1
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Yun SH, Khan IU, Noh B, Noh YS. Genomic overview of INA-induced NPR1 targeting and transcriptional cascades in Arabidopsis. Nucleic Acids Res 2024; 52:3572-3588. [PMID: 38261978 DOI: 10.1093/nar/gkae019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 12/20/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
The phytohormone salicylic acid (SA) triggers transcriptional reprogramming that leads to SA-induced immunity in plants. NPR1 is an SA receptor and master transcriptional regulator in SA-triggered transcriptional reprogramming. Despite the indispensable role of NPR1, genome-wide direct targets of NPR1 specific to SA signaling have not been identified. Here, we report INA (functional SA analog)-specific genome-wide targets of Arabidopsis NPR1 in plants expressing GFP-fused NPR1 under its native promoter. Analyses of NPR1-dependently expressed direct NPR1 targets revealed that NPR1 primarily activates genes encoding transcription factors upon INA treatment, triggering transcriptional cascades required for INA-induced transcriptional reprogramming and immunity. We identified genome-wide targets of a histone acetyltransferase, HAC1, including hundreds of co-targets shared with NPR1, and showed that NPR1 and HAC1 regulate INA-induced histone acetylation and expression of a subset of the co-targets. Genomic NPR1 targeting was principally mediated by TGACG-motif binding protein (TGA) transcription factors. Furthermore, a group of NPR1 targets mostly encoding transcriptional regulators was already bound to NPR1 in the basal state and showed more rapid and robust induction than other NPR1 targets upon SA signaling. Thus, our study unveils genome-wide NPR1 targeting, its role in transcriptional reprogramming, and the cooperativity between NPR1, HAC1, and TGAs in INA-induced immunity.
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Affiliation(s)
- Se-Hun Yun
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
| | - Irfan Ullah Khan
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
| | - Bosl Noh
- Research Institute of Basic Sciences, Seoul National University, Seoul 08826, Korea
| | - Yoo-Sun Noh
- School of Biological Sciences, Seoul National University, Seoul 08826, Korea
- Research Center for Plant Plasticity, Seoul National University, Seoul 08826, Korea
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2
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Lethe MCL, Bui D, Hu M, Wang X, Singh R, Chan CTY. Discovering New Substrates of a UDP-Glycosyltransferase with a High-Throughput Method. Int J Mol Sci 2024; 25:2725. [PMID: 38473971 PMCID: PMC10931590 DOI: 10.3390/ijms25052725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 02/16/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024] Open
Abstract
UDP-glycosyltransferases (UGTs) form a large enzyme family that is found in a wide range of organisms. These enzymes are known for accepting a wide variety of substrates, and they derivatize xenobiotics and metabolites for detoxification. However, most UGT homologs have not been well characterized, and their potential for biomedical and environmental applications is underexplored. In this work, we have used a fluorescent assay for screening substrates of a plant UGT homolog by monitoring the formation of UDP. We optimized the assay such that it could be used for high-throughput screening of substrates of the Medicago truncatula UGT enzyme, UGT71G1, and our results show that 34 of the 159 screened compound samples are potential substrates. With an LC-MS/MS method, we confirmed that three of these candidates indeed were glycosylated by UGT71G1, which includes bisphenol A (BPA) and 7-Ethyl-10-hydroxycamptothecin (SN-38); derivatization of these toxic compounds can lead to new environmental and medical applications. This work suggests that UGT homologs may recognize a substrate profile that is much broader than previously anticipated. Additionally, it demonstrates that this screening method provides a new means to study UDP-glycosyltransferases, facilitating the use of these enzymes to tackle a wide range of problems.
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Affiliation(s)
- Mary C. L. Lethe
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA;
| | - Dinh Bui
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
| | - Ming Hu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
| | - Xiaoqiang Wang
- Department of Biological Sciences, College of Science, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA;
| | - Rashim Singh
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, 4349 Martin Luther King Boulevard, Houston, TX 77204, USA; (D.B.); (M.H.); (R.S.)
- Sanarentero LLC, 514 N. Elder Grove Drive, Pearland, TX 77584, USA
| | - Clement T. Y. Chan
- Department of Biomedical Engineering, College of Engineering, University of North Texas, 3940 N Elm Street, Denton, TX 76207, USA;
- BioDiscovery Institute, University of North Texas, 1155 Union Circle #305220, Denton, TX 76203, USA
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3
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Baales J, Zeisler-Diehl VV, Kreszies T, Klaus A, Hochholdinger F, Schreiber L. Transcriptomic changes in barley leaves induced by alcohol ethoxylates indicate potential pathways of surfactant detoxification. Sci Rep 2024; 14:4535. [PMID: 38402319 PMCID: PMC10894278 DOI: 10.1038/s41598-024-54806-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/16/2024] [Indexed: 02/26/2024] Open
Abstract
Hardly anything is known regarding the detoxification of surfactants in crop plants, although they are frequently treated with agrochemical formulations. Therefore, we studied transcriptomic changes in barley leaves induced in response to spraying leaf surfaces with two alcohol ethoxylates (AEs). As model surfactants, we selected the monodisperse tetraethylene glycol monododecyl (C12E4) ether and the polydisperse BrijL4. Barley plants were harvested 8 h after spraying with a 0.1% surfactant solution and changes in gene expression were analysed by RNA-sequencing (RNA-Seq). Gene expression was significantly altered in response to both surfactants. With BrijL4 more genes (9724) were differentially expressed compared to C12E4 (6197). Gene families showing pronounced up-regulation were cytochrome P450 enzymes, monooxygenases, ABC-transporters, acetyl- and methyl- transferases, glutathione-S-transferases and glycosyltransferases. These specific changes in gene expression and the postulated function of the corresponding enzymes allowed hypothesizing three potential metabolic pathways of AE detoxification in barley leaves. (i) Up-regulation of P450 cytochrome oxidoreductases suggested a degradation of the lipophilic alkyl residue (dodecyl chain) of the AEs by ω- and β- oxidation. (ii) Alternatively, the polar PEG-chain of AEs could be degraded. (iii) Instead of surfactant degradation, a further pathway of detoxification could be the sequestration of AEs into the vacuole or the apoplast (cell wall). Thus, our results show that AEs lead to pronounced changes in the expression of genes coding for proteins potentially being involved in the detoxification of surfactants.
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Affiliation(s)
- Johanna Baales
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Viktoria V Zeisler-Diehl
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany
| | - Tino Kreszies
- Department of Crop Science, Plant Nutrition and Crop Physiology, University of Göttingen, Carl-Sprengel-Weg 1, 37075, Göttingen, Germany
| | - Alina Klaus
- Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Frank Hochholdinger
- Institute of Crop Science and Resource Conservation (INRES), Crop Functional Genomics, University of Bonn, 53113, Bonn, Germany
| | - Lukas Schreiber
- Department of Ecophysiology, Institute of Cellular and Molecular Botany, University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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4
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Vladejić J, Kovacik M, Zwyrtková J, Szurman-Zubrzycka M, Doležel J, Pecinka A. Zeocin-induced DNA damage response in barley and its dependence on ATR. Sci Rep 2024; 14:3119. [PMID: 38326519 PMCID: PMC10850495 DOI: 10.1038/s41598-024-53264-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
DNA damage response (DDR) is an essential mechanism by which living organisms maintain their genomic stability. In plants, DDR is important also for normal growth and yield. Here, we explored the DDR of a temperate model crop barley (Hordeum vulgare) at the phenotypic, physiological, and transcriptomic levels. By a series of in vitro DNA damage assays using the DNA strand break (DNA-SB) inducing agent zeocin, we showed reduced root growth and expansion of the differentiated zone to the root tip. Genome-wide transcriptional profiling of barley wild-type and plants mutated in DDR signaling kinase ATAXIA TELANGIECTASIA MUTATED AND RAD3-RELATED (hvatr.g) revealed zeocin-dependent, ATR-dependent, and zeocin-dependent/ATR-independent transcriptional responses. Transcriptional changes were scored also using the newly developed catalog of 421 barley DDR genes with the phylogenetically-resolved relationships of barley SUPRESSOR OF GAMMA 1 (SOG1) and SOG1-LIKE (SGL) genes. Zeocin caused up-regulation of specific DDR factors and down-regulation of cell cycle and histone genes, mostly in an ATR-independent manner. The ATR dependency was obvious for some factors associated with DDR during DNA replication and for many genes without an obvious connection to DDR. This provided molecular insight into the response to DNA-SB induction in the large and complex barley genome.
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Affiliation(s)
- Jovanka Vladejić
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Martin Kovacik
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
- Department of Cell Biology and Genetics, Faculty of Science, Palacký University, Olomouc, Czechia
| | - Jana Zwyrtková
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Miriam Szurman-Zubrzycka
- Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Jaroslav Doležel
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia
| | - Ales Pecinka
- Centre of Plant Structural and Functional Genomics, Institute of Experimental Botany of the Czech Academy of Sciences, Olomouc, Czechia.
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5
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Wu Y, Liu J, Jiao B, Wang T, Sun S, Huang B. Genome-Wide Analysis of Family-1 UDP-Glycosyltransferases in Potato ( Solanum tuberosum L.): Identification, Phylogenetic Analysis and Determination of Response to Osmotic Stress. Genes (Basel) 2023; 14:2144. [PMID: 38136966 PMCID: PMC10742590 DOI: 10.3390/genes14122144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/16/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Family-1 UDP-glycosyltransferases (UGTs) are the most common and functional glycosyltransferases in the plant world. UGT is closely related to plant growth and the response to abiotic stress. However, despite systematic research, our understanding of potato UGT genes is still unclear. In this study, we identified 174 potato UGT proteins based on their conserved plant secondary product glycosyltransferase (PSPG) motifs. Phylogenetic analyses were used to compare these proteins with Arabidopsis UGTs and other plant UGTs, and it was found that they could be clustered into 18 distinct groups. Patterns of intron gain/loss and intron phases within potato UGTs revealed highly conserved intron insertion events. The promoter cis-elements of these 174 UGT genes were systematically investigated. The promoter regions of these UGT genes are known to contain various classes of cis-acting compounds. These include elements that are light-responsive, phytohormone-responsive, and stress-responsive. Transcriptome data analysis established that 25, 10, 6, and 4 of these 174 UGT genes were specifically expressed in leaves, roots, stolons, and young tubers, respectively. The mannitol-treated transcriptomic data showed thirty-eight UGT genes were significantly upregulated. The quantitative real-time PCR results showed that the four genes were all responsive to osmotic stress under a 10% PEG6000 treatment. The results of our study provide a basis for clarifying the molecular mechanism of potato osmotic stress resistance and better understanding its function in the future.
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Affiliation(s)
- Yongchao Wu
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Jie Liu
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Baozhen Jiao
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Tingting Wang
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Sifan Sun
- School of Agriculture, Yunnan University, Kunming 650504, China
| | - Binquan Huang
- School of Agriculture, Yunnan University, Kunming 650504, China
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6
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Gharabli H, Della Gala V, Welner DH. The function of UDP-glycosyltransferases in plants and their possible use in crop protection. Biotechnol Adv 2023; 67:108182. [PMID: 37268151 DOI: 10.1016/j.biotechadv.2023.108182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 05/18/2023] [Accepted: 05/18/2023] [Indexed: 06/04/2023]
Abstract
Glycosyltransferases catalyse the transfer of a glycosyl moiety from a donor to an acceptor. Members of this enzyme class are ubiquitous throughout all kingdoms of life and are involved in the biosynthesis of countless types of glycosides. Family 1 glycosyltransferases, also referred to as uridine diphosphate-dependent glycosyltransferases (UGTs), glycosylate small molecules such as secondary metabolites and xenobiotics. In plants, UGTs are recognised for their multiple functionalities ranging from roles in growth regulation and development, in protection against pathogens and abiotic stresses and in adaptation to changing environments. In this study, we review UGT-mediated glycosylation of phytohormones, endogenous secondary metabolites, and xenobiotics and contextualise the role this chemical modification plays in the response to biotic and abiotic stresses and plant fitness. Here, the potential advantages and drawbacks of altering the expression patterns of specific UGTs along with the heterologous expression of UGTs across plant species to improve stress tolerance in plants are discussed. We conclude that UGT-based genetic modification of plants could potentially enhance agricultural efficiency and take part in controlling the biological activity of xenobiotics in bioremediation strategies. However, more knowledge of the intricate interplay between UGTs in plants is needed to unlock the full potential of UGTs in crop resistance.
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Affiliation(s)
- Hani Gharabli
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark
| | - Valeria Della Gala
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark
| | - Ditte Hededam Welner
- The Novo Nordisk Center for Biosustainability, Technical University of Denmark, Kemitorvet 220, Kgs. Lyngby DK-2800, Denmark.
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7
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Li T, Zhang K, Niu X, Chen W, Yang X, Gong X, Tu P, Wang Y, Liu W, Song Y. MS/MS fingerprint comparison between adjacent generations enables substructure identification: Flavonoid glycosides as cases. J Pharm Biomed Anal 2023; 234:115559. [PMID: 37393693 DOI: 10.1016/j.jpba.2023.115559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 06/20/2023] [Accepted: 06/27/2023] [Indexed: 07/04/2023]
Abstract
MS/MS spectrum matching currently serves as a favored means to identify the concerned metabolites attributing to the accessibility of several famous databases. However, the rule that takes the entire structure into account frequently leads to "0 hit" when inquiring MS/MS (usually MS2) spectrum in the databases. Conjugation plays an important role for the high-level structural diversity of metabolites in all organisms, and a given conjugate usually consists of two or more substructures. If MS3 spectra participate in database retrieval, the structural annotation potential of those databases should be dramatically expanded via identifying substructures. Attributing to the ubiquitous distribution pattern, flavonoid glycosides were deployed as the representative family to justify whether the primary fragment ion termed as Y0+, resulted from neutral loss of glycosyl residue(s), generated identical MS3 spectrum with MS2 spectrum of the aglycone cation namely [A+H]+. Because of owning unique ability to measure MS/MS spectrum with the exactly desired exciting energy, linear ion trap chamber of Qtrap-MS was responsible for generating the desired MS3 and MS2 spectra. When taking both m/z and ion intensity features into consideration, the findings included: 1) glycosides sharing identical aglycones produced the same MS3 spectra for Y0+; 2) different MS3 spectra for Y0+ occurred amongst glycosides bearing distinct, even isomeric, aglycones; 3) isomeric aglycones generated different MS2 spectra; and 4) MS3 spectra for Y0+ agreed with MS2 spectra of [A+H]+ when comparing paired glycoside and aglycone. Together, fingerprint comparison between MS3 and MS2 spectra could structurally annotate the substructures and further advance MS/MS spectrum matching towards the identification of, but not limited to, aglycones for flavonoid glycosides.
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Affiliation(s)
- Ting Li
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Ke Zhang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiaoya Niu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Wei Chen
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xiangfen Yang
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Xingcheng Gong
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Pengfei Tu
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China
| | - Yitao Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa 999078, Macao
| | - Wenjing Liu
- School of Pharmacy, Henan University of Chinese Medicine, Jinshui East Road, Zhengdong New District, Zhengzhou 450046, China.
| | - Yuelin Song
- Modern Research Center for Traditional Chinese Medicine, Beijing Research Institute of Chinese Medicine, Beijing University of Chinese Medicine, Beijing 100029, China.
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8
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Lelarge-Trouverie C, Cohen M, Trémulot L, Van Breusegem F, Mhamdi A, Noctor G. Metabolite modification in oxidative stress responses: A case study of two defense hormones. Free Radic Biol Med 2023; 196:145-155. [PMID: 36634883 DOI: 10.1016/j.freeradbiomed.2023.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 01/05/2023] [Accepted: 01/08/2023] [Indexed: 01/11/2023]
Abstract
Studies of the Arabidopsis cat2 mutant lacking the major leaf isoform of catalase have allowed the potential impact of intracellular H2O2 on plant function to be studied. Here, we report a robust analysis of modified gene expression associated with key families involved in metabolite modification in cat2. Through a combined transcriptomic and metabolomic analysis focused on the salicylic acid (SA) and jasmonic acid (JA) pathways, we report key features of the metabolic signatures linked to oxidative stress-induced signaling via these defence hormones and discuss the enzymes that are likely to be involved in determining these features. We provide evidence that specific UDP-glycosyl transferases contribute to the glucosylation of SA that accumulates as a result of oxidative stress in cat2. Glycosides of dihydroxybenzoic acids that accumulate alongside SA in cat2 are identified and, based on the expression of candidate genes, likely routes for their production are discussed. We also report that enhanced intracellular H2O2 triggers induction of genes encoding different enzymes that can metabolize JA. Integrated analysis of metabolite and transcript profiles suggests that a gene network involving specific hydrolases, hydroxylases, and sulfotransferases functions to limit accumulation of the most active jasmonates during oxidative stress.
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Affiliation(s)
- Caroline Lelarge-Trouverie
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Mathias Cohen
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Lug Trémulot
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université Paris-Saclay, 91405, Orsay cedex, France
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, VIB, 9052, Ghent, Belgium; VIB Center of Plant Systems Biology, 9052, Ghent, Belgium
| | - Amna Mhamdi
- Department of Plant Biotechnology and Bioinformatics, VIB, 9052, Ghent, Belgium; VIB Center of Plant Systems Biology, 9052, Ghent, Belgium
| | - Graham Noctor
- Institut des Sciences des Plantes de Paris-Saclay, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université Paris-Saclay, 91405, Orsay cedex, France; Institut Universitaire de France (IUF), France.
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9
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Knoch E, Kovács J, Deiber S, Tomita K, Shanmuganathan R, Serra Serra N, Okada K, Becker C, Schandry N. Transcriptional response of a target plant to benzoxazinoid and diterpene allelochemicals highlights commonalities in detoxification. BMC PLANT BIOLOGY 2022; 22:402. [PMID: 35974304 PMCID: PMC9382751 DOI: 10.1186/s12870-022-03780-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/28/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plants growing in proximity to other plants are exposed to a variety of metabolites that these neighbors release into the environment. Some species produce allelochemicals to inhibit growth of neighboring plants, which in turn have evolved ways to detoxify these compounds. RESULTS In order to understand how the allelochemical-receiving target plants respond to chemically diverse compounds, we performed whole-genome transcriptome analysis of Arabidopsis thaliana exposed to either the benzoxazinoid derivative 2-amino- 3H-phenoxazin-3-one (APO) or momilactone B. These two allelochemicals belong to two very different compound classes, benzoxazinoids and diterpenes, respectively, produced by different Poaceae crop species. CONCLUSIONS Despite their distinct chemical nature, we observed similar molecular responses of A. thaliana to these allelochemicals. In particular, many of the same or closely related genes belonging to the three-phase detoxification pathway were upregulated in both treatments. Further, we observed an overlap between genes upregulated by allelochemicals and those involved in herbicide detoxification. Our findings highlight the overlap in the transcriptional response of a target plant to natural and synthetic phytotoxic compounds and illustrate how herbicide resistance could arise via pathways involved in plant-plant interaction.
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Affiliation(s)
- Eva Knoch
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Judit Kovács
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Sebastian Deiber
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Keisuke Tomita
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Reshi Shanmuganathan
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Núria Serra Serra
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria
| | - Kazunori Okada
- Agro-Biotechnology Research Center (AgTECH), Graduate School of Agricultural and Life Sciences (GSALS), The University of Tokyo, Tokyo, 113-8657, Japan
| | - Claude Becker
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
| | - Niklas Schandry
- LMU Biocenter, Faculty of Biology, Ludwig-Maximilians-University Munich, 82152, Martinsried, Germany.
- Gregor Mendel Institute of Molecular Plant Biology GmbH, Austrian Academy of Sciences, Vienna BioCenter (VBC), 1030, Vienna, Austria.
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10
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Lin M, Jian JB, Zhou ZQ, Chen CH, Wang W, Xiong H, Mei ZN. Chromosome-level genome of Entada phaseoloides provides insights into genome evolution and triterpenoid saponins biosynthesis. Mol Ecol Resour 2022; 22:3049-3067. [PMID: 35661414 DOI: 10.1111/1755-0998.13662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 05/20/2022] [Accepted: 05/26/2022] [Indexed: 11/26/2022]
Abstract
As a medicinal herbal plant, Entada phaseoloides has high levels of secondary metabolites, particularly triterpenoid saponins, which are important resources for scientific research and medical applications. However, the lack of a reference genome for this genus has limited research on its evolution and utilization of its medicinal potential. In this study, we report a chromosome-scale genome assembly for E. phaseoloides using Illumina, Nanopore long reads, and high-throughput chromosome conformation capture technology. The assembled reference genome is 456.18 Mb (scaffold N50=30.9 Mb; contig N50=6.34 Mb) with 95.71 % of the sequences anchored onto 14 pseudochromosomes. E. phaseoloides was estimated to diverge from the Leguminosae lineage at approximately 72.0 million years ago. With the integration of transcriptomic and metabolomic data, gene expression patterns and metabolite profiling of E. phaseoloides were determined in different tissues. The pattern of gene expression and metabolic profile of the kernel were distinct from those of other tissues. Furthermore, the evolution of certain gene families involved in the biosynthesis of triterpenoid saponins and terpenes was analyzed and offer new insights into the formation of these two metabolites. Four CYP genes, one UGT gene and related transcription factors were identified as candidate genes contributing to regulation of triterpenoid saponins biosynthesis. As the first high-quality assembled reference genome in the genus Entada, it will not only provide new information for the evolutionary study of this genus and conservation biology of E. phaseoloides but also lay a foundation for the formation and utilization of secondary metabolites in medicinal plants.
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Affiliation(s)
- Min Lin
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Jian-Bo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, China.,Department of Biotechnology and Biomedicine, Technical University of Denmark, Lyngby, Denmark
| | - Zhu-Qing Zhou
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | | | - Wen Wang
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Hui Xiong
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
| | - Zhi-Nan Mei
- School of Pharmaceutical Sciences, South-Central University for Nationalities, Wuhan, China.,Institute of Ethnomedicine, South-Central University for Nationalities, Wuhan, China
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11
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Dimunová D, Matoušková P, Podlipná R, Boušová I, Skálová L. The role of UDP-glycosyltransferases in xenobiotic-resistance. Drug Metab Rev 2022; 54:282-298. [DOI: 10.1080/03602532.2022.2083632] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Diana Dimunová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Petra Matoušková
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Radka Podlipná
- Laboratory of Plant Biotechnologies, Institute of Experimental Botany, Czech Academy of Sciences, 165 02 Praha 6 - Lysolaje, Czech Republic
| | - Iva Boušová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
| | - Lenka Skálová
- Department of Biochemical Sciences, Faculty of Pharmacy, Charles University, Akademika Heyrovského 1203, 500 05 Hradec Králové, Czech Republic
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12
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Behr M, Speeckaert N, Kurze E, Morel O, Prévost M, Mol A, Mahamadou Adamou N, Baragé M, Renaut J, Schwab W, El Jaziri M, Baucher M. Leaf necrosis resulting from downregulation of poplar glycosyltransferase UGT72A2. TREE PHYSIOLOGY 2022; 42:1084-1099. [PMID: 34865151 DOI: 10.1093/treephys/tpab161] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 11/29/2021] [Indexed: 06/13/2023]
Abstract
Reactive species (RS) causing oxidative stress are unavoidable by-products of various plant metabolic processes, such as photosynthesis, respiration or photorespiration. In leaves, flavonoids scavenge RS produced during photosynthesis and protect plant cells against deleterious oxidative damages. Their biosynthesis and accumulation are therefore under tight regulation at the cellular level. Glycosylation has emerged as an essential biochemical reaction in the homeostasis of various specialized metabolites such as flavonoids. This article provides a functional characterization of the Populus tremula x P. alba (poplar) UGT72A2 coding for a UDP-glycosyltransferase that is localized in the chloroplasts. Compared with the wild type, transgenic poplar lines with decreased expression of UGT72A2 are characterized by reduced growth and oxidative damages in leaves, as evidenced by necrosis, higher content of glutathione and lipid peroxidation products as well as diminished soluble peroxidase activity and NADPH to NADP+ ratio under standard growing conditions. They furthermore display lower pools of phenolics, anthocyanins and total flavonoids but higher proanthocyanidins content. Promoter analysis revealed the presence of cis-elements involved in photomorphogenesis, chloroplast biogenesis and flavonoid biosynthesis. The UGT72A2 is regulated by the poplar MYB119, a transcription factor known to regulate the flavonoid biosynthesis pathway. Phylogenetic analysis and molecular docking suggest that UGT72A2 could glycosylate flavonoids; however, the actual substrate(s) was not consistently evidenced with either in vitro assays nor analyses of glycosylated products in leaves of transgenic poplar overexpressing or downregulated for UGT72A2. This article provides elements highlighting the importance of flavonoid glycosylation regarding protection against oxidative stress in poplar leaves and raises new questions about the link between this biochemical reaction and regulation of the redox homeostasis system.
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Affiliation(s)
- Marc Behr
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Nathanael Speeckaert
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Elisabeth Kurze
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Oriane Morel
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Martine Prévost
- Unité de recherche Structure et Fonction des Membranes Biologiques, Université libre de Bruxelles, Bruxelles, Belgium
| | - Adeline Mol
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Nassirou Mahamadou Adamou
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
- Laboratoire de Biotechnologie Végétale et Amélioration des Plantes (LABAP), Université Abdou Moumouni de Niamey, Niamey, Niger
| | - Moussa Baragé
- Laboratoire de Biotechnologie Végétale et Amélioration des Plantes (LABAP), Université Abdou Moumouni de Niamey, Niamey, Niger
| | - Jenny Renaut
- Luxembourg Institute of Science and Technology, 4422 Belvaux, Luxembourg
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, 85354 Freising, Germany
| | - Mondher El Jaziri
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
| | - Marie Baucher
- Laboratory of Plant Biotechnology, Université libre de Bruxelles, 12 rue des Profs Jeener et Brachet, Gosselies 6041, Belgium
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13
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The Phytotoxin Myrigalone A Triggers a Phased Detoxification Programme and Inhibits Lepidium sativum Seed Germination via Multiple Mechanisms including Interference with Auxin Homeostasis. Int J Mol Sci 2022; 23:ijms23094618. [PMID: 35563008 PMCID: PMC9104956 DOI: 10.3390/ijms23094618] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/12/2022] [Accepted: 04/13/2022] [Indexed: 02/01/2023] Open
Abstract
Molecular responses of plants to natural phytotoxins comprise more general and compound-specific mechanisms. How phytotoxic chalcones and other flavonoids inhibit seedling growth was widely studied, but how they interfere with seed germination is largely unknown. The dihydrochalcone and putative allelochemical myrigalone A (MyA) inhibits seed germination and seedling growth. Transcriptome (RNAseq) and hormone analyses of Lepidium sativum seed responses to MyA were compared to other bioactive and inactive compounds. MyA treatment of imbibed seeds triggered the phased induction of a detoxification programme, altered gibberellin, cis-(+)-12-oxophytodienoic acid and jasmonate metabolism, and affected the expression of hormone transporter genes. The MyA-mediated inhibition involved interference with the antioxidant system, oxidative signalling, aquaporins and water uptake, but not uncoupling of oxidative phosphorylation or p-hydroxyphenylpyruvate dioxygenase expression/activity. MyA specifically affected the expression of auxin-related signalling genes, and various transporter genes, including for auxin transport (PIN7, ABCG37, ABCG4, WAT1). Responses to auxin-specific inhibitors further supported the conclusion that MyA interferes with auxin homeostasis during seed germination. Comparative analysis of MyA and other phytotoxins revealed differences in the specific regulatory mechanisms and auxin transporter genes targeted to interfere with auxin homestasis. We conclude that MyA exerts its phytotoxic activity by multiple auxin-dependent and independent molecular mechanisms.
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14
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Cainelli N, Forestan C, Angeli D, Villegas TR, Costa F, Botton A, Rasori A, Bonghi C, Ruperti B. Transcriptomic Insights on the Preventive Action of Apple (cv Granny Smith) Skin Wounding on Superficial Scald Development. Int J Mol Sci 2021; 22:ijms222413425. [PMID: 34948219 PMCID: PMC8705499 DOI: 10.3390/ijms222413425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 12/03/2022] Open
Abstract
Superficial scald is a post-harvest chilling storage injury leading to browning of the surface of the susceptible cv Granny Smith apples. Wounding of skins has been reported to play a preventive role on scald development however its underlying molecular factors are unknown. We have artificially wounded the epidermal and sub-epidermal layers of apple skins consistently obtaining the prevention of superficial scald in the surroundings of the wounds during two independent vintages. Time course RNA-Seq analyses of the transcriptional changes in wounded versus unwounded skins revealed that two transcriptional waves occurred. An early wave included genes up-regulated by wounding already after 6 h, highlighting a specific transcriptional rearrangement of genes connected to the biosynthesis and signalling of JA, ethylene and ABA. A later transcriptional wave, occurring after three months of cold storage, included genes up-regulated exclusively in unwounded skins and was prevented from its occurrence in wounded skins. A significant portion of these genes was related to decay of tissues and to the senescence hormones ABA, JA and ethylene. Such changes suggest a wound-inducible reversed hormonal balance during post-harvest storage which may explain the local inhibition of scald in wounded tissues, an aspect that will need further studies for its mechanistic explanation.
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Affiliation(s)
- Nadia Cainelli
- Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università di Padova, 35122 Legnaro, PD, Italy; (N.C.); (A.B.); (A.R.); (C.B.)
| | - Cristian Forestan
- Dipartimento di Scienze e Tecnologie Agro-Alimentari, Università di Bologna, 40127 Bologna, BO, Italy;
| | - Dario Angeli
- Fondazione Edmund Mach, Centro di Trasferimento Tecnologico, 38010 San Michele all’Adige, TN, Italy; (D.A.); (T.R.V.)
| | - Tomas Roman Villegas
- Fondazione Edmund Mach, Centro di Trasferimento Tecnologico, 38010 San Michele all’Adige, TN, Italy; (D.A.); (T.R.V.)
| | - Fabrizio Costa
- Centro Agricoltura Alimenti Ambiente, 38098 San Michele all’Adige, TN, Italy;
| | - Alessandro Botton
- Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università di Padova, 35122 Legnaro, PD, Italy; (N.C.); (A.B.); (A.R.); (C.B.)
| | - Angela Rasori
- Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università di Padova, 35122 Legnaro, PD, Italy; (N.C.); (A.B.); (A.R.); (C.B.)
| | - Claudio Bonghi
- Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università di Padova, 35122 Legnaro, PD, Italy; (N.C.); (A.B.); (A.R.); (C.B.)
| | - Benedetto Ruperti
- Dipartimento di Agronomia, Animali, Alimenti, Risorse Naturali e Ambiente, Università di Padova, 35122 Legnaro, PD, Italy; (N.C.); (A.B.); (A.R.); (C.B.)
- Correspondence:
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15
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Reimer JJ, Thiele B, Biermann RT, Junker-Frohn LV, Wiese-Klinkenberg A, Usadel B, Wormit A. Tomato leaves under stress: a comparison of stress response to mild abiotic stress between a cultivated and a wild tomato species. PLANT MOLECULAR BIOLOGY 2021; 107:177-206. [PMID: 34677706 PMCID: PMC8553704 DOI: 10.1007/s11103-021-01194-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/16/2021] [Indexed: 05/03/2023]
Abstract
Tomato is one of the most produced crop plants on earth and growing in the fields and greenhouses all over the world. Breeding with known traits of wild species can enhance stress tolerance of cultivated crops. In this study, we investigated responses of the transcriptome as well as primary and secondary metabolites in leaves of a cultivated and a wild tomato to several abiotic stresses such as nitrogen deficiency, chilling or warmer temperatures, elevated light intensities and combinations thereof. The wild species responded different to varied temperature conditions compared to the cultivated tomato. Nitrogen deficiency caused the strongest responses and induced in particular the secondary metabolism in both species but to much higher extent in the cultivated tomato. Our study supports the potential of a targeted induction of valuable secondary metabolites in green residues of horticultural production, that will otherwise only be composted after fruit harvest. In particular, the cultivated tomato showed a strong induction in the group of mono caffeoylquinic acids in response to nitrogen deficiency. In addition, the observed differences in stress responses between cultivated and wild tomato can lead to new breeding targets for better stress tolerance.
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Affiliation(s)
- Julia J Reimer
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, PtJ, 52425, Jülich, Germany
| | - Björn Thiele
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Agrosphere (IBG-3), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Robin T Biermann
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Leibniz Institute of Vegetable and Ornamental Crops (IGZ) e.V., 14979, Großbeeren, Germany
| | - Laura V Junker-Frohn
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Anika Wiese-Klinkenberg
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
| | - Björn Usadel
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Plant Sciences (IBG-2), 52425, Jülich, Germany
- Forschungszentrum Jülich GmbH, Institute of Bio- and Geosciences, Bioinformatics (IBG-4), 52425, Jülich, Germany
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany
- Heinrich-Heine-University, Chair of Biological Data Science, 40225, Düsseldorf, Germany
| | - Alexandra Wormit
- Institute for Biology I, RWTH Aachen University, Worringer Weg 3, 52074, Aachen, Germany.
- Bioeconomy Science Center, c/o Forschungszentrum Jülich GmbH, 52425, Jülich, Germany.
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16
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Genome-Wide Association Study of QTLs Conferring Resistance to Bacterial Leaf Streak in Rice. PLANTS 2021; 10:plants10102039. [PMID: 34685848 PMCID: PMC8541590 DOI: 10.3390/plants10102039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/18/2021] [Accepted: 09/22/2021] [Indexed: 11/16/2022]
Abstract
Bacterial leaf streak (BLS) is a devastating rice disease caused by the bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), which can result in severe damage to rice production worldwide. Based on a total of 510 rice accessions, trialed in two seasons and using six different multi-locus GWAS methods (mrMLM, ISIS EM-BLASSO, pLARmEB, FASTmrMLM, FASTmrEMMA and pKWmEB), 79 quantitative trait nucleotides (QTNs) reflecting 69 QTLs for BLS resistance were identified (LOD > 3). The QTNs were distributed on all chromosomes, with the most distributed on chromosome 11, followed by chromosomes 1 and 5. Each QTN had an additive effect of 0.20 (cm) and explained, on average, 2.44% of the phenotypic variance, varying from 0.00–0.92 (cm) and from 0.00–9.86%, respectively. Twenty-five QTNs were detected by at least two methods. Among them, qnBLS11.17 was detected by as many as five methods. Most of the QTNs showed a significant interaction with their environment, but no QTNs were detected in both seasons. By defining the QTL range for each QTN according to the LD half-decay distance, a total of 848 candidate genes were found for nine top QTNs. Among them, more than 10% were annotated to be related to biotic stress resistance, and five showed a significant response to Xoc infection. Our results could facilitate the in-depth study and marker-assisted improvement of rice resistance to BLS.
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17
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Zhang Y, Liu C, Jin R, Wang Y, Cai T, Ren Z, Ma K, He S, Lee KS, Jin BR, Li J, Wan H. Dual oxidase-dependent reactive oxygen species are involved in the regulation of UGT overexpression-mediated clothianidin resistance in the brown planthopper, Nilaparvata lugens. PEST MANAGEMENT SCIENCE 2021; 77:4159-4167. [PMID: 33934482 DOI: 10.1002/ps.6453] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/26/2021] [Accepted: 05/02/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Uridine diphosphate-glycosyltransferases (UGTs) are phase II metabolic enzymes involved in metabolism of toxins and resistance to insecticides in insect pests. Reactive oxygen species (ROS) induced by xenobiotics are important for activation of detoxification pathways. However, relationships between ROS and UGTs involved in toxin metabolism and insecticide resistance remain unclear. RESULTS Here, involvement of dual oxidase (Duox)-dependent ROS in regulating UGT expression-mediated insecticide resistance in the brown planthopper (Nilaparvata lugens) was investigated. The overexpression of NlUGT386F2 contributed to the resistance of N. lugens to clothianidin. Furthermore, the ROS inhibitor (N-acetylcysteine) significantly reduced the expression of NlUGT386F2 and increased the susceptibility of N. lugens to clothianidin. Silencing the ROS producer Duox significantly increased the susceptibility of N. lugens to clothianidin through the down-regulation of NlUGT386F2 expression. CONCLUSION NlDuox-dependent ROS regulates NlUGT386F2 expression-mediated clothianidin resistance in brown planthopper. These observations further our understanding of the metabolism of toxins and of insecticide-resistance in insect pests.
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Affiliation(s)
- Yunhua Zhang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Chaoya Liu
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Ruoheng Jin
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yue Wang
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Tingwei Cai
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Zhijie Ren
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Kangsheng Ma
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Shun He
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Kwang S Lee
- College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Byung R Jin
- College of Natural Resources and Life Science, Dong-A University, Busan, Republic of Korea
| | - Jianhong Li
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
| | - Hu Wan
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, P. R. China
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18
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Sharma B, Seth R, Thakur S, Parmar R, Masand M, Devi A, Singh G, Dhyani P, Choudhary S, Sharma RK. Genome-wide transcriptional analysis unveils the molecular basis of organ-specific expression of isosteroidal alkaloids biosynthesis in critically endangered Fritillaria roylei Hook. PHYTOCHEMISTRY 2021; 187:112772. [PMID: 33873018 DOI: 10.1016/j.phytochem.2021.112772] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Revised: 04/03/2021] [Accepted: 04/04/2021] [Indexed: 06/12/2023]
Abstract
Fritillaria roylei Hook. is a critically endangered high altitude Himalayan medicinal plant species with rich source of pharmaceutically active structurally diverse steroidal alkaloids. Nevertheless, except few marker compounds, the chemistry of the plant remains unexplored. Therefore, in the current study, transcriptome sequencing efforts were made to elucidate isosteroidal alkaloids biosynthesis by creating first organ-specific genomic resource using bulb, stem, and leaf tissues derived from natural populations of Indian Himalayan region. Overall, 349.9 million high quality paired-end reads obtained using NovaSeq 6000 platform were assembled (de novo) into 82,848 unigenes and 31,061 isoforms. Functional annotation and organ specific differential expression (DE) analysis identified 2488 significant DE transcripts, grouped into three potential sub-clusters (sub-cluster I: 728 transcripts; sub-cluster II: 446 transcripts and Sub-cluster III: 1314 transcripts). Subsequently, pathway enrichment (GO, KEGG) and protein-protein network analysis revealed significantly higher enrichment of phenyl-propanoid and steroid backbone including terpenoid, sesquiterpenoid and triterpenoid biosynthesis in bulb. Additionally, upregulated expression of cytochrome P450, UDP-dependent Glucuronosyltransferase families and key transcription factor families (FAR1, bHLH, GRAS, C2H2, TCP and MYB) suggests 'bulb' as a primary site of MVA mediated isosteroidal alkaloids biosynthesis. The comprehensive elucidation of molecular insights in this study is a first step towards the understanding of isosteroidal alkaloid biosynthesis pathway in F. roylei. Furthermore, key genes and regulators identified here can facilitate metabolic engineering of potential bioactive compounds at industrial scale.
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Affiliation(s)
- Balraj Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Romit Seth
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India.
| | - Sapna Thakur
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Rajni Parmar
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Mamta Masand
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Amna Devi
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India
| | - Gopal Singh
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Praveen Dhyani
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Shruti Choudhary
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India
| | - Ram Kumar Sharma
- Biotechnology Department, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, Himachal Pradesh, 176061, India; Academy of Scientific and Innovative Research (AcSIR), CSIR-HRDC Campus, Ghaziabad, Uttar Pradesh, 201 002, India.
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19
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Zhang K, Sun Y, Li M, Long R. CrUGT87A1, a UDP-sugar glycosyltransferases (UGTs) gene from Carex rigescens, increases salt tolerance by accumulating flavonoids for antioxidation in Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 159:28-36. [PMID: 33321375 DOI: 10.1016/j.plaphy.2020.12.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 12/07/2020] [Indexed: 05/15/2023]
Abstract
Salt stress is a serious abiotic stressor impeding plant growth and crop production around the world. Plant glycosyltransferases are thought to serve important roles in dealing with stress conditions, however, the functional role of how UGTs cope with salt stress is not well understood. Carex rigescens (Franch.) V. Krecz, is a widely distributed species of turfgrass with strong salinity tolerance found in northern China. To investigate how the glycosyltransferase gene, CrUGT87A1, functions in C. rigescens, we performed analyses of cloning, transcriptional expression, subcellular localization, and overexpression. The full-length sequence of CrUGT87A1 is 1455 bp with a 1338 bp length ORF, which encodes 445 amino acids, while CrUGT87A1 was found to be a nuclear and plasmalemma-localized protein. We found that the transcriptional expression of CrUGT87A1 was up-regulated under ABA, heat, salt, and drought treatments in leaf tissues. CrUGT87A1 overexpression in Arabidopsis plants had a significantly higher germination rate, better growth and physiology, and a higher expression levels of transcripts related to salt stress-related genes under high-salinity conditions, suggesting that CrUGT87A1 is involved in salt tolerance. The transcriptional expression of genes related to flavonoid-synthesis related and the flavonoid content reflected higher accumulations of flavonoids in transgenic plants. Our study demonstrated that CrUGT87A1 could play an important role in resisting salt stress due to increased flavonoid accumulation, which can promote antioxidation when dealing with high-salinity conditions. This study advances our collective understanding of the functional role of UGTs and can be used to improve the salt tolerance and breeding of crops and plants.
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Affiliation(s)
- Kun Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China; College of Grassland Science and Technology, China Agricultural University, Beijing, 100093, PR China; College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, PR China
| | - Yan Sun
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100093, PR China
| | - Mingna Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
| | - Ruicai Long
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, PR China.
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20
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Islam MT, Gan HM, Ziemann M, Hussain HI, Arioli T, Cahill D. Phaeophyceaean (Brown Algal) Extracts Activate Plant Defense Systems in Arabidopsis thaliana Challenged With Phytophthora cinnamomi. FRONTIERS IN PLANT SCIENCE 2020; 11:852. [PMID: 32765538 PMCID: PMC7381280 DOI: 10.3389/fpls.2020.00852] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
Seaweed extracts are important sources of plant biostimulants that boost agricultural productivity to meet current world demand. The ability of seaweed extracts based on either of the Phaeophyceaean species Ascophyllum nodosum or Durvillaea potatorum to enhance plant growth or suppress plant disease have recently been shown. However, very limited information is available on the mechanisms of suppression of plant disease by such extracts. In addition, there is no information on the ability of a combination of extracts from A. nodosum and D. potatorum to suppress a plant pathogen or to induce plant defense. The present study has explored the transcriptome, using RNA-seq, of Arabidopsis thaliana following treatment with extracts from the two species, or a mixture of both, prior to inoculation with the root pathogen Phytophthora cinnamomi. Following inoculation, five time points (0-24 h post-inoculation) that represented early stages in the interaction of the pathogen with its host were assessed for each treatment and compared with their respective water controls. Wide scale transcriptome reprogramming occurred predominantly related to phytohormone biosynthesis and signaling, changes in metabolic processes and cell wall biosynthesis, there was a broad induction of proteolysis pathways, a respiratory burst and numerous defense-related responses were induced. The induction by each seaweed extract of defense-related genes coincident with the time of inoculation showed that the plants were primed for defense prior to infection. Each seaweed extract acted differently in inducing plant defense-related genes. However, major systemic acquired resistance (SAR)-related genes as well as salicylic acid-regulated marker genes (PR1, PR5, and NPR1) and auxin associated genes were found to be commonly up-regulated compared with the controls following treatment with each seaweed extract. Moreover, each seaweed extract suppressed P. cinnamomi growth within the roots of inoculated A. thaliana by the early induction of defense pathways and likely through ROS-based signaling pathways that were linked to production of ROS. Collectively, the RNA-seq transcriptome analysis revealed the induction by seaweed extracts of suites of genes that are associated with direct or indirect plant defense in addition to responses that require cellular energy to maintain plant growth during biotic stress.
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Affiliation(s)
- Md Tohidul Islam
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, Australia
- Department of Plant Pathology, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka, Bangladesh
| | - Han Ming Gan
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, Australia
| | - Mark Ziemann
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, Australia
| | | | - Tony Arioli
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, Australia
- Seasol International R&D Department, Bayswater, VIC, Australia
| | - David Cahill
- School of Life and Environmental Sciences, Deakin University, Waurn Ponds Campus, Geelong, VIC, Australia
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21
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Behr M, Neutelings G, El Jaziri M, Baucher M. You Want it Sweeter: How Glycosylation Affects Plant Response to Oxidative Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:571399. [PMID: 33042189 PMCID: PMC7525049 DOI: 10.3389/fpls.2020.571399] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 09/01/2020] [Indexed: 05/02/2023]
Abstract
Oxidative stress is a cellular threat which puts at risk the productivity of most of crops valorized by humankind in terms of food, feed, biomaterial, or bioenergy. It is therefore of crucial importance to understand the mechanisms by which plants mitigate the deleterious effects of oxidizing agents. Glycosylation of antioxidant molecules and phytohormones modifies their chemical properties as well as their cellular and histological repartition. This review emphasizes the mechanisms and the outcomes of this conjugation reaction on plant ability to face growing conditions favoring oxidative stress, in mirror with the activity of deglycosylating enzymes. Pioneer evidence bridging flavonoid, glycosylation, and redox homeostasis paved the way for numerous functional analyses of UDP-glycosyltransferases (UGTs), such as the identification of their substrates and their role to circumvent oxidative stress resulting from various environmental challenges. (De)glycosylation appears as a simple chemical reaction regulating the biosynthesis and/or the activity of a myriad of specialized metabolites partaking in response to pathogen and abiotic stresses. This outcome underlies the possibility to valorize UGTs potential to upgrade plant adaptation and fitness in a rising context of sub-optimal growing conditions subsequent to climate change.
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Affiliation(s)
- Marc Behr
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
| | - Godfrey Neutelings
- UGSF—Unité de Glycobiologie Structurale et Fonctionnelle, UMR 8576, Université de Lille, CNRS, Lille, France
| | - Mondher El Jaziri
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
| | - Marie Baucher
- Laboratoire de Biotechnologie Végétale, Université libre de Bruxelles, Gosselies, Belgium
- *Correspondence: Marie Baucher,
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22
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Zhao M, Jin J, Gao T, Zhang N, Jing T, Wang J, Ban Q, Schwab W, Song C. Glucosyltransferase CsUGT78A14 Regulates Flavonols Accumulation and Reactive Oxygen Species Scavenging in Response to Cold Stress in Camellia sinensis. FRONTIERS IN PLANT SCIENCE 2019; 10:1675. [PMID: 31929783 PMCID: PMC6941654 DOI: 10.3389/fpls.2019.01675] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 11/28/2019] [Indexed: 05/02/2023]
Abstract
Glycosyltransferases (UGTs) play diverse roles in cellular metabolism by altering regulatory metabolites activities. However, the physiological roles of most members of UGTs in crops in response to abiotic stresses are unknown. We have identified a novel glycosyltransferase CsUGT78A14 in tea crops, an important economic crops, whose expression is strongly induced by cold stress. Biochemical analyses confirmed that CsUGT78A14-1 showed the highest activity toward kaempferol and is involved in the biosynthesis of kaempferol-diglucoside, whereas the product of CsUGT78A14-2, which differs from CsUGT78A14-1 by a single amino acid, was identified as 3-O-glucoside. The accumulation of kaempferol monoglucosides and diglucosides was consistent with the expression levels of CsUGT78A14 in response to cold stress, as well as in different tissues and genotypes of tea plants. Down-regulation of CsUGT78A14 resulted in reduced accumulation of flavonols, reactive oxygen species (ROS) scavenging capacity and finally reduced tea plant stress tolerance under cold stress. The antioxidant capacity of flavonols aglycon was enhanced by glucosylation catalyzed by CsUGT78A14. The results demonstrate that CsUGT78A14 plays a critical role in cold stress by increasing flavonols accumulation and ROS scavenging capacity, providing novel insights into the biological role of UGTs and flavonoids in plants.
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Affiliation(s)
- Mingyue Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Jieyang Jin
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Ting Gao
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Na Zhang
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Tingting Jing
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Jingming Wang
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Qiuyan Ban
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
| | - Wilfried Schwab
- State Key Laboratory of Tea Plant Biology and Utilization, International Joint Laboratory on Tea Chemistry and Health Effects, Anhui Agricultural University, Hefei, China
- Biotechnology of Natural Products, Technische Universität München, 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, Hefei, China
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23
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Campos L, López-Gresa MP, Fuertes D, Bellés JM, Rodrigo I, Lisón P. Tomato glycosyltransferase Twi1 plays a role in flavonoid glycosylation and defence against virus. BMC PLANT BIOLOGY 2019; 19:450. [PMID: 31655554 PMCID: PMC6815406 DOI: 10.1186/s12870-019-2063-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 10/09/2019] [Indexed: 05/05/2023]
Abstract
BACKGROUND Secondary metabolites play an important role in the plant defensive response. They are produced as a defence mechanism against biotic stress by providing plants with antimicrobial and antioxidant weapons. In higher plants, the majority of secondary metabolites accumulate as glycoconjugates. Glycosylation is one of the commonest modifications of secondary metabolites, and is carried out by enzymes called glycosyltransferases. RESULTS Here we provide evidence that the previously described tomato wound and pathogen-induced glycosyltransferase Twi1 displays in vitro activity toward the coumarins scopoletin, umbelliferone and esculetin, and the flavonoids quercetin and kaempferol, by uncovering a new role of this gene in plant glycosylation. To test its activity in vivo, Twi1-silenced transgenic tomato plants were generated and infected with Tomato spotted wilt virus. The Twi1-silenced plants showed a differential accumulation of Twi1 substrates and enhanced susceptibility to the virus. CONCLUSIONS Biochemical in vitro assays and transgenic plants generation proved to be useful strategies to assign a role of tomato Twi1 in the plant defence response. Twi1 glycosyltransferase showed to regulate quercetin and kaempferol levels in tomato plants, affecting plant resistance to viral infection.
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Affiliation(s)
- Laura Campos
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - María Pilar López-Gresa
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Diana Fuertes
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - José María Bellés
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Ismael Rodrigo
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
| | - Purificación Lisón
- Instituto de Biología Molecular y Celular de Plantas, Universitat Politècnica de València-Consejo Superior de Investigaciones Científicas, Valencia, Spain
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24
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Sun G, Strebl M, Merz M, Blamberg R, Huang FC, McGraphery K, Hoffmann T, Schwab W. Glucosylation of the phytoalexin N-feruloyl tyramine modulates the levels of pathogen-responsive metabolites in Nicotiana benthamiana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:20-37. [PMID: 31124249 DOI: 10.1111/tpj.14420] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 05/07/2019] [Accepted: 05/14/2019] [Indexed: 05/03/2023]
Abstract
Enzyme promiscuity, a common property of many uridine diphosphate sugar-dependent glycosyltransferases (UGTs) that convert small molecules, significantly hinders the identification of natural substrates and therefore the characterization of the physiological role of enzymes. In this paper we present a simple but effective strategy to identify endogenous substrates of plant UGTs using LC-MS-guided targeted glycoside analysis of transgenic plants. We successfully identified natural substrates of two promiscuous Nicotiana benthamiana UGTs (NbUGT73A24 and NbUGT73A25), orthologues of pathogen-induced tobacco UGT (TOGT) from Nicotiana tabacum, which is involved in the hypersensitive reaction. While in N. tabacum, TOGT glucosylated scopoletin after treatment with salicylate, fungal elicitors and the tobacco mosaic virus, NbUGT73A24 and NbUGT73A25 produced glucosides of phytoalexin N-feruloyl tyramine, which may strengthen cell walls to prevent the intrusion of pathogens, and flavonols after agroinfiltration of the corresponding genes in N. benthamiana. Enzymatic glucosylation of fractions of a physiological aglycone library confirmed the biological substrates of UGTs. In addition, overexpression of both genes in N. benthamiana produced clear lesions on the leaves and led to a significantly reduced content of pathogen-induced plant metabolites such as phenylalanine and tryptophan. Our results revealed some additional biological functions of TOGT enzymes and indicated a multifunctional role of UGTs in plant resistance.
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Affiliation(s)
- Guangxin Sun
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Michael Strebl
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Maximilian Merz
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Robert Blamberg
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Fong-Chin Huang
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
| | - Kate McGraphery
- 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 Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Str. 1, 85354, Freising, Germany
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25
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Yuan L, Wang J, Xie S, Zhao M, Nie L, Zheng Y, Zhu S, Hou J, Chen G, Wang C. Comparative Proteomics Indicates That Redox Homeostasis Is Involved in High- and Low-Temperature Stress Tolerance in a Novel Wucai ( Brassica campestris L.) Genotype. Int J Mol Sci 2019; 20:ijms20153760. [PMID: 31374822 PMCID: PMC6696267 DOI: 10.3390/ijms20153760] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/28/2019] [Accepted: 07/30/2019] [Indexed: 02/06/2023] Open
Abstract
The genotype WS-1, previously identified from novel wucai germplasm, is tolerant to both low-temperature (LT) and high-temperature (HT) stress. However, it is unclear which signal transduction pathway or acclimation mechanisms are involved in the temperature-stress response. In this study, we used the proteomic method of tandem mass tag (TMT) coupled with liquid chromatography-mass spectrometry (LC-MS/MS) to identify 1022 differentially expressed proteins (DEPs) common to WS-1, treated with either LT or HT. Among these 1022 DEPs, 172 were upregulated in response to both LT and HT, 324 were downregulated in response to both LT and HT, and 526 were upregulated in response to one temperature stress and downregulated in response to the other. To illustrate the common regulatory pathway in WS-1, 172 upregulated DEPs were further analyzed. The redox homeostasis, photosynthesis, carbohydrate metabolism, heat-shockprotein, and chaperones and signal transduction pathways were identified to be associated with temperature stress tolerance in wucai. In addition, 35S:BcccrGLU1 overexpressed in Arabidopsis, exhibited higher reduced glutathione (GSH) content and reduced glutathione/oxidized glutathione (GSH/GSSG) ratio and less oxidative damage under temperature stress. This result is consistent with the dynamic regulation of the relevant proteins involved in redox homeostasis. These data demonstrate that maintaining redox homeostasis is an important common regulatory pathway for tolerance to temperature stress in novel wucai germplasm.
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Affiliation(s)
- Lingyun Yuan
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jie Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Shilei Xie
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Mengru Zhao
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Libing Nie
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Yushan Zheng
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Shidong Zhu
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Jinfeng Hou
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China
| | - Guohu Chen
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China
| | - Chenggang Wang
- College of Horticulture, Vegetable Genetics and Breeding Laboratory, Anhui Agricultural University, 130 West Changjiang Road, Hefei 230036, China.
- Provincial Engineering Laboratory for Horticultural Crop Breeding of Anhui, 130 West of Changjiang Road, Hefei 230036, China.
- Department of vegetable culture and breeding, Wanjiang Vegetable Industrial Technology Institute, Maanshan 238200, China.
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26
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Stringlis IA, de Jonge R, Pieterse CMJ. The Age of Coumarins in Plant-Microbe Interactions. PLANT & CELL PHYSIOLOGY 2019; 60:1405-1419. [PMID: 31076771 PMCID: PMC6915228 DOI: 10.1093/pcp/pcz076] [Citation(s) in RCA: 144] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/23/2019] [Indexed: 05/05/2023]
Abstract
Coumarins are a family of plant-derived secondary metabolites that are produced via the phenylpropanoid pathway. In the past decade, coumarins have emerged as iron-mobilizing compounds that are secreted by plant roots and aid in iron uptake from iron-deprived soils. Members of the coumarin family are found in many plant species. Besides their role in iron uptake, coumarins have been extensively studied for their potential to fight infections in both plants and animals. Coumarin activities range from antimicrobial and antiviral to anticoagulant and anticancer. In recent years, studies in the model plant species tobacco and Arabidopsis have significantly increased our understanding of coumarin biosynthesis, accumulation, secretion, chemical modification and their modes of action against plant pathogens. Here, we review current knowledge on coumarins in different plant species. We focus on simple coumarins and provide an overview on their biosynthesis and role in environmental stress responses, with special attention for the recently discovered semiochemical role of coumarins in aboveground and belowground plant-microbe interactions and the assembly of the root microbiome.
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Affiliation(s)
- Ioannis A Stringlis
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
- Corresponding author: E-mail, ; Fax,+31 30 253 2837
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
| | - Corn� M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Science4Life, Utrecht University, Padualaan 8, Utrecht, 3584 CH, The Netherlands
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27
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Chen L, Meng J, He XL, Zhang M, Luan YS. Solanum lycopersicum microRNA1916 targets multiple target genes and negatively regulates the immune response in tomato. PLANT, CELL & ENVIRONMENT 2019; 42:1393-1407. [PMID: 30362126 DOI: 10.1111/pce.13468] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 06/08/2023]
Abstract
MicroRNA1916 (miR1916) is one of the nonconserved miRNAs that respond to various stresses in plants, but little has been known at present about its mechanisms in biotic stresses. In this study, the expression of Solanum lycopersicum (sly)-miR1916 in tomato was found to be down-regulated after infection with Phytophthora infestans or Botrytis cinerea. Tomato plants that overexpressed sly-miR1916 displayed significant enhancement in susceptibility to P. infestans and B. cinerea infection, as well as increased tendency to produce reactive oxygen species. Silencing of sly-miR1916 by short tandem target mimic and artificial microRNA strategies caused the tomato plants to become more tolerant to adverse conditions. In addition, lower sly-miR1916 expression could up-regulate the expression of strictosidine synthase (STR-2), UDP-glycosyltransferases (UGTs), late blight resistance protein homolog R1B-16, disease resistance protein RPP13-like, and MYB transcription factor (MYB12), which ultimately resulted in the accumulation of α-tomatine and anthocyanins via STR-2, UGT, and MYB12. Furthermore, ectopic expression of sly-miR1916/STR-2 significantly changed the tolerance of tobacco to B. cinerea. Taken together, the results demonstrated that sly-miR1916 might regulate the expression of STR-2, UGT, and MYB12 in tomato plant, conferring sensitivity to biotic stress via modulating α-tomatine and anthocyanins.
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Affiliation(s)
- Lei Chen
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Jun Meng
- School of Computer Science and Technology, Dalian University of Technology, Dalian, 116024, China
| | - Xiao Li He
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Min Zhang
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
| | - Yu Shi Luan
- School of Life Sciences and Biotechnology, Dalian University of Technology, Dalian, 116024, China
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28
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McCabe CE, Cianzio SR, O'Rourke JA, Graham MA. Leveraging RNA-Seq to Characterize Resistance to Brown Stem Rot and the Rbs3 Locus in Soybean. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2018; 31:1083-1094. [PMID: 30004290 DOI: 10.1094/mpmi-01-18-0009-r] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Brown stem rot, caused by the fungus Phialophora gregata, reduces soybean yield by up to 38%. Although three dominant resistance loci have been identified (Rbs1 to Rbs3), the gene networks responsible for pathogen recognition and defense remain unknown. Further, identification and characterization of resistant and susceptible germplasm remains difficult. We conducted RNA-Seq of infected and mock-infected leaf, stem, and root tissues of a resistant (PI 437970, Rbs3) and susceptible (Corsoy 79) genotype. Combining historical mapping data with genotype expression differences allowed us to identify a cluster of receptor-like proteins that are candidates for the Rbs3 resistance gene. Reads mapping to the Rbs3 locus were used to identify potential novel single-nucleotide polymorphisms within candidate genes that could improve phenotyping and breeding efficiency. Comparing responses to infection revealed little overlap in differential gene expression between genotypes or tissues. Gene networks associated with defense, DNA replication, and iron homeostasis are hallmarks of resistance to P. gregata. This novel research demonstrates the utility of combining contrasting genotypes, gene expression, and classical genetic studies to characterize complex disease resistance loci.
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Affiliation(s)
- Chantal E McCabe
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
| | | | - Jamie A O'Rourke
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
| | - Michelle A Graham
- 1 United States Department of Agriculture-Agricultural Research Service Corn Insects and Crop Genetics Research Unit, Ames, IA 50011-1010, U.S.A. and Department of Agronomy, Iowa State University, Ames; and
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29
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Wozny D, Kramer K, Finkemeier I, Acosta IF, Koornneef M. Genes for seed longevity in barley identified by genomic analysis on near isogenic lines. PLANT, CELL & ENVIRONMENT 2018; 41:1895-1911. [PMID: 29744896 DOI: 10.1111/pce.13330] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 04/25/2018] [Accepted: 04/25/2018] [Indexed: 05/15/2023]
Abstract
Genes controlling differences in seed longevity between 2 barley (Hordeum vulgare) accessions were identified by combining quantitative genetics "omics" technologies in near isogenic lines (NILs). The NILs were derived from crosses between the spring barley landraces L94 from Ethiopia and Cebada Capa from Argentina. A combined transcriptome and proteome analysis on mature, nonaged seeds of the 2 parental lines and the L94 NILs by RNA-sequencing and total seed proteomic profiling identified the UDP-glycosyltransferase MLOC_11661.1 as candidate gene for the quantitative trait loci on 2H, and the NADP-dependent malic enzyme (NADP-ME) MLOC_35785.1 as possible downstream target gene. To validate these candidates, they were expressed in Arabidopsis under the control of constitutive promoters to attempt complementing the T-DNA knockout line nadp-me1. Both the NADP-ME MLOC_35785.1 and the UDP-glycosyltransferase MLOC_11661.1 were able to rescue the nadp-me1 seed longevity phenotype. In the case of the UDP-glycosyltransferase, with high accumulation in NILs, only the coding sequence of Cebada Capa had a rescue effect.
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Affiliation(s)
- Dorothee Wozny
- Institute Jean-Pierre Bourgin INRA Centre de Versailles-Grignon, Route de Saint-Cyr 10, Versailles Cedex, 78026, France
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Katharina Kramer
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Iris Finkemeier
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
- Institute for Plant Biology and Biotechnology, University of Münster, Schlossplatz 7, Münster, 48149, Germany
| | - Ivan F Acosta
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
| | - Maarten Koornneef
- Department Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Carl von-Linné-Weg 10, Köln, 50829, Germany
- Laboratory of Genetics, Wageningen University and Research, Droevendaalsesteeg 1, Wageningen, 6708 PB, The Netherlands
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Mehanathan M, Bedre R, Mangu V, Rajasekaran K, Bhatnagar D, Baisakh N. Identification of candidate resistance genes of cotton against Aspergillus flavus infection using a comparative transcriptomics approach. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:513-519. [PMID: 29692558 PMCID: PMC5911267 DOI: 10.1007/s12298-018-0522-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Revised: 01/23/2018] [Accepted: 02/15/2018] [Indexed: 06/08/2023]
Abstract
A comparative transcriptome analysis was performed using the genes significantly differentially expressed in cotton, corn and peanut in response to aflatoxin producing fungus Aspergillus flavus with an objective of identifying candidate resistance genes in cotton. Two-way analyses identified 732 unique genes to be differentially regulated by the fungus with only 26 genes common across all three crops that were considered candidate A. flavus resistance genes with an assumption that these genes have specific roles in conferring the resistance trait. Genes of membrane cellular component involved in DNA binding with involvement in defense responses were highly represented among the differentially expressed unique genes. Most (six) of these genes coded for 2-oxoglutarate (2OG) and Fe(II)-dependent oxygenase superfamily proteins. Genes encoding helix loop helix protein, alcohol dehydrogenase and UDP glycosylation transferase which were upregulated in response to both atoxigenic and toxigenic strains of A. flavus, could be potential resistance candidate genes for downstream functional manipulation to confer resistance.
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Affiliation(s)
- Muthamilarasan Mehanathan
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | - Renesh Bedre
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- Department of Plant Pathology and Microbiology, Texas A&M AgriLife Research, Weslaco, TX USA
| | - Venkata Mangu
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
- Department of Biochemistry, University of Pennsylvania, Philadelphia, PA USA
| | | | - Deepak Bhatnagar
- Southern Regional Research Center, USDA-ARS, New Orleans, LA USA
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Sciences, Louisiana State University Agricultural Center, Baton Rouge, LA USA
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Su X, Shen G, Di S, Dixon RA, Pang Y. Characterization of UGT716A1 as a Multi-substrate UDP:Flavonoid Glucosyltransferase Gene in Ginkgo biloba. FRONTIERS IN PLANT SCIENCE 2017; 8:2085. [PMID: 29270187 PMCID: PMC5725826 DOI: 10.3389/fpls.2017.02085] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 11/22/2017] [Indexed: 05/10/2023]
Abstract
Ginkgo biloba L., a "living fossil" and medicinal plant, is a well-known rich source of bioactive flavonoids. The molecular mechanism underlying the biosynthesis of flavonoid glucosides, the predominant flavonoids in G. biloba, remains unclear. To better understand flavonoid glucosylation in G. biloba, we generated a transcriptomic dataset of G. biloba leaf tissue by high-throughput RNA sequencing. We identified 25 putative UDP-glycosyltransferase (UGT) unigenes that are potentially involved in the flavonoid glycosylation. Among them, we successfully isolated and expressed eight UGT genes in Escherichia coli, and found that recombinant UGT716A1 protein was active toward broad range of flavonoid/phenylpropanoid substrates. In particular, we discovered the first recombinant UGT protein, UGT716A1 from G. biloba, possessing unique activity toward flavanol gallates that have been extensively documented to have significant bioactivity relating to human health. UGT716A1 expression level paralleled the flavonoid distribution pattern in G. biloba. Ectopic over-expression of UGT716A1 in Arabidopsis thaliana led to increased accumulation of several flavonol glucosides. Identification and comparison of the in vitro enzymatic activity of UGT716A1 homologs revealed a UGT from the primitive land species Physcomitrella patens also showed broader substrate spectrum than those from higher plants A. thaliana, Vitis vinifera, and Medicago truncatula. The characterization of UGT716A1 from G. biloba bridges a gap in the evolutionary history of UGTs in gymnosperms. We also discuss the implication of UGT716A1 for biosynthesis, evolution, and bioengineering of diverse glucosylated flavonoids.
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Affiliation(s)
- Xiaojia Su
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guoan Shen
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shaokang Di
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Richard A. Dixon
- BioDiscovery Institute and Department of Biological Sciences, University of North Texas, Denton TX, United States
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China
| | - Yongzhen Pang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
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Kost MA, Perales HR, Wijeratne S, Wijeratne AJ, Stockinger E, Mercer KL. Differentiated transcriptional signatures in the maize landraces of Chiapas, Mexico. BMC Genomics 2017; 18:707. [PMID: 28886704 PMCID: PMC5591509 DOI: 10.1186/s12864-017-4005-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 08/02/2017] [Indexed: 12/22/2022] Open
Abstract
Background Landrace farmers are the keepers of crops locally adapted to the environments where they are cultivated. Patterns of diversity across the genome can provide signals of past evolution in the face of abiotic and biotic change. Understanding this rich genetic resource is imperative especially since diversity can provide agricultural security as climate continues to shift. Results Here we employ RNA sequencing (RNA-seq) to understand the role that conditions that vary across a landscape may have played in shaping genetic diversity in the maize landraces of Chiapas, Mexico. We collected landraces from three distinct elevational zones and planted them in a midland common garden. Early season leaf tissue was collected for RNA-seq and we performed weighted gene co-expression network analysis (WGCNA). We then used association analysis between landrace co-expression module expression values and environmental parameters of landrace origin to elucidate genes and gene networks potentially shaped by environmental factors along our study gradient. Elevation of landrace origin affected the transcriptome profiles. Two co-expression modules were highly correlated with temperature parameters of landrace origin and queries into their ‘hub’ genes suggested that temperature may have led to differentiation among landraces in hormone biosynthesis/signaling and abiotic and biotic stress responses. We identified several ‘hub’ transcription factors and kinases as candidates for the regulation of these responses. Conclusions These findings indicate that natural selection may influence the transcriptomes of crop landraces along an elevational gradient in a major diversity center, and provide a foundation for exploring the genetic basis of local adaptation. While we cannot rule out the role of neutral evolutionary forces in the patterns we have identified, combining whole transcriptome sequencing technologies, established bioinformatics techniques, and common garden experimentation can powerfully elucidate structure of adaptive diversity across a varied landscape. Ultimately, gaining such understanding can facilitate the conservation and strategic utilization of crop genetic diversity in a time of climate change. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-4005-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew A Kost
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Hugo R Perales
- El Colegio de la Frontera Sur, Departmento de Agroecología, San Cristóbal de Las Casas, Chiapas, Mexico
| | - Saranga Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA
| | - Asela J Wijeratne
- Molecular Cellular and Imagining Center, The Ohio State University/OARDC, Wooster, OH, USA.,Department of Biological Sciences, Arkansas State University, Jonesboro, AR, USA
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, USA
| | - Kristin L Mercer
- Department of Horticulture and Crop Sciences, The Ohio State University, Columbus, OH, USA.
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Ruh M, Briand M, Bonneau S, Jacques MA, Chen NWG. Xanthomonas adaptation to common bean is associated with horizontal transfers of genes encoding TAL effectors. BMC Genomics 2017; 18:670. [PMID: 28854875 PMCID: PMC5577687 DOI: 10.1186/s12864-017-4087-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2017] [Accepted: 08/24/2017] [Indexed: 12/25/2022] Open
Abstract
Background Common bacterial blight is a devastating bacterial disease of common bean (Phaseolus vulgaris) caused by Xanthomonas citri pv. fuscans and Xanthomonas phaseoli pv. phaseoli. These phylogenetically distant strains are able to cause similar symptoms on common bean, suggesting that they have acquired common genetic determinants of adaptation to common bean. Transcription Activator-Like (TAL) effectors are bacterial type III effectors that are able to induce the expression of host genes to promote infection or resistance. Their capacity to bind to a specific host DNA sequence suggests that they are potential candidates for host adaption. Results To study the diversity of tal genes from Xanthomonas strains responsible for common bacterial blight of bean, whole genome sequences of 17 strains representing the diversity of X. citri pv. fuscans and X. phaseoli pv. phaseoli were obtained by single molecule real time sequencing. Analysis of these genomes revealed the existence of four tal genes named tal23A, tal20F, tal18G and tal18H, respectively. While tal20F and tal18G were chromosomic, tal23A and tal18H were carried on plasmids and shared between phylogenetically distant strains, therefore suggesting recent horizontal transfers of these genes between X. citri pv. fuscans and X. phaseoli pv. phaseoli strains. Strikingly, tal23A was present in all strains studied, suggesting that it played an important role in adaptation to common bean. In silico predictions of TAL effectors targets in the common bean genome suggested that TAL effectors shared by X. citri pv. fuscans and X. phaseoli pv. phaseoli strains target the promoters of genes of similar functions. This could be a trace of convergent evolution among TAL effectors from different phylogenetic groups, and comforts the hypothesis that TAL effectors have been implied in the adaptation to common bean. Conclusions Altogether, our results favour a model where plasmidic TAL effectors are able to contribute to host adaptation by being horizontally transferred between distant lineages. Electronic supplementary material The online version of this article (10.1186/s12864-017-4087-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mylène Ruh
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Martial Briand
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Sophie Bonneau
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Marie-Agnès Jacques
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France
| | - Nicolas W G Chen
- IRHS, INRA, AGROCAMPUS OUEST, Université d'Angers, SFR4207 QUASAV, 42, rue Georges Morel, 49071, Beaucouzé, France.
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Abdelrahman M, El-Sayed M, Sato S, Hirakawa H, Ito SI, Tanaka K, Mine Y, Sugiyama N, Suzuki M, Yamauchi N, Shigyo M. RNA-sequencing-based transcriptome and biochemical analyses of steroidal saponin pathway in a complete set of Allium fistulosum-A. cepa monosomic addition lines. PLoS One 2017; 12:e0181784. [PMID: 28800607 PMCID: PMC5553718 DOI: 10.1371/journal.pone.0181784] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 07/06/2017] [Indexed: 01/06/2023] Open
Abstract
The genus Allium is a rich source of steroidal saponins, and its medicinal properties have been attributed to these bioactive compounds. The saponin compounds with diverse structures play a pivotal role in Allium’s defense mechanism. Despite numerous studies on the occurrence and chemical structure of steroidal saponins, their biosynthetic pathway in Allium species is poorly understood. The monosomic addition lines (MALs) of the Japanese bunching onion (A. fistulosum, FF) with an extra chromosome from the shallot (A. cepa Aggregatum group, AA) are powerful genetic resources that enable us to understand many physiological traits of Allium. In the present study, we were able to isolate and identify Alliospiroside A saponin compound in A. fistulosum with extra chromosome 2A from shallot (FF2A) and its role in the defense mechanism against Fusarium pathogens. Furthermore, to gain molecular insight into the Allium saponin biosynthesis pathway, high-throughput RNA-Seq of the root, bulb, and leaf of AA, MALs, and FF was carried out using Illumina's HiSeq 2500 platform. An open access Allium Transcript Database (Allium TDB, http://alliumtdb.kazusa.or.jp) was generated based on RNA-Seq data. The resulting assembled transcripts were functionally annotated, revealing 50 unigenes involved in saponin biosynthesis. Differential gene expression (DGE) analyses of AA and MALs as compared with FF (as a control) revealed a strong up-regulation of the saponin downstream pathway, including cytochrome P450, glycosyltransferase, and beta-glucosidase in chromosome 2A. An understanding of the saponin compounds and biosynthesis-related genes would facilitate the development of plants with unique saponin content and, subsequently, improved disease resistance.
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Affiliation(s)
- Mostafa Abdelrahman
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
- Botany Department, Faculty of Science, Aswan University, Aswan, Egypt
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | - Magdi El-Sayed
- Botany Department, Faculty of Science, Aswan University, Aswan, Egypt
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, Aoba-ku, Sendai, Japan
| | | | - Shin-ichi Ito
- Laboratory of Molecular Plant Pathology, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
| | - Keisuke Tanaka
- The NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Yoko Mine
- Department of Agriculture, Faculty of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Nobuo Sugiyama
- Department of Agriculture, Faculty of Agriculture, Tokyo University of Agriculture, Tokyo, Japan
| | - Minoru Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Naoki Yamauchi
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
| | - Masayoshi Shigyo
- Laboratory of Vegetable Crop Science, College of Agriculture, Graduate School of Sciences and Technology for Innovation, Japan
- * E-mail:
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Liu Y, Zhang Z, Fu J, Wang G, Wang J, Liu Y. Transcriptome Analysis of Maize Immature Embryos Reveals the Roles of Cysteine in Improving Agrobacterium Infection Efficiency. FRONTIERS IN PLANT SCIENCE 2017; 8:1778. [PMID: 29089955 PMCID: PMC5651077 DOI: 10.3389/fpls.2017.01778] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 09/29/2017] [Indexed: 05/14/2023]
Abstract
Maize Agrobacterium-mediated transformation efficiency has been greatly improved in recent years. Antioxidants, such as, cysteine, can significantly improve maize transformation frequency through improving the Agrobacterium infection efficiency. However, the mechanism underlying the transformation improvement after cysteine exposure has not been elucidated. In this study, we showed that the addition of cysteine to the co-cultivation medium significantly increased the Agrobacterium infection efficiency of hybrid HiII and inbred line Z31 maize embryos. Reactive oxygen species contents were higher in embryos treated with cysteine than that without cysteine. We further investigated the mechanism behind cysteine-related infection efficiency increase using transcriptome analysis. The results showed that the cysteine treatment up-regulated 939 genes and down-regulated 549 genes in both Z31 and HiII. Additionally, more differentially expressed genes were found in HiII embryos than those in Z31 embryos, suggesting that HiII was more sensitive to the cysteine treatment than Z31. GO analysis showed that the up-regulated genes were mainly involved in the oxidation reduction process. The up-regulation of these genes could help maize embryos to cope with the oxidative stress stimulated by Agrobacterium infection. The down-regulated genes were mainly involved in the cell wall and membrane metabolism, such as, aquaporin and expansin genes. Decreased expression of these cell wall integrity genes could loosen the cell wall, thereby improving the entry of Agrobacterium into plant cells. This study offers insight into the role of cysteine in improving Agrobacterium-mediated transformation of maize immature embryos.
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Affiliation(s)
- Yan Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhiqiang Zhang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Guoying Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jianhua Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
- *Correspondence: Jianhua Wang
| | - Yunjun Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Yunjun Liu
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Dmitriev AA, Krasnov GS, Rozhmina TA, Kishlyan NV, Zyablitsin AV, Sadritdinova AF, Snezhkina AV, Fedorova MS, Yurkevich OY, Muravenko OV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax. FRONTIERS IN PLANT SCIENCE 2016; 7:1920. [PMID: 28066475 PMCID: PMC5174120 DOI: 10.3389/fpls.2016.01920] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 12/02/2016] [Indexed: 05/19/2023]
Abstract
About 30% of the world's ice-free land area is occupied by acid soils. In soils with pH below 5, aluminum (Al) releases to the soil solution, and becomes highly toxic for plants. Therefore, breeding of varieties that are resistant to Al is needed. Flax (Linum usitatissimum L.) is grown worldwide for fiber and seed production. Al toxicity in acid soils is a serious problem for flax cultivation. However, very little is known about mechanisms of flax resistance to Al and the genetics of this resistance. In the present work, we sequenced 16 transcriptomes of flax cultivars resistant (Hermes and TMP1919) and sensitive (Lira and Orshanskiy) to Al, which were exposed to control conditions and aluminum treatment for 4, 12, and 24 h. In total, 44.9-63.3 million paired-end 100-nucleotide reads were generated for each sequencing library. Based on the obtained high-throughput sequencing data, genes with differential expression under aluminum exposure were revealed in flax. The majority of the top 50 up-regulated genes were involved in transmembrane transport and transporter activity in both the Al-resistant and Al-sensitive cultivars. However, genes encoding proteins with glutathione transferase and UDP-glycosyltransferase activity were in the top 50 up-regulated genes only in the flax cultivars resistant to aluminum. For qPCR analysis in extended sampling, two UDP-glycosyltransferases (UGTs), and three glutathione S-transferases (GSTs) were selected. The general trend of alterations in the expression of the examined genes was the up-regulation under Al stress, especially after 4 h of Al exposure. Moreover, in the flax cultivars resistant to aluminum, the increase in expression was more pronounced than that in the sensitive cultivars. We speculate that the defense against the Al toxicity via GST antioxidant activity is the probable mechanism of the response of flax plants to aluminum stress. We also suggest that UGTs could be involved in cell wall modification and protection from reactive oxygen species (ROS) in response to Al stress in L. usitatissimum. Thus, GSTs and UGTs, probably, play an important role in the response of flax to Al via detoxification of ROS and cell wall modification.
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Affiliation(s)
- Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
- All-Russian Research Institute for FlaxTorzhok, Russia
| | | | | | - Asiya F. Sadritdinova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | | | - Maria S. Fedorova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga Y. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Nadezhda L. Bolsheva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of SciencesMoscow, Russia
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Dumas AS, Taconnat L, Barbas E, Rigaill G, Catrice O, Bernard D, Benamar A, Macherel D, El Amrani A, Berthomé R. Unraveling the early molecular and physiological mechanisms involved in response to phenanthrene exposure. BMC Genomics 2016; 17:818. [PMID: 27769163 PMCID: PMC5073745 DOI: 10.1186/s12864-016-3133-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/27/2016] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND Higher plants have to cope with increasing concentrations of pollutants of both natural and anthropogenic origin. Given their capacity to concentrate and metabolize various compounds including pollutants, plants can be used to treat environmental problems - a process called phytoremediation. However, the molecular mechanisms underlying the stabilization, the extraction, the accumulation and partial or complete degradation of pollutants by plants remain poorly understood. RESULTS Here, we determined the molecular events involved in the early plant response to phenanthrene, used as a model of polycyclic aromatic hydrocarbons. A transcriptomic and a metabolic analysis strongly suggest that energy availability is the crucial limiting factor leading to high and rapid transcriptional reprogramming that can ultimately lead to death. We show that the accumulation of phenanthrene in leaves inhibits electron transfer and photosynthesis within a few minutes, probably disrupting energy transformation. CONCLUSION This kinetic analysis improved the resolution of the transcriptome in the initial plant response to phenanthrene, identifying genes that are involved in primary processes set up to sense and detoxify this pollutant but also in molecular mechanisms used by the plant to cope with such harmful stress. The identification of first events involved in plant response to phenanthrene is a key step in the selection of candidates for further functional characterization, with the prospect of engineering efficient ecological detoxification systems for polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Anne-Sophie Dumas
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France
| | - Ludivine Taconnat
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
| | - Evangelos Barbas
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
- Present Address: Laboratory of Forest Genetics and Tree Breeding, AUTH, University Campus, 54124, Thessaloniki, Greece
| | - Guillem Rigaill
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France
| | - Olivier Catrice
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR INRA 441/CNRS 2594, CS 52627, 31326, Castanet Tolosan cedex, France
| | - Delphine Bernard
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France
- Present Address: Laboratoire de Génétique Moléculaire et de Génétique Epidémiologique, INSERM U1078, 46, rue Felix Le Dantec, CS 51819, 29218, Brest Cedex 2, France
| | - Abdelilah Benamar
- Université d'Angers, UMR 1345, Institut de Recherche en Horticulture et Semences (IRHS), Bat ARES, 16 Boulevard Lavoisier, 49045, Angers cedex, France
| | - David Macherel
- Université d'Angers, UMR 1345, Institut de Recherche en Horticulture et Semences (IRHS), Bat ARES, 16 Boulevard Lavoisier, 49045, Angers cedex, France
| | - Abdelhak El Amrani
- Université de Rennes 1, CNRS/OSUR/UMR 6553, Ecosystèmes-Biodiversité-Evolution, campus de Beaulieu, Bâtiment 14A, 35042, Rennes cedex, France.
| | - Richard Berthomé
- Institute of Plant Sciences Paris Saclay (IPS2), UMR 9213/UMR1403, Université Paris Sud, CNRS, INRA, Université d'Evry, Université Paris Diderot, Sorbonne Paris Cité, Bâtiment 630, 91405, Orsay, France.
- Laboratoire des Interactions Plantes Micro-organismes (LIPM), UMR INRA 441/CNRS 2594, CS 52627, 31326, Castanet Tolosan cedex, France.
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Utsumi Y, Tanaka M, Kurotani A, Yoshida T, Mochida K, Matsui A, Ishitani M, Sraphet S, Whankaew S, Asvarak T, Narangajavana J, Triwitayakorn K, Sakurai T, Seki M. Cassava (Manihot esculenta) transcriptome analysis in response to infection by the fungus Colletotrichum gloeosporioides using an oligonucleotide-DNA microarray. JOURNAL OF PLANT RESEARCH 2016; 129:711-726. [PMID: 27138000 DOI: 10.1007/s10265-016-0828-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 02/14/2016] [Indexed: 05/04/2023]
Abstract
Cassava anthracnose disease (CAD), caused by the fungus Colletotrichum gloeosporioides f. sp. Manihotis, is a serious disease of cassava (Manihot esculenta) worldwide. In this study, we established a cassava oligonucleotide-DNA microarray representing 59,079 probes corresponding to approximately 30,000 genes based on original expressed sequence tags and RNA-seq information from cassava, and applied it to investigate the molecular mechanisms of resistance to fungal infection using two cassava cultivars, Huay Bong 60 (HB60, resistant to CAD) and Hanatee (HN, sensitive to CAD). Based on quantitative real-time reverse transcription PCR and expression profiling by the microarray, we showed that the expressions of various plant defense-related genes, such as pathogenesis-related (PR) genes, cell wall-related genes, detoxification enzyme, genes related to the response to bacterium, mitogen-activated protein kinase (MAPK), genes related to salicylic acid, jasmonic acid and ethylene pathways were higher in HB60 compared with HN. Our results indicated that the induction of PR genes in HB60 by fungal infection and the higher expressions of defense response-related genes in HB60 compared with HN are likely responsible for the fungal resistance in HB60. We also showed that the use of our cassava oligo microarray could improve our understanding of cassava molecular mechanisms related to environmental responses and development, and advance the molecular breeding of useful cassava plants.
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Affiliation(s)
- Yoshinori Utsumi
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Maho Tanaka
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Atsushi Kurotani
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Takuhiro Yoshida
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Keiichi Mochida
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
- Biomass Research Platform Team, RIKEN Biomass Engineering Program, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Akihiro Matsui
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan
| | - Manabu Ishitani
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira, Apartado Aéreo 6713, Cali, Colombia
| | - Supajit Sraphet
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Sukhuman Whankaew
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Thipa Asvarak
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, 10400, Thailand
| | - Jarunya Narangajavana
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, 10400, Thailand
| | - Kanokporn Triwitayakorn
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, 73170, Thailand
| | - Tetsuya Sakurai
- Integrated Genome Informatics Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Research and Education Faculty, Multidisciplinary Science Cluster, Interdisciplinary Science Unit, 200 Otsu, Monobe, Nankoku, Kochi, 783-8502, Japan.
| | - Motoaki Seki
- Plant Genomic Network Research Team, RIKEN Center for Sustainable Resource Science, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045, Japan.
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST), 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan.
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan.
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Gao L, Wang Y, Li Z, Zhang H, Ye J, Li G. Gene Expression Changes during the Gummosis Development of Peach Shoots in Response to Lasiodiplodia theobromae Infection Using RNA-Seq. Front Physiol 2016; 7:170. [PMID: 27242544 PMCID: PMC4861008 DOI: 10.3389/fphys.2016.00170] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 04/25/2016] [Indexed: 01/31/2023] Open
Abstract
Lasiodiplodia theobromae is a causal agent of peach (Prunus persica L.) tree gummosis, a serious disease affecting peach cultivation and production. However, the molecular mechanism underlying the pathogenesis remains unclear. RNA-Seq was performed to investigate gene expression in peach shoots inoculated or mock-inoculated with L. theobromae. A total of 20772 genes were detected in eight samples; 4231, 3750, 3453, and 3612 differentially expressed genes were identified at 12, 24, 48, and 60 h after inoculation, respectively. Furthermore, 920 differentially co-expressed genes (515 upregulated and 405 downregulated) were found, respectively. Gene ontology annotation revealed that phenylpropanoid biosynthesis and metabolism, uridine diphosphate-glucosyltransferase activity, and photosynthesis were the most differentially regulated processes during gummosis development. Significant differences were also found in the expression of genes involved in glycometabolism and in ethylene and jasmonic acid biosynthesis and signaling. These data illustrate the dynamic changes in gene expression in the inoculated peach shoots at the transcriptome level. Overall, gene expression in defense response and glycometabolism might result in the gummosis of peach trees induced by L. theobromae.
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Affiliation(s)
- Lei Gao
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University Wuhan, China
| | - Yuting Wang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University Wuhan, China
| | - Zhi Li
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Horticulture, Northwest Agriculture and Forestry University Yangling, China
| | - He Zhang
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University Wuhan, China
| | - Junli Ye
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University Wuhan, China
| | - Guohuai Li
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University Wuhan, China
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40
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Song C, Zhao S, Hong X, Liu J, Schulenburg K, Schwab W. A UDP-glucosyltransferase functions in both acylphloroglucinol glucoside and anthocyanin biosynthesis in strawberry (Fragaria × ananassa). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 85:730-42. [PMID: 26859691 DOI: 10.1111/tpj.13140] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Revised: 02/01/2016] [Accepted: 02/03/2016] [Indexed: 05/02/2023]
Abstract
Physiologically active acylphloroglucinol (APG) glucosides were recently found in strawberry (Fragaria sp.) fruit. Although the formation of the APG aglycones has been clarified, little is known about APG glycosylation in plants. In this study we functionally characterized ripening-related glucosyltransferase genes in Fragaria by comprehensive biochemical analyses of the encoded proteins and by a RNA interference (RNAi) approach in vivo. The allelic proteins UGT71K3a/b catalyzed the glucosylation of diverse hydroxycoumarins, naphthols and flavonoids as well as phloroglucinols, enzymatically synthesized APG aglycones and pelargonidin. Total enzymatic synthesis of APG glucosides was achieved by co-incubation of recombinant dual functional chalcone/valerophenone synthase and UGT71K3 proteins with essential coenzyme A esters and UDP-glucose. An APG glucoside was identified in strawberry fruit which has not yet been reported in other plants. Suppression of UGT71K3 activity in transient RNAi-silenced fruits led to a loss of pigmentation and a substantial decrease of the levels of various APG glucosides and an anthocyanin. Metabolite analyses of transgenic fruits confirmed UGT71K3 as a UDP-glucose:APG glucosyltransferase in planta. These results provide the foundation for the breeding of fruits with improved health benefits and for the biotechnological production of bioactive natural products.
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Affiliation(s)
- Chuankui Song
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
| | - Shuai Zhao
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
| | - Xiaotong Hong
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
| | - Jingyi Liu
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
| | - Katja Schulenburg
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
| | - Wilfried Schwab
- Biotechnology of Natural Products, Technische Universität München, Liesel-Beckmann-Strasse 1, Freising, 85354, Germany
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Le Roy J, Huss B, Creach A, Hawkins S, Neutelings G. Glycosylation Is a Major Regulator of Phenylpropanoid Availability and Biological Activity in Plants. FRONTIERS IN PLANT SCIENCE 2016; 7:735. [PMID: 27303427 PMCID: PMC4880792 DOI: 10.3389/fpls.2016.00735] [Citation(s) in RCA: 203] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2016] [Accepted: 05/12/2016] [Indexed: 05/18/2023]
Abstract
The phenylpropanoid pathway in plants is responsible for the biosynthesis of a huge amount of secondary metabolites derived from phenylalanine and tyrosine. Both flavonoids and lignins are synthesized at the end of this very diverse metabolic pathway, as well as many intermediate molecules whose precise biological functions remain largely unknown. The diversity of these molecules can be further increased under the action of UDP-glycosyltransferases (UGTs) leading to the production of glycosylated hydroxycinnamates and related aldehydes, alcohols and esters. Glycosylation can change phenylpropanoid solubility, stability and toxic potential, as well as influencing compartmentalization and biological activity. (De)-glycosylation therefore represents an extremely important regulation point in phenylpropanoid homeostasis. In this article we review recent knowledge on the enzymes involved in regulating phenylpropanoid glycosylation status and availability in different subcellular compartments. We also examine the potential link between monolignol glycosylation and lignification by exploring co-expression of lignin biosynthesis genes and phenolic (de)glycosylation genes. Of the different biological roles linked with their particular chemical properties, phenylpropanoids are often correlated with the plant's stress management strategies that are also regulated by glycosylation. UGTs can for instance influence the resistance of plants during infection by microorganisms and be involved in the mechanisms related to environmental changes. The impact of flavonoid glycosylation on the color of flowers, leaves, seeds and fruits will also be discussed. Altogether this paper underlies the fact that glycosylation and deglycosylation are powerful mechanisms allowing plants to regulate phenylpropanoid localisation, availability and biological activity.
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Widdup EE, Chatfield-Reed K, Henry D, Chua G, Samuel MA, Muench DG. Identification of detoxification pathways in plants that are regulated in response to treatment with organic compounds isolated from oil sands process-affected water. CHEMOSPHERE 2015; 139:47-53. [PMID: 26052061 DOI: 10.1016/j.chemosphere.2015.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/16/2015] [Accepted: 05/18/2015] [Indexed: 06/04/2023]
Abstract
Bitumen mining in the Athabasca oil sands region of northern Alberta results in the accumulation of large volumes of oil sands process-affected water (OSPW). The acid-extractable organic (AEO) fraction of OSPW contains a variety of compounds, including naphthenic acids, aromatics, and sulfur- and nitrogen-containing compounds that are toxic to aquatic and terrestrial organisms. We have studied the effect of AEO treatment on the transcriptome of root and shoot tissues in seedlings of the model plant, Arabidopsis thaliana. Several genes encoding enzymes involved in the xenobiotic detoxification pathway were upregulated, including cytochrome P450s (CYPs), UDP-dependent glycosyltransferases (UGTs), glutathione-S-transferases (GSTs), and membrane transporters. In addition, gene products involved in oxidative stress, β-oxidation, and glucosinolate degradation were also upregulated, indicating other potential mechanisms of the adaptive response to AEO exposure. These results provide insight into the pathways that plants use to detoxify the organic acid component of OSPW. Moreover, this study advances our understanding of genes that could be exploited to potentially develop phytoremediation and biosensing strategies for AEO contaminants resulting from oil sands mining.
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Affiliation(s)
- Ellen E Widdup
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Kate Chatfield-Reed
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Darren Henry
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada
| | - Gordon Chua
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
| | - Marcus A Samuel
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
| | - Douglas G Muench
- Department of Biological Sciences, University of Calgary, 2500 University Dr. NW, Calgary, Alberta T2N1N4, Canada.
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Garg A, Agrawal L, Misra RC, Sharma S, Ghosh S. Andrographis paniculata transcriptome provides molecular insights into tissue-specific accumulation of medicinal diterpenes. BMC Genomics 2015; 16:659. [PMID: 26328761 PMCID: PMC4557604 DOI: 10.1186/s12864-015-1864-y] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2015] [Accepted: 08/18/2015] [Indexed: 12/15/2022] Open
Abstract
Background Kalmegh (Andrographis paniculata) has been widely exploited in traditional medicine for the treatment of infectious diseases and health disorders. Ent-labdane-related diterpene (ent-LRD) specialized (i.e., secondary) metabolites of kalmegh such as andrographolide, neoandrographolide and 14-deoxy-11,12-didehydroandrographolide, are known for variety of pharmacological activities. However, due to the lack of genomic and transcriptomic information, underlying molecular basis of ent-LRDs biosynthesis has remained largely unknown. To identify candidate genes of the ent-LRD biosynthetic pathway, we performed comparative transcriptome analysis using leaf and root tissues that differentially accumulate ent-LRDs. Results De novo assembly of Illumina HiSeq2000 platform-generated paired-end sequencing reads resulted into 69,011 leaf and 64,244 root transcripts which were assembled into a total of 84,628 unique transcripts. Annotation of these transcripts to the Uniprot, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active Enzymes (CAZy) databases identified candidate transcripts of the ent-LRD biosynthetic pathway. These included transcripts that encode enzymes of the plastidial 2C-methyl-D-erythritol-4-phosphate pathway which provides C5 isoprenoid precursors for the ent-LRDs biosynthesis, geranylgeranyl diphosphate synthase, class II diterpene synthase (diTPS), cytochrome P450 monooxygenase and glycosyltransferase. Three class II diTPSs (ApCPS1, ApCPS2 and ApCPS3) that showed distinct tissue-specific expression profiles and are phylogenetically related to the dicotyledon ent-copalyl diphosphate synthases, are identified. ApCPS1, ApCPS2 and ApCPS3 encode for 832-, 817- and 797- amino acids proteins of 55–63 % identity, respectively. Spatio-temporal patterns of transcripts and ent-LRDs accumulation are consistent with the involvement of ApCPS1 in general (i.e., primary) metabolism for the biosynthesis of phytohormone gibberellin, ApCPS2 in leaf specialized ent-LRDs biosynthesis and ApCPS3 in root diterpene biosynthesis. Moreover, simple sequence repeats (SSRs) that might assist in genotyping and developing specific chemotypes were identified in transcripts of the specialized metabolic pathways, including ent-LRDs. Conclusions Comparative analysis of root and leaf transcriptomes disclosed novel genes of the ent-LRD biosynthetic pathway, including three class II diTPSs that showed discrete spatio-temporal expression patterns; thus, suggesting their participation into distinct diterpene metabolic pathways of kalmegh. Overall, these results will be useful in understanding molecular basis of the medicinal ent-LRDs biosynthesis and developing breeding strategies for improving their yields. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1864-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anchal Garg
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
| | - Lalit Agrawal
- Council of Scientific and Industrial Research-National Botanical Research Institute, Lucknow, 226001, India.
| | - Rajesh Chandra Misra
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
| | - Shubha Sharma
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
| | - Sumit Ghosh
- Biotechnology Division, Council of Scientific and Industrial Research-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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Yan L, Wang X, Liu H, Tian Y, Lian J, Yang R, Hao S, Wang X, Yang S, Li Q, Qi S, Kui L, Okpekum M, Ma X, Zhang J, Ding Z, Zhang G, Wang W, Dong Y, Sheng J. The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb. MOLECULAR PLANT 2015; 8:922-34. [PMID: 25825286 DOI: 10.1016/j.molp.2014.12.011] [Citation(s) in RCA: 152] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/15/2014] [Accepted: 12/16/2014] [Indexed: 05/05/2023]
Abstract
Dendrobium officinale Kimura et Migo is a traditional Chinese orchid herb that has both ornamental value and a broad range of therapeutic effects. Here, we report the first de novo assembled 1.35 Gb genome sequences for D. officinale by combining the second-generation Illumina Hiseq 2000 and third-generation PacBio sequencing technologies. We found that orchids have a complete inflorescence gene set and have some specific inflorescence genes. We observed gene expansion in gene families related to fungus symbiosis and drought resistance. We analyzed biosynthesis pathways of medicinal components of D. officinale and found extensive duplication of SPS and SuSy genes, which are related to polysaccharide generation, and that the pathway of D. officinale alkaloid synthesis could be extended to generate 16-epivellosimine. The D. officinale genome assembly demonstrates a new approach to deciphering large complex genomes and, as an important orchid species and a traditional Chinese medicine, the D. officinale genome will facilitate future research on the evolution of orchid plants, as well as the study of medicinal components and potential genetic breeding of the dendrobe.
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Affiliation(s)
- Liang Yan
- College of Life Science, Jilin University, Changchun 130012, China; Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Xiao Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Hui Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Tian
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jinmin Lian
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Ruijuan Yang
- Pu'er Institute of Pu-er Tea, Pu'er 665000, China
| | - Shumei Hao
- Yunnan University, Kunming 650091, China
| | - Xuanjun Wang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Shengchao Yang
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Qiye Li
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Shuai Qi
- Agri-Biotech Lab, Kunming 650502, China
| | - Ling Kui
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Moses Okpekum
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Xiao Ma
- Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajin Zhang
- School of Science and Information Engineering, Yunnan Agricultural University, Kunming 650201, China
| | - Zhaoli Ding
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Guojie Zhang
- China National GeneBank-Shenzhen, BGI-Shenzhen, Shenzhen 518083, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China
| | - Yang Dong
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), Kunming, Yunnan 650223, China; Laboratory of Applied Genomics and Synthetic Biology, College of Life Science, Kunming University of Science and Technology, Kunming 650500, China.
| | - Jun Sheng
- College of Life Science, Jilin University, Changchun 130012, China; Key Laboratory of Puerh Tea Science, Ministry of Education, Yunnan Agricultural University, Kunming 650201, China.
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Noctor G, Lelarge-Trouverie C, Mhamdi A. The metabolomics of oxidative stress. PHYTOCHEMISTRY 2015; 112:33-53. [PMID: 25306398 DOI: 10.1016/j.phytochem.2014.09.002] [Citation(s) in RCA: 123] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Revised: 09/02/2014] [Accepted: 09/04/2014] [Indexed: 05/20/2023]
Abstract
Oxidative stress resulting from increased availability of reactive oxygen species (ROS) is a key component of many responses of plants to challenging environmental conditions. The consequences for plant metabolism are complex and manifold. We review data on small compounds involved in oxidative stress, including ROS themselves and antioxidants and redox buffers in the membrane and soluble phases, and we discuss the wider consequences for plant primary and secondary metabolism. While metabolomics has been exploited in many studies on stress, there have been relatively few non-targeted studies focused on how metabolite signatures respond specifically to oxidative stress. As part of the discussion, we present results and reanalyze published datasets on metabolite profiles in catalase-deficient plants, which can be considered to be model oxidative stress systems. We emphasize the roles of ROS-triggered changes in metabolites as potential oxidative signals, and discuss responses that might be useful as markers for oxidative stress. Particular attention is paid to lipid-derived compounds, the status of antioxidants and antioxidant breakdown products, altered metabolism of amino acids, and the roles of phytohormone pathways.
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Affiliation(s)
- Graham Noctor
- Institut de Biologie des Plantes, UMR8618 CNRS, Université de Paris sud, 91405 Orsay Cedex, France.
| | | | - Amna Mhamdi
- Institut de Biologie des Plantes, UMR8618 CNRS, Université de Paris sud, 91405 Orsay Cedex, France
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Vermeirssen V, De Clercq I, Van Parys T, Van Breusegem F, Van de Peer Y. Arabidopsis ensemble reverse-engineered gene regulatory network discloses interconnected transcription factors in oxidative stress. THE PLANT CELL 2014; 26:4656-79. [PMID: 25549671 PMCID: PMC4311199 DOI: 10.1105/tpc.114.131417] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Revised: 11/27/2014] [Accepted: 12/10/2014] [Indexed: 05/19/2023]
Abstract
The abiotic stress response in plants is complex and tightly controlled by gene regulation. We present an abiotic stress gene regulatory network of 200,014 interactions for 11,938 target genes by integrating four complementary reverse-engineering solutions through average rank aggregation on an Arabidopsis thaliana microarray expression compendium. This ensemble performed the most robustly in benchmarking and greatly expands upon the availability of interactions currently reported. Besides recovering 1182 known regulatory interactions, cis-regulatory motifs and coherent functionalities of target genes corresponded with the predicted transcription factors. We provide a valuable resource of 572 abiotic stress modules of coregulated genes with functional and regulatory information, from which we deduced functional relationships for 1966 uncharacterized genes and many regulators. Using gain- and loss-of-function mutants of seven transcription factors grown under control and salt stress conditions, we experimentally validated 141 out of 271 predictions (52% precision) for 102 selected genes and mapped 148 additional transcription factor-gene regulatory interactions (49% recall). We identified an intricate core oxidative stress regulatory network where NAC13, NAC053, ERF6, WRKY6, and NAC032 transcription factors interconnect and function in detoxification. Our work shows that ensemble reverse-engineering can generate robust biological hypotheses of gene regulation in a multicellular eukaryote that can be tested by medium-throughput experimental validation.
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Affiliation(s)
- Vanessa Vermeirssen
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Inge De Clercq
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Thomas Van Parys
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Gent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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Sun H, Wang L, Zhang B, Ma J, Hettenhausen C, Cao G, Sun G, Wu J, Wu J. Scopoletin is a phytoalexin against Alternaria alternata in wild tobacco dependent on jasmonate signalling. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:4305-15. [PMID: 24821958 PMCID: PMC4112635 DOI: 10.1093/jxb/eru203] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Alternaria alternata (tobacco pathotype) is a necrotrophic fungus causing severe losses in Nicotiana species by infection of mature leaves. Similar to what has been observed in cultivated tobacco, N. tabacum, young leaves of wild tobacco, N. attenuata, were more resistant to A. alternata than mature leaves, and this was correlated with stronger blue fluorescence induced after infection. However, the nature of the fluorescence-emitting compound, its role in defence, and its regulation were not clear. Silencing feruloyl-CoA 6'-hydroxylase 1 (F6'H1), the gene encoding the key enzyme for scopoletin biosynthesis, by virus-induced gene silencing (VIGS) revealed that the blue fluorescence was mainly emitted by scopoletin and its β-glycoside form, scopolin. Further analysis showed that scopoletin exhibited strong antifungal activity against A. alternata in vitro and in vivo. Importantly, jasmonic acid (JA) levels were highly elicited in young leaves but much less in mature leaves after infection; and fungus-elicited scopoletin was absent in JA-deficient plants, but was largely restored with methyl jasmonate treatments. Consistent with this, plants strongly impaired in JA biosynthesis and perception were highly susceptible to A. alternata in the same way scopoletin/scopolin-depleted VIGS F6'H1 plants. Furthermore, silencing MYC2, a master regulator of most JA responses, reduced A. alternata-induced NaF6'H1 transcripts and scopoletin. Thus, it is concluded that JA signalling is activated in N. attenuata leaves after infection, which subsequently regulates scopoletin biosynthesis for the defence against A. alternata partly through MYC2, and higher levels of scopoletin accumulated in young leaves account for their strong resistance.
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Affiliation(s)
- Huanhuan Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Lei Wang
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Baoqin Zhang
- Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian 116023, China
| | - Junhong Ma
- Yunnan Academy of Tobacco Agricultural Science, Yuantong Street 33, 650031, Kunming, China
| | - Christian Hettenhausen
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Guoyan Cao
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Guiling Sun
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Jianqiang Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
| | - Jinsong Wu
- Key Laboratory of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Lanhei Road 132, 650201, Kunming, China
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Noctor G, Mhamdi A, Foyer CH. The roles of reactive oxygen metabolism in drought: not so cut and dried. PLANT PHYSIOLOGY 2014; 164:1636-48. [PMID: 24715539 PMCID: PMC3982730 DOI: 10.1104/pp.113.233478] [Citation(s) in RCA: 293] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 03/05/2014] [Indexed: 05/18/2023]
Abstract
Drought is considered to cause oxidative stress, but the roles of oxidant-induced modifications in plant responses to water deficit remain obscure. Key unknowns are the roles of reactive oxygen species (ROS) produced at specific intracellular or apoplastic sites and the interactions between the complex, networking antioxidative systems in restricting ROS accumulation or in redox signal transmission. This Update discusses the physiological aspects of ROS production during drought, and analyzes the relationship between oxidative stress and drought from different but complementary perspectives. We ask to what extent redox changes are involved in plant drought responses and discuss the roles that different ROS-generating processes may play. Our discussion emphasizes the complexity and the specificity of antioxidant systems, and the likely importance of thiol systems in drought-induced redox signaling. We identify candidate drought-responsive redox-associated genes and analyze the potential importance of different metabolic pathways in drought-associated oxidative stress signaling.
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Affiliation(s)
| | - Amna Mhamdi
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (G.N., A.M.); and
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (C.H.F.)
| | - Christine H. Foyer
- Institut de Biologie des Plantes, Unité Mixte de Recherche 8618 Centre National de la Recherche Scientifique, Université de Paris-Sud, 91405 Orsay cedex, France (G.N., A.M.); and
- Centre for Plant Sciences, University of Leeds, Leeds LS2 9JT, United Kingdom (C.H.F.)
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