Science Munich CiPSM at the Department of Pharmacy-Center for Drug Research, Ludwig-Maximilians-Universität München, Butenandtstr. 5-13, 81377 Munich, Germany.
| | - Stefanie Kellner
- Department of Chemistry, Ludwig Maximilians University Munich, Butenandtstr. 5-13, 81377 Munich, Germany.
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Methyl Jasmonate Changes the Composition and Distribution Rather than the Concentration of Defence Compounds: a Study on Pyrrolizidine Alkaloids. J Chem Ecol 2018; 45:136-145. [PMID: 30284188 DOI: 10.1007/s10886-018-1020-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2018] [Revised: 09/17/2018] [Accepted: 09/24/2018] [Indexed: 10/28/2022]
Abstract
In this study we investigated the effect of methyl jasmonate (MeJA) application on pyrrolizidine alkaloid (PA) concentration and composition of two closely related Jacobaea species. In addition, we examined whether MeJA application affected herbivory of the polyphagous leaf feeding herbivore Spodoptera exigua. A range of concentrations of MeJA was added to the medium of Jacobaea vulgaris and J. aquatica tissue culture plants grown under axenic conditions. PA concentrations were measured in roots and shoots using LC-MS/MS. In neither species MeJA application did affect the total PA concentration at the whole plant level. In J. vulgaris the total PA concentration decreased in roots but increased in shoots. In J. aquatica a similar non-significant trend was observed. In both Jacobaea species MeJA application induced a strong shift from senecionine- to erucifoline-like PAs, while the jacobine- and otosenine-like PAs remained largely unaffected. The results show that MeJA application does not necessarily elicits de novo synthesis, but rather leads to PA conversion combined with reallocation of certain PAs from roots to shoots. S. exigua preferred feeding on control leaves of J. aquatica over MeJA treated leaves, while for J. vulgaris both the control and MeJA treated leaves were hardly eaten. This suggests that the MeJA-induced increase of erucifoline-like PAs can play a role in resistance of J. aquatica to S. exigua. In J. vulgaris resistance to S. exigua may already be high due to the presence of jacobine-like PAs or other resistance factors.
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21
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Dynamic modeling of subcellular phenylpropanoid metabolism in Arabidopsis lignifying cells. Metab Eng 2018; 49:36-46. [DOI: 10.1016/j.ymben.2018.07.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Revised: 06/16/2018] [Accepted: 07/08/2018] [Indexed: 12/15/2022]
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