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Barreda L, Brosse C, Boutet S, Perreau F, Rajjou L, Lepiniec L, Corso M. Specialized metabolite modifications in Brassicaceae seeds and plants: diversity, functions and related enzymes. Nat Prod Rep 2024; 41:834-859. [PMID: 38323463 DOI: 10.1039/d3np00043e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
Covering: up to 2023Specialized metabolite (SM) modifications and/or decorations, corresponding to the addition or removal of functional groups (e.g. hydroxyl, methyl, glycosyl or acyl group) to SM structures, contribute to the huge diversity of structures, activities and functions of seed and plant SMs. This review summarizes available knowledge (up to 2023) on SM modifications in Brassicaceae and their contribution to SM plasticity. We give a comprehensive overview on enzymes involved in the addition or removal of these functional groups. Brassicaceae, including model (Arabidopsis thaliana) and crop (Brassica napus, Camelina sativa) plant species, present a large diversity of plant and seed SMs, which makes them valuable models to study SM modifications. In this review, particular attention is given to the environmental plasticity of SM and relative modification and/or decoration enzymes. Furthermore, a spotlight is given to SMs and related modification enzymes in seeds of Brassicaceae species. Seeds constitute a large reservoir of beneficial SMs and are one of the most important dietary sources, providing more than half of the world's intake of dietary proteins, oil and starch. The seed tissue- and stage-specific expressions of A. thaliana genes involved in SM modification are presented and discussed in the context of available literature. Given the major role in plant phytochemistry, biology and ecology, SM modifications constitute a subject of study contributing to the research and development in agroecology, pharmaceutical, cosmetics and food industrial sectors.
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Affiliation(s)
- Léa Barreda
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Céline Brosse
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Stéphanie Boutet
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - François Perreau
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Loïc Rajjou
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Loïc Lepiniec
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
| | - Massimiliano Corso
- Université Paris-Saclay, INRAE, AgroParisTech, Institut Jean-Pierre Bourgin (IJPB), 78000 Versailles, France.
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Rates ADB, Cesarino I. Pour some sugar on me: The diverse functions of phenylpropanoid glycosylation. JOURNAL OF PLANT PHYSIOLOGY 2023; 291:154138. [PMID: 38006622 DOI: 10.1016/j.jplph.2023.154138] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 11/06/2023] [Indexed: 11/27/2023]
Abstract
The phenylpropanoid metabolism is the source of a vast array of specialized metabolites that play diverse functions in plant growth and development and contribute to all aspects of plant interactions with their surrounding environment. These compounds protect plants from damaging ultraviolet radiation and reactive oxygen species, provide mechanical support for the plants to stand upright, and mediate plant-plant and plant-microorganism communications. The enormous metabolic diversity of phenylpropanoids is further expanded by chemical modifications known as "decorative reactions", including hydroxylation, methylation, glycosylation, and acylation. Among these modifications, glycosylation is the major driving force of phenylpropanoid structural diversification, also contributing to the expansion of their properties. Phenylpropanoid glycosylation is catalyzed by regioselective uridine diphosphate (UDP)-dependent glycosyltransferases (UGTs), whereas glycosyl hydrolases known as β-glucosidases are the major players in deglycosylation. In this article, we review how the glycosylation process affects key physicochemical properties of phenylpropanoids, such as molecular stability and solubility, as well as metabolite compartmentalization/storage and biological activity/toxicity. We also summarize the recent knowledge on the functional implications of glycosylation of different classes of phenylpropanoid compounds. A balance of glycosylation/deglycosylation might represent an essential molecular mechanism to regulate phenylpropanoid homeostasis, allowing plants to dynamically respond to diverse environmental signals.
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Affiliation(s)
- Arthur de Barros Rates
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil
| | - Igor Cesarino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, 05508-090, São Paulo, Brazil; Synthetic and Systems Biology Center, InovaUSP, Avenida Professor Lucio Martins Rodrigues 370, 05508-020, São Paulo, Brazil.
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3
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Wouters M, Bastiaanse H, Rombauts S, de Vries L, De Pooter T, Strazisar M, Neutelings G, Vanholme R, Boerjan W. Suppression of the Arabidopsis cinnamoyl-CoA reductase 1-6 intronic T-DNA mutation by epigenetic modification. PLANT PHYSIOLOGY 2023; 192:3001-3016. [PMID: 37139862 PMCID: PMC7614886 DOI: 10.1093/plphys/kiad261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/10/2023] [Accepted: 04/10/2023] [Indexed: 05/05/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) transfer DNA (T-DNA) insertion collections are popular resources for fundamental plant research. Cinnamoyl-CoA reductase 1 (CCR1) catalyzes an essential step in the biosynthesis of the cell wall polymer lignin. Accordingly, the intronic T-DNA insertion mutant ccr1-6 has reduced lignin levels and shows a stunted growth phenotype. Here, we report restoration of the ccr1-6 mutant phenotype and CCR1 expression levels after a genetic cross with a UDP-glucosyltransferase 72e1 (ugt72e1),-e2,-e3 T-DNA mutant. We discovered that the phenotypic recovery was not dependent on the UGT72E family loss of function but due to an epigenetic phenomenon called trans T-DNA suppression. Via trans T-DNA suppression, the gene function of an intronic T-DNA mutant was restored after the introduction of an additional T-DNA sharing identical sequences, leading to heterochromatinization and splicing out of the T-DNA-containing intron. Consequently, the suppressed ccr1-6 allele was named epiccr1-6. Long-read sequencing revealed that epiccr1-6, not ccr1-6, carries dense cytosine methylation over the full length of the T-DNA. We showed that the SAIL T-DNA in the UGT72E3 locus could trigger the trans T-DNA suppression of the GABI-Kat T-DNA in the CCR1 locus. Furthermore, we scanned the literature for other potential cases of trans T-DNA suppression in Arabidopsis and found that 22% of the publications matching our query report on double or higher-order T-DNA mutants that meet the minimal requirements for trans T-DNA suppression. These combined observations indicate that intronic T-DNA mutants need to be used with caution since methylation of intronic T-DNA might derepress gene expression and can thereby confound results.
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Affiliation(s)
- Marlies Wouters
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Héloïse Bastiaanse
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Stéphane Rombauts
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Lisanne de Vries
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Tim De Pooter
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Mojca Strazisar
- Neuromics Support Facility, VIB Center for Molecular Neurology, VIB, Antwerp, Belgium
- Department of Biomedical Sciences, University of Antwerp, Antwerp, Belgium
| | - Godfrey Neutelings
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576, CNRS, Université de Lille, Lille, France
| | - Ruben Vanholme
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wout Boerjan
- VIB Center for Plants Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
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Sun G, Liao J, Kurze E, Hoffmann TD, Steinchen W, McGraphery K, Habegger R, Marek L, Catici DAM, Ludwig C, Jing T, Hoffmann T, Song C, Schwab W. Apocarotenoids are allosteric effectors of a dimeric plant glycosyltransferase involved in defense and lignin formation. THE NEW PHYTOLOGIST 2023; 238:2080-2098. [PMID: 36908092 DOI: 10.1111/nph.18875] [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: 10/18/2022] [Accepted: 03/02/2023] [Indexed: 05/04/2023]
Abstract
Glycosyltransferases are nature's versatile tools to tailor the functionalities of proteins, carbohydrates, lipids, and small molecules by transferring sugars. Prominent substrates are hydroxycoumarins such as scopoletin, which serve as natural plant protection agents. Similarly, C13-apocarotenoids, which are oxidative degradation products of carotenoids/xanthophylls, protect plants by repelling pests and attracting pest predators. We show that C13-apocarotenoids interact with the plant glycosyltransferase NbUGT72AY1 and induce conformational changes in the enzyme catalytic center ultimately reducing its inherent UDP-α-d-glucose glucohydrolase activity and increasing its catalytic activity for productive hydroxycoumarin substrates. By contrast, C13-apocarotenoids show no effect on the catalytic activity toward monolignol lignin precursors, which are competitive substrates. In vivo studies in tobacco plants (Nicotiana benthamiana) confirmed increased glycosylation activity upon apocarotenoid supplementation. Thus, hydroxycoumarins and apocarotenoids represent specialized damage-associated molecular patterns, as they each provide precise information about the plant compartments damaged by pathogen attack. The molecular basis for the C13-apocarotenoid-mediated interplay of two plant protective mechanisms and their function as allosteric enhancers opens up potential applications of the natural products in agriculture and pharmaceutical industry.
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Affiliation(s)
- Guangxin Sun
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Jieren Liao
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Elisabeth Kurze
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35043, Marburg, Germany
| | - Kate McGraphery
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ruth Habegger
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Ludwig Marek
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Dragana A M Catici
- Center for Protein Assemblies (CPA), Technical University of Munich, Ernst-Otto-Fischer-Str. 8, 85748, Garching, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), School of Life Sciences Weihenstephan, Technische Universität München, Gregor-Mendel-Str. 4, 85354, Freising, Germany
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Thomas Hoffmann
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036, Hefei, Anhui, China
| | - Wilfried Schwab
- Biotechnology of Natural Products, School of Life Sciences Weihenstephan, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
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5
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Liao J, Sun G, Kurze E, Steinchen W, Hoffmann TD, Song C, Zou Z, Hoffmann T, Schwab WG. Subfunctionalization of a monolignol to a phytoalexin glucosyltransferase is accompanied by substrate inhibition. PLANT COMMUNICATIONS 2023; 4:100506. [PMID: 36566353 DOI: 10.1016/j.xplc.2022.100506] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 11/16/2022] [Accepted: 12/16/2022] [Indexed: 05/11/2023]
Abstract
Uridine diphosphate-dependent glycosyltransferases (UGTs) mediate the glycosylation of plant metabolites, thereby altering their physicochemical properties and bioactivities. Plants possess numerous UGT genes, with the encoded enzymes often glycosylating multiple substrates and some exhibiting substrate inhibition kinetics, but the biological function and molecular basis of these phenomena are not fully understood. The promiscuous monolignol/phytoalexin glycosyltransferase NbUGT72AY1 exhibits substrate inhibition (Ki) at 4 μM scopoletin, whereas the highly homologous monolignol StUGT72AY2 is inhibited at 190 μM. We therefore used hydrogen/deuterium exchange mass spectrometry and structure-based mutational analyses of both proteins and introduced NbUGT72AY1 residues into StUGT72AY2 and vice versa to study promiscuity and substrate inhibition of UGTs. A single F87I and chimeric mutant of NbUGT72AY1 showed significantly reduced scopoletin substrate inhibition, whereas its monolignol glycosylation activity was almost unaffected. Reverse mutations in StUGT72AY2 resulted in increased scopoletin glycosylation, leading to enhanced promiscuity, which was accompanied by substrate inhibition. Studies of 3D structures identified open and closed UGT conformers, allowing visualization of the dynamics of conformational changes that occur during catalysis. Previously postulated substrate access tunnels likely serve as drainage channels. The results suggest a two-site model in which the second substrate molecule binds near the catalytic site and blocks product release. Mutational studies showed that minor changes in amino acid sequence can enhance the promiscuity of the enzyme and add new capabilities such as substrate inhibition without affecting existing functions. The proposed subfunctionalization mechanism of expanded promiscuity may play a role in enzyme evolution and highlights the importance of promiscuous enzymes in providing new functions.
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Affiliation(s)
- Jieren Liao
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Guangxin Sun
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Elisabeth Kurze
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wieland Steinchen
- Center for Synthetic Microbiology (SYNMIKRO) & Faculty of Chemistry, Philipps-University Marburg, Karl-von-Frisch-Straße 14, 35043 Marburg, Germany
| | - Timothy D Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Chuankui Song
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, 230036 Hefei, Anhui, P. R. China
| | - Zhiwei Zou
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Thomas Hoffmann
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany
| | - Wilfried G Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354 Freising, Germany.
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Pancaldi F, van Loo EN, Senio S, Al Hassan M, van der Cruijsen K, Paulo MJ, Dolstra O, Schranz ME, Trindade LM. Syntenic Cell Wall QTLs as Versatile Breeding Tools: Intraspecific Allelic Variability and Predictability of Biomass Quality Loci in Target Plant Species. PLANTS (BASEL, SWITZERLAND) 2023; 12:779. [PMID: 36840127 PMCID: PMC9961111 DOI: 10.3390/plants12040779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Syntenic cell wall QTLs (SQTLs) can identify genetic determinants of biomass traits in understudied species based on results from model crops. However, their effective use in plant breeding requires SQTLs to display intraspecific allelic variability and to predict causative loci in other populations/species than the ones used for SQTLs identification. In this study, genome assemblies from different accessions of Arabidopsis, rapeseed, tomato, rice, Brachypodium and maize were used to evaluate the intraspecific variability of SQTLs. In parallel, a genome-wide association study (GWAS) on cell wall quality traits was performed in miscanthus to verify the colocalization between GWAS loci and miscanthus SQTLs. Finally, an analogous approach was applied on a set of switchgrass cell wall QTLs retrieved from the literature. These analyses revealed large SQTLs intraspecific genetic variability, ranging from presence-absence gene variation to SNPs/INDELs and changes in coded proteins. Cell wall genes displaying gene dosage regulation, such as PAL and CAD, displayed presence-absence variation in Brachypodium and rapeseed, while protein INDELs were detected for the Brachypodium homologs of the rice brittle culm-like 8 locus, which may likely impact cell wall quality. Furthermore, SQTLs significantly colocalized with the miscanthus and switchgrass QTLs, with relevant cell wall genes being retained in colocalizing regions. Overall, SQTLs are useful tools to screen germplasm for relevant genes and alleles to improve biomass quality and can increase the efficiency of plant breeding in understudied biomass crops.
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Affiliation(s)
- Francesco Pancaldi
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Eibertus N. van Loo
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sylwia Senio
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Mohamad Al Hassan
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Kasper van der Cruijsen
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria-João Paulo
- Biometris, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Oene Dolstra
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - M. Eric Schranz
- Biosystematics, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Luisa M. Trindade
- Plant Breeding, Wageningen University & Research, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
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Li N, Zhou D, Li N, Kong S, Shang J, Zhu W, Wang J, Ma S. Identification of the egusi seed trait locus (eg) and its suppressor gene associated with the thin seed coat trait in watermelon. FRONTIERS IN PLANT SCIENCE 2023; 14:1018975. [PMID: 36794224 PMCID: PMC9923051 DOI: 10.3389/fpls.2023.1018975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 01/04/2023] [Indexed: 06/18/2023]
Abstract
Egusi watermelon has a unique egusi seed type, which could be useful for breeding both edible seeds and edible flesh in watermelon. However, the genetic basis of the unique egusi seed type is not clear. In the present study, we first reported that at least two genes with inhibitory epistasis were responsible for the thin seed coat (unique egusi seed type) in watermelon. Inheritance analysis of five populations, including F2, BC, and BCF2, suggested that the thin seed coat trait was controlled by a suppressor gene together with the egusi seed locus (eg) in egusi watermelon. Based on high-throughput sequencing technology, two quantitative trait loci located on chromosome 1 and chromosome 6 were identified for the thin seed coat trait in watermelon. One of the loci, the eg locus on chromosome 6, was finely mapped to a genomic region of 15.7 kb, which contained only one candidate gene. Comparative transcriptome analysis highlighted differentially expressed genes involved in cellulose and lignin synthesis between watermelon genotypes varying in the thickness of the seed coat and provided several potential candidate genes for the thin seed coat trait. Taken together, our data suggest that at least two genes are complementarily involved in the thin seed coat trait and will be useful for cloning novel genes. The results presented here provide a new reference for uncovering egusi seed genetic mechanisms and valuable information for marker-assisted selection in seed coat breeding.
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Affiliation(s)
- Na Li
- *Correspondence: Na Li, ; Shuangwu Ma,
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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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Wu J, Zhu W, Shan X, Liu J, Zhao L, Zhao Q. Glycoside-specific metabolomics combined with precursor isotopic labeling for characterizing plant glycosyltransferases. MOLECULAR PLANT 2022; 15:1517-1532. [PMID: 35996753 DOI: 10.1016/j.molp.2022.08.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 07/19/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
Glycosylation by uridine diphosphate-dependent glycosyltransferases (UGTs) in plants contributes to the complexity and diversity of secondary metabolites. UGTs are generally promiscuous in their use of acceptors, making it challenging to reveal the function of UGTs in vivo. Here, we described an approach that combined glycoside-specific metabolomics and precursor isotopic labeling analysis to characterize UGTs in Arabidopsis. We revisited the UGT72E cluster, which has been reported to catalyze the glycosylation of monolignols. Glycoside-specific metabolomics analysis reduced the number of differentially accumulated metabolites in the ugt72e1e2e3 mutant by at least 90% compared with that from traditional untargeted metabolomics analysis. In addition to the two previously reported monolignol glycosides, a total of 62 glycosides showed reduced accumulation in the ugt72e1e2e3 mutant, 22 of which were phenylalanine-derived glycosides, including 5-OH coniferyl alcohol-derived and lignan-derived glycosides, as confirmed by isotopic tracing of [13C6]-phenylalanine precursor. Our method revealed that UGT72Es could use coumarins as substrates, and genetic evidence showed that UGT72Es endowed plants with enhanced tolerance to low iron availability under alkaline conditions. Using the newly developed method, the function of UGT78D2 was also evaluated. These case studies suggest that this method can substantially contribute to the characterization of UGTs and efficiently investigate glycosylation processes, the complexity of which have been highly underestimated.
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Affiliation(s)
- Jie Wu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Wentao Zhu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaotong Shan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jinyue Liu
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Lingling Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Qiao Zhao
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China; Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China.
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Wang H, Feng X, Zhang Y, Wei D, Zhang Y, Jin Q, Cai Y. PbUGT72AJ2-Mediated Glycosylation Plays an Important Role in Lignin Formation and Stone Cell Development in Pears (Pyrus bretschneideri). Int J Mol Sci 2022; 23:ijms23147893. [PMID: 35887241 PMCID: PMC9318811 DOI: 10.3390/ijms23147893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 12/04/2022] Open
Abstract
Glycosylation is necessary for many processes of plant secondary metabolism. It can maintain plant homeostasis and is of great significance to normal plant growth and development. At present, the significance of glycosylation for lignin biosynthesis has been proven in some plants, but it has not yet been reported in pears. We used in situ hybridization, in vitro expression, substrate catalysis, transgenic Arabidopsisthaliana, and transient transformation of pear fruit in our investigation, which was predicated on the identification of a gene PbUGT72AJ2 that may be involved in lignin monolignol glycosylation according to our previous work. These results revealed that PbUGT72AJ2 transcripts were localized to some pulp cell walls, lignin deposition, and stone cell areas of pear fruit. The recombinant PbUGT72AJ2-pGEX4T-1 protein had activity against coniferyl alcohol and sinapyl alcohol, and its catalytic efficiency against coniferyl alcohol was higher than that against sinapyl alcohol. When PbUGT72AJ2 was transferred into Arabidopsisthaliana mutants, it was found that some characteristics of Arabidopsisthalianaugt72e3 mutants were restored. In Arabidopsisthaliana, overexpression of PbUGT72AJ2 enhanced the contents of coniferin and syringin, whereas lignification did not change significantly. Transient transformation of pear fruit showed that when PbUGT72AJ2 in pear fruit was silenced by RNA interference, the content of lignin and stone cells in pear fruit increased, whereas the gene PbUGT72AJ2 was overexpressed in pear fruit, and there was almost no change in the pear fruit compared with the control. Lignin deposition in pear fruit was closely related to stone cell development. In this study, we proved that PbUGT72AJ2 plays an important role in lignin deposition and stone cell development in pear fruit, which provides a molecular biological basis for improving pear fruit quality at the molecular level.
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Affiliation(s)
- Han Wang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Xiaofeng Feng
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yingjie Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Dongyi Wei
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yang Zhang
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Qing Jin
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
| | - Yongping Cai
- School of Life Sciences, Anhui Agricultural University, Hefei 230036, China; (H.W.); (X.F.); (Y.Z.); (D.W.); (Y.Z.); (Q.J.)
- Anhui Provincial Engineering Technology Research Center for Development & Utilization of Regional Characteristic Plants, Anhui Agricultural University, No. 130, Changjiang West Road, Hefei 230036, China
- Correspondence:
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UGT72, a Major Glycosyltransferase Family for Flavonoid and Monolignol Homeostasis in Plants. BIOLOGY 2022; 11:biology11030441. [PMID: 35336815 PMCID: PMC8945231 DOI: 10.3390/biology11030441] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/07/2022] [Accepted: 03/11/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Phenylpropanoids are specialized metabolites playing crucial roles in plant developmental processes and in plant defense towards pathogens. The attachment of sugar moieties to these small hydrophobic molecules renders them more hydrophilic and increases their solubility. The UDP-glycosyltransferase 72 family (UGT72) of plants has been shown to glycosylate mainly two classes of phenylpropanoids, (i) the monolignols that are the building blocks of lignin, the second most abundant polymer after cellulose, and (ii) the flavonoids, which play determinant roles in plant interactions with other organisms and in response to stress. The purpose of this review is to bring an overview of the current knowledge of the UGT72 family and to highlight its role in the homeostasis of these molecules. Potential applications in pharmacology and in wood, paper pulp, and bioethanol production are given within the perspectives. Abstract Plants have developed the capacity to produce a diversified range of specialized metabolites. The glycosylation of those metabolites potentially decreases their toxicity while increasing their stability and their solubility, modifying their transport and their storage. The UGT, forming the largest glycosyltransferase superfamily in plants, combine enzymes that glycosylate mainly hormones and phenylpropanoids by using UDP-sugar as a sugar donor. Particularly, members of the UGT72 family have been shown to glycosylate the monolignols and the flavonoids, thereby being involved in their homeostasis. First, we explore primitive UGTs in algae and liverworts that are related to the angiosperm UGT72 family and their role in flavonoid homeostasis. Second, we describe the role of several UGT72s glycosylating monolignols, some of which have been associated with lignification. In addition, the role of other UGT72 members that glycosylate flavonoids and are involved in the development and/or stress response is depicted. Finally, the importance to explore the subcellular localization of UGTs to study their roles in planta is discussed.
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Morel O, Lion C, Neutelings G, Stefanov J, Baldacci‐Cresp F, Simon C, Biot C, Hawkins S, Spriet C. REPRISAL: mapping lignification dynamics using chemistry, data segmentation, and ratiometric analysis. PLANT PHYSIOLOGY 2022; 188:816-830. [PMID: 34687294 PMCID: PMC8825451 DOI: 10.1093/plphys/kiab490] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 10/05/2021] [Indexed: 05/04/2023]
Abstract
This article describes a methodology for detailed mapping of the lignification capacity of plant cell walls that we have called "REPRISAL" for REPorter Ratiometrics Integrating Segmentation for Analyzing Lignification. REPRISAL consists of the combination of three separate approaches. In the first approach, H*, G*, and S* monolignol chemical reporters, corresponding to p-coumaryl alcohol, coniferyl alcohol, and sinapyl alcohol, are used to label the growing lignin polymer in a fluorescent triple labeling strategy based on the sequential use of three main bioorthogonal chemical reactions. In the second step, an automatic parametric and/or artificial intelligence segmentation algorithm is developed that assigns fluorescent image pixels to three distinct cell wall zones corresponding to cell corners, compound middle lamella and secondary cell walls. The last step corresponds to the exploitation of a ratiometric approach enabling statistical analyses of differences in monolignol reporter distribution (ratiometric method [RM] 1) and proportions (RM 2) within the different cell wall zones. We first describe the use of this methodology to map developmentally related changes in the lignification capacity of wild-type Arabidopsis (Arabidopsis thaliana) interfascicular fiber cells. We then apply REPRISAL to analyze the Arabidopsis peroxidase (PRX) mutant prx64 and provide further evidence for the implication of the AtPRX64 protein in floral stem lignification. In addition, we also demonstrate the general applicability of REPRISAL by using it to map lignification capacity in poplar (Populus tremula × Populus alba), flax (Linum usitatissimum), and maize (Zea mays). Finally, we show that the methodology can be used to map the incorporation of a fucose reporter into noncellulosic cell wall polymers.
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Affiliation(s)
- Oriane Morel
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
- Institute of Biophysics, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Cedric Lion
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
| | - Godfrey Neutelings
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
| | - Jonathan Stefanov
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41—UMS 2014—PLBS, Lille F-59000, France
| | - Fabien Baldacci‐Cresp
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
| | - Clemence Simon
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41—UMS 2014—PLBS, Lille F-59000, France
| | - Christophe Biot
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
- Author for communication:
| | - Simon Hawkins
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
| | - Corentin Spriet
- Univ. Lille, CNRS, UMR 8576—UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, Lille F 59000, France
- Univ. Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41—UMS 2014—PLBS, Lille F-59000, France
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Genome-wide identification and expression analysis of glycosyltransferase gene family 1 in Quercus robur L. J Appl Genet 2021; 62:559-570. [PMID: 34241817 DOI: 10.1007/s13353-021-00650-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 10/20/2022]
Abstract
Glycosyltransferase gene family 1, also known as uridine diphosphate glycosyltransferase (UGT), is the largest glycosyltransferase family in plants, playing a vital role in their growth and development. In this study, 244 UGT genes with conserved PSPG motifs were identified in the genome of Quercus robur L. The collinearity analysis results showed that tandem repeat was the main way of UGT genes expansion in Q. robur, with 21 groups of 55 tandem repeat genes. UGT genes were divided into 15 subgroups A-P; group K was lost, and the gene structure and conserved domain of the same subgroup were basically the same. Cis-element analysis showed that upstream 2,000 bp promoter sequence of UGT genes contained light response elements, plant hormone response elements, and stress-related cis-elements, which indicated that UGT genes of Q. robur might be regulated by various metabolic pathways. In particular, some UGTs in group L of Q. robur contained a conserved promoter structure. The expression pattern analysis results demonstrated that UGT genes of groups B, D, E, and I were differentially expressed under Tortrix viridana L. stress. The expression of UGTs in group E decreased under stress, the expression of group L increased, and that of genes in groups D and B were different. The functions of UGT genes in E and L groups are relatively conservative, and their functions may also conserve among species. The study results have a particular reference value for further research on the function of Q. robur UGT genes.
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